Journal of the American Chemical Society October 9, 2013 Volume 135(Issue 40) pp:15251-15256
Publication Date(Web):September 17, 2013
DOI:10.1021/ja408422y
The ability to predict mode/bond selectivity and energy disposal is of central importance for controlling chemical reactions. We argue that the transition state plays a critical role in state-to-state reactivity and propose a simple sudden model based on coupling with the reaction coordinate at the transition state. The applicability of this so-called sudden vector projection (SVP) model is examined for several prototypical atom–triatom, namely, X + H2O (X = H, F, O(3P), and Cl) reactions. It is shown that the SVP model is capable of qualitatively predicting experimental and full-dimensional quantum dynamical results, including those reported in this work, for these polyatomic reactions. These results, and those for other reactions, suggest that the SVP model offers a general paradigm for understanding quantum state resolved reactivity in bimolecular reactions.
Co-reporter:Changjian Xie, Brian K. Kendrick, David R. Yarkony, and Hua Guo
Journal of Chemical Theory and Computation May 9, 2017 Volume 13(Issue 5) pp:1902-1902
Publication Date(Web):March 31, 2017
DOI:10.1021/acs.jctc.7b00124
As a manifestation of the molecular Aharonov–Bohm effect, tunneling-facilitated dissociation under a conical intersection (CI) requires the inclusion of the geometric phase (GP) to ensure a single-valued adiabatic wave function encircling the CI. In this work, we demonstrate using a simple two-dimensional model that the GP induces destructive interference for vibrational states with even quanta in the coupling mode, but it leads to constructive interference for those with odd quanta. The interference patterns are manifested in tunneling wave functions and clearly affect the tunneling lifetime. It is further shown that the inclusion of the diagonal Born–Oppenheimer correction is necessary for agreement with exact results.
Co-reporter:Changjian Xie, Bin Jiang, Jacek Kłos, Praveen Kumar, Millard H. Alexander, Bill Poirier, and Hua Guo
The Journal of Physical Chemistry A July 6, 2017 Volume 121(Issue 26) pp:4930-4930
Publication Date(Web):June 14, 2017
DOI:10.1021/acs.jpca.7b04629
The fragmentation dynamics of predissociative SO2(C̃1B2) is investigated on an accurate adiabatic potential energy surface (PES) determined from high level ab initio data. This singlet PES features non-C2v equilibrium geometries for SO2, which are separated from the SO(X̃3Σ–) + O(3P) dissociation limit by a barrier resulting from a conical intersection with a repulsive singlet state. The ro-vibrational state distribution of the SO fragment is determined quantum mechanically for many predissociative states of several sulfur isotopomers of SO2. Significant rotational and vibrational excitations are found in the SO fragment. It is shown that these fragment internal state distributions are strongly dependent on the predissociative vibronic states, and the excitation typically increases with the photon energy.
Co-reporter:Junxiang Zuo, Changjian Xie, Hua Guo, and Daiqian Xie
The Journal of Physical Chemistry Letters July 20, 2017 Volume 8(Issue 14) pp:3392-3392
Publication Date(Web):July 7, 2017
DOI:10.1021/acs.jpclett.7b01296
The thermal rate coefficients of a prototypical bimolecular reaction are determined on an accurate ab initio potential energy surface (PES) using ring polymer molecular dynamics (RPMD). It is shown that quantum effects such as tunneling and zero-point energy (ZPE) are of critical importance for the HCl + OH reaction at low temperatures, while the heavier deuterium substitution renders tunneling less facile in the DCl + OH reaction. The calculated RPMD rate coefficients are in excellent agreement with experimental data for the HCl + OH reaction in the entire temperature range of 200–1000 K, confirming the accuracy of the PES. On the other hand, the RPMD rate coefficients for the DCl + OH reaction agree with some, but not all, experimental values. The self-consistency of the theoretical results thus allows a quality assessment of the experimental data.
Co-reporter:Praveen Kumar;Jacek Kłos;Bill Poirier;Bin Jiang;Millard H. Alexander
The Journal of Physical Chemistry A February 9, 2017 Volume 121(Issue 5) pp:1012-1021
Publication Date(Web):January 9, 2017
DOI:10.1021/acs.jpca.6b12958
The high resolution spectroscopy of the SO2 molecule is of great topical interest, in a wide variety of contexts ranging from origins of higher life, to astrophysics of the interstellar medium, to environmental chemistry. In particular, the C̃1B2 ← X̃1A1 UV photoabsorption spectrum has received considerable attention. This spectrum exhibits a highly regular progression of ∼20 or so strong peaks, spaced roughly 350 cm–1 apart, which is comparable to the C̃1B2 bending vibrational frequency. Accordingly, they have for decades been largely attributed to the (1, v2′, 2) ← (0, 0, 0) bend progression. Using a highly accurate new ab initio potential energy surface (PES) for the C̃1B2 state, we compute vibrational energy levels and wave functions, and compare with a photoabsorption calculation obtained using the same PES and corresponding C̃1B2 ← X̃1A1 transition dipole surface (TDS). We find that the above putative assignment is incorrect, contradicting even general qualitative trends—thus necessitating a very different dynamical picture for this highly unusual molecule.
Co-reporter:Brian Kolb, Xuan Luo, Xueyao Zhou, Bin JiangHua Guo
The Journal of Physical Chemistry Letters February 2, 2017 Volume 8(Issue 3) pp:
Publication Date(Web):January 19, 2017
DOI:10.1021/acs.jpclett.6b02994
Ab initio molecular dynamics (AIMD) simulations of molecule–surface scattering allow first-principles characterization of the dynamics. However, the large number of density functional theory calculations along the trajectories is very costly, limiting simulations of long-time events and giving rise to poor statistics. To avoid this computational bottleneck, we report here the development of a high-dimensional molecule–surface interaction potential energy surface (PES) with movable surface atoms, using a machine learning approach. With 60 degrees of freedom, this PES allows energy transfer between the energetic impinging molecule and thermal surface atoms. Classical trajectory calculations for the scattering of DCl from Au(111) on this PES are found to agree well with AIMD simulations, with ∼105-fold acceleration. Scattering of HCl from Au(111) is further investigated and compared with available experimental results.
Co-reporter:Brian Kolb, Paul Marshall, Bin Zhao, Bin Jiang, and Hua Guo
The Journal of Physical Chemistry A April 6, 2017 Volume 121(Issue 13) pp:2552-2552
Publication Date(Web):March 13, 2017
DOI:10.1021/acs.jpca.7b01182
Representation of multidimensional global potential energy surfaces suitable for spectral and dynamical calculations from high-level ab initio calculations remains a challenge. Here, we present a detailed study on constructing potential energy surfaces using a machine learning method, namely, Gaussian process regression. Tests for the 3A″ state of SH2, which facilitates the SH + H ↔ S(3P) + H2 abstraction reaction and the SH + H′ ↔ SH′ + H exchange reaction, suggest that the Gaussian process is capable of providing a reasonable potential energy surface with a small number (∼1 × 102) of ab initio points, but it needs substantially more points (∼1 × 103) to converge reaction probabilities. The implications of these observations for construction of potential energy surfaces are discussed.
Chemical Physics Letters 2017 Volume 683(Volume 683) pp:
Publication Date(Web):1 September 2017
DOI:10.1016/j.cplett.2017.02.026
•Tunneling lifetime of phenol (S1) is computed on two sets of coupled potential energy surfaces.•The diabatic and various adiabatic treatments were compared.•The results suggest the importance of including the geometric phase and diagonal Born-Oppenheimer correction in the adiabatic treatment.The nonadiabatic tunneling-facilitated photodissociation of phenol is investigated using a reduced-dimensional quantum model on two ab initio-based coupled potential energy surfaces (PESs). Although dynamics occurs largely on the lower adiabat, the proximity to a conical intersection between the S1 and S2 states requires the inclusion of both the geometric phase (GP) and diagonal Born-Oppenheimer correction (DBOC). The lifetime of the lowest-lying vibronic state is computed using the diabatic and various adiabatic models. The GP and DBOC terms are found to be essential on one set of PESs, but have a small impact on the other.Download high-res image (87KB)Download full-size image
Physical Chemistry Chemical Physics 2017 vol. 19(Issue 45) pp:30540-30550
Publication Date(Web):2017/11/22
DOI:10.1039/C7CP05993K
A fifteen-dimensional global potential energy surface for the dissociative chemisorption of methane on the rigid Ni(111) surface is developed by a high fidelity fit of ∼200 000 DFT energy points computed using a specific reaction parameter density functional designed to reproduce experimental data. The permutation symmetry and surface periodicity are rigorously enforced using the permutation invariant polynomial-neural network approach. The fitting accuracy of the potential energy surface is thoroughly investigated by examining both static and dynamical attributes of CHD3 dissociation on the frozen surface. This potential energy surface is expected to be chemically accurate as after correction for surface temperature effects it reproduces the measured initial sticking probabilities of CHD3 on Ni(111) for various incidence conditions.
Chemical Society Reviews 2017 vol. 46(Issue 24) pp:7650-7667
Publication Date(Web):2017/12/11
DOI:10.1039/C7CS00684E
The dynamics of chemical reactions are often governed by transient species, including the transition state for activated bimolecular reactions. Such transient species are difficult to study experimentally, but it has proven valuable to prepare and probe transition-state dynamics by the photodetachment of anions with an equilibrium geometry similar to the neutral transition state. In this review, recent experimental advances in photoelectron and photoelectron–photofragment coincidence spectroscopy are discussed, as well as the latest progress in the calculation of multidimensional potential energy surfaces and quantum dynamics calculations that have enabled an extension of studies of transition-state dynamics to increasingly multidimensional polyatomic systems. Examples of important dynamical effects such as mode specificity, tunneling, resonance and product energy disposal in reaction dynamics are discussed.
Co-reporter:Bin Jiang, Minghui Yang, Daiqian Xie and Hua Guo
Chemical Society Reviews 2016 vol. 45(Issue 13) pp:3621-3640
Publication Date(Web):23 Jun 2015
DOI:10.1039/C5CS00360A
Dissociative chemisorption is the initial and often rate-limiting step in many heterogeneous processes. As a result, an in-depth understanding of the reaction dynamics of such processes is of great importance for the establishment of a predictive model of heterogeneous catalysis. Overwhelming experimental evidence has suggested that these processes have a non-statistical nature and excitations in various reactant modes have a significant impact on reactivity. A comprehensive characterization of the reaction dynamics requires a quantum mechanical treatment on a global potential energy surface. In this review, we summarize recent progress in constructing high-dimensional potential energy surfaces for polyatomic molecules interacting with transition metal surfaces based on the plane-wave density functional theory and in quantum dynamical studies of dissociative chemisorption on these potential energy surfaces. A special focus is placed on the mode specificity and bond selectivity in these gas–surface collisional processes, and their rationalization in terms of the recently proposed Sudden Vector Projection model.
Co-reporter:Changjian Xie; Jianyi Ma; Xiaolei Zhu; David R. Yarkony; Daiqian Xie
Journal of the American Chemical Society 2016 Volume 138(Issue 25) pp:7828-7831
Publication Date(Web):June 9, 2016
DOI:10.1021/jacs.6b03288
Using recently developed full-dimensional coupled quasi-diabatic ab initio potential energy surfaces including four electronic (1ππ, 1ππ*, 11πσ*, and 21πσ*) states, the tunneling dynamics of phenol photodissociation via its first excited singlet state (S1 ← S0) is investigated quantum mechanically using a three-dimensional model. The lifetimes of several low-lying vibrational states are examined and compared with experiment. The deuteration of the phenoxyl hydrogen is found to dramatically increase the lifetime, attesting to the tunneling nature of the nonadiabatic dissociation. Importantly, it is shown that owing to the conical intersection topography tunneling in this system cannot be described in the standard adiabatic approximation, which eschews the geometric phase effect since the nonadiabatically computed lifetimes, validated by comparison with experiment, differ significantly from those obtained in that limit.
Chemical Science 2016 vol. 7(Issue 7) pp:3992-4003
Publication Date(Web):13 Apr 2016
DOI:10.1039/C6SC01066K
It has been long established that the transition state for an activated reaction controls the overall reactivity, serving as the bottleneck for reaction flux. However, the role of the transition state in regulating quantum state resolved reactivity has only been addressed more recently, thanks to advances in both experimental and theoretical techniques. In this perspective, we discuss some recent advances in understanding mode-specific reaction dynamics in bimolecular reactions, mainly focusing on the X + H2O/CH4 (X = H, F, Cl, and O(3P)) systems, extensively studied in our groups. These advances shed valuable light on the importance of the transition state in mode-specific and steric dynamics of these prototypical reactions. It is shown that many mode-specific phenomena can be understood in terms of a transition-state based model, which assumes in the sudden limit that the ability of a reactant mode for promoting the reaction stems from its coupling with the reaction coordinate at the transition state. Yet, in some cases the long-range anisotropic interactions in the entrance (or exit) valley, which govern how the trajectories reach (or leave) the transition state, also come into play, thus modifying the reactive outcomes.
Co-reporter:Hongwei Song, Anyang Li, Hua Guo, Yuntao Xu, Bo Xiong, Yih-Chung Chang and C. Y. Ng
Physical Chemistry Chemical Physics 2016 vol. 18(Issue 32) pp:22509-22515
Publication Date(Web):22 Jul 2016
DOI:10.1039/C6CP04598G
To understand the dynamics of H3O+ formation, we report a combined experimental–theoretical study of the rovibrationally state-selected ion–molecule reactions H2O+(X2B1; v1+v2+v3+; NKa+Kc++) + H2 (D2) → H3O+ (H2DO+) + H (D), where (v1+v2+v3+) = (000), (020), and (100) and NKa+Kc++ = 000, 111, and 211. Both quantum dynamics and quasi-classical trajectory calculations were carried out on an accurate full-dimensional ab initio global potential energy surface, which involves nine degrees of freedom. The theoretical results are in good agreement with experimental measurements of the initial state specific integral cross-sections for the formation of H3O+ (H2DO+) and thus provide valuable insights into the surprising rotational enhancement and vibrational inhibition effects in these prototypical ion–molecule reactions that play a key role in the interstellar generation of OH and H2O species.
The Journal of Physical Chemistry A 2016 Volume 120(Issue 27) pp:4742-4748
Publication Date(Web):January 5, 2016
DOI:10.1021/acs.jpca.5b11574
Initial state selected time-dependent wave packet and quasi-classical trajectory methods are employed to study the effects of reactant rotational excitations and isotopic substitutions on the title reaction. The coupled-channel (CC) and/or centrifugal sudden (CS) integral cross sections are calculated quantum mechanically. It was found that the CS cross sections are slightly smaller than the CC counterparts over the collision energy range studied. The quantum dynamical and quasi-classical trajectory results agree reasonably well and both indicate that the rotational excitation of H2 enhances the reaction in all energies, whereas the rotational excitation of OH+ promotes the reaction more strongly at low collision energies but has a negligible effect at high collision energies. In addition, there exist significant isotopic substitution effects: The reaction cross section of the D2 + OH+ reaction is much lower than those of the H2 + OH+ and HD + OH+ reactions, which are quite close.
Co-reporter:Frédéric A. L. Mauguière, Peter Collins, Stamatis Stamatiadis, Anyang Li, Gregory S. Ezra, Stavros C. Farantos, Zeb C. Kramer, Barry K. Carpenter, Stephen Wiggins, and Hua Guo
The Journal of Physical Chemistry A 2016 Volume 120(Issue 27) pp:5145-5154
Publication Date(Web):February 26, 2016
DOI:10.1021/acs.jpca.6b00682
The roaming mechanism in the reaction H + MgH →Mg + HH is investigated by classical and quantum dynamics employing an accurate ab initio three-dimensional ground electronic state potential energy surface. The reaction dynamics are explored by running trajectories initialized on a four-dimensional dividing surface anchored on three-dimensional normally hyperbolic invariant manifold associated with a family of unstable orbiting periodic orbits in the entrance channel of the reaction (H + MgH). By locating periodic orbits localized in the HMgH well or involving H orbiting around the MgH diatom, and following their continuation with the total energy, regions in phase space where reactive or nonreactive trajectories may be trapped are found. In this way roaming reaction pathways are deduced in phase space. Patterns similar to periodic orbits projected into configuration space are found for the quantum bound and resonance eigenstates. Roaming is attributed to the capture of the trajectories in the neighborhood of certain periodic orbits. The complex forming trajectories in the HMgH well can either return to the radical channel or “roam” to the MgHH minimum from where the molecule may react.
The Journal of Physical Chemistry A 2016 Volume 120(Issue 19) pp:2991-2998
Publication Date(Web):September 30, 2015
DOI:10.1021/acs.jpca.5b08491
A full-dimensional potential energy surface is developed for dioxirane based on a high-fidelity fit of ∼46,000 ab initio points at the CCSD(T)-F12a/AVTZ level. The ro-vibrational levels of dioxirane were computed using the MULTIMODE method on this potential energy surface, and the agreement with the available experimental microwave spectrum is quite satisfactory. In addition, dipole moment surfaces have been constructed from ab initio data, and they allow the prediction of the infrared (IR) spectrum.
Co-reporter:Donald J. Arseneau and Donald G. Fleming, Yongle Li , Jun Li, Yury V. Suleimanov , Hua Guo
The Journal of Physical Chemistry B 2016 Volume 120(Issue 8) pp:1641-1648
Publication Date(Web):October 20, 2015
DOI:10.1021/acs.jpcb.5b08368
The rate constant for the H atom abstraction reaction from methane by the muonic helium atom, Heμ + CH4 → HeμH + CH3, is reported at 500 K and compared with theory, providing an important test of both the potential energy surface (PES) and reaction rate theory for the prototypical polyatomic CH5 reaction system. The theory used to characterize this reaction includes both variational transition-state (CVT/μOMT) theory (VTST) and ring polymer molecular dynamics (RPMD) calculations on a recently developed PES, which are compared as well with earlier calculations on different PESs for the H, D, and Mu + CH4 reactions, the latter, in particular, providing for a variation in atomic mass by a factor of 36. Though rigorous quantum calculations have been carried out for the H + CH4 reaction, these have not yet been extended to the isotopologues of this reaction (in contrast to H3), so it is important to provide tests of less rigorous theories in comparison with kinetic isotope effects measured by experiment. In this regard, the agreement between the VTST and RPMD calculations and experiment for the rate constant of the Heμ + CH4 reaction at 500 K is excellent, within 10% in both cases, which overlaps with experimental error.
The Journal of Physical Chemistry Letters 2016 Volume 7(Issue 2) pp:327-331
Publication Date(Web):January 6, 2016
DOI:10.1021/acs.jpclett.5b02737
The influence of electron–hole pairs in dissociative chemisorption of a polyatomic molecule (water) on metal surfaces is assessed for the first time using a friction approach. The atomic local density dependent friction coefficients computed based on a free electron gas embedding model are employed in classical molecular dynamics simulations of the water dissociation dynamics on rigid Ni(111) using a recently developed nine dimensional interaction potential energy surface for the system. The results indicate that nonadiabatic effects are relatively small and they do not qualitatively alter the mode specificity in the dissociation.
Co-reporter:Yan Wang, Hongwei Song, István Szabó, Gábor Czakó, Hua Guo, and Minghui Yang
The Journal of Physical Chemistry Letters 2016 Volume 7(Issue 17) pp:3322-3327
Publication Date(Web):August 9, 2016
DOI:10.1021/acs.jpclett.6b01457
Despite its importance in chemistry, the microscopic dynamics of bimolecular nucleophilic substitution (SN2) reactions is still not completely elucidated. In this publication, the dynamics of a prototypical SN2 reaction (F– + CH3Cl → CH3F + Cl–) is investigated using a high-dimensional quantum mechanical model on an accurate potential energy surface (PES) and further analyzed by quasi-classical trajectories on the same PES. While the indirect mechanism dominates at low collision energies, the direct mechanism makes a significant contribution. The reactivity is found to depend on the specific reactant vibrational mode excitation. The mode specificity, which is more prevalent in the direct reaction, is rationalized by a transition-state-based model.
Co-reporter:Changjian Xie, Bin Jiang, Minghui Yang, and Hua Guo
The Journal of Physical Chemistry A 2016 Volume 120(Issue 33) pp:6521-6528
Publication Date(Web):August 3, 2016
DOI:10.1021/acs.jpca.6b06450
The F + CHD3 → HF/DF + CD3/CHD2 reaction is studied using a state-to-state quasi-classical trajectory method on a recently developed ab initio based full-dimensional potential energy surface. Consistent with sudden vector projection model predictions, the HF/DF products are highly excited in both vibrational and rotational modes, while the CD3/CHD2 product internal excitation is mostly in the umbrella/out-of-plane mode. Furthermore, the C–H stretching vibration in the CHD3 reactant is found to behave as an active mode for the HF + CD3 channel, leading to additional excitation in the HF product but having almost no impact on CD3 vibrational state distributions. On the other hand, this mode acts as a spectator for the DF + CHD2 channel, exerting little influence on the DF and other CHD2 vibrational modes except an extra quantum excitation in the C–H stretching mode. The calculated vibrational state resolved differential cross sections are in good agreement with available experimental results at Ec = 9.00 kcal/mol.
The Journal of Physical Chemistry A 2016 Volume 120(Issue 14) pp:2185-2193
Publication Date(Web):March 29, 2016
DOI:10.1021/acs.jpca.6b01946
Vibrational energy levels of the ammonium cation (NH4+) and its deuterated isotopomers are calculated using a numerically exact kinetic energy operator on a recently developed nine-dimensional permutation invariant semiglobal potential energy surface fitted to a large number of high-level ab initio points. Like CH4, the vibrational levels of NH4+ and ND4+ exhibit a polyad structure, characterized by a collective quantum number P = 2(v1 + v3) + v2 + v4. The low-lying vibrational levels of all isotopomers are assigned and the agreement with available experimental data is better than 1 cm–1.
Co-reporter:Yury V. Suleimanov, F. Javier Aoiz , Hua Guo
The Journal of Physical Chemistry A 2016 Volume 120(Issue 43) pp:8488-8502
Publication Date(Web):September 14, 2016
DOI:10.1021/acs.jpca.6b07140
This Feature Article presents an overview of the current status of ring polymer molecular dynamics (RPMD) rate theory. We first analyze the RPMD approach and its connection to quantum transition-state theory. We then focus on its practical applications to prototypical chemical reactions in the gas phase, which demonstrate how accurate and reliable RPMD is for calculating thermal chemical reaction rate coefficients in multifarious cases. This review serves as an important checkpoint in RPMD rate theory development, which shows that RPMD is shifting from being just one of recent novel ideas to a well-established and validated alternative to conventional techniques for calculating thermal chemical rate coefficients. We also hope it will motivate further applications of RPMD to various chemical reactions.
Journal of the American Chemical Society 2015 Volume 137(Issue 50) pp:15964-15970
Publication Date(Web):November 27, 2015
DOI:10.1021/jacs.5b11404
Energy flow and sequestration at the state-to-state level are investigated for a prototypical four-atom reaction, H2 + OH → H + H2O, using a transition-state wave packet (TSWP) method. The product state distribution is found to depend strongly on the reactant vibrational excitation, indicating mode specificity at the state-to-state level. From a local-mode perspective, it is shown that the vibrational excitation of the H2O product derives from two different sources, one attributable to the energy flow along the reaction coordinate into the newly formed OH bond and the other due to the sequestration of the vibrational energy in the OH spectator moiety during the reaction. The analysis provided a unified interpretation of some seemingly contradicting experimental observations. It is further shown that the transfer of vibrational energy from the OH reactant to H2O product is gated by the transition state, accomplished coherently by multiple TSWPs with the corresponding OH vibrational excitation.
Physical Chemistry Chemical Physics 2015 vol. 17(Issue 6) pp:4259-4267
Publication Date(Web):22 Dec 2014
DOI:10.1039/C4CP05165C
Bond-selective reaction dynamics of the title reaction is investigated using full-dimensional quantum dynamical (QD) and quasi-classical trajectory (QCT) methods on a newly constructed ab initio global potential energy surface. Both QD and QCT results indicate that excitation of the local OH vibration in the HOD reactant renders the reaction strongly bond selective, with the OD/OH branching ratio in quantitative agreement with the experiment. In addition, the reactivity is found to be greatly enhanced with the reactant vibrational excitation, thanks to the change of a direct rebound mechanism to a capture mechanism. The QCT calculations also yield product state distributions, which show that the HCl product is vibrationally and rotationally hot while the OD co-product is internally cold. The bond selectivity, vibrational enhancement, and product energy disposal are rationalized by the Sudden Vector Projection model.
Co-reporter:Bin Jiang, Xixi Hu, Sen Lin, Daiqian Xie and Hua Guo
Physical Chemistry Chemical Physics 2015 vol. 17(Issue 36) pp:23346-23355
Publication Date(Web):07 Aug 2015
DOI:10.1039/C5CP03324A
Cobalt is a widely used catalyst for many heterogeneous reactions, including the Fischer–Tropsch (FT) process, which converts syngas (H2 and CO) to higher hydrocarbons. As a result, a better understanding of the key chemical steps on the Co surface, such as the dissociative chemisorption of H2 as an initial step of the FT process, is of fundamental importance. Here, we report an accurate full-dimensional global potential energy surface for the dissociative chemisorption of H2 on the rigid Co(0001) surface constructed from more than 3000 density functional theory points. The high-fidelity potential energy surface was obtained using the permutation invariant polynomial-neural network method, which preserves both the permutation symmetry of H2 and translational symmetry of the Co(0001) surface. The reaction path features a very low barrier on the top site. Full-dimensional quantum dynamical calculations provide insights into the dissociation dynamics and influence of the initial vibrational, rotational, and orientational degrees of freedom.
Chemical Physics Letters 2015 Volume 624() pp:102-106
Publication Date(Web):16 March 2015
DOI:10.1016/j.cplett.2015.02.027
•Bending mode of 1,3-dipoles promotes 1,3-dipolar cycloaddition reactions.•Mode specificity in 1,3-dipolar cycloaddition reactions can be predicted from SVP model.•Such predictions only need information on the transition state and can thus be made without doing trajectory calculations.Mode specificity in the cycloaddition of 1,3-dipoles to ethene and ethyne is investigated with the newly proposed Sudden Vector Projection (SVP) model, which attributes the promoting ability of a reactant mode to its projection onto the reaction coordinate at the transition state. The SVP model revealed that dipole bending and translational modes have large components in the reaction coordinate, consistent with the recent direct dynamics studies. It further identified several other promoting modes. The success of the SVP model is encouraging as it requires no dynamics calculations, and as a result it can be applied to many reactions.
The Journal of Physical Chemistry Letters 2015 Volume 6(Issue 23) pp:4822-4826
Publication Date(Web):November 18, 2015
DOI:10.1021/acs.jpclett.5b02366
The photodetachment of the FH2O– anion is investigated quantum mechanically on accurate full-dimensional potential energy surfaces of the two lowest-lying electronic states of FH2O. The calculated photoelectron spectrum possesses both broad and sharp features, corresponding to reactive and nonreactive Feshbach resonances. The former extend to both reactant and product channels over the transition state, while the latter are supported by a hydrogen bonded HO–HF well in the product channel. Many of the resonances are assignable with quantum numbers for the stretching and bending modes of the HO–HF complex as well as the H–F vibration. The implications of these resonances in the F + H2O ↔ HF + HO reaction are discussed.
Co-reporter:Jun Li, Bin Jiang, Hongwei Song, Jianyi Ma, Bin Zhao, Richard Dawes, and Hua Guo
The Journal of Physical Chemistry A 2015 Volume 119(Issue 20) pp:4667-4687
Publication Date(Web):April 17, 2015
DOI:10.1021/acs.jpca.5b02510
We survey the recent advances in theoretical understanding of quantum state resolved dynamics, using the title reactions as examples. It is shown that the progress was made possible by major developments in two areas. First, an accurate analytical representation of many high-level ab initio points over a large configuration space can now be made with high fidelity and the necessary permutation symmetry. The resulting full-dimensional global potential energy surfaces enable dynamical calculations using either quasi-classical trajectory or more importantly quantum mechanical methods. The second advance is the development of accurate and efficient quantum dynamical methods, which are necessary for providing a reliable treatment of quantum effects in reaction dynamics such as tunneling, resonances, and zero-point energy. The powerful combination of the two advances has allowed us to achieve a quantitatively accurate characterization of the reaction dynamics, which unveiled rich dynamical features such as steric steering, strong mode specificity, and bond selectivity. The dependence of reactivity on reactant modes can be rationalized by the recently proposed sudden vector projection model, which attributes the mode specificity and bond selectivity to the coupling of reactant modes with the reaction coordinate at the relevant transition state. The deeper insights provided by these theoretical studies have advanced our understanding of reaction dynamics to a new level.
The Journal of Physical Chemistry A 2015 Volume 119(Issue 24) pp:6188-6194
Publication Date(Web):May 19, 2015
DOI:10.1021/acs.jpca.5b03740
The vibrational and rotational mode specificity of the Cl + H2O → HCl + OH reaction is studied on a recently constructed ab initio based global potential energy surface using an initial state selected Chebyshev real wave packet method. The full-dimensional quantum dynamical results under the centrifugal sudden and/or J-shifting approximations indicate that this reaction is enhanced strongly by excitations of the stretching modes of the H2O reactant but only weakly by bending excitations. On the other hand, combination modes are found to enhance the reaction more than the sum of individual excitations. In addition, rotational excitation of the H2O reactant slightly inhibits the reactivity. The observed mode specificity is consistent with the predictions of the recently proposed Sudden Vector Projection model, which attributes the promotional effects of the reactant modes to their couplings with the reaction coordinate at the transition state.
Co-reporter:Lindong Zou, Jun Li, Hui Wang, Jianyi Ma, and Hua Guo
The Journal of Physical Chemistry A 2015 Volume 119(Issue 28) pp:7316-7324
Publication Date(Web):January 21, 2015
DOI:10.1021/jp512557k
Full-dimensional quantum dynamics studies of the photodetachment of HCO2– and DCO2– are reported using a wave-packet method on an accurate global potential energy surface of the neutral HOCO/HCO2 system. The calculated photoelectron spectra reproduced both the positions and widths of the main HCO2 and DCO2 peaks observed in experiment. Specifically, both the 2A1 and 2B2 resonance peaks of the neutral radicals were identified in our simulations thanks to the adiabatic PES that captures both the 2A1 and 2B2 minima. The narrow widths and isotope effect of the lowest resonances are indicative of tunneling-facilitated predissociation. Furthermore, the dissociation product CO2 was found to be excited in both its symmetric stretching and bending modes, which are coupled via a strong Fermi resonance, but rotationally cold, in good agreement with the recent photoelectron–photodetachment coincidence experiments.
Co-reporter:Lifen Guo, Huixian Han, Jianyi Ma, and Hua Guo
The Journal of Physical Chemistry A 2015 Volume 119(Issue 31) pp:8488-8496
Publication Date(Web):June 24, 2015
DOI:10.1021/acs.jpca.5b05061
Vinylidene is a high-energy isomer of acetylene, and the rearrangement of bonds in the two species serves as a prototype for isomerization reactions. Here, a full-dimensional quantum mechanical study of the vinylidene vibration is carried out on a recently developed global acetylene–vinylidene potential energy surface by simulating the photodetachment dynamics of the vinylidene anion. Several low-lying vibrational levels of the anion were first determined on a new ab initio based potential energy surface, and their photoelectron spectra were obtained within the Condon approximation. The vibrational features of the vinylidene isomer are found to agree well with the experiment in both positions and intensities, validating the global acetylene–vinylidene potential energy surface.
Co-reporter:Hongwei Song, Soo-Ying Lee, Yunpeng Lu, and Hua Guo
The Journal of Physical Chemistry A 2015 Volume 119(Issue 50) pp:12224-12230
Publication Date(Web):August 5, 2015
DOI:10.1021/acs.jpca.5b06230
Full-dimensional quantum dynamical calculations are carried out to study the mode specificity, bond selectivity, and isotopic branching ratio of the Cl + HOD reaction on an accurate global potential energy surface. Total reaction cross sections have been computed for several low-lying vibrational states of HOD. Our results confirm the experimental observed vibrationally promoted bond cleavage, in which the breaking of the OH(OD) bond is strongly enhanced by the OH(OD) excitation. These results are rationalized by the recently proposed sudden vector projection model. In addition, the OH/OD branching ratio as a function of energy is investigated and rationalized by a reorientation effect.
The Journal of Physical Chemistry Letters 2015 Volume 6(Issue 4) pp:676-680
Publication Date(Web):February 3, 2015
DOI:10.1021/acs.jpclett.5b00071
The full-dimensional quantum dynamics of the F + H2O → HF + OH reaction is investigated at the state-to-state level for the first time using a transition-state wave packet method on an accurate global potential energy surface. It is found that the H2O rotation enhances the reactivity and the product-state distribution is dominated by HF vibrational excitation while the OH moiety serves effectively as a spectator. These observations underscore the transition-state control of the reaction dynamics, as both the H2O rotational and HF vibrational modes are strongly coupled to the reaction coordinate at the transition state. It is also shown that the transition-state dominance of the reaction dynamics is modulated by other features on the potential energy surface, such as the prereaction well.
Co-reporter:Huixian Han, Hongwei Song, Jun Li, and Hua Guo
The Journal of Physical Chemistry A 2015 Volume 119(Issue 14) pp:3400-3406
Publication Date(Web):March 17, 2015
DOI:10.1021/acs.jpca.5b01835
A nine-dimensional potential energy surface (PES) for the ammonium cation has been constructed by fitting ∼30 000 AE-CCSD(T)-F12a/cc-pCVTZ-F12 points up to 32 262 cm–1 (4.0 eV) from the minimum. The fitting using the permutation invariant polynomial-neural network method has high fidelity, with a root-mean-square error of merely 2.34 cm–1. The low-lying vibrational energy levels of NH4+ have been determined quantum mechanically using both Jacobi and normal coordinates, and the fundamental frequencies are in excellent agreement with available experimental data.
The Journal of Physical Chemistry A 2015 Volume 119(Issue 5) pp:826-831
Publication Date(Web):January 12, 2015
DOI:10.1021/jp512021m
The dynamics and mode specificity of the HCl + OH → Cl + H2O reaction are investigated using a full-dimensional quantum dynamics method on an accurate global potential energy surface. It is shown that the vibrational excitation of the HCl reactant greatly enhances the reactivity while the OH vibrational excitation has little effect. The surprising HCl vibrational enhancement of this early barrier reaction contradicts a naive extension of Polanyi’s rules, but can be explained by the sudden vector projection model, which attributes the promotional effect of the HCl vibration to its strong coupling with the reaction coordinate at the transition state. In addition, it is found that the fundamental and overtone excitations of the HCl reactant change the reaction mechanism from a direct barrier crossing process to a capture-like process.
Accounts of Chemical Research 2014 Volume 47(Issue 12) pp:3679
Publication Date(Web):November 13, 2014
DOI:10.1021/ar500350f
ConspectusMode specificity is defined by the differences in reactivity due to excitations in various reactant modes, while bond selectivity refers to selective bond breaking in a reaction. These phenomena not only shed light on reaction dynamics but also open the door for laser control of reactions. The existence of mode specificity and bond selectivity in a reaction indicates that not all forms of energy are equivalent in promoting the reactivity, thus defying a statistical treatment. They also allow the enhancement of reactivity and control product branching ratio. As a result, they are of central importance in chemistry.This Account discusses recent advances in our understanding of these nonstatistical phenomena. In particular, the newly proposed sudden vector projection (SVP) model and its applications are reviewed. The SVP model is based on the premise that the collision in many direct reactions is much faster than intramolecular vibrational energy redistribution in the reactants. In such a sudden limit, the coupling of a reactant mode with the reaction coordinate at the transition state, which dictates its ability to promote the reaction, is approximately quantified by the projection of the former onto the latter. The SVP model can be considered as a generalization of the venerable Polanyi’s rules, which are based on the location of the barrier. The SVP model is instead based on properties of the saddle point and as a result capable of treating the translational, rotational, and multiple vibrational modes in reactions involving polyatomic reactants. In case of surface reactions, the involvement of surface atoms can also be examined. Taking advantage of microscopic reversibility, the SVP model has also been used to predict product energy disposal in reactions. This simple yet powerful rule of thumb has been successfully demonstrated in many reactions including uni- and bimolecular reactions in the gas phase and gas–surface reactions. The success of the SVP model underscores the importance of the transition state in controlling mode-specific and bond-selective chemistry.
Journal of the American Chemical Society 2014 Volume 137(Issue 1) pp:50-53
Publication Date(Web):December 3, 2014
DOI:10.1021/ja510736d
The lowest-lying singlet states of the simplest Criegee intermediate (CH2OO) have been characterized along the O–O dissociation coordinate using explicitly correlated MRCI-F12 electronic structure theory and large active spaces. It is found that a high-level treatment of dynamic electron-correlation is essential to accurately describe these states. A significant well on the B-state is identified at the MRCI-F12 level with an equilibrium structure that differs substantially from that of the ground X-state. This well is presumably responsible for the apparent vibrational structure in some experimental UV absorption spectra, analogous to the structured Huggins band of the iso-electronic ozone. The B-state potential in the Franck–Condon region is sufficiently accurate that an absorption spectrum calculated with a one-dimensional model agrees remarkably well with experiment.
Physical Chemistry Chemical Physics 2014 vol. 16(Issue 14) pp:6753-6763
Publication Date(Web):12 Feb 2014
DOI:10.1039/C4CP00241E
Extensive ab initio calculations of the stationary points in the NH4(X2A1) system are reported using both coupled cluster and multi-reference configuration interaction methods. In addition, more than 100000 points are generated over a large configuration space and energy range (6 eV) using the explicitly correlated unrestricted coupled cluster method with single, double, and perturbative triple excitations with the augmented correlation-consistent polarized triple zeta basis set (UCCSD(T)-F12a/aug-cc-pVTZ). Using the recently proposed permutation-invariant polynomial neural network (PIP-NN) method, these points are accurately fit to an analytical form with a total root mean squared error (RMSE) of 3.4 meV (0.08 kcal mol−1). Both the abstraction and exchange channels as well as the metastable ammonium radical (NH4) are included in this potential energy surface. Transition-state theory and quasi-classical trajectory calculations have been performed to obtain the rate constants for the abstraction reaction and its reverse. Comparison with available experimental results is satisfactory, providing supporting evidence for the accuracy of the potential.
Physical Chemistry Chemical Physics 2014 vol. 16(Issue 45) pp:24704-24715
Publication Date(Web):09 Oct 2014
DOI:10.1039/C4CP03761H
A six-dimensional potential energy surface (PES) for H2 dissociation on rigid Ag(111) is developed by fitting ∼4000 plane-wave density functional theory points using the recently proposed permutation invariant polynomial-neural network (PIP-NN) method, which enforces both the surface periodicity and molecular permutation symmetry. Quantum reactive scattering calculations on the PIP-NN PES yielded dissociative sticking probabilities for both H2 and D2. Good agreement with experiment was achieved at high collision energies, but the agreement is less satisfactory at low collision energies, due apparently to the neglect of surface temperature in our model. The dissociation is activated by both vibrational and translational excitations, with roughly equal efficacies. Rotational and alignment effects were examined and found to be quite similar to hydrogen dissociation on Ag(100) and Cu(111).
Co-reporter:Hongwei Song, Jun Li, Minghui Yang, Yunpeng Lu and Hua Guo
Physical Chemistry Chemical Physics 2014 vol. 16(Issue 33) pp:17770-17776
Publication Date(Web):11 Jul 2014
DOI:10.1039/C4CP02227K
Reaction dynamics and mode specificity in the H2 + NH2 → H + NH3 reaction are investigated in full dimensionality on a recent ab initio based global potential energy surface. Integral cross sections from several low-lying vibrational states of both reagents have been calculated under the centrifugal sudden or J-shifting approximations, using an initial state selected time-dependent wave packet method. This nine-dimensional system provides an ideal proving ground to test our recently proposed Sudden Vector Projection (SVP) model. Our results indicate that vibrational excitation of H2 enhances the reactivity. On the other hand, excitation of either the symmetric or antisymmetric stretching mode of NH2 inhibits the reaction, while excitation of its bending mode has a negligible effect. Furthermore, all vibrational modes are less effective than translational energy in promoting the reaction. These mode-specific features are rationalized with the SVP model.
Co-reporter:Yongle Li, Yury V. Suleimanov, and Hua Guo
The Journal of Physical Chemistry Letters 2014 Volume 5(Issue 4) pp:700-705
Publication Date(Web):January 31, 2014
DOI:10.1021/jz500062q
The thermal rate constants of two prototypical insertion-type reactions, namely, N/O + H2 → NH/OH + H, are investigated with ring polymer molecular dynamics (RPMD) on full-dimensional potential energy surfaces using recently developed RPMDrate code. It is shown that the unique ability of the RPMD approach among the existing theoretical methods to capture the quantum effects, e.g., tunneling and zero-point energy, as well as recrossing dynamics quantum mechanically with ring-polymer trajectories leads to excellent agreement with rigorous quantum dynamics calculations. The present result is encouraging for future applications of the RPMD method and the RPMDrate code to complex-forming chemical reactions involving polyatomic reactants.Keywords: insertion reaction; path integral; rate coefficients; tunneling; zero-point energy;
Co-reporter:Jun Li, Stuart Carter, Joel M. Bowman, Richard Dawes, Daiqian Xie, and Hua Guo
The Journal of Physical Chemistry Letters 2014 Volume 5(Issue 13) pp:2364-2369
Publication Date(Web):June 19, 2014
DOI:10.1021/jz501059m
The ro-vibrational spectrum of the simplest Criegee intermediate (CH2OO) has been determined quantum mechanically based on nine-dimensional potential energy and dipole surfaces for its ground electronic state. The potential energy surface is fitted to more than 50 000 high-level ab initio points with a root-mean-square error of 25 cm–1, using a recently proposed permutation invariant polynomial neural network method. The calculated rotational constants, vibrational frequencies, and spectral intensities of CH2OO are in excellent agreement with experiment. The potential energy surface provides a valuable platform for studying highly excited vibrational and unimolecular reaction dynamics of this important molecule.Keywords: ab initio calculations; Criegee intermediate; potential energy surface; ro-vibrational spectrum;
Co-reporter:Changjian Xie, Jianyi Ma, Xiaolei Zhu, Dong Hui Zhang, David R. Yarkony, Daiqian Xie, and Hua Guo
The Journal of Physical Chemistry Letters 2014 Volume 5(Issue 7) pp:1055-1060
Publication Date(Web):March 10, 2014
DOI:10.1021/jz500227d
Full-dimensional state-to-state quantum dynamics of the photodissociation of NH3(Ã1A2″) is investigated on newly developed coupled diabatic potential energy surfaces. For the first time, the rovibrational distributions of the nonadiabatically produced NH2(X̃2B1) product have been determined quantum mechanically. In agreement with experimental observations, NH2(X̃2B1) produced from the 00 and 21 states of NH3(Ã1A2″) was found to be dominated by its ground vibrational state with an N = Ka propensity, shedding light on the quantum-state-resolved nonadiabatic dynamics facilitated by conical intersections and setting the stage for the elucidation of vibrationally mediated photodissociation.Keywords: conical intersection; nonadiabatic transition; photodissociation; product state distribution; reaction dynamics;
The Journal of Physical Chemistry C 2014 Volume 118(Issue 46) pp:26851-26858
Publication Date(Web):October 24, 2014
DOI:10.1021/jp5090839
Dissociative chemisorption of water is a key step in many heterogeneous catalytic processes such as water–gas shift and steam reformation. As a result, a better understanding of the mechanism and dynamics of these processes is important for developing a predictive model of catalysis. In this work, we use the recently proposed Sudden Vector Projection (SVP) model to predict mode specificity, bond selectivity, normal scaling behavior, and surface lattice effects in water dissociative chemisorption on Ni(111), Cu(111), Pt(111), and Pt(110)-(1 × 2), based on direct plane-wave density functional theory calculations. While mode specificity and bond selectivity are similar on these surfaces, the SVP model predicts significant differences in the reaction promoting effects of kinetic energies in the surface normal and along the surface plane, signifying the different characters of the transition state on these metal surfaces. Furthermore, the involvement of surface atoms is shown, which predicts significant surface temperature effects.
Co-reporter:Yongle Li, Yury V. Suleimanov, William H. Green, and Hua Guo
The Journal of Physical Chemistry A 2014 Volume 118(Issue 11) pp:1989-1996
Publication Date(Web):February 24, 2014
DOI:10.1021/jp501043z
Thermal rate coefficients and kinetic isotope effect have been calculated for prototypical heavy–light–heavy polyatomic bimolecular reactions Cl + CH4/CD4 → HCl/DCl + CH3/CD3, using a recently proposed quantum dynamics approach: ring polymer molecular dynamics (RPMD). Agreement with experimental rate coefficients, which are quite scattered, is satisfactory. However, differences up to 50% have been found between the RPMD results and those obtained from the harmonic variational transition-state theory on one of the two full-dimensional potential energy surfaces used in the calculations. Possible reasons for such discrepancy are discussed. The present work is an important step in a series of benchmark studies aimed at assessing accuracy for RPMD for chemical reaction rates, which demonstrates that this novel method is a quite reliable alternative to previously developed techniques based on transition-state theory.
The Journal of Physical Chemistry A 2014 Volume 118(Issue 13) pp:2419-2425
Publication Date(Web):March 11, 2014
DOI:10.1021/jp501255t
A simple model is proposed to predict mode specificity and product energy disposal in unimolecular dissociation reactions. This so-called Sudden Vector Projection (SVP) model quantifies the coupling of a reactant or product mode with the reaction coordinate at the transition state by projecting the corresponding normal mode vector onto the imaginary frequency mode at the saddle point. Due to the sudden assumption, SVP predictions for mode specificity are expected to be valid only when the reactant molecule has weak intermodal coupling. On the other hand, the sudden limit is generally satisfied for its predictions of product energy disposal in unimolecular reactions with a tight barrier. The SVP model is applied to several prototypical systems and the agreement with available experimental and theoretical results is satisfactory.
The Journal of Physical Chemistry A 2014 Volume 118(Issue 47) pp:11168-11176
Publication Date(Web):October 24, 2014
DOI:10.1021/jp5100507
An accurate full-dimensional global potential energy surface (PES) is developed for the title reaction. The PES was based on ∼30 000 points at the Davidson corrected multireference configuration interaction level with the aug-cc-pVQZ basis set (MRCI+Q/AVQZ). The ab initio points were fitted using the permutation invariant polynomial-neural network (PIP-NN) method with a root-mean-square error of about 3.0 meV or 24 cm–1. The kinetics of the OH+ + H2 and OH+ + D2 reactions were investigated on the PIP-NN PES using a quasi-classical trajectory method and the calculated thermal rate coefficients are in good agreement with the available experimental data. Furthermore, it is predicted based on the PES using the Sudden Vector Projection model that the rotational excitation of OH+ enhances the reaction at low collision energies.
Co-reporter:Shaun G. Ard, Anyang Li, Oscar Martinez Jr., Nicholas S. Shuman, Albert A. Viggiano, and Hua Guo
The Journal of Physical Chemistry A 2014 Volume 118(Issue 49) pp:11485-11489
Publication Date(Web):November 14, 2014
DOI:10.1021/jp510399v
Thermal rate coefficients for the title reactions computed using a quasi-classical trajectory method on an accurate global potential energy surface fitted to ∼81,000 high-level ab initio points are compared with experimental values measured between 100 and 600 K using a variable temperature selected ion flow tube instrument. Excellent agreement is found across the entire temperature range, showing a subtle, but unusual temperature dependence of the rate coefficients. For both reactions the temperature dependence has a maximum around 350 K, which is a result of H2O+ rotations increasing the reactivity, while kinetic energy is decreasing the reactivity. A strong isotope effect is found, although the calculations slightly overestimate the kinetic isotope effect. The good experiment–theory agreement not only validates the accuracy of the potential energy surface but also provides more accurate kinetic data over a large temperature range.
Co-reporter:Jianyi Ma, Changjian Xie, Xiaolei Zhu, David R. Yarkony, Daiqian Xie, and Hua Guo
The Journal of Physical Chemistry A 2014 Volume 118(Issue 51) pp:11926-11934
Publication Date(Web):July 18, 2014
DOI:10.1021/jp5057122
Vibrationally mediated photodissociation of NH3 and ND3 in the A band allows the exploration of the excited-state potential energy surface in regions that are not accessible from the ground vibrational state of these polyatomic systems. Using our recently developed coupled ab initio potential energy surfaces in a quasi-diabatic representation, we report here a full-dimensional quantum characterization of the à ← X̃ absorption spectra for vibrationally excited NH3 and ND3 and the corresponding nonadiabatic dissociation dynamics into the NH2(Ã2A1) + H and NH2(X̃2B1) + H channels. The predissociative resonances in the absorption spectra have been assigned with appropriate quantum numbers. The NH2(Ã2A1)/NH2(X̃2B1) branching ratio was found to be mildly sensitive to the initial vibrational excitation prior to photolysis. Implications for interpreting experimental data are discussed.
Co-reporter:P. Morten Hundt;Bin Jiang;Maarten E. van Reijzen;Rainer D. Beck
Science 2014 Vol 344(6183) pp:504-507
Publication Date(Web):02 May 2014
DOI:10.1126/science.1251277
Vibrating Water Apart
The main route for producing hydrogen for industrial chemical synthesis is steam reforming, in which water and methane react at high temperatures on nickel catalysts to produce hydrogen and carbon dioxide. For both water and methane, the initial dissociation step can be promoted by the translational energy of a molecule as well as its internal vibrational energy, and fundamental studies of these reactions try to determine the relative contributions of these pathways. Although the methane reaction has been well studied, only recently have lasers been available to excite the higher stretching vibrations of water. Hundt et al. (p. 504) now report a joint experimental and theoretical study of D2O dissociation on the Ni(111) surface. For a given input of energy, vibrational energy was more effective for surmounting the reaction barrier than translational energy.
Co-reporter:Rico Otto;Jianyi Ma;Amelia W. Ray;Jennifer S. Daluz;Jun Li;Robert E. Continetti
Science 2014 Volume 343(Issue 6169) pp:
Publication Date(Web):
DOI:10.1126/science.1247424
Abstract
The study of gas-phase reaction dynamics has advanced to a point where four-atom reactions are the proving ground for detailed comparisons between experiment and theory. Here, a combined experimental and theoretical study of the dissociation dynamics of the tetra-atomic FH2O system is presented, providing snapshots of the F + H2O → HF + OH reaction. Photoelectron-photofragment coincidence measurements of the dissociative photodetachment (DPD) of the F¯(H2O) anion revealed various dissociation pathways along different electronic states. A distinct photoelectron spectrum of stable FH–OH complexes was also measured and attributed to long-lived Feshbach resonances. Comparison to full-dimensional quantum calculations confirms the sensitivity of the DPD measurements to the subtle dynamics on the low-lying FH2O potential energy surfaces over a wide range of nuclear configurations and energies.
Journal of the American Chemical Society 2013 Volume 135(Issue 3) pp:982-985
Publication Date(Web):January 9, 2013
DOI:10.1021/ja311159j
The exothermic F + H2O → HF + OH reaction has a decidedly “early” or “reactant-like” barrier. According to a naïve interpretation of the Polanyi’s rules, translational energy would be more effective than vibrational energy in promoting such reactions. However, we demonstrate here using both quasi-classical trajectory and full-dimensional quantum wave packet methods on an accurate global potential energy surface that excitations in the H2O vibrational degrees of freedom have higher efficacy in enhancing the reactivity of the title reaction than the same amount of translational energy, thus providing a counter-example to Polanyi’s rules. This enhancement of reactivity is analyzed using a vibrational adiabatic model, which sheds light on the surprising mode selectivity in this reaction.
Co-reporter:Bin Jiang, Rui Liu, Jun Li, Daiqian Xie, Minghui Yang and Hua Guo
Chemical Science 2013 vol. 4(Issue 8) pp:3249-3254
Publication Date(Web):28 May 2013
DOI:10.1039/C3SC51040A
Dissociative chemisorption of CH4 on transition-metal surfaces, representing the rate-limiting step in methane steam reforming, has been shown experimentally to be strongly mode selective. To understand the mode selectivity, a twelve-dimensional global potential energy surface is developed for CH4 interacting with a rigid Ni(111) surface based on a large number of density functional theory points. The reaction dynamics is investigated using an eight-dimensional quantum model, which includes representatives of all four vibrational modes of methane. After correcting for surface effects, key experimental observations, including the mode selectivity, are well reproduced. These theoretical results, along with mechanistic analysis, provide insights into this industrially important heterogeneous reaction.
The low (3.84 kcal mol−1) transition state for the F + H2O → HF + HO reaction on the ground electronic state potential energy surface is pre-staged by a relatively deep (2.67 kcal mol−1) van der Waals well in the entrance channel. Quasi-classical trajectory studies indicated that this pre-reaction van der Waals complex “guides” trajectories towards the “reactant-like” transition state. Such a stereodynamic effect is shown to enhance the reactivity at low collision energies, resulting in a pronounced peak in the excitation function. A similar enhancement effect was also found in quantum dynamic calculations.
The bond selectivity in dissociative chemisorption of HOD on Cu(111) is investigated using a six-dimensional quantum model. It includes all vibrational modes of the impinging molecule on a density functional theory based interaction potential between the molecule and metal surface. It is shown that excitations in the HOD local stretching modes selectively enhance cleavage of the excited bond. This pronounced bond selectivity is attributed to a “late” or “product-like” barrier on the potential energy surface for the dissociative chemisorption and the slow intramolecular vibrational energy redistribution in the water molecule. The existence of mode and bond selectivities also underscores the inadequacy of statistical based transition-state theory in describing this industrially important surface reaction.
Co-reporter:Ryan S. Johnson, Andrew DeLaRiva, Valerie Ashbacher, Barr Halevi, Charles J. Villanueva, Gregory K. Smith, Sen Lin, Abhaya K. Datye and Hua Guo
Physical Chemistry Chemical Physics 2013 vol. 15(Issue 20) pp:7768-7776
Publication Date(Web):19 Mar 2013
DOI:10.1039/C3CP00126A
The effect of Zn on the CO adsorption and oxidation reaction is examined experimentally and theoretically on two PdZn catalysts with different compositions, namely the intermetallic 1:1 β-PdZn and α-PdZn as a solid solution of 9 at% Zn in Pd. These bimetallic catalysts, made using an aerosol derived method, are homogeneous in phase and composition so that the measured reactivity excludes support effects. Both specific reactivities for CO oxidation on these two PdZn catalysts were measured. It was found that the initial rates are high and different between these catalysts, presumably due to the weakening of the CO adsorption and easier binding of oxygen to Pd sites modified by Zn. However, the rates decrease with time and become comparable to that on Pd at the steady state. With the help of density functional theory, it was suggested that the transient kinetics are due to the oxidation of Zn during the catalysis, which yields pure Pd where the reaction takes place.
Co-reporter:Anyang Li, Hua Guo, Zhigang Sun, Jacek Kłos and Millard H. Alexander
Physical Chemistry Chemical Physics 2013 vol. 15(Issue 37) pp:15347-15355
Publication Date(Web):17 Jul 2013
DOI:10.1039/C3CP51870A
The state-to-state reaction dynamics of the title reaction is investigated on the ground electronic state potential energy surface using two quantum dynamical methods. The results obtained using the Chebyshev real wave packet method are in excellent agreement with those obtained using the time-independent method, except at low translational energies. It is shown that this exothermic hydrogen abstraction reaction is direct, resulting in a strong back-scattered bias in the product angular distribution. The HF product is highly excited internally. Agreement with available experimental data is only qualitative. We discuss several possible causes of disagreement with experiment.
Co-reporter:Julien Daranlot, Xixi Hu, Changjian Xie, Jean-Christophe Loison, Philippe Caubet, Michel Costes, Valentine Wakelam, Daiqian Xie, Hua Guo and Kevin M. Hickson
Physical Chemistry Chemical Physics 2013 vol. 15(Issue 33) pp:13888-13896
Publication Date(Web):11 Jul 2013
DOI:10.1039/C3CP52535J
Rate constants for the potentially important interstellar N(4S) + CH(X2Πr) reaction have been measured in a continuous supersonic flow reactor over the range 56 K ≤ T ≤ 296 K using the relative rate technique employing both the N(4S) + OH(X2Πi) and N(4S) + CN(X2Σ+) reactions as references. Excess concentrations of atomic nitrogen were produced by the microwave discharge method upstream of the Laval nozzle and CH and OH radicals were created by the in situ pulsed laser photolysis of suitable precursor molecules. In parallel, quantum dynamics calculations of the title reaction have been performed based on accurate global potential energy surfaces for the 13A′ and 13A′′ states of HCN and HNC, brought about through a hierarchical construction scheme. Both adiabatic potential energy surfaces are barrierless, each one having two deep potential wells suggesting that this reaction is dominated by a complex-forming mechanism. The experimental and theoretical work are in excellent agreement, predicting a positive temperature dependence of the rate constant, in contrast to earlier experimental work at low temperature. The effects of the new low temperature rate constants on interstellar N2 formation are tested using a dense cloud model, yielding N2 abundances 10–20% lower than previously predicted.
The Journal of Physical Chemistry C 2013 Volume 117(Issue 31) pp:16127-16135
Publication Date(Web):July 16, 2013
DOI:10.1021/jp405720c
The mode and bond selectivities in methane dissociative chemisorption on Ni(111) are studied using a quasi-classical trajectory (QCT) method on a twelve-dimensional global potential energy surface based on a large number of density functional theory points. The calculated reaction probabilities near and above the reaction barrier reproduced the general trends observed in experimental investigations of various vibrationally excited CH4, CHD3, and CH2D2 species on nickel surfaces. The mechanism of these mode and bond selectivities is analyzed using the recently proposed sudden vector projection model.
Co-reporter:Yongle Li, Yury V. Suleimanov, Minghui Yang, William H. Green, and Hua Guo
The Journal of Physical Chemistry Letters 2013 Volume 4(Issue 1) pp:48-52
Publication Date(Web):December 12, 2012
DOI:10.1021/jz3019513
The thermal rate constant of the O(3P) + CH4 → OH + CH3 reaction is investigated with ring polymer molecular dynamics on a full-dimensional potential energy surface. Good agreement with experimental and full-dimensional quantum multiconfiguration time-dependent Hartree results between 300 and 1500 K was obtained. It is shown that quantum effects, for example, tunneling and zero-point energy, can be effectively and efficiently included in this path-integral based approach implemented with classical trajectories. Convergence with respect to the number of beads is rapid, suggesting wide applicability for other reactions involving polyatomic molecules.Keywords: combustion; path integral; reaction rates; tunneling; zero-point energy;
The Journal of Physical Chemistry C 2013 Volume 117(Issue 1) pp:451-459
Publication Date(Web):December 10, 2012
DOI:10.1021/jp310600q
Methanol decomposition on noble metal surfaces is an important industrial process and prototype for understanding heterogeneous catalysis. Despite many advances, the role played by surface defects and structural sensitivity is still not fully understood. In this work, methanol decomposition on a stepped palladium surface, Pd(211), is investigated using periodic density functional theory (DFT). The activation barriers and thermochemistry for relevant elementary steps leading to the final decomposition products CO and H2 are obtained. Similar to the previous theoretical results on flat Pd surfaces, the initial C–H bond scission is preferred on Pd(211) because it has a lower barrier than those for the initial O–H and C–O scissions. It was also found that the barriers for the C–H or O–H bond scissions are lowered at the step sites. Finally, kinetic Monte Carlo simulations on a realistic Pd surface reproduce the temperature-programmed desorption spectrum for methanol decomposition but only when modified DFT data are used. These simulations show that most of the reaction occurs at under-coordinated sites.
The Journal of Physical Chemistry A 2013 Volume 117(Issue 24) pp:5052-5060
Publication Date(Web):May 28, 2013
DOI:10.1021/jp4049988
The dynamics of the H + MgH → Mg + H2 reaction at low collision energies is analyzed with both quasi-classical trajectory and quantum wave packet methods on an improved potential-energy surface for the ground electronic state of MgH2. Three microscopic reaction channels, namely, direct abstraction, roaming via a loose roaming transition state, and complex decaying via a tight transition state, are identified. It is shown that the reaction is dominated at low collision energies by the direct abstraction channel, whereas the roaming channel is responsible for about 20% of the reaction flux. The pathway via the tight transition state plays almost no role at the energy of study. The two dominant channels produce similar highly excited vibrational distributions for the H2 product. Finally, it is shown that roaming is manifested quantum-mechanically by a large-amplitude vibration that emerges just below the reaction threshold and is guided by the roaming transition state. Its continuation into the continuum leads to roaming resonances.
Co-reporter:Linsen Zhou, Bin Jiang, Daiqian Xie, and Hua Guo
The Journal of Physical Chemistry A 2013 Volume 117(Issue 32) pp:6940-6947
Publication Date(Web):December 4, 2012
DOI:10.1021/jp310546g
The photodissociation of H2O in its B band is a prototype for nonadiabatic reaction dynamics. In addition to dissociation via the adiabatic pathway to the OH(Ã2Σ+) + H fragments, it also produces the OH(X̃2Π) + H fragments through two nonadiabatic pathways: the B̃ → X̃ transition via two conical intersections and the B̃ → Ã transition via a Renner–Teller pair. In this work, the state-to-state dissociation dynamics in all three channels are investigated with a full-dimensional quantum mechanical model using a set of coupled diabatic potential energy surfaces determined at the internally contracted multireference configuration interaction level with the aug-cc-pVQZ basis set. The inclusion of all relevant electronic states not only results in an improved agreement with the latest experimental data but also sheds valuable insights into the competition between the two coexisting nonadiabatic pathways.
Co-reporter:Jose C. Corchado and Joaquin Espinosa-Garcia, Jun Li and Hua Guo
The Journal of Physical Chemistry A 2013 Volume 117(Issue 46) pp:11648-11654
Publication Date(Web):December 4, 2012
DOI:10.1021/jp310503d
Quasi-classical trajectory studies have been carried out for the HO + CO → H + CO2 reaction and H + CO2 inelastic collision on a recently developed global potential energy surface based on a large number of high-level ab initio points. The CO2 vibrational state distributions for these processes have been determined using an original normal-mode analysis method. It was found that the CO2 product of the reaction is highly excited in both the Fermi-linked bending and symmetric stretching modes, but little population was found in the antisymmetric stretching mode. The substantial excitation of the CO2 vibration, while consistent with the geometry of the transition state in the exit channel, is in disagreement with available experimental data. For the inelastic collision, the CO2 is much less excited despite much higher total energies. In addition, excitations in all vibrational modes were found, in good agreement with experiment.
Physical Chemistry Chemical Physics 2012 vol. 14(Issue 35) pp:12090-12093
Publication Date(Web):25 Jul 2012
DOI:10.1039/C2CP41621B
The title reaction is thought to be responsible for the production of molecular nitrogen in interstellar clouds. In this work, we report quantum capture calculations on a new two-dimensional potential energy surface determined by interpolating high-level ab initio data. The low-temperature rate constant calculated using a capture model is quite large and has a positive temperature dependence, in agreement with a recent experiment. The origin of the aforementioned behaviors of the rate constant is analyzed.
Co-reporter:Rui Liu, Minghui Yang, Gábor Czakó, Joel M. Bowman, Jun Li, and Hua Guo
The Journal of Physical Chemistry Letters 2012 Volume 3(Issue 24) pp:3776-3780
Publication Date(Web):December 4, 2012
DOI:10.1021/jz301735m
The dynamics of a combustion reaction, namely, O(3P) + CH4 → OH + CH3, is investigated with an eight-dimensional quantum model that includes representatives of all vibrational modes of CH4 and with a full-dimensional quasi-classical trajectory (QCT) method. The calculated excitation functions for the ground vibrational state CH4 agree well with experiment. Both quantum and QCT results suggest that excitation of the stretching modes of CH4 enhances the reaction, while the bending and umbrella modes have a smaller impact on reactivity, again consistent with experimental findings. However, none of the vibrational excitations has comparable efficiency in promoting the reaction as translational energy.Keywords: combustion; methane; mode-specific reactivity; quantum scattering; reaction dynamics;
The dissociative chemisorption of water is an important step in many heterogeneous catalytic processes. Here, the mode selectivity
of this process was examined quantum mechanically on a realistic potential energy surface determined by fitting planewave
density functional calculations spanning a large configuration space. The quantum dynamics of the surface reaction were characterized
by a six-dimensional model including all important internal coordinates of H2O and its distance to the surface. It was found that excitations in all three vibrational modes are capable of enhancing reactivity
more effectively than increasing translational energy, consistent with the “late” transition state in the reaction path.
The Journal of Physical Chemistry Letters 2012 Volume 3(Issue 17) pp:2482-2486
Publication Date(Web):August 21, 2012
DOI:10.1021/jz301064w
Full-dimensional quantum dynamics of the HO + CO → H + CO2 reaction is investigated on a recent global potential energy surface based on a large number of ab initio points. The J = 0 reaction probability is small and essentially a monotonically increasing function with energy, superimposed by overlapping resonances. The reactivity is considerably enhanced by OH vibrational excitation while relatively insensitive to CO vibrational excitation. The rate constant estimated by the J-shifting approximation indicates a much better agreement with experiment than that obtained on a previous potential energy surface.Keywords: combustion reaction; mode selectivity; quantum reactive scattering; rate constant; tunneling;
Co-reporter:Jun Li, Changjian Xie, Jianyi Ma, Yimin Wang, Richard Dawes, Daiqian Xie, Joel M. Bowman, and Hua Guo
The Journal of Physical Chemistry A 2012 Volume 116(Issue 21) pp:5057-5067
Publication Date(Web):May 10, 2012
DOI:10.1021/jp302278r
We report extensive quasi-classical trajectory calculations of the HO + CO → H + CO2 reaction on a newly developed potential energy surface based on a large number of UCCSD(T)-F12/AVTZ calculations. This complex-forming reaction is known for its unusual kinetics and dynamics because of its unique potential energy surface, which is dominated by the HOCO wells flanked by an entrance channel bottleneck and a transition state leading to the H + CO2 products. It was found that the thermal rate coefficients are in reasonably good agreement with known experimental data in both low and high pressure limits. Excitation of the OH vibration is shown to enhance reactivity, due apparently to its promoting effect over the transition state between the HOCO intermediate and the H + CO2 product. On the other hand, neither CO vibrational excitation nor rotational excitation in either CO or OH has a significant effect on reactivity, in agreement with experiment. However, significant discrepancies have been found between theory and the available molecular beam experiments. For example, the calculated translational energy distribution of the products substantially underestimates the experiment. In addition, the forward bias in the differential cross section observed in the experiment was not reproduced theoretically. While the origin of the discrepancies is still not clear, it is argued that a quantum mechanical treatment of the dynamics might be needed.
Co-reporter:Corey M. Johnson ; Arthur F. Monzingo ; Zhihong Ke ; Dae-Wi Yoon ; Thomas W. Linsky ; Hua Guo ; Jon D. Robertus ;Walter Fast
Journal of the American Chemical Society 2011 Volume 133(Issue 28) pp:10951-10959
Publication Date(Web):June 1, 2011
DOI:10.1021/ja2033684
Small molecules capable of selective covalent protein modification are of significant interest for the development of biological probes and therapeutics. We recently reported that 2-methyl-4-bromopyridine is a quiescent affinity label for the nitric oxide controlling enzyme dimethylarginine dimethylaminohydrolase (DDAH) (Johnson, C. M.; Linsky, T. W.; Yoon, D. W.; Person, M. D.; Fast, W. J. Am. Chem. Soc.2011, 133, 1553–1562). Discovery of this novel protein modifier raised the possibility that the 4-halopyridine motif may be suitable for wider application. Therefore, the inactivation mechanism of the related compound 2-hydroxymethyl-4-chloropyridine is probed here in more detail. Solution studies support an inactivation mechanism in which the active site Asp66 residue stabilizes the pyridinium form of the inactivator, which has enhanced reactivity toward the active site Cys, resulting in covalent bond formation, loss of the halide, and irreversible inactivation. A 2.18 Å resolution X-ray crystal structure of the inactivated complex elucidates the orientation of the inactivator and its covalent attachment to the active site Cys, but the structural model does not show an interaction between the inactivator and Asp66. Molecular modeling is used to investigate inactivator binding, reaction, and also a final pyridinium deprotonation step that accounts for the apparent differences between the solution-based and structural studies with respect to the role of Asp66. This work integrates multiple approaches to elucidate the inactivation mechanism of a novel 4-halopyridine “warhead,” emphasizing the strategy of using pyridinium formation as a “switch” to enhance reactivity when bound to the target protein.
Co-reporter:Zhihong Ke ; Gregory K. Smith ; Yingkai Zhang
Journal of the American Chemical Society 2011 Volume 133(Issue 29) pp:11103-11105
Publication Date(Web):June 28, 2011
DOI:10.1021/ja204378q
The newly discovered bacterial phosphothreonine lyases perform a post-translational modification of host cell signaling proteins through a novel catalytic mechanism that irreversibly removes the phosphate group from a phosphorylated threonine via β-elimination. This “eliminylation” reaction is shown by ab initio QM/MM studies to proceed via an E1cB-like pathway, in which the carbanion intermediate is stabilized by an enzyme oxyanion hole provided by Lys104 and Tyr158 of SpvC.
Methyl formate has been proposed to be an intermediate in methanol steam reforming (MSR) on copper catalysts. We show here using plane-wave density functional theory that methyl formate can indeed be formed by reaction between formaldehyde and methoxyl. However, this reaction competes unfavorable with that between formaldehyde and hydroxyl, which explains why methyl formate is only observed in the absence of water. Methyl formate can be further hydrolyzed by a surface OH species to produce formic acid, which can dehydrogenate to produce CO2. This process has a lower overall barrier than MSR, thus consistent with the experimental observation that the steam reforming of methyl formate is faster than MSR. However, this hydrolysis process might have difficulties competing with desorption of methyl formate, which has a small adsorption energy. Our theoretical model, which is consistent with all experimental observations related to methyl formate in MSR, thus assigns a minor role for the methyl formate pathway.Keywords: Cu(111); DFT; methanol steam reforming; methyl formate;
Co-reporter:Sen Lin, Ryan S. Johnson, Gregory K. Smith, Daiqian Xie and Hua Guo
Physical Chemistry Chemical Physics 2011 vol. 13(Issue 20) pp:9622-9631
Publication Date(Web):13 Apr 2011
DOI:10.1039/C1CP20067D
Plane-wave density functional theory calculations have been carried out to explore possible pathways in methanol steam reforming (MSR) on Cu(111). We focus on reactions involving the adsorbed formaldehyde intermediate (CH2O) produced by methanol decomposition and the surface hydroxyl (OH) species generated by dissociative adsorption of H2O. Several possible pathways leading to the H2 + CO2 products have been identified. The two most likely pathways involve the formate (CHOO), rather than the carboxyl (COOH), intermediate, and they possess barriers lower than that of the rate-limiting step of MSR, namely the dehydrogenation of adsorbed methoxyl (CH3O) species.
Chemical Physics Letters 2011 Volume 511(4–6) pp:193-195
Publication Date(Web):5 August 2011
DOI:10.1016/j.cplett.2011.06.069
Abstract
A full-dimensional quantum dynamics study of the photodetachment of HCO2− is reported using an exact wavepacket method. The calculated photodetachment spectrum identified several HCO2 resonances observed in the experiment, but with quantitatively different intensities, indicating imperfection in the HCO2 potential-energy surface. The narrow widths of the lowest resonances indicate slow tunneling-facilitated predissociation. The dissociation of these resonances yields CO2 not only in its ground vibrational state, but also in excited ones, particularly at high energies. Both the symmetric stretching and bending modes, which are coupled via Fermi resonance, are found to be excited.
Co-reporter:Gregory K. Smith, Sen Lin, Wenzhen Lai, Abhaya Datye, Daiqian Xie, Hua Guo
Surface Science 2011 Volume 605(7–8) pp:750-759
Publication Date(Web):April 2011
DOI:10.1016/j.susc.2011.01.014
Recent experiments suggested that PdZn alloy on ZnO support is a very active and selective catalyst for methanol steam reforming (MSR). To gain insight into MSR mechanism on this catalyst, plane-wave density functional theory calculations were carried out on the initial steps of MSR on both PdZn and ZnO surfaces. Our calculations indicate that the dissociation of both methanol and water is highly activated on flat surfaces of PdZn such as (111) and (100), while the dissociation barriers can be lowered significantly by surface defects, represented here by the (221), (110), and (321) faces of PdZn. The corresponding processes on the polar Zn-terminated ZnO(0001) surfaces are found to have low or null barriers. Implications of these results for both MSR and low temperature mechanisms are discussed.Research highlights►CH3OH and H2O dissociations on defect-free PdZn surfaces are highly activated. ►Defects on PdZn surfaces lower these barriers. ►CH3OH and H2O dissociations on the ZnO(0001) surface have relatively low barriers.
Co-reporter:Zhihong Ke and Hua Guo, Daiqian Xie , Shenglong Wang and Yingkai Zhang
The Journal of Physical Chemistry B 2011 Volume 115(Issue 13) pp:3725-3733
Publication Date(Web):March 11, 2011
DOI:10.1021/jp200843s
The first step of the hydrolytic deimination of l-arginine catalyzed by arginine deiminase is examined using ab initio quantum mechanical/molecular mechanical molecular dynamics simulations. Two possible protonation states of the nucleophilic Cys406 residue were investigated, and the corresponding activation free energies were obtained via umbrella sampling. Our calculations indicated a reaction free-energy barrier of 21.3 kcal/mol for the neutral cysteine, which is in reasonably good agreement with the experimental kcat value of 6.3 s−1, i.e., a barrier of 16.7 kcal/mol. On the other hand, the deprotonated Cys nucleophile yields a free-energy barrier of 6.7 kcal/mol, much lower than the experimental result. The reaction free-energy barriers along with other data suggest that the Cys nucleophile is dominated by its protonated state in the Michaelis complex, and the reaction barrier corresponds largely to its deprotonation.
We report a hybrid quantum mechanical and molecular mechanical study of the catalysis of anthrax lethal factor. The calculations suggest that the zinc peptidase uses the same general base-general acid mechanism as in thermolysin and carboxypeptidase A, in which a zinc-bound water is activated by Glu687 to nucleophilically attack the scissile carbonyl carbon in the substrate. The catalysis is aided by an oxyanion hole formed by the zinc ion and the side chain of Tyr728, which provide stabilization for the fractionally charged carbonyl oxygen. The assigned role of Tyr728 differs from previous suggestions but is consistent with the established mechanism of other zinc proteases.
The Journal of Physical Chemistry C 2011 Volume 115(Issue 42) pp:20583-20589
Publication Date(Web):September 18, 2011
DOI:10.1021/jp206511q
PdZn alloy has been shown to catalyze methanol steam reforming (MSR), producing hydrogen gas and carbon dioxide with high selectivity. Despite many studies, the mechanism for MSR on this catalyst is still not completely understood. In this work, several possible pathways of MSR are explored using a plane-wave density functional theory. The focus is placed on the reaction network starting from a facile reaction between adsorbed formaldehyde and hydroxyl species, produced from the decomposition of methanol and water, respectively. These pathways were found to have barriers lower than the rate-limiting step, namely, the dehydrogenation of methoxyl, and they involve species that have been detected in various experiments. Interestingly, the reaction pathways share many similarities with the MSR process on copper, which is the traditional catalyst for MSR.
Journal of the American Chemical Society 2010 Volume 132(Issue 51) pp:17986-17988
Publication Date(Web):December 7, 2010
DOI:10.1021/ja104241g
QM/MM studies of the hydrolysis of a β-lactam antibiotic molecule (biapenem) catalyzed by a monozinc β-lactamase (CphA) have revealed the complete reaction mechanism and shown that an experimentally determined enzyme−intermediate complex is a stable intermediate or product in a minor pathway.
Co-reporter:Wenzhen Lai, Shi Ying Lin, Daiqian Xie and Hua Guo
The Journal of Physical Chemistry A 2010 Volume 114(Issue 9) pp:3121-3126
Publication Date(Web):November 11, 2009
DOI:10.1021/jp908688a
The nonadiabatic photodissociation dynamics of the Ã-state ammonia (NH3) was investigated using a four-dimensional wave packet model. The branching ratio between the excited NH2(Ã2A1) and ground NH2(X̃2B1) products was obtained as a function of energy for photodissociation mediated by several low-lying vibrational states in the ground electronic state of NH3. The calculated results could not fully account for the experimental observations of strong mode specificity in nonadiabatic dynamics but agree qualitatively with a recent trajectory-based coupled-surface study using the same potential energy surfaces. Several possible sources of inaccuracy are discussed.
Co-reporter:Reinhard Schinke;Zhigang Sun;Shi Ying Lin;Lan Liu;Dong H. Zhang
PNAS 2010 Volume 107 (Issue 2 ) pp:555-558
Publication Date(Web):2010-01-12
DOI:10.1073/pnas.0911356107
The O + O2 exchange reaction is a prerequisite for the formation of ozone in Earth’s atmosphere. We report here state-to-state differential
and integral cross sections for several O + O2 isotope-exchange reactions obtained by dynamically exact quantum scattering calculations at collision energies relevant to
atmospheric conditions. These reactions are shown to be highly nonstatistical, evidenced by dominant forward scattering and
deviation of the integral cross section from the statistical limit. Mechanistic analyses revealed that the nonstatistical
channel is facilitated by short-lived osculating resonances. The theoretical results provided an in-depth interpretation of
a recent molecular beam experiment of the exchange reaction and shed light on the initial step of ozone recombination.
Co-reporter:Shi Ying Lin and Hua Guo, Bin Jiang, Shulan Zhou, and Daiqian Xie
The Journal of Physical Chemistry A 2010 Volume 114(Issue 36) pp:9655-9661
Publication Date(Web):April 16, 2010
DOI:10.1021/jp100976g
This publication examines the influence of electronically nonadiabatic Renner−Teller coupling between the two lowest-lying electronic states of NH2 on state-to-state reaction dynamics. The fully Coriolis coupled quantum mechanical calculations were carried out on the recently developed NH2 potential energy surfaces of both the X̃2A″ and Ã2A′ states. It is shown that the Renner−Teller coupling has a dramatic effect on the low-lying ro-vibrational states on the excited Ã2A′ potential, but its impact on the differential and integral cross sections of the N(2D) + H2 → NH(X̃3Σ−) + H reaction is relatively minor.
Co-reporter:Shanshan Wu, Chunchun Zhang, Dingguo Xu and Hua Guo
The Journal of Physical Chemistry B 2010 Volume 114(Issue 28) pp:9259-9267
Publication Date(Web):June 28, 2010
DOI:10.1021/jp101448j
The catalytic mechanism of carboxypeptidase A (CPA) for the hydrolysis of ester substrates is investigated using hybrid quantum mechanical/molecular mechanical (QM/MM) methods and high-level density functional theory. The prevailing mechanism was found to utilize an active-site water molecule assisted by Glu270, and this so-called promoted-water pathway is similar to that in the CPA catalyzed proteolytic reaction (D. Xu and H. Guo, J. Am. Chem. Soc. 2009, 131, 9780). On the other hand, our simulations indicated the existence of an alternative pathway due to direct nucleophilic attack of Glu270 on the scissile carbonyl carbon. This so-called nucleophilic pathway, which is not viable in proteolytic reactions, leads to a stable acyl−enzyme complex. However, the nucleophilic pathway is nonproductive as it is blocked by a high barrier in the deacylation step. On the basis of results reported here and in our earlier publication, a unified model is proposed to account for nearly all experimental observations concerning the catalysis of CPA.
Journal of the American Chemical Society 2009 Volume 131(Issue 28) pp:9780-9788
Publication Date(Web):June 24, 2009
DOI:10.1021/ja9027988
Carboxypeptidase A is a zinc-containing enzyme that cleaves the C-terminal residue in a polypeptide substrate. Despite much experimental work, there is still a significant controversy concerning its catalytic mechanism. In this study, the carboxypeptidase A-catalyzed hydrolysis of the hippuryl-l-Phe molecule (kcat = 17.7 ± 0.7 s−1) is investigated using both density functional theory and a hybrid quantum mechanical/molecular mechanical approach. The enzymatic reaction was found to proceed via a promoted-water pathway with Glu270 serving as the general base and general acid. Free-energy calculations indicate that the first nucleophilic addition step is rate-limiting, with a barrier of 17.9 kcal/mol. Besides activating the zinc-bound water nucleophile, the zinc cofactor also serves as an electrophilic catalyst that stabilizes the substrate carbonyl oxygen during the formation of the tetrahedral intermediate. In the Michaelis complex, Arg127, rather than Zn(II), is responsible for the polarization of the substrate carbonyl and it also serves as the oxyanion hole. As a result, its mutation leads to a higher free-energy barrier, in agreement with experimental observations.
The Journal of Physical Chemistry A 2009 Volume 113(Issue 16) pp:4285-4293
Publication Date(Web):March 11, 2009
DOI:10.1021/jp810948k
The authors report accurate quantum dynamics calculations for the title reaction on the three lowest electronic state potentials. The adiabatic pathway on the ground electronic state (11A′) of H2O has a complex-forming mechanism, manifested by rotationally hot and vibrationally cold OH products with a nearly forward−backward symmetric angular distribution. As energy increases, the adiabatic pathway via the 11A′′ state and nonadiabatic pathway via the 21A′ state become significant. The former has an abstraction mechanism and produces an exclusively backward differential cross section. On the other hand, the latter has essentially the same dynamic signatures of the ground-state pathway. The inclusion of the two excited-state pathways is necessary to quantitatively reproduce the observed rise in the integral cross section at high energies and the increasingly backward bias in the differential cross section. It is also found that the inclusion of the excited-state dynamics, particularly the nonadiabatic 21A′ pathway, greatly improves the agreement with the measured rate constant.
The Journal of Physical Chemistry A 2009 Volume 113(Issue 26) pp:7314-7321
Publication Date(Web):March 16, 2009
DOI:10.1021/jp810990j
We report global potential energy surfaces for both the ground (X̃1A′) and the excited (Ã1A′′) electronic states of HGeBr as well as the transition dipole moment surface between them using an internally contracted multireference configuration interaction method with the Davidson correction and an augmented correlation-consistent polarized valence quadruple-ζ basis set. Vibrational energy levels of HGeBr and DGeBr are calculated on both the ground and the excited electronic states and found in good agreement with the available experimental band origins. In addition, the Ã1A′′−X̃1A′ absorption and emission spectra of the two isotopomers were obtained, and an excellent agreement with the available experimental spectra was found.
Co-reporter:Ling Li, Zhimin Li, Canhui Wang, Dingguo Xu, Patrick S. Mariano, Hua Guo and Debra Dunaway-Mariano
Biochemistry 2008 Volume 47(Issue 16) pp:
Publication Date(Web):March 27, 2008
DOI:10.1021/bi7023496
l-Arginine deiminase (ADI) catalyzes the hydrolysis of l-arginine to form l-citrulline and ammonia via two partial reactions. A working model of the ADI catalytic mechanism assumes nucleophilic catalysis by a stringently conserved active site Cys and general acid−general base catalysis by a stringently conserved active site His. Accordingly, in the first partial reaction, the Cys attacks the substrate guanidino Cζ atom to form a tetrahedral covalent adduct, which is protonated by the His at the departing ammonia group to facilitate the formation of the Cys-S-alkylthiouronium intermediate. In the second partial reaction, the His activates a water molecule for nucleophilic addition at the thiouronium Cζ atom to form the second tetrahedral intermediate, which eliminates the Cys in formation of the l-citrulline product. The absence of a basic residue near the Cys thiol suggested that the electrostatic environment of the Cys thiol, in the enzyme–substrate complex, stabilizes the Cys thiolate anion. The studies described in this paper explore the mechanism of stabilization of the Cys thiolate. First, the log(kcat/Km) and log kcat pH rate profiles were measured for several structurally divergent ADIs to establish the pH range for ADI catalysis. All ADIs were optimally active at pH 5, which suggested that the Cys pKa is strongly perturbed by the prevailing electrostatics of the ADI active site. The pKa of the Bacillus cereus ADI (BcADI) was determined by UV−pH titration to be 9.6. In contrast, the pKa determined by iodoacetamide Cys alkylation is 6.9. These results suggest that the negative electrostatic field from the two opposing Asp carboxylates perturbs the Cys pKa upward in the apoenzyme and that the binding of the iodoacetamide (a truncated analogue of the citrulline product) between the Cys thiol and the two Asp carboxylates shields the Cys thiol, thereby reducing its pKa. It is hypothesized that the bound positively charged guanidinium group of the l-arginine substrate further stabilizes the Cys thiolate. The so-called “substrate-assisted” Cys ionization, first reported by Fast and co-workers to operate in the related enzyme dimethylarginine dimethylaminohydrolase [Stone, E. M., Costello, A. L., Tierney, D. L., and Fast, W. (2006) Biochemistry 45, 5618–5630], was further explored computationally in ADI by using an ab initio quantum mechanics/molecular mechanics method. The energy profiles for formation of the tetrahedral intermediate in the first partial reaction were calculated for three different reaction scenarios. From these results, we conclude that catalytic turnover commences from the active configuration of the ADI(l-arginine) complex which consists of the Cys thiolate (nucleophile) and His imidazolium ion (general acid) and that the energy barriers for the nucleophilic addition of Cys thiolate to the thiouronium Cζ atom and His imidazolium ion-assisted elimination from the tetrahedral intermediate are small.
Co-reporter:Jessica Momb, Canhui Wang, Dali Liu, Pei W. Thomas, Gregory A. Petsko, Hua Guo, Dagmar Ringe and Walter Fast
Biochemistry 2008 Volume 47(Issue 29) pp:
Publication Date(Web):July 15, 2008
DOI:10.1021/bi8003704
The N-acyl-l-homoserine lactone hydrolases (AHL lactonases) have attracted considerable attention because of their ability to quench AHL-mediated quorum-sensing pathways in Gram-negative bacteria and because of their relation to other enzymes in the metallo-β-lactamase superfamily. To elucidate the detailed catalytic mechanism of AHL lactonase, mutations are made on residues that presumably contribute to substrate binding and catalysis. Steady-state kinetic studies are carried out on both the wild-type and mutant enzymes using a spectrum of substrates. Two mutations, Y194F and D108N, present significant effects on the overall catalysis. On the basis of a high-resolution structural model of the enzyme−product complex, a hybrid quantum mechanical/molecular mechanical method is used to model the substrate binding orientation and to probe the effect of the Y194F mutation. Combining all experimental and computational results, we propose a detailed mechanism for the ring-opening hydrolysis of AHL substrates as catalyzed by the AHL lactonase from Bacillus thuringiensis. Several features of the mechanism that are also found in related enzymes are discussed and may help to define an evolutionary thread that connects the hydrolytic enzymes of this mechanistically diverse superfamily.
Co-reporter:Shulan Zhou, Daiqian Xie, Dingguo Xu, Hua Guo, Robert W. Field
Chemical Physics Letters 2008 Volume 455(4–6) pp:145-150
Publication Date(Web):10 April 2008
DOI:10.1016/j.cplett.2008.02.064
We report a new ab initio potential energy surface of the excited (A˜1A″) state of HCN/HNC and the transition dipole function to the ground (X˜1A′) state at the MRCI/aug-cc-pVTZ level of theory. Resonance emission spectra from several low-lying and predissociative vibrational states of the HNC(A˜1A″) isomer are calculated, which show the dominance of the C–N progressions, due apparently to the large difference in the equilibrium C–N bond lengths in the two electronic states.A˜1A″→X˜1A′ emission spectra from the HNC isomer are calculated using ab initio potential and transition dipole
Chemical Physics Letters 2008 Volume 453(4–6) pp:140-144
Publication Date(Web):3 March 2008
DOI:10.1016/j.cplett.2008.01.030
We report exact J = 0 quantum reaction probability for the title reaction using a wave packet method. It is shown that the reaction is almost completely dominated by the capture of the reactants, because of its large exothermicity and barrierless nature. As a result, the integral cross section can be accurately determined by capture probabilities. The calculated quantum rate constant is in good agreement with the earlier quasi-classical trajectory results except at low temperatures. The discrepancy is discussed.Quantum integral cross section and rate constant for C + OH → H + CO reaction are reported.
Co-reporter:Lidong Zhang, Daiqian Xie, Dingguo Xu and Hua Guo
Chemical Communications 2007 (Issue 16) pp:1638-1640
Publication Date(Web):06 Feb 2007
DOI:10.1039/B617946K
Supermolecule density functional theory calculations show that solvent is responsible for the concerted transition state in alkaline hydrolysis of p-nitrophenyl phosphate suggested by heavy atom kinetic isotope effects.
Chemical Physics Letters 2007 Volume 439(4–6) pp:280-283
Publication Date(Web):11 May 2007
DOI:10.1016/j.cplett.2007.03.103
We investigate the isotopic variation of the C∼-state absorption spectrum of sulfur dioxide (SO2). Low-lying vibrational energy levels of four isotopomers were obtained using the Lanczos method on a recent ab initio potential energy surface of the C∼-state of SO2. The corresponding absorption spectra up to 185 nm were determined using a Chebyshev method with ab initio transition dipole functions. Implications for the recently observed mass-independent isotope effects are discussed.Absorption spectra of SO2 isotopomers indicate that the observed mass-independent mass effects are unlikely due to photoexcitation.
Co-reporter:Jian Wang;Hao Li;Bihshow Lou Dr.;Liansuo Zu Dr.;Wei Wang Dr.
Chemistry - A European Journal 2006 Volume 12(Issue 16) pp:
Publication Date(Web):31 MAR 2006
DOI:10.1002/chem.200600115
Chiral (S)-pyrrolidine trifluoromethanesulfonamide has been shown to serve as an effective catalyst for direct Michael addition reactions of aldehydes and ketones with nitroolefins. A wide range of aldehydes and ketones as Michael donors and nitroolefins as acceptors participate in the process, which proceeds with high levels of enantioselectivity (up to 99 % ee) and diastereoselectivity (up to 50:1 d.r.). The methodology has been employed successfully in an efficient synthesis of the potent H3 agonist Sch 50917. In addition, a practical three-step procedure for the preparation of (S)-pyrrolidine trifluoromethanesulfonamide has been developed. The high levels of stereochemical control attending Michael addition reactions catalyzed by this pyrrolidine sulfonamide, have been investigated by using ab initio and density functional methods. Transition state structures for the rate-limiting CC bond-forming step, corresponding to re- and si-face addition to the reactive conformation of the key enamine intermediates have been calculated. Analysis of these structures indicates that hydrogen bonding plays an important role in catalysis and that the energy barrier for si-face attack in reactions of aldehydes to form 2R,3S products is lower than that for the re-face attack leading to 2S,3R products. In contrast, the energy barrier for re-face addition is lower than that for si-face addition in reactions of ketones. The computational results, which are in good agreement with the experimental observations, are discussed in the context of the stereochemical course of these Michael addition reactions.
Co-reporter:Dingguo Xu, Hua Guo, Jiali Gao and Qiang Cui
Chemical Communications 2004 (Issue 7) pp:892-893
Publication Date(Web):05 Mar 2004
DOI:10.1039/B401159G
Calculated using a QM/MM method, the free energy profile for the conversion of 4-chlorobenzoate to 4-hydroxybenzoate catalyzed by 4-chlorobenzoyl-CoA dehalogenase indicates the existence of a stable Meisenheimer complex.
Chemical Physics Letters 2003 Volume 377(5–6) pp:582-588
Publication Date(Web):22 August 2003
DOI:10.1016/S0009-2614(03)01184-9
We report an empirically adjusted potential energy surface for C2H2 that describes acetylene/vinylidene isomerization. This new surface is based on a very recent fit to extensive ab initio electronic calculations obtained at the CCSD(T) level of theory, with an aug-cc-pVTZ basis [Chem. Phys. Lett. 368 (2003) 421]. The adjustments are made by a coordinate-scaling procedure that has been used previously to empirically adjust potentials. The adjustments are made based on full-dimensional converged quantum mechanical calculations of acetylene vibrational levels that have been accurately determined experimentally.
Co-reporter:Cheng Zhou, Daiqian Xie, Rongqing Chen, Guosen Yan, Hua Guo, Vivian Tyng, Michael E Kellman
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 2002 Volume 58(Issue 4) pp:727-746
Publication Date(Web):1 March 2002
DOI:10.1016/S1386-1425(01)00666-7
We report a refined potential energy function for the ground electronic state of CS2 based on a least-squares fitting to several low-lying experimental vibrational frequencies. Energy levels up to 20,000 cm−1 have been obtained on this empirical potential using the Lanczos algorithm and potential optimized discrete variable representation. Among them, 329 levels below 10,000 cm−1 are assigned with approximate normal mode quantum numbers , based on expectation values of one-dimensional (1D) reference Hamiltonians. An effective Hamiltonian is extracted from these assigned levels. The agreement with experimental data, including those of several isotopically substituted species, is excellent. In addition, some Fermi and anharmonic resonances are analyzed. The nearest neighbor level spacing and Δ3 distributions indicated that the vibrational spectrum of CS2 is largely regular in the energy range up to 20,000 cm−1. Semiclassical phase space analysis, including bifurcation analysis of the spectroscopic Hamiltonian, is used to interpret subtle anomalies signaled by expectation values used in normal mode assignments. The meaning of Fermi resonance is clarified by contrasting the semiclassical analysis of CS2 and CO2.
Chemical Physics Letters 2001 Volume 345(5–6) pp:517-524
Publication Date(Web):21 September 2001
DOI:10.1016/S0009-2614(01)00924-1
We report a new three-dimensional ab initio potential energy surface of the first excited singlet (11A′′) state of HCN. More than one thousand potential points have been calculated at the multi-reference configuration interaction level employing a large basis set. Variational calculations of the predissociative resonances of both HCN and DCN are performed on the three-dimensional spline fitted potential energy surface, which yield both positions and widths. Fairly good agreement with experiment confirms the accuracy of our new potential energy. These resonances provide valuable information on the photodissociation dynamics of HCN/DCN in the 11A″ state.
Co-reporter:Daiqian Xie, Hua Guo, Ota Bludský, Petr Nachtigall
Chemical Physics Letters 2000 Volume 329(5–6) pp:503-510
Publication Date(Web):27 October 2000
DOI:10.1016/S0009-2614(00)01049-6
Abstract
We report here an analytical fit of the transition dipole moments between and electronic states of SO2 calculated using a high level ab initio method. The absorption spectrum as well as the resonance emission spectra from several low-lying vibrational levels are calculated using a newly developed ab initio potential energy surface (PES) and the transition dipole functions. The calculated spectra are in semi-quantitative agreement with available experimental data. A strong non-Condon effect is found for the emission spectra.
We present a classical trajectory study of the collision-induced desorption of rare gas (Rg=Ar, Xe) atoms from Pt(111) by ‘hot’ O atoms generated by photodissociating coadsorbed O2. Empirical potential energy functions are used to describe the Rg/O/Pt(111) systems. The calculated angular and translational energy distributions of the desorbed Ar and Xe are in good agreement with experimental observations. It is found that the desorption dynamics involves two collisions. The first collision between O and Rg supplies the necessary kinetic energy for desorption, whereas the second collision between the departing Rg atom and a coadsorbed Rg atom results in a desorption angle of 25–35° from the surface normal for Ar and 35–45° for Xe. The light oxygen atom is found to chatter between the Xe atom and the surface during an O–Xe collision, enhancing the energy transfer.
Co-reporter:Hua Guo, Peter Saalfrank, Tamar Seideman
Progress in Surface Science 1999 Volume 62(7–8) pp:239-303
Publication Date(Web):December 1999
DOI:10.1016/S0079-6816(99)00013-1
The absorption of photons by an adsorbate/substrate complex may induce a wide range of physical and chemical processes, such as desorption, dissociation and reactions. Although several of these processes have analogs in the gas phase, the presence of the surface opens new reaction pathways that are not available in the gas phase. These unique pathways can be used to control reactivity, product selectivity and yield, or to explore new reactions. Stimulated by the surge in experimental studies of surface photochemistry, various theoretical models have been recently developed to elucidate observations and explore new opportunities. In this review, we survey recent advances in the theoretical characterization of photoinduced chemical and physical processes occurring on solid surfaces. Our discussions are focused on two prototypical processes. The adsorbate photodissociation on insulator surfaces provides an ideal probe of the nonelectronic interaction with the substrate. Photochemical processes on conductors, on the other hand, highlight the excitation and relaxation processes induced by substrate hot carriers. The issues addressed here include excitation and relaxation mechanisms, the role played by internal modes of the adsorbate and energy transfer between the admolecule and the substrate. Both classical and quantum models are used in describing these processes.
Recent experiments suggested that PdZn alloy on ZnO support is a very active and selective catalyst for methanol steam reforming (MSR). To gain insight into MSR mechanism on this catalyst, plane-wave density functional theory calculations were carried out on the initial steps of MSR on both PdZn and ZnO surfaces. Our calculations indicate that the dissociation of both methanol and water is highly activated on flat surfaces of PdZn such as (111) and (100), while the dissociation barriers can be lowered significantly by surface defects, represented here by the (221), (110), and (321) faces of PdZn. The corresponding processes on the polar Zn-terminated ZnO(0001) surfaces are found to have low or null barriers. Implications of these results for both MSR and low temperature mechanisms are discussed.Download high-res image (178KB)Download full-size imageResearch highlights►CH3OH and H2O dissociations on defect-free PdZn surfaces are highly activated. ►Defects on PdZn surfaces lower these barriers. ►CH3OH and H2O dissociations on the ZnO(0001) surface have relatively low barriers.
The ability to predict mode/bond selectivity and energy disposal is of central importance for controlling chemical reactions. We argue that the transition state plays a critical role in state-to-state reactivity and propose a simple sudden model based on coupling with the reaction coordinate at the transition state. The applicability of this so-called sudden vector projection (SVP) model is examined for several prototypical atom–triatom, namely, X + H2O (X = H, F, O(3P), and Cl) reactions. It is shown that the SVP model is capable of qualitatively predicting experimental and full-dimensional quantum dynamical results, including those reported in this work, for these polyatomic reactions. These results, and those for other reactions, suggest that the SVP model offers a general paradigm for understanding quantum state resolved reactivity in bimolecular reactions.
Physical Chemistry Chemical Physics 2015 - vol. 17(Issue 6) pp:NaN4267-4267
Publication Date(Web):2014/12/22
DOI:10.1039/C4CP05165C
Bond-selective reaction dynamics of the title reaction is investigated using full-dimensional quantum dynamical (QD) and quasi-classical trajectory (QCT) methods on a newly constructed ab initio global potential energy surface. Both QD and QCT results indicate that excitation of the local OH vibration in the HOD reactant renders the reaction strongly bond selective, with the OD/OH branching ratio in quantitative agreement with the experiment. In addition, the reactivity is found to be greatly enhanced with the reactant vibrational excitation, thanks to the change of a direct rebound mechanism to a capture mechanism. The QCT calculations also yield product state distributions, which show that the HCl product is vibrationally and rotationally hot while the OD co-product is internally cold. The bond selectivity, vibrational enhancement, and product energy disposal are rationalized by the Sudden Vector Projection model.
Co-reporter:Hongwei Song, Jun Li, Minghui Yang, Yunpeng Lu and Hua Guo
Physical Chemistry Chemical Physics 2014 - vol. 16(Issue 33) pp:NaN17776-17776
Publication Date(Web):2014/07/11
DOI:10.1039/C4CP02227K
Reaction dynamics and mode specificity in the H2 + NH2 → H + NH3 reaction are investigated in full dimensionality on a recent ab initio based global potential energy surface. Integral cross sections from several low-lying vibrational states of both reagents have been calculated under the centrifugal sudden or J-shifting approximations, using an initial state selected time-dependent wave packet method. This nine-dimensional system provides an ideal proving ground to test our recently proposed Sudden Vector Projection (SVP) model. Our results indicate that vibrational excitation of H2 enhances the reactivity. On the other hand, excitation of either the symmetric or antisymmetric stretching mode of NH2 inhibits the reaction, while excitation of its bending mode has a negligible effect. Furthermore, all vibrational modes are less effective than translational energy in promoting the reaction. These mode-specific features are rationalized with the SVP model.
Chemical Science (2010-Present) 2013 - vol. 4(Issue 2) pp:NaN632-632
Publication Date(Web):2012/10/31
DOI:10.1039/C2SC21457A
The low (3.84 kcal mol−1) transition state for the F + H2O → HF + HO reaction on the ground electronic state potential energy surface is pre-staged by a relatively deep (2.67 kcal mol−1) van der Waals well in the entrance channel. Quasi-classical trajectory studies indicated that this pre-reaction van der Waals complex “guides” trajectories towards the “reactant-like” transition state. Such a stereodynamic effect is shown to enhance the reactivity at low collision energies, resulting in a pronounced peak in the excitation function. A similar enhancement effect was also found in quantum dynamic calculations.
Co-reporter:Ryan S. Johnson, Andrew DeLaRiva, Valerie Ashbacher, Barr Halevi, Charles J. Villanueva, Gregory K. Smith, Sen Lin, Abhaya K. Datye and Hua Guo
Physical Chemistry Chemical Physics 2013 - vol. 15(Issue 20) pp:NaN7776-7776
Publication Date(Web):2013/03/19
DOI:10.1039/C3CP00126A
The effect of Zn on the CO adsorption and oxidation reaction is examined experimentally and theoretically on two PdZn catalysts with different compositions, namely the intermetallic 1:1 β-PdZn and α-PdZn as a solid solution of 9 at% Zn in Pd. These bimetallic catalysts, made using an aerosol derived method, are homogeneous in phase and composition so that the measured reactivity excludes support effects. Both specific reactivities for CO oxidation on these two PdZn catalysts were measured. It was found that the initial rates are high and different between these catalysts, presumably due to the weakening of the CO adsorption and easier binding of oxygen to Pd sites modified by Zn. However, the rates decrease with time and become comparable to that on Pd at the steady state. With the help of density functional theory, it was suggested that the transient kinetics are due to the oxidation of Zn during the catalysis, which yields pure Pd where the reaction takes place.
Physical Chemistry Chemical Physics 2014 - vol. 16(Issue 14) pp:NaN6763-6763
Publication Date(Web):2014/02/12
DOI:10.1039/C4CP00241E
Extensive ab initio calculations of the stationary points in the NH4(X2A1) system are reported using both coupled cluster and multi-reference configuration interaction methods. In addition, more than 100000 points are generated over a large configuration space and energy range (6 eV) using the explicitly correlated unrestricted coupled cluster method with single, double, and perturbative triple excitations with the augmented correlation-consistent polarized triple zeta basis set (UCCSD(T)-F12a/aug-cc-pVTZ). Using the recently proposed permutation-invariant polynomial neural network (PIP-NN) method, these points are accurately fit to an analytical form with a total root mean squared error (RMSE) of 3.4 meV (0.08 kcal mol−1). Both the abstraction and exchange channels as well as the metastable ammonium radical (NH4) are included in this potential energy surface. Transition-state theory and quasi-classical trajectory calculations have been performed to obtain the rate constants for the abstraction reaction and its reverse. Comparison with available experimental results is satisfactory, providing supporting evidence for the accuracy of the potential.
Co-reporter:Bin Jiang, Minghui Yang, Daiqian Xie and Hua Guo
Chemical Society Reviews 2016 - vol. 45(Issue 13) pp:NaN3640-3640
Publication Date(Web):2015/06/23
DOI:10.1039/C5CS00360A
Dissociative chemisorption is the initial and often rate-limiting step in many heterogeneous processes. As a result, an in-depth understanding of the reaction dynamics of such processes is of great importance for the establishment of a predictive model of heterogeneous catalysis. Overwhelming experimental evidence has suggested that these processes have a non-statistical nature and excitations in various reactant modes have a significant impact on reactivity. A comprehensive characterization of the reaction dynamics requires a quantum mechanical treatment on a global potential energy surface. In this review, we summarize recent progress in constructing high-dimensional potential energy surfaces for polyatomic molecules interacting with transition metal surfaces based on the plane-wave density functional theory and in quantum dynamical studies of dissociative chemisorption on these potential energy surfaces. A special focus is placed on the mode specificity and bond selectivity in these gas–surface collisional processes, and their rationalization in terms of the recently proposed Sudden Vector Projection model.
Co-reporter:Sen Lin, Ryan S. Johnson, Gregory K. Smith, Daiqian Xie and Hua Guo
Physical Chemistry Chemical Physics 2011 - vol. 13(Issue 20) pp:NaN9631-9631
Publication Date(Web):2011/04/13
DOI:10.1039/C1CP20067D
Plane-wave density functional theory calculations have been carried out to explore possible pathways in methanol steam reforming (MSR) on Cu(111). We focus on reactions involving the adsorbed formaldehyde intermediate (CH2O) produced by methanol decomposition and the surface hydroxyl (OH) species generated by dissociative adsorption of H2O. Several possible pathways leading to the H2 + CO2 products have been identified. The two most likely pathways involve the formate (CHOO), rather than the carboxyl (COOH), intermediate, and they possess barriers lower than that of the rate-limiting step of MSR, namely the dehydrogenation of adsorbed methoxyl (CH3O) species.
Co-reporter:Julien Daranlot, Xixi Hu, Changjian Xie, Jean-Christophe Loison, Philippe Caubet, Michel Costes, Valentine Wakelam, Daiqian Xie, Hua Guo and Kevin M. Hickson
Physical Chemistry Chemical Physics 2013 - vol. 15(Issue 33) pp:NaN13896-13896
Publication Date(Web):2013/07/11
DOI:10.1039/C3CP52535J
Rate constants for the potentially important interstellar N(4S) + CH(X2Πr) reaction have been measured in a continuous supersonic flow reactor over the range 56 K ≤ T ≤ 296 K using the relative rate technique employing both the N(4S) + OH(X2Πi) and N(4S) + CN(X2Σ+) reactions as references. Excess concentrations of atomic nitrogen were produced by the microwave discharge method upstream of the Laval nozzle and CH and OH radicals were created by the in situ pulsed laser photolysis of suitable precursor molecules. In parallel, quantum dynamics calculations of the title reaction have been performed based on accurate global potential energy surfaces for the 13A′ and 13A′′ states of HCN and HNC, brought about through a hierarchical construction scheme. Both adiabatic potential energy surfaces are barrierless, each one having two deep potential wells suggesting that this reaction is dominated by a complex-forming mechanism. The experimental and theoretical work are in excellent agreement, predicting a positive temperature dependence of the rate constant, in contrast to earlier experimental work at low temperature. The effects of the new low temperature rate constants on interstellar N2 formation are tested using a dense cloud model, yielding N2 abundances 10–20% lower than previously predicted.
Co-reporter:Bin Jiang, Rui Liu, Jun Li, Daiqian Xie, Minghui Yang and Hua Guo
Chemical Science (2010-Present) 2013 - vol. 4(Issue 8) pp:NaN3254-3254
Publication Date(Web):2013/05/28
DOI:10.1039/C3SC51040A
Dissociative chemisorption of CH4 on transition-metal surfaces, representing the rate-limiting step in methane steam reforming, has been shown experimentally to be strongly mode selective. To understand the mode selectivity, a twelve-dimensional global potential energy surface is developed for CH4 interacting with a rigid Ni(111) surface based on a large number of density functional theory points. The reaction dynamics is investigated using an eight-dimensional quantum model, which includes representatives of all four vibrational modes of methane. After correcting for surface effects, key experimental observations, including the mode selectivity, are well reproduced. These theoretical results, along with mechanistic analysis, provide insights into this industrially important heterogeneous reaction.
Chemical Science (2010-Present) 2013 - vol. 4(Issue 1) pp:NaN508-508
Publication Date(Web):2012/10/23
DOI:10.1039/C2SC21393A
The bond selectivity in dissociative chemisorption of HOD on Cu(111) is investigated using a six-dimensional quantum model. It includes all vibrational modes of the impinging molecule on a density functional theory based interaction potential between the molecule and metal surface. It is shown that excitations in the HOD local stretching modes selectively enhance cleavage of the excited bond. This pronounced bond selectivity is attributed to a “late” or “product-like” barrier on the potential energy surface for the dissociative chemisorption and the slow intramolecular vibrational energy redistribution in the water molecule. The existence of mode and bond selectivities also underscores the inadequacy of statistical based transition-state theory in describing this industrially important surface reaction.
Co-reporter:Lidong Zhang, Daiqian Xie, Dingguo Xu and Hua Guo
Chemical Communications 2007(Issue 16) pp:NaN1640-1640
Publication Date(Web):2007/02/06
DOI:10.1039/B617946K
Supermolecule density functional theory calculations show that solvent is responsible for the concerted transition state in alkaline hydrolysis of p-nitrophenyl phosphate suggested by heavy atom kinetic isotope effects.
Physical Chemistry Chemical Physics 2012 - vol. 14(Issue 35) pp:NaN12093-12093
Publication Date(Web):2012/07/25
DOI:10.1039/C2CP41621B
The title reaction is thought to be responsible for the production of molecular nitrogen in interstellar clouds. In this work, we report quantum capture calculations on a new two-dimensional potential energy surface determined by interpolating high-level ab initio data. The low-temperature rate constant calculated using a capture model is quite large and has a positive temperature dependence, in agreement with a recent experiment. The origin of the aforementioned behaviors of the rate constant is analyzed.
Co-reporter:Anyang Li, Hua Guo, Zhigang Sun, Jacek Kłos and Millard H. Alexander
Physical Chemistry Chemical Physics 2013 - vol. 15(Issue 37) pp:NaN15355-15355
Publication Date(Web):2013/07/17
DOI:10.1039/C3CP51870A
The state-to-state reaction dynamics of the title reaction is investigated on the ground electronic state potential energy surface using two quantum dynamical methods. The results obtained using the Chebyshev real wave packet method are in excellent agreement with those obtained using the time-independent method, except at low translational energies. It is shown that this exothermic hydrogen abstraction reaction is direct, resulting in a strong back-scattered bias in the product angular distribution. The HF product is highly excited internally. Agreement with available experimental data is only qualitative. We discuss several possible causes of disagreement with experiment.
Physical Chemistry Chemical Physics 2016 - vol. 18(Issue 43) pp:NaN29835-29835
Publication Date(Web):2016/10/06
DOI:10.1039/C6CP06232F
The lowest triplet state of the H2O2 system features multiple reaction channels, including several relevant to the combustion of H2. To accurately map out the global potential energy surface, ∼28000 geometries were sampled over a large configuration space including all important asymptotes, and electronic energies at these points were calculated at the level of the explicitly correlated version of the multi-reference configuration interaction (MRCI-F12) method. A new multi-channel global potential energy surface was constructed by fitting the ab initio data set using a permutation invariant polynomial-neural network method, resulting in a total root mean square fitting error of only 6.7 meV (0.15 kcal mol−1). Various kinetics and dynamical properties of several relevant reactions were calculated on the new MRCI potential energy surface, and compared with the available experimental results.
Physical Chemistry Chemical Physics 2014 - vol. 16(Issue 45) pp:NaN24715-24715
Publication Date(Web):2014/10/09
DOI:10.1039/C4CP03761H
A six-dimensional potential energy surface (PES) for H2 dissociation on rigid Ag(111) is developed by fitting ∼4000 plane-wave density functional theory points using the recently proposed permutation invariant polynomial-neural network (PIP-NN) method, which enforces both the surface periodicity and molecular permutation symmetry. Quantum reactive scattering calculations on the PIP-NN PES yielded dissociative sticking probabilities for both H2 and D2. Good agreement with experiment was achieved at high collision energies, but the agreement is less satisfactory at low collision energies, due apparently to the neglect of surface temperature in our model. The dissociation is activated by both vibrational and translational excitations, with roughly equal efficacies. Rotational and alignment effects were examined and found to be quite similar to hydrogen dissociation on Ag(100) and Cu(111).
Co-reporter:Bin Jiang, Xixi Hu, Sen Lin, Daiqian Xie and Hua Guo
Physical Chemistry Chemical Physics 2015 - vol. 17(Issue 36) pp:NaN23355-23355
Publication Date(Web):2015/08/07
DOI:10.1039/C5CP03324A
Cobalt is a widely used catalyst for many heterogeneous reactions, including the Fischer–Tropsch (FT) process, which converts syngas (H2 and CO) to higher hydrocarbons. As a result, a better understanding of the key chemical steps on the Co surface, such as the dissociative chemisorption of H2 as an initial step of the FT process, is of fundamental importance. Here, we report an accurate full-dimensional global potential energy surface for the dissociative chemisorption of H2 on the rigid Co(0001) surface constructed from more than 3000 density functional theory points. The high-fidelity potential energy surface was obtained using the permutation invariant polynomial-neural network method, which preserves both the permutation symmetry of H2 and translational symmetry of the Co(0001) surface. The reaction path features a very low barrier on the top site. Full-dimensional quantum dynamical calculations provide insights into the dissociation dynamics and influence of the initial vibrational, rotational, and orientational degrees of freedom.
Co-reporter:Hongwei Song, Anyang Li, Hua Guo, Yuntao Xu, Bo Xiong, Yih-Chung Chang and C. Y. Ng
Physical Chemistry Chemical Physics 2016 - vol. 18(Issue 32) pp:NaN22515-22515
Publication Date(Web):2016/07/22
DOI:10.1039/C6CP04598G
To understand the dynamics of H3O+ formation, we report a combined experimental–theoretical study of the rovibrationally state-selected ion–molecule reactions H2O+(X2B1; v1+v2+v3+; NKa+Kc++) + H2 (D2) → H3O+ (H2DO+) + H (D), where (v1+v2+v3+) = (000), (020), and (100) and NKa+Kc++ = 000, 111, and 211. Both quantum dynamics and quasi-classical trajectory calculations were carried out on an accurate full-dimensional ab initio global potential energy surface, which involves nine degrees of freedom. The theoretical results are in good agreement with experimental measurements of the initial state specific integral cross-sections for the formation of H3O+ (H2DO+) and thus provide valuable insights into the surprising rotational enhancement and vibrational inhibition effects in these prototypical ion–molecule reactions that play a key role in the interstellar generation of OH and H2O species.
Co-reporter:Huixian Han, Benjamin Alday, Nicholas S. Shuman, Justin P. Wiens, Jürgen Troe, Albert A. Viggiano and Hua Guo
Physical Chemistry Chemical Physics 2016 - vol. 18(Issue 45) pp:NaN31071-31071
Publication Date(Web):2016/10/18
DOI:10.1039/C6CP05867A
To provide a deeper understanding of the kinetics of electron attachment to CF3, the six-dimensional potential energy surfaces of both CF3 and CF3− were developed by fitting ∼3000 ab initio points per surface at the AE-CCSD(T)-F12a/AVTZ level using the permutation invariant polynomial-neural network (PIP-NN) approach. The fitted potential energy surfaces for CF3 and CF3− had root mean square fitting errors relative to the ab initio calculations of 1.2 and 1.8 cm−1, respectively. The main active mode for the crossing between the two potential energy surfaces was identified as the umbrella bending mode of CF3 in C3v symmetry. The lowest energy crossing point is located at RCF = 1.306 Å and θFCF = 113.6° with the energy of 0.051 eV above the minimum of the CF3 electronic surface. This value is only slightly larger than the experimental data 0.026 ± 0.01 eV determined by kinetic modeling of electron attachment to CF3. The small discrepancy between the theoretical and experimentally measured values is analyzed.
Chemical Science (2010-Present) 2016 - vol. 7(Issue 7) pp:NaN4003-4003
Publication Date(Web):2016/04/13
DOI:10.1039/C6SC01066K
It has been long established that the transition state for an activated reaction controls the overall reactivity, serving as the bottleneck for reaction flux. However, the role of the transition state in regulating quantum state resolved reactivity has only been addressed more recently, thanks to advances in both experimental and theoretical techniques. In this perspective, we discuss some recent advances in understanding mode-specific reaction dynamics in bimolecular reactions, mainly focusing on the X + H2O/CH4 (X = H, F, Cl, and O(3P)) systems, extensively studied in our groups. These advances shed valuable light on the importance of the transition state in mode-specific and steric dynamics of these prototypical reactions. It is shown that many mode-specific phenomena can be understood in terms of a transition-state based model, which assumes in the sudden limit that the ability of a reactant mode for promoting the reaction stems from its coupling with the reaction coordinate at the transition state. Yet, in some cases the long-range anisotropic interactions in the entrance (or exit) valley, which govern how the trajectories reach (or leave) the transition state, also come into play, thus modifying the reactive outcomes.
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