Co-reporter:Guang-Shuang-Mu Lin, Changjian Xie, and Daiqian Xie
The Journal of Physical Chemistry A November 9, 2017 Volume 121(Issue 44) pp:8432-8432
Publication Date(Web):October 18, 2017
DOI:10.1021/acs.jpca.7b09070
New reduced three-dimensional (3D) diabatic potential energy surfaces (PESs) involving the 1ππ, 1ππ*, and 1πσ* states for the nonadiabatic photodissociation C6H5SH(S0) + hv → C6H5SH(1ππ*/1πσ*) → H + C6H5S•(A/X) were constructed at a high computational level, namely explicitly correlated multireference configuration interaction (MRCI-F12) method with the cc-pVTZ-F12 basis. The diabatization of the PESs was achieved by a simple, efficient, and reliable “regularized diabatization” method [Köppel, H.; Gronki, J.; Mahapatra, S. J. Chem. Phys. 2001, 115, 2377–2388]. The dissociation energy of the S0 state and the excitation energies of the excited S1 and S2 states were found to be in reasonably good agreement with the experimental values. The vibronic energy levels of the thiophenol (PhSH) and deuterated thiophenol (PhSD) for S0 and S1 states were calculated using a three-dimensional model, and they are in reasonably good agreement with the available experimental results, which validate the high accuracy of the adiabatic PESs and the reasonability of the diabatic couplings.
Co-reporter:Guang-Shuang-Mu Lin, Changjian Xie, and Daiqian Xie
The Journal of Physical Chemistry A November 9, 2017 Volume 121(Issue 44) pp:8432-8432
Publication Date(Web):October 18, 2017
DOI:10.1021/acs.jpca.7b09070
New reduced three-dimensional (3D) diabatic potential energy surfaces (PESs) involving the 1ππ, 1ππ*, and 1πσ* states for the nonadiabatic photodissociation C6H5SH(S0) + hv → C6H5SH(1ππ*/1πσ*) → H + C6H5S•(A/X) were constructed at a high computational level, namely explicitly correlated multireference configuration interaction (MRCI-F12) method with the cc-pVTZ-F12 basis. The diabatization of the PESs was achieved by a simple, efficient, and reliable “regularized diabatization” method [Köppel, H.; Gronki, J.; Mahapatra, S. J. Chem. Phys. 2001, 115, 2377–2388]. The dissociation energy of the S0 state and the excitation energies of the excited S1 and S2 states were found to be in reasonably good agreement with the experimental values. The vibronic energy levels of the thiophenol (PhSH) and deuterated thiophenol (PhSD) for S0 and S1 states were calculated using a three-dimensional model, and they are in reasonably good agreement with the available experimental results, which validate the high accuracy of the adiabatic PESs and the reasonability of the diabatic couplings.
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.
Physical Chemistry Chemical Physics 2017 vol. 19(Issue 20) pp:12826-12837
Publication Date(Web):2017/05/24
DOI:10.1039/C7CP01697B
The dissociative chemisorption dynamics of CO on rigid Co(110) is investigated using a quasi-classical trajectory method on a new global six-dimensional potential energy surface (PES). The PES is fit using a neural network method to represent 24 630 density functional energies in various configurations. The reaction path features deep chemisorption wells and a late barrier for dissociation, agreeing well with previous calculations. The activation energy for dissociation ranges from 0.1 eV at the hollow site to 2.46 eV on the top site, indicating a highly corrugated PES. Effects of the incidence energy of the impinging molecule, its initial orientation, vibrational and rotational excitations, and site specificity are examined. Despite the presence of a low barrier, the initial dissociation probability is very small, even at high incident energies, as a large percentage of trajectories is either trapped or desorbed back to the gas phase. The low reactivity is attributed to inefficient energy transfer into the dissociation reaction coordinate in the chemisorption well where thermal equilibrium is not reached. This system underscores the importance of dynamics in understanding reactions at gas–surface interfaces and in kinetic modeling of catalytic processes.
Physical Chemistry Chemical Physics 2017 vol. 19(Issue 15) pp:9770-9777
Publication Date(Web):2017/04/12
DOI:10.1039/C7CP00920H
A new and more accurate full-dimensional global potential energy surface (PES) for the ground electronic state of the ClH2O system is developed by fitting 15 777 points obtained using an explicitly correlated unrestricted coupled-cluster method with single, double, and perturbative triple excitations (UCCSD(T)-F12b). The fitting is carried out using the permutation invariant polynomial-neural network (PIP-NN) method and has an error of 6.9 meV. The new PES has a slightly lower barrier for the atmospherically important HCl + OH → Cl + H2O reaction than the previous PES based on multi-reference configuration interaction (MRCI) calculations. As a result, it should provide a better characterization of the kinetics. Quantum dynamical calculations of reaction probabilities for both the forward and reverse reactions are performed on this new PES and compared with those on the MRCI PES. They reveal notable differences, resulting apparently from subtle differences in the PESs.
We investigated the co-assembly of nanoparticles P and amphiphilic diblock copolymers AB in selective solvents using a dissipative particle dynamics (DPD) method. By controlling the nanoparticle concentration and the interaction parameter between the hydrophobic blocks and the solvents, we found that the aggregation morphology can be changed from rod-like micelles to disk-like micelles and further to vesicles. The ratio of the hydrophobic/hydrophilic block and the nanoparticle concentration largely affects the structural characteristics of vesicles and the dispersion of nanoparticles. Copolymers with a longer hydrophobic block length are more likely to form vesicles with a smaller aqueous cavity size and vesicle size as well as a thicker wall. At the same time, the nanoparticles in the hydrophobic membrane tend to locate closer to the center of the vesicle and they become more compactly organized. A significant discovery has found that the larger the nanoparticle concentration, the smaller the aqueous cavity and the larger the vesicle size. We can also locate the nanoparticles at the center of spherical micelles or the hydrophobic membranes of vesicles by varying the nanoparticle concentration. This provides an effective and simple method to prepare size-controlled vesicles containing nanoparticles, project the localization of nanoparticles within the vesicles, and even tune the distance between the nanoparticles.
Co-reporter:Changjian Xie; Jianyi Ma; Xiaolei Zhu; David R. Yarkony; Daiqian Xie;Hua Guo
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.
Co-reporter:Junxiang Zuo, Yongle Li, Hua Guo, and Daiqian Xie
The Journal of Physical Chemistry A 2016 Volume 120(Issue 20) pp:3433-3440
Publication Date(Web):May 5, 2016
DOI:10.1021/acs.jpca.6b03488
Thermal rate coefficients at temperatures between 200 and 1000 K are calculated for the HCl + OH → Cl + H2O reaction on a recently developed permutation invariant potential energy surface, using ring polymer molecular dynamics (RPMD). Large deviations from the Arrhenius limit are found at low temperatures, suggesting significant quantum tunneling. Agreement with available experimental rate coefficients is generally satisfactory, although the deviation becomes larger at lower temperatures. The theory–experiment discrepancy is attributed to the remaining errors in the potential energy surface, which is known to slightly overestimate the barrier. In the deep tunneling region, RPMD performs better than traditional transition-state theory with semiclassical tunneling corrections.
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.
Co-reporter:Wen-Sheng Zou, Sen Lin, Jia-Yuan Li, Hong-Qing Wei, Xiao-Qin Zhang, Dong-Xu Shen, Jun-Qin Qiao, Hong-Zhen Lian, Dai-Qian Xie and Xin Ge
New Journal of Chemistry 2015 vol. 39(Issue 1) pp:262-272
Publication Date(Web):09 Oct 2014
DOI:10.1039/C4NJ01396D
In this paper, a strong halogen bond (XB) donor (iodine) and photoinduced electron transfer (PET) molecule (ciprofloxacin, Cip) were selected with the objective to investigate halogen bonding under weakly alkaline conditions. A series of experimental characterization techniques was employed to elucidate the interaction mechanism of the XB, in combination with theoretical calculations. It is found that new UV-Vis absorption peaks and the fluorescence enhancement with the mixing of Cip and iodine are attributed to the disruption of the PET charge separation process through the halogen bonding interaction. The 2:1 stoichiometry of the XB complex (I2:Cip) was attested using a modified Benesi–Hildebrand method. 1H NMR spectra showed that the iodine molecule can interact with three nitrogen atoms of Cip to form three XBs. FT-IR spectra indicated that the nitrogen atom of the imino group is the preferential interaction site of the XB. Notably, direct analysis in real time-mass spectrometry (DART-MS) gave a distinct quasi-molecular ion of the supramolecular complex (Cip + I) in solution. Meanwhile, density functional theory (DFT), taking into account the dispersion energy, revealed that the formation of an I⋯N XB not only disrupts the PET charge separation process of Cip to enhance fluorescence but also induces the cleavage of an iodine molecule (I–I) to produce a triiodine anion (I3−) XB. This explained why I3− was observed in UV-Vis and DART-MS as well as in the crystal, and how the fourth iodine atom involved in the self-assembly of the XB existed stably. Moreover, a developed optosensor based on halogen bonding has been successfully used to analyze commercial Cip·HCl capsules, suggesting the potential applicability of halogen bonding in real pharmaceutical analyses.
The Journal of Physical Chemistry A 2015 Volume 119(Issue 50) pp:12062-12072
Publication Date(Web):July 23, 2015
DOI:10.1021/acs.jpca.5b05029
The photodissociation dynamics for the ground and three fundamental vibrational states of HOD were explored from quantum dynamical calculations including the electronic X̃, Ã, and B̃ states. The calculations were based on a Chebyshev real wave packet method. Due to the different shapes of the initial vibrational wave functions and isotopic effect, the calculated absorption spectra, product state distributions, and branching ratios show different dynamic features. The initial bending excited vibtaional state (0, 1, 0) generates a bimodal behavior on the absorption spectrum and an inverted vibrational population of OD(X̃) fragment at some total energies. The rotational state distributions from four vibrational states have two different behaviors. One has a single broad peak, whereas the other one has a bimodal structure. Large OD(Ã)/OD(X̃) ratios are found for photodissociation from four vibrational states at high total energies, which indicate that the H atom dissociates mainly via the adiabatic pathway. We also calculated the OD/OH isotopic branching ratios from four vibrational states and found that the OD + H production channel is dominant over the OH + D channel in the energy range considered. The calculated results are consistent with the available observed ones.
Co-reporter:Jean-Christophe Loison, Xixi Hu, Shanyu Han, Kevin M. Hickson, Hua Guo and Daiqian Xie
Physical Chemistry Chemical Physics 2014 vol. 16(Issue 27) pp:14212-14219
Publication Date(Web):04 Jun 2014
DOI:10.1039/C4CP01801J
Rate constants for the N(4S) + C2(1Σg+) reaction have been measured in a continuous supersonic flow reactor over the range 57 K ≤ T ≤ 296 K by the relative rate technique employing the N(4S) + OH(X2Π) → H(2S) + NO(X2Π) reaction as a reference. Excess concentrations of atomic nitrogen were produced by the microwave discharge method and C2 and OH radicals were created by the in situ pulsed laser photolysis of precursor molecules C2Br4 and H2O2 respectively. In parallel, quantum dynamics calculations were performed based on an accurate global potential energy surfaces for the three lowest lying quartet states of the C2N molecule. The 14A′′ potential energy surface is barrierless, having two deep potential wells corresponding to the NCC and CNC intermediates. Both the experimental and theoretical work show that the rate constant decreases to low temperature, although the experimentally measured values fall more rapidly than the theoretical ones except at the lowest temperatures. Astrochemical simulations indicate that this reaction could be the dominant source of CN in dense interstellar clouds.
Co-reporter:Guang-Shuang-Mu Lin, Linsen Zhou, and Daiqian Xie
The Journal of Physical Chemistry A 2014 Volume 118(Issue 39) pp:9220-9227
Publication Date(Web):May 15, 2014
DOI:10.1021/jp503062s
The state-to-state photodissociation dynamics for the vibrationally excited H2O in its second absorption band has been investigated on the recent three-dimensional potential energy surfaces based on a large number of high-level ab initio points. The photodissociassion dynamics from three fundamental vibrational states of H2O were explored from quantum dynamical calculations including the electronic X̃ and B̃ states on the basis of a Chebyshev real wave packet method. Because of the different shapes of various initial vibrational wave functions, the photoexcited wavepackets access different portions of the upper-state potential energy surface, which yields different absorption spectra, ro-vibrational distributions, and branching ratios. The bending excited vibrational state (0,1,0) generates two lobes with a shallow minimum on the absorption spectrum, a dominant vibrational inverted population OH(X̃, ν = 1) fragment at higher energy, and a nearly single rotational product propensity. The bond-stretching vibrational states (0,0,1) and (1,0,0) show a high OH(Ã)/OH(X̃) ratio at short photon wavelength, which indicates that dissociation proceeds mainly via the adiabatic channel.
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;
Science China Chemistry 2014 Volume 57( Issue 1) pp:87-99
Publication Date(Web):2014 January
DOI:10.1007/s11426-013-4976-8
Much progress has been achieved for both experimental and theoretical studies on the dissociative chemisorption of molecules on surfaces. Quantum state-resolved experimental data has provided unprecedented details for these fundamental steps in heterogeneous catalysis, while the quantitative dynamics is still not fully understood in theory. An in-depth understanding of experimental observations relies on accurate dynamical calculations, in which the potential energy surface and adequate quantum mechanical implementation are desired. This article summarizes the current methodologies on the construction of potential energy surfaces and the quantum mechanical treatments, some of which are promising for future applications. The challenges in this field are also addressed.
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: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.
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.
Co-reporter:Mengying Xiao, Jiannan Liu, Jiexin Yang, Rong Wang and Daiqian Xie
Soft Matter 2013 vol. 9(Issue 8) pp:2434-2442
Publication Date(Web):11 Jan 2013
DOI:10.1039/C2SM26882E
Our recent simulation study on mechanisms of vesicle formation in ABA triblock copolymer system has revealed the factors or conditions that lead to the transition from mechanism I (a bilayer membrane closing pathway) to mechanism II (a nucleation and growth pathway). The spontaneous vesicle formation involves many metastable states and the two mechanisms do not each lead to a unique intermediate structure, but have a transition period. In this paper, we use dissipative particle dynamics (DPD) simulations to further investigate the effect of vesicle size and hydrophobicity of the blocks on membrane characteristics, with the aim of understanding and controlling the structures of block copolymer vesicle and its formation in different scales, and to try to connect our simulation results to previous experimental studies. We have evaluated the thickness of the hydrophobic layer and observed two types of dependence on the vesicle size. Our results indicate that as the degree of hydrophobicity of the blocks increases, from a totally strong-behavior to a totally weak-behavior relationship, the transformation is observed in large sized vesicles first and then in small sized vesicles. Two characteristics, the chain compaction of the vesicles and the area densities of the inner corona, are thought to be important in controlling the membrane thickness, which are proposed to explain the size-dependent behaviors of bilayer thickness. Finally, the fraction of bridges Φb is also calculated. In our model, Φb increases with an increase in vesicle size for a given system and fixed interaction and decreases with an increase in the degree of hydrophobicity of the blocks.
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:Andrew R. Whitehill;Xixi Hu;Shuhei Ono;Changjian Xie;Hua Guo
PNAS 2013 Volume 110 (Issue 44 ) pp:17697-17702
Publication Date(Web):2013-10-29
DOI:10.1073/pnas.1306979110
Signatures of mass-independent isotope fractionation (MIF) are found in the oxygen (16O,17O,18O) and sulfur (32S, 33S, 34S, 36S) isotope systems and serve as important tracers of past and present atmospheric processes. These unique isotope signatures
signify the breakdown of the traditional theory of isotope fractionation, but the physical chemistry of these isotope effects
remains poorly understood. We report the production of large sulfur isotope MIF, with Δ33S up to 78‰ and Δ36S up to 110‰, from the broadband excitation of SO2 in the 250–350-nm absorption region. Acetylene is used to selectively trap the triplet-state SO2 (3B1), which results from intersystem crossing from the excited singlet (1A2/1B1) states. The observed MIF signature differs considerably from that predicted by isotopologue-specific absorption cross-sections
of SO2 and is insensitive to the wavelength region of excitation (above or below 300 nm), suggesting that the MIF originates not
from the initial excitation of SO2 to the singlet states but from an isotope selective spin–orbit interaction between the singlet (1A2/1B1) and triplet (3B1) manifolds. Calculations based on high-level potential energy surfaces of the multiple excited states show a considerable
lifetime anomaly for 33SO2 and 36SO2 for the low vibrational levels of the 1A2 state. These results demonstrate that the isotope selectivity of accidental near-resonance interactions between states is
of critical importance in understanding the origin of MIF in photochemical systems.
Chinese Journal of Chemistry 2012 Volume 30( Issue 9) pp:2036-2040
Publication Date(Web):
DOI:10.1002/cjoc.201200714
Abstract
Pure In2O3 is considered as an efficient methanol steam reforming catalyst. Despite of several studies in the past decades, the mechanism of MSR on In2O3 is still not fully understood. In this work, a periodic density functional theory study of the initial dissociation of methanol and water over the In2O3 (110) surface is presented. The activation energy barriers and thermochemistry for several elementary steps are reported. It is found that the energy barriers for OH bond cleavage of both CH3OH and H2O to produce CH3O and OH species at a surface In-O pair site are very low, indicating that In2O3 (110) can facilely catalyze these two important processes at low temperatures. In addition, the subsequent dehydrogenation of CH3O to CH2O is also found to proceed with a low barrier.
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.
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:Huixian Han, Bingbing Suo, Daiqian Xie, Yibo Lei, Yubin Wang and Zhenyi Wen
Physical Chemistry Chemical Physics 2011 vol. 13(Issue 7) pp:2723-2731
Publication Date(Web):10 Dec 2010
DOI:10.1039/C0CP01300E
Configuration-based multi-reference second order perturbation theory (CB-MRPT2) and multi-reference configuration interaction with single and double excitations (MRCISD) have been used to calculate the bending and dissociation potential energy curves (PECs) of ozone. Based on these PECs, equilibrium structures, vertical and adiabatic transition energies of the ground state and several low-lying excited states, as well as intersections and avoided crossings among the states displayed on the PECs are investigated. The energy separation of the open and ring structures and the dissociation energy of the ground state 1A1 are determined by reference-selected MRCISD. Furthermore, one-dimensional cuts along the dissociation reaction coordinate for the lowest four electronic states of O3 with 1A′ symmetry and possible pre-dissociations are studied. The Hartley band may be pre-dissociable, and the pre-dissociation limit is found to be 3871 cm−1, which corresponds to symmetric stretching quanta nss ≈ 6.
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.
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:Lecheng Wang, Daiqian Xie, Hua Guo, Hui Li, Robert J. Le Roy, Pierre-Nicholas Roy
Journal of Molecular Spectroscopy 2011 Volume 267(1–2) pp:136-143
Publication Date(Web):May–June 2011
DOI:10.1016/j.jms.2011.03.007
Using an improved path integral Monte Carlo method, finite-temperature structural and dynamical properties of 4HeN–N2O clusters (N ⩽ 40) are investigated. The simulations employed a newly developed He–N2O interaction potential obtained at the CCSD(T) level. Good agreement with experimental observations was obtained for the evolution of the effective rotational constant as a function of cluster size. In particular, the experimentally observed turnaround at N = 6 for the effective rotational constant Beff is attributed to filling of the “donut” ring structure around the equator of the linear impurity molecule, and a second extremum in Beff for cluster sizes near N = 10 is associated with the emergence of superfluidity of the quantum solvent. A careful comparison with properties of HeN–CO2 clusters suggests that the difference between the renormalized rotational constants of the two impurity molecules is due to the anisotropy of the solute–solvent interaction potential.Graphical abstractCalculated rotational constants of HeN–N2O clusters were obtained from fitting to orientation correlation functions and from the two-fluid model. The corresponding values from Boltzmann simulations are included as a benchmark for gauging the effect of bosonic exchange.Highlights► The simulation results are in good agreement with known experimental data. ► A detailed analysis of the superfluid response has been performed. ► Difference in rotational dynamics between HeN–N2O and HeN–CO2 has been elucidated.
Chemical Physics Letters 2011 Volume 511(4–6) pp:229-234
Publication Date(Web):5 August 2011
DOI:10.1016/j.cplett.2011.06.067
Abstract
We present a new potential energy surface for Kr–CO2 which incorporates its dependence on the asymmetric Q3 normal mode with CO2 in both ground (υ3 = 0) and the first excited (υ3 = 1) states were generated by integration of this potential over the Q3 coordinate. Each potential is found to have a T-shaped global minimum. The radial DVR/angular FBR method are applied to calculate the rovibrational energy levels. The calculated band origin shifts, microwave and infrared spectra are in good agreement with the available experiment values.
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.
Co-reporter:Xuefeng Ren, Daiqian Xie, and Jun Zeng
The Journal of Physical Chemistry A 2011 Volume 115(Issue 36) pp:10129-10135
Publication Date(Web):August 11, 2011
DOI:10.1021/jp2033609
In red fluorescent proteins such as DsRed, an acylimine is formed from the Phe65-Gln66 linkage in GFP-like immature form, while it shows a cis configuration in its mature state. To date, the relationship between acylimine formation and trans–cis isomerization is still unresolved. We have calculated bond rotation profiles for mature and immature chromophores within the protein using our own n-layered integrated molecular orbital and molecular mechanism (ONIOM) approach. The results suggested that the isomerization is barrierless in acylimine formed in the mature state, suggesting that the acylimine formation precedes the trans–cis isomerization in DsRed chromophores. Further decomposition analysis of electrostatic contributions from individual residues has identified several residues and a specific water molecule which could play key roles in controlling the rate of the trans–cis isomerization of peptide bond in immature GFP-like protein. The results also highlight the importance of Gln66-like of tripeptide motif (chromophore) in the maturation of red fluorescent proteins. In view of the considerable interest in developing red fluorescent proteins for numerous biotechnological applications, these results should be useful for design of novel fluorescent proteins.
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:Weizhong Yan, Daiqian Xie and Jun Zeng
Physical Chemistry Chemical Physics 2009 vol. 11(Issue 29) pp:6042-6050
Publication Date(Web):12 May 2009
DOI:10.1039/B903544C
Fluorescent proteins are commonly used as molecular labels, noninvasive markers of gene expression, and reporters of environmental conditions in live cells. We investigate the structural and spectroscopic properties of the chromophore of a far-red fluorescent protein eqFP611. Both the cis and trans isomers of the chromophore are examined within the protein for which both anionic and neutral states of protonation are considered. Spectroscopic properties are examined using time-dependent density functional theory (TDDFT), employing the B3LYP, PBE and B3PW91 density functionals. Intermolecular and long-range contributions to the structure and spectroscopy were treated using the own n-layered integrated molecular orbital and molecular mechanics (ONIOM) approach. The results indicated that the chromophore before excitation is in an anionic, protonated state, with the long-range contributions inducing a blue shift in the absorption and fluorescence maxima of the chromophore. Moreover, the calculated changes of the lowest π–π* excitation energy upon isomerization match the observed shift from 559 to 600 nm in the absorption maximum of the system following prolonged irradiation. Furthermore, decomposition analysis of the electrostatic contributions from individual residues indicated that the interactions from four residues Arg92, Lys67, Glu145, and His197 to the chromophore play a key role in the absorption and fluorescence spectra of eqFP611, suggesting that mutations at these sites should provide very useful mechanistic information.
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:Zhihong Ke, Shenglong Wang, Daiqian Xie and Yingkai Zhang
The Journal of Physical Chemistry B 2009 Volume 113(Issue 52) pp:16705-16710
Publication Date(Web):October 21, 2009
DOI:10.1021/jp9080614
Protein arginine deiminase 4 (PAD4) catalyzes the citrullination of the peptidylarginine via two successive stages: deimination and hydrolysis. Herein, by employing state-of-the-art Born−Oppenheimer ab initio QM/MM molecular dynamics simulations with the umbrella sampling method, we characterized the catalytic mechanism of the hydrolysis reaction: first, the nucleophilic attack of a water molecule to the Cζ of the thiouronium intermediate yields a stable tetrahedral intermediate, and then the S−Cζ bond breaks to generate the final product, citrulline. Throughout the hydrolysis reaction, His471 and Asp473 play pivotal catalytic roles by first enhancing the nucleophilic ability of the active water through forming shorter and low-barrier hydrogen bonds and then by serving as proton-accepting groups to deprotonate the water molecule, which is consistent with experimental findings. At the transition state, the spontaneous proton transfer among the reactive water, His471 and Asp473 have been observed. The determined overall free energy barrier for this hydrolysis stage is 16.5 kcal·mol−1, which is lower than the barrier of 20.9 kcal·mol−1 for the deimination stage determined previously with the same computational approach [J. Phys. Chem. B 2009, 113, 12750−12758]. Thus, the rate-determining step of the PAD4-catalyzed citrullination is the first step of the deimination. Our current work further demonstrates the strength and applicability of the ab initio QM/MM MD approach in simulating enzyme reactions.
Co-reporter:Zhihong Ke, Yanzi Zhou, Po Hu, Shenglong Wang, Daiqian Xie and Yingkai Zhang
The Journal of Physical Chemistry B 2009 Volume 113(Issue 38) pp:12750-12758
Publication Date(Web):June 9, 2009
DOI:10.1021/jp903173c
The protein arginine deiminase 4 (PAD4) catalyzes the citrullination of the peptidylarginine and plays a critical role in rheumatoid arthritis (RA) and gene regulation. Understanding its catalytic mechanism is not only of fundamental importance but also of significant medical interest for the rational design of new inhibitors. By employing on-the-fly Born−Oppenheimer ab initio QM/MM molecular dynamics simulations, we have demonstrated that it is unlikely for the active site cysteine and histidine to exist as a thiolate−imidazolium ion pair in the PAD4 Michaelis reactant complex. Instead, a substrate-assisted proton transfer mechanism for the deimination reaction step has been characterized: both Cys645 and His471 in the PAD4 active site are neutral prior to the reaction; the deprotonation of Cys645 by the substrate arginine occurs in concert with the nucleophilic addition of the Cys thiolate to Cζ of the substrate, and leads to a covalent tetrahedral intermediate; then, the Cζ−Nη1 bond cleaves and the resulted ammonia is displaced by a solvent water molecule. The initial deprotonation and nucleophilic attack step is found to be rate-determining. The computed free energy barrier with B3LYP(6-31G*) QM/MM MD simulations and umbrella sampling is 20.9 kcal·mol−1, consistent with the experimental kinetic data. During the deimination, His471 plays an important role in stabilizing the transition state through the formation of the hydrogen bond with the guanidinium group. Our current studies further demonstrated the viability and strength of the ab initio QM/MM molecular dynamics approach in simulating enzyme reactions.
Co-reporter:Wenzhen Lai, Wuying Huang and Daiqian Xie
Physical Chemistry Chemical Physics 2008 vol. 10(Issue 12) pp:1669-1674
Publication Date(Web):08 Feb 2008
DOI:10.1039/B718477H
Ab
initio total-energy density functional theory calculations with supercell models have been employed to investigate the R30° and (2 × 2) structures of K on the Pb(111) surface. Four “on-surface” sites and a substitutional site were considered. The calculations showed that the substitutional site is more stable than all the on-surface sites, due to its low vacancy formation energy. The calculated R30° geometry agrees well with the LEED results. The density-of-states analysis indicates that the K atom loses part of its loosely bound valence s electron. From the electron density distributions, it was found that the lowering of the work function after the substitutional adsorption can be attributed to the dipole moment, associated with the positively polarized adsorbate atom that is characterized by charge depletion from the K vacuum sides and charge accumulation in the region between K and Pb atoms. Our results indicate that the bonding of K with the Pb(111) surface has a mixed ionic and metallic bond character.
The adsorption and dissociation of NH3 on Ir(1 0 0) have been investigated using the periodic density functional calculations. The recombination desorption of N2 has also been studied. The corresponding reaction energies, the structure of the transition states and the activation energies were determined. The calculated activation barrier for NHx (x = 1–3) dehydrogenation is between 0.83 and 1.09 eV including the zero point energy correction. The NH3 desorption energy of 0.95 eV is close to the NH3 dehydrogenation barrier of 0.91 eV, which indicates that the desorption and dissociation of NH3 on Ir(1 0 0) is very competitive, consistent with the recent experimental results. The N–H bond cleavage in NH3 is found to be the rate limiting step. The activation energy for the recombinative desorption of N2 is significantly lower than those for the NHx dehydrogenation. Moreover, it was found that the zero point energy has a large contribution to the reaction energies and activation barriers.
The adsorption and dissociation of NH3 on Ir{110}(1×2) have been investigated using the density-functional calculations at a coverage of 0.25 ML. The adsorption sites, energy, and geometries were obtained for NH3, NH2, and H adsorptions on the surface. The transition state for NH3 dissociation on Ir{110}(1×2) was also identified. It was found that NH3 is adsorbed preferentially at the ridge atop site, while NH2 and H are adsorbed at the ridge bridge site. The activation barrier of NH3 dissociation is 78.4 kJ/mol, which is very close to the NH3 adsorption energy of 90.0 kJ/mol. This indicates that the desorption and dissociation of NH3 on Ir{110}(1×2) are very competitive, which is consistent with the recent experimental results.
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.
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 2007 Volume 68(Issue 5) pp:1287-1295
Publication Date(Web):31 December 2007
DOI:10.1016/j.saa.2007.02.005
In the present study, density functional theory calculations with the combined Becke's three-parameter exchange functional in combination with the Lee, Yang, and Parr correlation functional (B3LYP) exchange-correlation energy functions were performed by using the 6-311G** basis set to study the structure and vibrational spectra of 10,10,2,6,5-pentamethyl-1-hydroxychroman (a model of α-tocopherol). The fully optimized geometry of the molecule was found to be very consistent with the X-ray crystal structure. The predicted vibrational frequencies made it possible to give a reliable assignment of the IR spectrum of the molecule according to the potential energy distributions (PEDs).
Science China Chemistry 2007 Volume 50( Issue 1) pp:7-10
Publication Date(Web):2007 February
DOI:10.1007/s11426-007-0006-z
The potential energy surfaces for the electronic ground state of the HXeCl and HXeF molecules are constructed by using the internally contracted multi-reference configuration interaction with the Davidson correction (icMRCl+Q) method and large basis sets. The stabilities and dissociation barriers are identified from the potential energy surfaces. The three-body dissociation channel is found to be the dominate dissociation channel for HXeCl, while two dissociation channels are possible and competitive for HXeF. Based on the obtained potentials, vibrational energy levels of HXeCl and HXeF are calculated using the Lanczos algorithm. Our theoretical results are in good agreement with the available observed values. Particularly, the calculated fundamental frequency of the H—Xe stretching vibration including the Xe matrix effect of HXeCl is found to be 1666.6 cm−1, which is only 17.6 cm−1 higher than the recently observed value of 1649 cm−1.
Co-reporter:Minghui Qiu;Zefeng Ren;Li Che;Dongxu Dai;Steve A. Harich;Xiuyan Wang;Xueming Yang;Chuanxiu Xu;Magnus Gustafsson;Rex T. Skodje;Zhigang Sun;Dong H. Zhang
Science 2006 Vol 311(5766) pp:1440-1443
Publication Date(Web):10 Mar 2006
DOI:10.1126/science.1123452
Abstract
Reaction resonances, or transiently stabilized transition-state structures, have proven highly challenging to capture experimentally. Here, we used the highly sensitive H atom Rydberg tagging time-of-flight method to conduct a crossed molecular beam scattering study of the F + H2 → HF + H reaction with full quantum-state resolution. Pronounced forward-scattered HF products in the v′ = 2 vibrational state were clearly observed at a collision energy of 0.52 kcal/mol; this was attributed to both the ground and the first excited Feshbach resonances trapped in the peculiar HF(v′ = 3)-H′ vibrationally adiabatic potential, with substantial enhancement by constructive interference between the two resonances.
The adsorption of methyl on Ni(1 0 0) has been investigated using density functional theory calculations based on plane-wave expansion and pseudo-potential treatment. It was found that the bridge site with one of the hydrogen atoms near top site is most favorable. The calculated C–H symmetric stretching frequencies for the preferred bridge site showed a significant mode softening, thanks to the three-center bonding between C–H and Ni. The coadsorption of methyl and hydrogen on Ni(1 0 0) has also been calculated. The methyl at a bridge site with coadsorbed hydrogen at a hollow site was found to be preferred. In addition, the dissociation of methane on Ni(1 0 0) has been studied and the barrier height was found to be 0.73 eV, in good agreement with the recent experimental value of 0.61 eV.
The adsorption of methyl on the Rh(1 1 1) surface at the coverage of 0.25 ML has been investigated by using ab initio total energy calculations. It was found that the fcc hollow site (with H near top) is preferred over the less stable top site by only about 10 meV. An energy barrier of 0.461 eV was identified for methyl diffusion from fcc hollow to top sites. Our calculated results are similar to those reported by Walter and Rappe [Surf. Sci. 549 (2004) 265] at the coverage of 0.33 ML except for the second most stable site and variations in mode softening. It was indicated that the diffusion pathway is coverage-dependent. The calculated C–H stretching frequencies revealed that significant mode softening occurs for hollow site adsorption with H near top. It was turned out that the C–H symmetric stretching frequencies decreased significantly as the coverage increases from 0.25 to 0.33 ML. The DOS analysis has shown that the 2a1, 1e and 3a1 orbitals of CH3 are involved in bonding with the metal and the most significant contribution to CH3–Rh bonding comes from the 3a1 orbital.
Chemical Physics Letters 2003 Volume 368(3–4) pp:377-383
Publication Date(Web):17 January 2003
DOI:10.1016/S0009-2614(02)01849-3
Abstract
Solvent effects on the lowest excitation of 1,2,3-triazine have been studied using a method previously developed for estimating solvent shifts of species that have strong specific interactions with the solvent. The liquid structures are obtained from Monte Carlo simulations on dilute aqueous solutions of 1,2,3-triazine. Three hydrogen bonds to the ground state are found to be consistent with observed solvent shifts, and hydrogen bonding to the excited state is shown to be strong with one linear hydrogen bond to each symmetric nitrogen atom. The calculations provide a molecular analysis of the solvent shifts of the triazines in dilute solutions.
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.
Co-reporter:Junxiang Zuo, Bin Zhao, Hua Guo and Daiqian Xie
Physical Chemistry Chemical Physics 2017 - vol. 19(Issue 15) pp:NaN9777-9777
Publication Date(Web):2017/03/13
DOI:10.1039/C7CP00920H
A new and more accurate full-dimensional global potential energy surface (PES) for the ground electronic state of the ClH2O system is developed by fitting 15777 points obtained using an explicitly correlated unrestricted coupled-cluster method with single, double, and perturbative triple excitations (UCCSD(T)-F12b). The fitting is carried out using the permutation invariant polynomial-neural network (PIP-NN) method and has an error of 6.9 meV. The new PES has a slightly lower barrier for the atmospherically important HCl + OH → Cl + H2O reaction than the previous PES based on multi-reference configuration interaction (MRCI) calculations. As a result, it should provide a better characterization of the kinetics. Quantum dynamical calculations of reaction probabilities for both the forward and reverse reactions are performed on this new PES and compared with those on the MRCI PES. They reveal notable differences, resulting apparently from subtle differences in the PESs.
Co-reporter:Xixi Hu, Yipeng Zhou, Bin Jiang, Hua Guo and Daiqian Xie
Physical Chemistry Chemical Physics 2017 - vol. 19(Issue 20) pp:NaN12837-12837
Publication Date(Web):2017/04/13
DOI:10.1039/C7CP01697B
The dissociative chemisorption dynamics of CO on rigid Co(110) is investigated using a quasi-classical trajectory method on a new global six-dimensional potential energy surface (PES). The PES is fit using a neural network method to represent 24630 density functional energies in various configurations. The reaction path features deep chemisorption wells and a late barrier for dissociation, agreeing well with previous calculations. The activation energy for dissociation ranges from 0.1 eV at the hollow site to 2.46 eV on the top site, indicating a highly corrugated PES. Effects of the incidence energy of the impinging molecule, its initial orientation, vibrational and rotational excitations, and site specificity are examined. Despite the presence of a low barrier, the initial dissociation probability is very small, even at high incident energies, as a large percentage of trajectories is either trapped or desorbed back to the gas phase. The low reactivity is attributed to inefficient energy transfer into the dissociation reaction coordinate in the chemisorption well where thermal equilibrium is not reached. This system underscores the importance of dynamics in understanding reactions at gas–surface interfaces and in kinetic modeling of catalytic processes.
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.
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: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.
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: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:Huixian Han, Bingbing Suo, Daiqian Xie, Yibo Lei, Yubin Wang and Zhenyi Wen
Physical Chemistry Chemical Physics 2011 - vol. 13(Issue 7) pp:NaN2731-2731
Publication Date(Web):2010/12/10
DOI:10.1039/C0CP01300E
Configuration-based multi-reference second order perturbation theory (CB-MRPT2) and multi-reference configuration interaction with single and double excitations (MRCISD) have been used to calculate the bending and dissociation potential energy curves (PECs) of ozone. Based on these PECs, equilibrium structures, vertical and adiabatic transition energies of the ground state and several low-lying excited states, as well as intersections and avoided crossings among the states displayed on the PECs are investigated. The energy separation of the open and ring structures and the dissociation energy of the ground state 1A1 are determined by reference-selected MRCISD. Furthermore, one-dimensional cuts along the dissociation reaction coordinate for the lowest four electronic states of O3 with 1A′ symmetry and possible pre-dissociations are studied. The Hartley band may be pre-dissociable, and the pre-dissociation limit is found to be 3871 cm−1, which corresponds to symmetric stretching quanta nss ≈ 6.
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:Weizhong Yan, Daiqian Xie and Jun Zeng
Physical Chemistry Chemical Physics 2009 - vol. 11(Issue 29) pp:NaN6050-6050
Publication Date(Web):2009/05/12
DOI:10.1039/B903544C
Fluorescent proteins are commonly used as molecular labels, noninvasive markers of gene expression, and reporters of environmental conditions in live cells. We investigate the structural and spectroscopic properties of the chromophore of a far-red fluorescent protein eqFP611. Both the cis and trans isomers of the chromophore are examined within the protein for which both anionic and neutral states of protonation are considered. Spectroscopic properties are examined using time-dependent density functional theory (TDDFT), employing the B3LYP, PBE and B3PW91 density functionals. Intermolecular and long-range contributions to the structure and spectroscopy were treated using the own n-layered integrated molecular orbital and molecular mechanics (ONIOM) approach. The results indicated that the chromophore before excitation is in an anionic, protonated state, with the long-range contributions inducing a blue shift in the absorption and fluorescence maxima of the chromophore. Moreover, the calculated changes of the lowest π–π* excitation energy upon isomerization match the observed shift from 559 to 600 nm in the absorption maximum of the system following prolonged irradiation. Furthermore, decomposition analysis of the electrostatic contributions from individual residues indicated that the interactions from four residues Arg92, Lys67, Glu145, and His197 to the chromophore play a key role in the absorption and fluorescence spectra of eqFP611, suggesting that mutations at these sites should provide very useful mechanistic information.
Co-reporter:Wenzhen Lai, Wuying Huang and Daiqian Xie
Physical Chemistry Chemical Physics 2008 - vol. 10(Issue 12) pp:NaN1674-1674
Publication Date(Web):2008/02/08
DOI:10.1039/B718477H
Ab
initio total-energy density functional theory calculations with supercell models have been employed to investigate the R30° and (2 × 2) structures of K on the Pb(111) surface. Four “on-surface” sites and a substitutional site were considered. The calculations showed that the substitutional site is more stable than all the on-surface sites, due to its low vacancy formation energy. The calculated R30° geometry agrees well with the LEED results. The density-of-states analysis indicates that the K atom loses part of its loosely bound valence s electron. From the electron density distributions, it was found that the lowering of the work function after the substitutional adsorption can be attributed to the dipole moment, associated with the positively polarized adsorbate atom that is characterized by charge depletion from the K vacuum sides and charge accumulation in the region between K and Pb atoms. Our results indicate that the bonding of K with the Pb(111) surface has a mixed ionic and metallic bond character.
![4H-Imidazol-4-one,3,5-dihydro-5-[(4-hydroxyphenyl)methylene]-3-methyl-2-(1-propen-1-yl)-](http://img.cochemist.com/ccimg/433300/433218-99-6.png)
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![4H-Imidazol-4-one,3,5-dihydro-5-[(4-hydroxyphenyl)methylene]-2,3-dimethyl-](http://img.cochemist.com/ccimg/184400/184302-39-4.png)
![4H-Imidazol-4-one,3,5-dihydro-5-[(4-hydroxyphenyl)methylene]-2,3-dimethyl-](http://img.cochemist.com/ccimg/184400/184302-39-4_b.png)
