Co-reporter:Yirong Mo, Huaiyu Zhang, Peifeng Su, Peter D. Jarowski and Wei Wu
Chemical Science 2016 vol. 7(Issue 9) pp:5872-5878
Publication Date(Web):20 May 2016
DOI:10.1039/C6SC00454G
Electron conjugation stabilizes unsaturated systems and diminishes the differences among bond distances. Experimentally, Kistiakowsky and coworkers first measured and noticed the difference between the hydrogenation heats of carbon–carbon double bonds in conjugated systems. For instance, the hydrogenation heat of butadiene is 57.1 kcal mol−1, which is less than two times that of the hydrogenation heat of 1-butene (30.3 kcal mol−1), and the difference (3.5 kcal mol−1) is the extra stabilization due to the resonance between two double bonds in the former, and is referred to as the experimental resonance energy. Following Kistiakowsky's definition, Rogers et al. studied the stepwise hydrogenation of 1,3-butadiyne and concluded that there is no conjugation stabilization in this molecule. This claim received objections instantly, but Rogers and coworkers further showed the destabilizing conjugation in 2,3-butanedione and cyanogen. Within resonance theory, the conjugation energy is derived “by subtracting the actual energy of the molecule in question from that of the most stable contributing structure.” The notable difference between the experimental and theoretical resonance energies lies in that the former needs other real reference molecules while the latter does not. Here we propose and validate a new concept, intramolecular multi-bond strain, which refers to the repulsion among π bonds. The π–π repulsion, which is contributed to by both Pauli exchange and electrostatic interaction, is quantified with the B4H2 model system (16.9 kcal mol−1), and is compared with the σ–σ repulsion in B2H4 (7.7 kcal mol−1). The significance of the π–π repulsion can be demonstrated by the much longer carbon–nitrogen bond in nitrobenzene (1.486 Å) than in aniline (1.407 Å), the very long and weak nitrogen–nitrogen bond (1.756 Å) in dinitrogen tetroxide, and the instability of long polyynes. This new concept successfully reconciles the discrepancy between experimental and theoretical conjugation energies. However, we maintain that by definition, electron conjugation must be stabilizing.
Co-reporter:Jing Huang, Chunsen Li, Binju Wang, Dina A. Sharon, Wei Wu, and Sason Shaik
ACS Catalysis 2016 Volume 6(Issue 4) pp:2694
Publication Date(Web):March 11, 2016
DOI:10.1021/acscatal.5b02825
The enzyme SyrB2 employs an FeIV–oxo species to achieve selective C–H halogenation of l-threonine. Herein, we use combined quantum mechanical/molecular mechanical (QM/MM) calculations and molecular dynamics (MD) simulations to decipher the mechanism of selective halogenation by SyrB2. Our QM/MM calculations show the presence of three Cl–FeIV–oxo isomers which interconvert, and only the one having its oxo ligand pointing toward the target C–H bond is active during the hydrogen atom abstraction (H-abstraction) process. The fate of the formed Cl–FeIII–OH/R• intermediate is determined by a hydrogen-bonding interaction between the Arg254 residue and the OH ligand of Cl–FeIII–OH. The hydrogen bond not only prevents the OH group from participating in the followup rebound step to form a hydroxylated product but also facilitates the isomerization of the Cl–FeIII–OH/R• intermediate so that the Cl is directed toward the alkyl radical. The role of Arg254 in regulating the selectivity of chlorination is further discussed and connected to the experimentally observed effect of mutations of Arg247 (Arg247Glu and Arg247Ala) in the related CurA halogenase. The Ala118Asp and Ala118Glu mutants of SyrB2 were investigated by MD simulations, and they were found to suppress the H-bonding interaction of Arg254 with Cl–FeIII–OH: this result is in accord with their experimentally observed suppressed chlorination activity. This novel mechanism highlights the role of the H-bonding interaction between the protein and a reaction intermediate.Keywords: hydrogen bond; MD simulation; nonheme enzymes; protein environment; QM/MM calculation; reaction mechanism; selective chlorination; SyrB2 enzyme
Co-reporter:Huaiyu Zhang; Wei Wu;Basil M. Ahmed; Gellert Mezei; Yirong Mo
Chemistry - A European Journal 2016 Volume 22( Issue 22) pp:
Publication Date(Web):
DOI:10.1002/chem.201601555
Co-reporter:Huaiyu Zhang; Wei Wu;Basil M. Ahmed; Gellert Mezei; Yirong Mo
Chemistry - A European Journal 2016 Volume 22( Issue 22) pp:
Publication Date(Web):
DOI:10.1002/chem.201601574
Abstract
Invited for the cover of this issue are the teams led by Wei Wu (Xiamen University) and Yirong Mo (University of Western Michigan). The image depicts how π electron pairs (white figures) are more stable when the σ lone pairs (red figures) are separated. Read the full text of the article at 10.1002/chem.201600509.
Co-reporter:Huaiyu Zhang; Wei Wu;Basil M. Ahmed; Gellert Mezei; Yirong Mo
Chemistry - A European Journal 2016 Volume 22( Issue 22) pp:7415-7421
Publication Date(Web):
DOI:10.1002/chem.201600509
Abstract
The adjacent lone pair (ALP) effect is an experimental phenomenon in certain nitrogenous heterocyclic systems exhibiting the preference of the products with lone pairs separated over other isomers with lone pairs adjacent. A theoretical elucidation of the ALP effect requires the decomposition of intramolecular energy terms and the isolation of lone pair–lone pair interactions. Here we used the block-localized wavefunction (BLW) method within the ab initio valence bond (VB) theory to derive the strictly localized orbitals which are used to accommodate one-atom centered lone pairs and two-atom centered σ or π bonds. As such, interactions among electron pairs can be directly derived. Two-electron integrals between adjacent lone pairs do not support the view that the lone pair–lone pair repulsion is responsible for the ALP effect. Instead, the disabling of π conjugation greatly diminishes the ALP effect, indicating that the reduction of π conjugation in deprotonated forms with two σ lone pairs adjacent is one of the major causes for the ALP effect. Further electrostatic potential analysis and intramolecular energy decomposition confirm that the other key factor is the favorable electrostatic attraction within the isomers with lone pairs separated.
Co-reporter:Zhenhua Chen, Chen Zhou, and Wei Wu
Journal of Chemical Theory and Computation 2015 Volume 11(Issue 9) pp:4102-4108
Publication Date(Web):July 20, 2015
DOI:10.1021/acs.jctc.5b00416
In this work, a hierarchy of valence bond (VB) methods based on the concept of seniority number, defined as the number of singly occupied orbitals in a determinant or an orbital configuration, is proposed and applied to the studies of the potential energy curves (PECs) of H8, N2, and C2 molecules. It is found that the seniority-based VB expansion converges more rapidly toward the full configuration interaction (FCI) or complete active space self-consistent field (CASSCF) limit and produces more accurate PECs with smaller nonparallelity errors than its molecular orbital (MO) theory-based analogue. Test results reveal that the nonorthogonal orbital-based VB theory provides a reverse but more efficient way to truncate the complete active Hilbert space by seniority numbers.
Co-reporter:Huaiyu Zhang, David Danovich, Wei Wu, Benoît Braïda, Philippe C. Hiberty, and Sason Shaik
Journal of Chemical Theory and Computation 2014 Volume 10(Issue 6) pp:2410-2418
Publication Date(Web):May 13, 2014
DOI:10.1021/ct500367s
The charge-shift bonding (CSB) concept was originally discovered through valence bond (VB) calculations. Later, CSB was found to have signatures in atoms-in-molecules and electron-localization-function and in experimental electron density measurements. However, the CSB concept has never been derived from a molecular orbital (MO)-based theory. We now provide a proof of principle that an MO-based approach enables one to derive the CSB family alongside the distinctly different classical family of covalent bonds. In this bridging energy decomposition analysis, the covalent–ionic resonance energy, RECS, of a bond is extracted by cloning an MO-based purely covalent reference state, which is a constrained two-configuration wave function. The energy gap between this reference state and the variational TCSCF ground state yields numerical values for RECS, which correlate with the values obtained at the VBSCF level. This simple MO-based method, which only takes care of static electron correlation, is already sufficient for distinguishing the classical covalent or polar-covalent bonds from charge-shift bonds. The equivalence of the VB and MO-based methods is further demonstrated when both methods are augmented by dynamic correlation. Thus, it is shown from both MO and VB perspectives that the bonding in the CSB family does not arise from electron correlation. Considering that the existence of the CSB family is associated also with quite a few experimental observations that we already reviewed (Shaik, S., Danovich, D., Wu, W., and Hiberty, P. C. Nat. Chem., 2009, 1, 443−449), the new bonding concept has passed by now two stringent tests. This derivation, on the one hand, supports the new concept and on the other, it creates bridges between the two main theories of electronic structure.
Co-reporter:Changwei Wang, Fuming Ying, Wei Wu, and Yirong Mo
The Journal of Organic Chemistry 2014 Volume 79(Issue 4) pp:1571-1581
Publication Date(Web):January 23, 2014
DOI:10.1021/jo402306e
The block-localized wave function (BLW) method, which can derive optimal electron-localized state with intramolecular electron delocalization completely deactivated, has been combined with the polarizable continuum model (PCM) to probe the variation of the anomeric effect in solution. Currently both the hyperconjugation and electrostatic models have been called to interpret the anomeric effect in carbohydrate molecules. Here we employed the BLW-PCM scheme to analyze the energy differences between α and β anomers of substituted tetrahydropyran C5OH9Y (Y = F, Cl, OH, NH2, and CH3) and tetrahydrothiopyran C5SH9Y (Y = F, Cl, OH, and CH3) in solvents including chloroform, acetone, and water. In accord with literature, our computations show that for anomeric systems the conformational preference is reduced in solution and the magnitude of reduction increases as the solvent polarity increases. Significantly, on one hand the solute–solvent interaction diminishes the intramolecular electron delocalization in β anomers more than in α anomers, thus destabilizing β anomers relatively. But on the other hand, it reduces the steric effect in β anomers much more than α anomers and thus stabilizes β anomers relatively more, leading to the overall reduction of the anomeric effect in anomeric systems in solutions.
Co-reporter:Jing Huang;FuMing Ying;PeiFeng Su
Science China Chemistry 2014 Volume 57( Issue 10) pp:1409-1417
Publication Date(Web):2014 October
DOI:10.1007/s11426-014-5192-x
In this paper, a combined QM/MM/PCM approach, named VBEFP/PCM, is presented for ab initio VB study with a solvent effect incorporated. In VBEFP/PCM, both short-range and long-range solvent effects are taken into account by effective fragment potential (EFP) and polarizable continuum model (PCM), respectively, while the solute molecules are described by valence bond (VB) wave function. Furthermore, VBEFP/PCM, along with VBPCM and VBEFP, is employed for the n→π* vertical excitation of formaldehyde and acetone molecules in aqueous solution. The computational results show that VBEFP/PCM can provide the appropriate solvent shifts, whereas VBPCM underestimates the solvent shifts due to its lack of short-range solvent effect. The VBEFP results strongly rely upon the description of the short-range solvent effect. To explore the role of the solute’s electronic structure in the solvent shift, resonance energy analysis during the excitation is performed. It was found that the solute’s electronic polarization plays the most important role in the solvent shift. The resonance controls the variation of the solute’s wave function during the n→* vertical excitation, which leads to the blue solvent shifts.
Co-reporter:Fuming Ying, Peifeng Su, Zhenhua Chen, Sason Shaik, and Wei Wu
Journal of Chemical Theory and Computation 2012 Volume 8(Issue 5) pp:1608-1615
Publication Date(Web):March 12, 2012
DOI:10.1021/ct200803h
A new ab initio valence bond method with density-functional-based correlation correction, so-called DFVB, is presented. In the DFVB method, the dynamic correlation energy is taken into account by use of density correlation functional(s), while the static correlation energy is covered by the VBSCF wave function. Owing to incorporation of DFT methods, DFVB provides an economic route to improving the accuracy of ab initio VB theory. Various tests of the method are presented, including the spectroscopic parameters of a series of diatomic molecules, the dipole moments of the NF molecule for different electronic states, and the singlet–triplet gaps of the diradical species, chemical reactions barriers, and total charge-shift resonance energies. These tests show that DFVB is capable of providing high accuracy with relatively low computational cost by comparison to the currently existing post-VBSCF methods.
Co-reporter:Alessandro Cembran, Makenzie R. Provorse, Changwei Wang, Wei Wu, and Jiali Gao
Journal of Chemical Theory and Computation 2012 Volume 8(Issue 11) pp:4347-4358
Publication Date(Web):September 4, 2012
DOI:10.1021/ct3004595
A critical element in theoretical characterization of the mechanism of proton-coupled electron transfer (PCET) reactions, including hydrogen atom transfer (HAT), is the formulation of the electron and proton localized diabatic states, based on which a More O’Ferrall–Jencks diagram can be represented to determine the stepwise and concerted nature of the reaction. Although the More O’Ferrall–Jencks diabatic states have often been used empirically to develop theoretical models for PCET reactions, the potential energy surfaces for these states have never been determined directly based on first principles calculations using electronic structure theory. The difficulty is due to a lack of practical method to constrain electron and proton localized diabatic states in wave function or density functional theory. Employing a multistate density functional theory (MSDFT), in which the electron and proton localized diabatic configurations are constructed through block-localization of Kohn–Sham orbitals, we show that distinction between concerted proton–electron transfer (CPET) and HAT, which are not distinguishable experimentally from phenomenological kinetic data, can be made by examining the third dimension of a More O’Ferrall–Jencks diagram that includes both the ground and excited state potential surfaces. In addition, we formulate a pair of effective two-state valence bond models to represent the CPET and HAT mechanisms. We found that the lower energy of the CPET and HAT effective diabatic states at the intersection point can be used as an energetic criterion to distinguish the two mechanisms. In the isoelectronic series of hydrogen exchange reaction in (PhX)2H•, where X = O, NH, and CH2, there is a continuous transition from a CPET mechanism for the phenoxy radical–phenol pair to a HAT process for benzyl radical and toluene, while the reaction between PhNH2 and PhNH• has a mechanism intermediate of CPET and HAT. The electronically nonadiabatic nature of the CPET mechanism in the phenol system can be attributed to the overlap interactions between the ground and excited state surfaces, resulting in roughly orthogonal minimum energy paths on the adiabatic ground and excited state potential energy surfaces. On the other hand, the minimum energy path on the adiabatic ground state for the HAT mechanism coincides with that on the excited state, producing a large electronic coupling that separates the two surfaces by more than 120 kcal/mol.
Co-reporter:Wei Wu, Peifeng Su, Sason Shaik, and Philippe C. Hiberty
Chemical Reviews 2011 Volume 111(Issue 11) pp:7557
Publication Date(Web):August 18, 2011
DOI:10.1021/cr100228r
Co-reporter:Changwei Wang ; Fuming Ying ; Wei Wu ;Yirong Mo
Journal of the American Chemical Society 2011 Volume 133(Issue 34) pp:13731-13736
Publication Date(Web):July 27, 2011
DOI:10.1021/ja205613x
The anomeric effect plays a central role in carbohydrate chemistry, but its origin is controversial, and both the hyperconjugation model and the electrostatic model have been proposed to explain this phenomenon. Recently, Cocinero et al. designed a peptide sensor, which can bind to a sugar molecule methyl d-galactose, and claimed that the anomeric effect can be sensed by the spectral changes from the β- to the α-complex, which are ultimately attributed to the lone pair electron density change on the endocyclic oxygen atom [Nature2011, 469, 76; J. Am. Chem. Soc.2011, 133, 4548]. Here, we provide strong computational evidence showing that the observed spectral changes simply come from the conformational differences between the α- and β-anomers, as the replacement of the endocyclic oxygen atom with a methylene group, which disables both the endo- and the exo-anomeric effects in methyl d-galactose, leads to similar spectral shifts. In other words, the “sensor” cannot probe the anomeric effect as claimed. We further conducted detailed energetic and structural analyses to support our arguments.
Co-reporter:Peifeng Su, Jifang Wu, Junjing Gu, Wei Wu, Sason Shaik, and Philippe C. Hiberty
Journal of Chemical Theory and Computation 2011 Volume 7(Issue 1) pp:121-130
Publication Date(Web):December 20, 2010
DOI:10.1021/ct100577v
The ab initio VB study for the electronic structure of the C2 molecule in the ground state is presented in this work. VB calculations involving 78 chemically relevant VB structures can predict the bonding energy of C2 quite well. Sequentially, a VBCIS calculation provides spectroscopic parameters that are very close to full CI calculated values in the same basis set. Furthermore, the analysis of the bonding scheme shows that a triply bonded structure is the major one in terms of weights, and the lowest in energy at the equilibrium distance. The second structure in terms of weights is an ethylene-like structure, displaying a σ + π double bond. The structure with two suspended π bonds but no σ bond contributes only marginally to the ground state. This ordering of weights for the VB structures describing the C2 molecule is shown to be consistent with the shape of the molecular orbitals and with the multireference character of the ground state. With the triply bonded bonding scheme, the natures of the π and σ bonds are investigated, and then the corresponding “in situ” bond strengths are estimated. The contribution of the covalent-ionic resonance energy to π and σ bonding is revealed and discussed.
Co-reporter:ZhenHua Chen;QianEr Zhang
Science China Chemistry 2009 Volume 52( Issue 11) pp:
Publication Date(Web):2009 November
DOI:10.1007/s11426-009-0265-y
This paper presents an efficient algorithm for energy gradients in valence bond self-consistent field (VBSCF) method with non-orthogonal orbitals. The frozen core approximation method is extended to the case of non-orthogonal orbitals. The expressions for the total energy and its gradients are presented by introducing auxiliary orbitals, where inactive orbitals are orthogonal, while active orbitals are non-orthogonal themselves but orthogonal to inactive orbitals. It is shown that our new algorithm has a low scaling of (Na + 1)m4, where Na and m are the numbers of the active orbitals and basis functions, respectively, and is more efficient than the existing VBSCF algorithms.
Co-reporter:Lixian Zhang;Fuming Ying ;PhilippeC. Hiberty;Sason Shaik
Chemistry - A European Journal 2009 Volume 15( Issue 12) pp:2979-2989
Publication Date(Web):
DOI:10.1002/chem.200802134
Co-reporter:Shulin Gao, Wei Wu and Yirong Mo
The Journal of Physical Chemistry A 2009 Volume 113(Issue 28) pp:8108-8117
Publication Date(Web):June 25, 2009
DOI:10.1021/jp903059w
The B−Hδ−···δ+H−P dihydrogen bonding (DHB) in ion pair complexes [(CF3)3BH−][HPH3−n(Me)n+] (n = 0−3) and its role in the combination of proton and hydride with the release of H2 or, reversibly, the heterolytic activation of H2 by Lewis pairs (CF3)3BPH3−n(Me)n have been theoretically investigated at the MP2 and DFT levels. It is found that the B−H···H−P bonds behave similarly to those in neutral pairs and ion−molecule complexes in most respects, such as the linearity of the H···H−P moiety, the characteristics of the electron transfer and rearrangement, and the topological properties of the DHB critical point, except that in certain cases, a blue-shifting of the H-bond vibrational frequency is observed. In [(CF3)3BH−][HPH3−n(Me)n+], the proton shifting within the complexes leads to the formation of the dihydrogen complex B(CF3)3(η2-H2), which is followed by a subsequent H2 release. The stability of B(CF3)3(η2-H2) (De/D0 = 10.8/6.0 kcal/mol) makes the proton−hydride combination proceed in a fashion similar to the protonation reactions in transition-metal hydrides rather than those in group 13 hydrides EH4− (E = B, Al, Ga). As for the H2-splitting reaction R3BPR′3 + H2 → [R3BH−][HPR′3+], classical Lewis pair (CLP) (CF3)3BPH3 exhibits a high barrier and results in an unstable ion pair product [(CF3)3BH−][HPH3+] compared with the “frustrated Lewis pair” (FLP) (C6F5)3BP(tBu)3. A detailed analysis of the mechanistic aspects of H2 activation by (CF3)3BPH3 and (C6F5)3BP(tBu)3, supported by another CLP (CF3)3BP(tBu)3 which has a binding energy comparable to (CF3)3BPH3 but a reaction exothermicity comparable to (C6F5)3BP(tBu)3, allows us to suggest that the low stability of FLP (C6F5)3BP(tBu)3 is the determining factor for the low reaction barrier. The relative stability and other properties of the ion pair products [R3BH−][HPR′3+] have also been analyzed. Results strongly support the view proposed by Rokob et al. [Rokob, T. A.; Hamza, A.; Stirling, A.; Soos, T.; Papai, I. Angew. Chem., Int. Ed. 2008, 47, 2435] that the frustration energy lowers the energy barrier and increases the exothermicity of the reaction.
Co-reporter:Chunsen Li ;Kyung-Bin Cho Dr.;Sason Shaik
Chemistry - A European Journal 2009 Volume 15( Issue 34) pp:8492-8503
Publication Date(Web):
DOI:10.1002/chem.200802215
Abstract
Two types of tertiary amine oxidation processes, namely, N-dealkylation and N-oxygenation, by compound I (Cpd I) of cytochrome P450 are studied theoretically using hybrid DFT calculations. All the calculations show that both N-dealkylation and N-oxygenation of trimethylamine (TMA) proceed preferentially from the low-spin (LS) state of Cpd I. Indeed, the computed kinetic isotope effects (KIEs) for the rate-controlling hydrogen abstraction step of dealkylation show that only the KIELS fits the experimental datum, whereas the corresponding value for the high-spin (HS) process is much higher. These results second those published before for N,N-dimethylaniline (DMA), and as such, they further confirm the conclusion drawn then that KIEs can be a sensitive probe of spin state reactivity. The ferric-carbinolamine of TMA decomposes most likely in a non-enzymatic reaction since the FeO bond dissociation energy (BDE) is negative. The computational results reveal that in the reverse reaction of N-oxygenation, the N-oxide of aromatic amine can serve as a better oxygen donor than that of aliphatic amine to generate Cpd I. This capability of the N-oxo derivatives of aromatic amines to transfer oxygen to the heme, and thereby generate Cpd I, is in good accord with experimental data previously reported.
Co-reporter:Wei Wu ;Ben Ma;Judy I-ChiaWu;PaulvonRagué Schleyer ;Yirong Mo
Chemistry - A European Journal 2009 Volume 15( Issue 38) pp:9730-9736
Publication Date(Web):
DOI:10.1002/chem.200900586
Abstract
Dewar proposed the σ-aromaticity concept to explain the seemingly anomalous energetic and magnetic behavior of cyclopropane in 1979. While a detailed, but indirect energetic evaluation in 1986 raised doubts—“There is no need to involve ‘σ-aromaticity’,”—other analyses, also indirect, resulted in wide-ranging estimates of the σ-aromatic stabilization energy. Moreover, the aromatic character of “in-plane”, “double”, and cyclically delocalized σ-electron systems now seems well established in many types of molecules. Nevertheless, the most recent analysis of the magnetic properties of cyclopropane (S. Pelloni, P. Lazzeretti, R. Zanasi, J. Phys. Chem. A2007, 111, 8163–8169) challenged the existence of an induced σ-ring current, and provided alternative explanations for the abnormal magnetic behavior. Likewise, the present study, which evaluates the σ-aromatic stabilization of cyclopropane directly for the first time, fails to find evidence for a significant energetic effect. According to ab initio valence bond (VB) computations at the VBSCF/cc-PVTZ level, the σ-aromatic stabilization energy of cyclopropane is, at most, 3.5 kcal mol−1 relative to propane, and is close to zero when n-butane is used as reference. Trisilacyclopropane also has very little σ-aromatic stabilization, compared to Si3H8 (6.3 kcal mol−1) and Si4H10 (4.2 kcal mol−1). Alternative interpretations of the energetic behavior of cyclopropane (and of cyclobutane, as well as their silicon counterparts) are supported.
Co-reporter:Zhenhua Chen, Jinshuai Song, Sason Shaik, Philippe C. Hiberty and Wei Wu
The Journal of Physical Chemistry A 2009 Volume 113(Issue 43) pp:11560-11569
Publication Date(Web):July 1, 2009
DOI:10.1021/jp903011j
A post-VBSCF method, called valence bond second-order perturbation theory (VBPT2), is developed in this paper and is shown to be (i) economical and (ii) at par with more sophisticated VB and MO-based methods. The VBPT2 method starts with VBSCF using a minimal structure set. Subsequently, the Møller−Plesset (MP) partition of the zeroth-order Hamiltonian is obtained by introducing a generalized Fock matrix constructed from the VBSCF density matrix. The first-order wave function is expressed in terms of singly and doubly excited VB structures, which are generated by replacing occupied orbitals by virtual orbitals, the latter being defined as orthogonal to the occupied orbitals. The VBPT2 method retains the simplicity of a VB presentation by condensing contributions from the excited structures into the minimal number of fundamental structures that are involved in the VBSCF calculation. The method is tested by calculating the bond energies of H2, F2, N2, O2, the barrier of identity hydrogen abstraction reaction, the atomization energy and a potential energy curve for the water molecule and the structural weights and covalent−ionic resonance energy of F2. It is shown that the VBPT2 method gives results in good agreement with those of the VBCI method and molecular-orbital based methods such as MRPT and MRCI at the same truncation levels. However, the computational effort is greatly reduced, compared to that of VBCI. Future potential directions for the development of the VBPT2 method are outlined.
Co-reporter:Wei Wu ;Junjing Gu;Jinshuai Song;Sason Shaik ;PhilippeC. Hiberty
Angewandte Chemie International Edition 2009 Volume 48( Issue 8) pp:1407-1410
Publication Date(Web):
DOI:10.1002/anie.200804965
Co-reporter:Wei Wu ;Junjing Gu;Jinshuai Song;Sason Shaik ;PhilippeC. Hiberty
Angewandte Chemie 2009 Volume 121( Issue 8) pp:1435-1438
Publication Date(Web):
DOI:10.1002/ange.200804965
Co-reporter:Junjing Gu, Yonghui Lin, Ben Ma, Wei Wu and Sason Shaik
Journal of Chemical Theory and Computation 2008 Volume 4(Issue 12) pp:2101-2107
Publication Date(Web):November 6, 2008
DOI:10.1021/ct800341z
The ab initio valence bond (VB) methods, VBSCF and VBCI, are applied to the ground states and the covalent excited states of polyenes C2nH2n+2 (n = 2−8) and polyenyl radicals C2n-1H2n+1 (n = 2−8). The excitation energy gap was computed at the ab initio VB level, which is in good agreement with the semiempirical VB method, VBDFT(s), and the experimental values as well as with the molecular orbital theory based methods, CASPT3 and MRCI. The ab initio VB wave functions of systems are also in very good agreement with those of the VBDFT(s) method, even though the former is based on the ab initio VB scheme while the latter is a semiempirical Hückel type method, in which no orbital optimization procedure is performed. The computational results show that the ab initio VB method is capable now of providing numerical accuracy not only for bond forming and breaking processes, as shown in the past, but also for excitation energies, as shown here. In addition, the computational results validate the efficiency of the VBDFT(s) method, which is a simple VB model with less computational effort but which provides intuitive insights into the excited states of conjugated molecules.
Co-reporter:Chunsen Li;Lixian Zhang;Chi Zhang;Hajime Hirao Dr.;Sason Shaik Dr.
Angewandte Chemie 2008 Volume 120( Issue 43) pp:
Publication Date(Web):
DOI:10.1002/ange.200890269
No abstract is available for this article.
Co-reporter:Chunsen Li;Lixian Zhang;Chi Zhang;Hajime Hirao Dr.;Sason Shaik Dr.
Angewandte Chemie International Edition 2008 Volume 47( Issue 43) pp:
Publication Date(Web):
DOI:10.1002/anie.200890215
No abstract is available for this article.
Co-reporter:Peifeng Su ;Sason Shaik ;Philippe C. Hiberty
ChemPhysChem 2008 Volume 9( Issue 10) pp:1442-1452
Publication Date(Web):
DOI:10.1002/cphc.200800143
Abstract
The electronic structures of the three lowest-lying states of NF are investigated by means of modern valence bond (VB) methods such as the VB self-consistent field (VBSCF), breathing orbital VB (BOVB), and VB configuration interaction (VBCI) methods. The wave functions for the three states are expressed in terms of 9–12 VB structures, which can be further condensed into three or four classical Lewis structures, whose weights are quantitatively estimated. Despite the compactness of the wave functions, the BOVB and VBCI methods reproduce the spectroscopic properties and dipole moments of the three states well, in good agreement with previous computational studies and experimental values. By analogy to the isoelectronic O2 molecule, the ground state 3Σ− possesses both a σ bond and 3-electron π bonds. However, here the polar σ bond contributes the most to the overall bonding. It is augmented by a fractional (19 %) contribution of three-electron π bonding that arises from π charge transfer from fluorine to nitrogen. In the singlet 1Δ and 1Σ+ excited states the π-bonding component is classically covalent, and it contributes 28 % and 37 % to the overall bonding picture for the two states, respectively. The resonance energies are calculated and reveal that π bonding contributes at least 24, 35 and 42 kcal mol−1 to the total bonding energies of the 3Σ−, 1Δ and 1Σ+ states, respectively. Some unusual properties of the NF molecule, like the equilibrium distance shortening and bonding energy increasing upon excitation, the counterintuitive values of the dipole moments and the reversal of the dipole moments as the bond is stretched, are interpreted in the light of the simple valence bond picture. The overall polarity of the molecule is very small in the ground state, and is opposite to the relative electronegativity of N vs F in the singlet excited states. The values of the dipole moments in the three states are quantitatively accounted for by the calculated weights of the VB structures.
Co-reporter:Peifeng Su;Fuming Ying ;Philippe C. Hiberty ;Sason Shaik
ChemPhysChem 2007 Volume 8(Issue 18) pp:2603-2614
Publication Date(Web):5 DEC 2007
DOI:10.1002/cphc.200700626
The recently developed (L. Song, W. Wu, Q. Zhang, S. Shaik, J. Phys. Chem. A2004, 108, 6017–6024) valence bond method coupled to a polarized continuum model (VBPCM) is applied to the Menshutkin reaction, NH3+CH3ClCH3NH3++Cl−, in the gas phase and in aqueous solution. The computed barriers and reaction energies at the level of the breathing orbital VB method (P. C. Hiberty, J. P. Flament, E. Noizet, Chem. Phys. Lett.1992, 189, 259), BOVB and VBPCM//BOVB, are comparable to CCSD(T) and CCSD(T)//PCM results and to experimental values in solution. The gas-phase reaction is endothermic and leads to an ion-pair complex via a late transition state. By contrast, the reaction in the aqueous phase is exothermic and leads to separate solvated ions as reaction products, via an early transition state. The VB calculations provide also the reactivity parameters needed to apply the valence bond state correlation diagram method, VBSCD (S. Shaik, A. Shurki, Angew. Chem. Int. Ed.1999, 38, 586). It is shown that the reactivity parameters along with their semiempirical derivations provide together a satisfactory qualitative and quantitative account of the barriers.
Co-reporter:Chunsen Li;Lixian Zhang;Chi Zhang;Hajime Hirao Dr.;Sason Shaik Dr.
Angewandte Chemie International Edition 2007 Volume 46(Issue 43) pp:
Publication Date(Web):20 SEP 2007
DOI:10.1002/anie.200702867
Clarifying a conundrum: The question of whether Compound I or Compound 0 (Cpd I or Cpd 0) is the reactive oxidant in the sulfoxidation of thiafatty acids by P450 is addressed by theory, which demonstrates that Cpd I leads to an extremely fast process, while Cpd 0 is at least six orders of magnitude slower. Most likely, thiafatty acids promote Cpd I formation even in the TA mutant of P450BM3.
Co-reporter:Chunsen Li;Lixian Zhang;Chi Zhang;Hajime Hirao Dr.;Sason Shaik Dr.
Angewandte Chemie 2007 Volume 119(Issue 43) pp:
Publication Date(Web):20 SEP 2007
DOI:10.1002/ange.200702867
Des Rätsels Lösung: Wirkt Verbindung I (Cpd I) oder Verbindung 0 (Cpd 0) als reaktive Spezies bei der Sulfoxidation von Thiafettsäuren durch P450? Theoretische Untersuchungen zeigen, dass Cpd I um mindestens sechs Größenordnungen schneller reagiert als Cpd 0. Vermutlich fördern die Thiafettsäuren die Bildung von Cpd I selbst in der TA-Mutante von P450BM3.
Co-reporter:Lingchun Song Dr. ;Philippe C. Hiberty ;Sason Shaik
Chemistry - A European Journal 2006 Volume 12(Issue 28) pp:
Publication Date(Web):28 JUL 2006
DOI:10.1002/chem.200600372
The recently developed (L. Song, W. Wu, Q. Zhang, S. Shaik, J. Phys. Chem. A2004, 108, 6017) valence bond method coupled with a polarized continuum model (VBPCM) has been applied to the identity SN2 reaction of halides in the gas phase and in aqueous solution. The barriers computed at the level of the breathing orbital VB method (P. C. Hiberty, J. P. Flament, E. Noizet, Chem. Phys. Lett.1992, 189, 259), BOVB and VBPCM//BOVB, are comparable to CCSD(T) and CCSD(T)//PCM results and to experimentally derived barriers in solution (W. J. Albery, M. M. Kreevoy, Adv. Phys. Org. Chem.1978, 16, 85). The reactivity parameters needed to apply the valence bond state correlation diagram (VBSCD) method (S. Shaik, J. Am. Chem. Soc.1984, 106, 1227), were also determined by VB calculations. It has been shown that the reactivity parameters along with their semiempirical derivations provide a satisfactory qualitative and quantitative account of the barriers.
Co-reporter:Yirong Mo ;Lingchun Song Dr.;Menghai Lin ;Qianer Zhang ;Jiali Gao
Angewandte Chemie International Edition 2004 Volume 43(Issue 15) pp:
Publication Date(Web):30 MAR 2004
DOI:10.1002/anie.200352931
Steric effect dominates: Ab initio valence bond and block-localized wavefunction methods are used to estimate the contributions of hyperconjugation and steric effects to the ethane rotation barrier. The results show that hyperconjugation stabilizes the staggered conformer by about 4 kJ mol−1 relative to the eclipsed form (see picture) and steric hindrance is the major driving force behind the favoring of the staggered conformation in ethane.
Co-reporter:Yan Luo;Lingchun Song Dr. Dr.;David Danovich Dr.;Sason Shaik Dr.
ChemPhysChem 2004 Volume 5(Issue 4) pp:
Publication Date(Web):14 APR 2004
DOI:10.1002/cphc.200300935
The semiempirical valence bond (VB) method, VBDFT(s), is applied to the ground states and the covalent excited states of polyenyl radicals C2n−1H2n+1(n=2–13). The method uses a single scalable parameter with a value that carries over from the study of the covalent excited states of polyenes (W. Wu, D. Danovich, A. Shurki, S. Shaik, J. Phys. Chem. A, 2000, 104, 8744). Whenever comparison is possible, the VB excitation energies are found to be in good accord with sophisticated molecular orbital (MO)-based methods like CASPT2. The symmetry-adapted Rumer structures are used to discuss the state-symmetry and VB constitution of the ground and excited states, and the expansion to VB determinants is used to gain insight on spin density patterns. The theory helps to understand in a coherent and lucid manner the properties of polyenyl radicals, such as the makeup of the various states, their geometries and energies, and the distribution of the unpaired electrons (the neutral solitons).
Co-reporter:Yirong Mo ;Lingchun Song Dr.;Menghai Lin ;Qianer Zhang ;Jiali Gao
Angewandte Chemie 2004 Volume 116(Issue 15) pp:
Publication Date(Web):30 MAR 2004
DOI:10.1002/ange.200352931
Abgedreht: Ab-initio-VB- und -BLW-Methoden werden zur Abschätzung der Beiträge von Hyperkonjugation sowie von sterischen Effekten zur Rotationsbarriere in Ethan verwendet. Die Ergebnisse belegen, dass Hyperkonjugation das gestaffelte Konformer mit etwa 4 kJ mol−1 gegenüber der ekliptischen Form stabilisiert (siehe Bild). Sterische Hinderung ist allerdings das wichtigste Kriterium für die Bevorzugung der gestaffelten Konformation in Ethan. BLW=Block-localized wavefunction.
Co-reporter:Liao Xin-Li;Mo Yi-Rong;Wu Wei;Zhang Qian-Er
Chinese Journal of Chemistry 2003 Volume 21(Issue 3) pp:225-231
Publication Date(Web):26 AUG 2010
DOI:10.1002/cjoc.20030210304
Ab initio valence bond method is employed to quantitatively study the concepts of ionic resonance energy and ionicity of a chemical bond in the cases of hydrides XH (X = Li, Be, B, C, N, O, F) and fluorides XF (X = Li, Be, B). By establishing the relationship between resonance and stability, and comparing the calculated ionicities with Pauling's earlier estimations in the above diatomic molecules, the merits of Pauling's classical resonance theory were demonstrated at the ab initio level.
Co-reporter:Liao, Xin-Ll;Mo, Yi-Rong;Wu, Wd;Zhang, Qian-Er
Chinese Journal of Chemistry 2003 Volume 21(Issue 8) pp:
Publication Date(Web):26 AUG 2010
DOI:10.1002/cjoc.20030210806
Co-reporter:Lingchun Song Dr. ;Philippe C. Hiberty ;David Danovich Dr.;Sason Shaik
Chemistry - A European Journal 2003 Volume 9(Issue 18) pp:
Publication Date(Web):11 SEP 2003
DOI:10.1002/chem.200305093
One of the landmark achievements of quantum chemistry, specifically of MO-based methods that include electron correlation, was the precise calculation of the barrier for the hydrogen-exchange reaction (B. Liu, J. Chem. Phys.1973, 58, 1925; P. Siegbahn, B. Liu, J. Chem. Phys.1978, 68, 2457). This paper reports an accurate calculation of this barrier by two recently developed VB methods that use only the eight classical VB structures. To our knowledge, the present work is the first accurate ab initio VB barrier that matches an experimental value. Along with the accurate barrier, the VB method provides accurate bond energies and diabatic quantities that enable the barrier height to be analyzed by the VB state correlation diagram approach, VBSCD (S. Shaik, A. Shurki, Angew. Chem.1999, 111, 616; Angew. Chem. Int. Ed. Engl.1999, 38, 586). This is a proof of principal that VB theory with appropriate account of dynamic electron correlation can achieve quantitative accuracy of reaction barriers, and still retain a compact and interpretable wave function. A sample of SN2 barriers and dihalogen bonding energies, which are close to CCSD(T) and G2(+) values, show that the H3 problem is not an isolated case, and while it is premature to conclude that VB theory has come of age, the occurrence of this event is clearly within sight.
Co-reporter:Yirong Mo, Huaiyu Zhang, Peifeng Su, Peter D. Jarowski and Wei Wu
Chemical Science (2010-Present) 2016 - vol. 7(Issue 9) pp:NaN5878-5878
Publication Date(Web):2016/05/20
DOI:10.1039/C6SC00454G
Electron conjugation stabilizes unsaturated systems and diminishes the differences among bond distances. Experimentally, Kistiakowsky and coworkers first measured and noticed the difference between the hydrogenation heats of carbon–carbon double bonds in conjugated systems. For instance, the hydrogenation heat of butadiene is 57.1 kcal mol−1, which is less than two times that of the hydrogenation heat of 1-butene (30.3 kcal mol−1), and the difference (3.5 kcal mol−1) is the extra stabilization due to the resonance between two double bonds in the former, and is referred to as the experimental resonance energy. Following Kistiakowsky's definition, Rogers et al. studied the stepwise hydrogenation of 1,3-butadiyne and concluded that there is no conjugation stabilization in this molecule. This claim received objections instantly, but Rogers and coworkers further showed the destabilizing conjugation in 2,3-butanedione and cyanogen. Within resonance theory, the conjugation energy is derived “by subtracting the actual energy of the molecule in question from that of the most stable contributing structure.” The notable difference between the experimental and theoretical resonance energies lies in that the former needs other real reference molecules while the latter does not. Here we propose and validate a new concept, intramolecular multi-bond strain, which refers to the repulsion among π bonds. The π–π repulsion, which is contributed to by both Pauli exchange and electrostatic interaction, is quantified with the B4H2 model system (16.9 kcal mol−1), and is compared with the σ–σ repulsion in B2H4 (7.7 kcal mol−1). The significance of the π–π repulsion can be demonstrated by the much longer carbon–nitrogen bond in nitrobenzene (1.486 Å) than in aniline (1.407 Å), the very long and weak nitrogen–nitrogen bond (1.756 Å) in dinitrogen tetroxide, and the instability of long polyynes. This new concept successfully reconciles the discrepancy between experimental and theoretical conjugation energies. However, we maintain that by definition, electron conjugation must be stabilizing.
![N-(3-METHYLBUTANOYL)-L-VALYL-N-[(3S,4S)-1-{[(2S)-1-{[(2S,3S)-1-CA<WBR />RBOXY-2-HYDROXY-5-METHYL-3-HEXANYL]AMINO}-1-OXO-2-PROPANYL]AMINO}<WBR />-3-HYDROXY-6-METHYL-1-OXO-4-HEPTANYL]-L-VALINAMIDE](http://img.cochemist.com/ccimg/39400/39324-30-6.png)
![N-(3-METHYLBUTANOYL)-L-VALYL-N-[(3S,4S)-1-{[(2S)-1-{[(2S,3S)-1-CA<WBR />RBOXY-2-HYDROXY-5-METHYL-3-HEXANYL]AMINO}-1-OXO-2-PROPANYL]AMINO}<WBR />-3-HYDROXY-6-METHYL-1-OXO-4-HEPTANYL]-L-VALINAMIDE](http://img.cochemist.com/ccimg/39400/39324-30-6_b.png)
![Tetracyclo[6.1.0.02,4.05,7]nona-1,4,7-triene](http://img.cochemist.com/ccimg/123400/123334-84-9.png)
![Tetracyclo[6.1.0.02,4.05,7]nona-1,4,7-triene](http://img.cochemist.com/ccimg/123400/123334-84-9_b.png)
![Tetracyclo[8.2.0.02,5.06,9]dodeca-1,3,5,7,9,11-hexaene](/data/chemimg/2713800/69038-28-4.png)
![Tetracyclo[8.2.0.02,5.06,9]dodeca-1,3,5,7,9,11-hexaene](/data/chemimg/2713800/69038-28-4_b.png)
![Tetracyclo[8.2.0.02,5.06,9]dodeca-1,5,9-triene](http://img.cochemist.com/ccimg/60400/60323-52-6.png)
![Tetracyclo[8.2.0.02,5.06,9]dodeca-1,5,9-triene](http://img.cochemist.com/ccimg/60400/60323-52-6_b.png)
