Does the topological approach characterize the hydrogen bond?

 The topological analysis of the electron localization function has been applied to complexes representative of the weak, medium and strong hydrogen bond. For both the weak and the medium hydrogen bonds, the number of basins in the complexes is the sum of those of the moieties. In this case, the formation of a weak or a medium hydrogen-bonded complex does not involve a chemical reaction. In the weak hydrogen bond case, the reduction of the localization domain yields two domains in the first step, which can be partitioned afterwards into valence and core domains. In contrast, for medium complexes the core–valence separation is the first event which occurs during the reduction process and therefore the complex should be considered as a single molecular species. Moreover, the analysis of the basin population variance indicates in this case a noticeable delocalization between the V(A, H) and V(B) basins. Finally, the symmetrical strong hydrogen bond has a protonated basin V(H) at the bond midpoint. Such a topology corresponds to an incomplete proton transfer and to a rather covalent bond. Received: 19 April 1999 / Accepted: 22 July 1999 / Published online: 17 January 2000     

Computational insight into the effect of C(19) substituents on [1,7]-hydrogen shift in previtamin D

 B3LYP calculations in conjunction with natural bond orbital population analysis have been performed for a previtamin D model and corresponding transition structures for the [1,7]-hydrogen migration. In addition the 19,19-difluoro, 19-methoxy and 19-fluoro substituted analogs were investigated. The calculated activation barriers decrease in the following order: CHF₂>CH₃>CH₂OCH₃ (24.8, 23.5 and 20.1 kcal/mol). This is in qualitative agreement with experiments. It has been suggested that a decrease of the barrier by a 19-methoxy substituent and its increase by a 19,19-difluoro substituent are phenomena of different origin. In the case of 19-methoxy substitution, the effect is due to the charge redistribution in the triene system and the decrease of the C(19)–H bond energy. The effect of two fluorine substituents at C-19 on the activation barrier is suggested to originate from the combination and balance of several factors: electrostatic repulsion between the negative fluorine atom and the π-electron cloud over the conjugated system, an increase of the HOMO–LUMO gap, and geminal difluoro substitution affecting C–F and C–C bond energies. Received: 17 May 2002 / Accepted: 11 September 2002 / Published online: 14 February 2003     

HCN(HNC)与NH3, H2O和HF分子间相互作用的理论研究

在MP2/aug-cc-pVTZ水平上, 对HCN(HNC)与NH3, H2O和HF分子间可能存在的氢键型复合物进行了全自由度能量梯度优化, 通过在相同水平上的频率验证分析发现了稳定的分子间相互作用形式是HCN(HNC)作为质子供体或作为质子受体形成的复合物. 基组重叠误差对总相互作用能的影响均小于3.34 kJ/mol. 通过自然键轨道(NBO)分析, 研究了单体和复合物中的原子电荷和电荷转移对分子间相互作用的影响. 对称性匹配微扰理论(SAPT, Symmetry Adapted Perturbation Theory)能量分解结果表明, 在分子间相互作用中, 静电作用与诱导作用占主导地位, 而诱导作用与复合物的电荷转移之间具有良好的正相关性.     

Internal rotation in squaramide and related compounds. A theoretical ab initio study

The structural and energetic changes associated with C–N bond rotation in a squaric acid derivative as well as in formamide, 3-aminoacrolein and vinylamine have been studied theoretically using ab initio molecular orbital methods. Geometry optimizations at the MP2(full)/6-31+G* level confirmed an increase in the C–N bond length and a smaller decrease in the C=O length on going from the equilibrium geometry to the twisted transition state. Other geometrical changes are also discussed. Energies calculated at the QCISD(T)/6-311+G** level, including zero-point-energy correction, show barrier heights decreasing in the order formamide, squaric acid derivative, 3-aminoacrolein and vinylamine. The origin of the barriers were examined using the atoms-in-molecules approach of Bader and the natural bond orbital population analysis. The calculations agree with Pauling's resonance model, and the main contributing factor of the barrier is assigned to the loss of conjugation on rotating the C–N bond. Finally, molecular interaction potential calculations were used to study the changes in the nucleophilicity of N and O (carbonyl) atoms upon C–N rotation, and to obtain a picture of the abilities of the molecules to act in nonbonded interactions, in particular hydrogen bonds. The molecular interaction potential results confirm the suitability of squaramide units for acting as binding units in host–guest chemistry. Received: 13 March 2002 / Accepted: 23 June 2002 / Published online: 21 August 2002     

Computational modeling of enzymatic keto-enol isomerization reactions

Catalysis of proton abstraction from nonacidic carbon atoms adjacent to a carbonyl or carboxylate group is a fundamental reaction in enzymology that has been extensively studied during the last few decades. Enzymes catalyzing these reactions, which normally involve labile enolic intermediates, need to overcome large pK _a differences between the reacting groups as well as high intrinsic free-energy barriers. Here, we present an overview of results from recent computer simulation studies of keto-enol isomerization reactions catalyzed by the enzymes glyoxalase I, triosephopsphate isomerase and ketosteroid isomerase. For all three enzymes it is found that electrostatic stabilization of the transient enolate intermediates, either by charge–charge interactions or by hydrogen bonding, accounts for the main part of the activation free-energy barrier reduction. Another catalytic effect observed in all cases is the reduction of the reorganization energy by the enzyme active site. Some other factors that have been proposed to be important for these reactions are also discussed and evaluated. Received: 3 January 2002 / Accepted: 13 May 2002 / Published online: 29 July 2002     

Infrared spectra of CO in absorption and evaluation of radial functions for potential energy and electric dipolar moment

From quantum-chemical calculations of rotational g factor and new experimental measurements of strengths of lines in infrared spectra of vibration–rotational bands v′–0 in absorption, with 1≤v′≤4, of ¹²C¹⁶O, and from analysis of 16,947 frequencies and wave numbers assigned to pure rotational and vibration–rotational transitions within electronic ground state X ¹Σ⁺, including new measurements of band 4–0 of ¹²C¹⁶O, we evaluate radial functions for potential energy and electric dipolar moment, the latter both in polynomial form and as a rational function that has qualitatively correct behaviour under limiting conditions. Received: 8 November 2001 / Accepted: 5 February 2002 / Published online: 14 August 2002     

An atom-in-molecules and electron-localization-function study of the interaction between O2 and VxOy+/VxOy (x = 1, 2, y = 1–5) clusters

 The most stable structures of V _x O _y ⁺/V _x O _y (x=1, 2, y=1–5) clusters and their interaction with O₂ are determined by density functional calculations, the B3LYP functional with the 6-31G* basis set. The nature of the bonding of these clusters and the interaction with O₂ have been studied by topological analysis in the framework of both the atoms-in-molecules theory of Bader and the Becke–Edgecombe electron localization function. Bond critical points are localized by means of the analysis of the electron density gradient field, ∇ρ(r), and the electron localization function gradient field, ∇η(r). The values of the electron density properties, i.e., electron density, ρ(r), Laplacian of the electron density, ∇²ρ(r), and electron localization function, η(r), allow the nature of the bonds to be characterized, and linear correlation is found for the results obtained in both gradient fields. Vanadium-oxygen interactions are characterized as unshared-electron interactions, and linear correlation is observed between the electron density properties and the V–O bond length. In contrast, O₂ units involve typical shared-electron interactions, as for the dioxygen molecule. Four different vanadium–oxygen interactions are found and characterized: a molecular O₂ interaction, a peroxo O₂ ²⁻ interaction, a superoxo O₂ ⁻ interaction and a side-on O₂ ⁻ interaction. Received: 15 October 2001 / Accepted: 30 January 2002 / Published online: 24 June 2002     

A theoretical study of photoinduced electron transfer between tetracyanoethylene and arene

 Ab initio calculations have been performed to investigate the state transition in photoinduced electron transfer reactions between tetracyanoethylene and biphenyl as well as naphthalene. Face-to-face conformations of electron donor–acceptor (EDA) complexes were selected for this purpose. The geometries of the EDA complexes were determined by using the isolated optimized geometries of the donor and the acceptor to search for the maximum stabilization energy along the center-to-center distance. The correction of interaction energies for basis set superposition error was considered by using counterpoise methods. The ground and excited states of the EDA complexes were optimized with complete-active-space self-consistent-field calculations. The theoretical study of the ground state and excited states of the EDA complex in this work reveals that the S₁ and S₂ states of the EDA complexes are charge–transfer (CT) excited states, and CT absorption which corresponds to the S₀→S₁ and S₀→S₂ transitions arise from π−π^* excitation. On the basis of an Onsager model, CT absorption in dichloromethane was investigated by considering the solvent reorganization energy. Detailed discussions on the excited state and on the CT absorptions were made. Received: 30 April 2001 / Accepted: 18 October 2001 / Published online: 9 January 2002     

A small-core multiconfiguration Dirac–Hartree–Fock-adjusted pseudopotential for Tl – application to TlX (X = F, Cl, Br, I)

 A relativistic pseudopotential of the energy-consistent variety simulating the Tl²¹⁺ (1s– 4f) core has been generated by adjustment to multiconfiguration Dirac–Hartree–Fock data based on the Dirac–Coulomb–Breit Hamiltonian. Valence ab initio calculations using this pseudopotential have been performed for atomic excitation energies and for spectroscopic constants of the X0⁺ and A0⁺ states of TlX (X = F, Cl, Br, I). Comparison is made to experiment and to four-component density functional results. Received: 22 June 1999 / Accepted: 5 August 1999 / Published online: 15 December 1999     

Investigation of the S<Subscript>0</Subscript>S<Subscript>1</Subscript> excitation in bacteriorhodopsin with the ONIOM(MO:MM) hybrid method

 We have investigated the S₀ and S₁ electronic states in bacteriorhodopsin using a variety of QM/MM levels. The decomposition of the calculated excitation energies into electronic and electrostatic components shows that the interaction of the chromophore with the protein electric field increases the excitation energy, while polarization effects are negligible. Therefore, the experimentally observed reduction in excitation energy from solution phase to protein environment (the Opsin shift) does not come from the electrostatic interaction with the protein environment, but from either the interaction ofthe chromophore with the solvent or counter ion, or structural effects. Our high-level ONIOM(TD– B3LYP:Amber) calculation predicts the excitation energy within 8 kcal/mol from experiment, the discrepancy probably being caused by the neglect of polarization of the protein environment. In addition, we have shown that the level of optimization is extremely critical for the calculation of accurate excitation energies in bacteriorhodopsin. Received: 13 October 2001 / Accepted: 6 September 2002 / Published online: 3 February 2003 Contribution to the Proceedings of the Symposium on Combined QM/MM Methods at the 222nd National Meeting of the American Chemical Society, 2001 Correspondence to: K. Morokuma e-mail: morokuma@emory.edu     

Triel–hydride triel bond between ZX3 (Z = B and Al; X = H and Me) and THMe3 (T = Si,Ge and Sn)

Complexes between THMe₃ (T = Si, Ge and Sn) and ZX₃ (Z = B and Al; X = H and Me) have been characterized using MP2/aug‐cc‐pVTZ calculations. These complexes are chiefly stabilized by a triel–hydride triel bond with the T–H bond pointing to the π‐hole on the triel atom. The triel–hydride interaction is mainly attributed to the charge transfer from the T–H bond orbital to the empty p orbital of the triel atom. These complexes are very stable with a large interaction energy (>10 kcal mol^?1) excluding THMe₃···BMe₃ (T = Si and Ge), indicating that the sp²‐hydridized triel atom has a strong affinity for the T–H bond. The formation of THMe₃···BH₃ results in proton transfer, characterized by conversion of orbital interaction and large charge transfer (ca 0.5e). The large deformation is primarily responsible for the abnormally greater interaction energy in THMe₃···BH₃ (>30 kcal mol^?1) than in the AlH₃ analogue. Methyl substitution on the triel atom weakens the triel–hydride interaction and causes a larger interaction energy in THMe₃···AlMe₃ with respect to its BMe₃ counterpart. Most of these interactions possess characteristics of covalent bonds. Polarization makes a contribution to the stability of most complexes nearly equivalent to the electrostatic term.     

Ab initio and density functional theory studies on the mechanism of nucleophilic vinylic substitution of 4<Emphasis Type="Italic">H</Emphasis>-pyran-4-one and 2-methyl-4<Emphasis Type="Italic">H</Emphasis>-pyran-4-one with ammonia

 Nucleophilic vinylic substitutions of 4H-pyran-4-one and 2-methyl-4H-pyran-4-one with ammonia were calculated by the B3LYP method using the 6-31G(d,p) basis set. Bulk solvent effects of aqueous solution were estimated by the polarized continuum and Poisson–Boltzmann self-consistent reaction field models using the 6-311+G(d,p) basis set. In the gas phase different mechanisms were found for the two reaction systems calculated. The reaction of 4H-pyran-4-one proceeds through enol, whereas a feasible path for the less reactive 2-methyl-4H-pyran-4-one is the mechanism through a keto intermediate. Addition of ammonia in concert with proton transfer is the rate-determining step ofthe reaction. The mechanism proceeding either by a bimolecular nucleophilic substitution (S_N2) or by one involving a tetrahedral zwitterionic intermediate is shown to be unlikely in the gas phase or nonpolar solution. The effects of bulk solvent not only consist in a reduction of the various activation barriers by about 25–40 kJ mol⁻¹ but also in a change in the reaction mechanism. Received 26 May 2002 / Accepted 26 July 2002 / Published online: 14 February 2003     

Recent advances in quantum mechanical/molecular mechanical calculations of enzyme catalysis: hydrogen tunnelling in liver alcohol dehydrogenase and inhibition of elastase by α-ketoheterocycles

 Hybrid quantum mechanical (QM)/molecular mechanical (MM) calculations are used to study two aspects of enzyme catalysis, Kinetic isotope effects associated with the hydride ion transfer step in the reduction of benzyl alcohol by liver alcohol dehydrogenase are studied by employing variational transition-state theory and optimised multidimensional tunnelling. With the smaller QM region, described at the Hartree–Fock ab initio level, together with a parameterised zinc atom charge, good agreement with experiment is obtained. A comparison is made with the proton transfer in methylamine dehydrogenase. The origin of the large range in pharmacological activity shown by a series of α-ketoheterocycle inhibitors of the serine protease, elastase, is investigated by both force field and QM/MM calculations. Both models point to two different inhibition mechanisms being operative. Initial QM/MM calculations suggest that these are binding, and reaction to form a tetrahedral intermediate, the latter process occurring for only the more potent set of inhibitors. Recieved 3 October 2001 / Accepted: 6 September 2002 / Published online: 31 January 2003 Contribution to the Proceedings of the Symposium on Combined QM/MM Methods at the 222nd National Meeting of the American Chemical Society, 2001 Correspondence to: I. H. Hillier Acknowledgements. We thank EPSRC and BBSRC for support of the research and D.G. Truhlar for the use of the POLYRATE code.     

A DFT study of pyramidalized alkenes: 7-oxasesquinorbornenes and 7,7′-dioxasesquinorbornenes

  DFT calculations of 7′–oxasesquinorbornenes and 7,7′-dioxasesquinorbornenes using the B3LYP/6–31G* method are reported. All the investigated structures (syn- and anti- derivatives) showed significant non-planarity of the central double bond, with the exception of those anti-derivatives possessing symmetrical structures. The influence of the replacement of the methylene groups at position 7- of the norbornene fragment with oxygen and the introduction of second and third (peripheral) double bonds and benzene rings on the molecular and electronic structures of these molecules have also been investigated. Received: 11 November 2002 / Accepted: 6 June 2002 / Published online: 29 April 2003     

Aconityl-derived polymers for biomedical applications. Modeling study of cis–trans isomerisation

 Soluble polymers have been prepared that are designed to undergo enhanced rates of hydrolysis at pH values less than that observed in blood circulation. The degradable element in the polymer mainchain is derived from cis-aconityl acid and is defined by a carboxylic acid pendent functionality (C-4) that is cis across a double bond to an amide at C-1 in the polymer mainchain. While degradation studies in vitro have confirmed these polymers do undergo enhanced rates of degradation at acidic pH values, there is also increasing evidence that during the degradation process the double bond isomerises to the trans configuration and thus prevents the full degradation of a polymer. From a molecular modelling perspective we are seeking to understand the propensity for this cis–trans isomerisation and the mechanism of this cis–trans isomerisation is discussed. Received: 29 April 2002 / Accepted: 6 September 2002 / Published online: 14 February 2003     

Theoretical Studies on the Dihydrogen Bonding Between Shortchain Hydrocarbon and Magnesium Hydride

The C--H…H dihydrogen-bonded complexes of methane, ethylene, acetylene, and their derivatives with magnesium hydride were systematically investigated at MP2/aug-cc-PVTZ level. The results confirm that the strength of dihydrogen bonding increases in the following order of proton donors： C（sp3）-H〈C（sp2）-H〈C（sp）-H and chlorine substituents enhance the C-H…H interaction. In the majority of the complexes with a cyclic structure, the Mg-H proton-accepting bond is more sensitive to the surroundings than C-H proton-donating bond. The nature of the electrostatic interaction in these C-H…H dihydrogen bonds was also unveiled by means of the atoms in mo- lecules（AIM） analysis. The natural bond orbital（NBO） analysis suggests that the charge transfer in the cyclic com- plexes is characteristic of dual-channel. The direction of the net charge transfer in the cyclic complexes is contrary to that previously found in dihydrogen bonded systems.     

Structures,vibrational frequencies,topologies, and energies of hydrogen bonds in cysteine‐formaldehyde complexes

The hydrogen bonding interactions between cysteine (Cys) and formaldehyde (FA) were studied with density functional theory regarding their geometries, energies, vibrational frequencies, and topological features of the electron density. The quantum theory of atoms in molecules and natural bond orbital analyses were employed to elucidate the interaction characteristics in the Cys‐FA complexes. The intramolecular hydrogen bonds (H‐bonds) formed between the hydroxyl and the N atom of cysteine moiety in some Cys‐FA complexes were strengthened because of the cooperativity. Most of intermolecular H‐bonds involve the O atom of cysteine/FA moiety as proton acceptors, while the strongest H‐bond involves the O atom of FA moiety as proton acceptor, which indicates that FA would rather accept proton than providing one. The H‐bonds formed between the CH group of FA and the S atom of cysteine in some complexes are so weak that no hydrogen bonding interactions exist among them. In most of complexes, the orbital interaction of H‐bond is predominant during the formation of complex. The electron density (ρ_b) and its Laplace (?²ρ_b) at the bond critical point significantly correlate with the H‐bond parameter δR, while a linearly relationship between the second‐perturbation energy E(2) and ρ_b has been found as well. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012