Valence bond theory for chemical dynamics

This essay provides a perspective on several issues in valence bond theory: the physical significance of semilocal bonding orbitals, the capability of valence bond concepts to explain systems with multireferences character, the use of valence bond theory to provide analytical representations of potential energy surfaces for chemical dynamics by the method of semiempirical valence bond potential energy surfaces (an early example of specific reaction parameters), by multiconfiguration molecular mechanics, by the combined valence bond-molecular mechanics method, and by the use of valence bond states as coupled diabatic states for describing electronically nonadiabatic processes (photochemistry). The essay includes both ab initio and semiempirical approaches.     

Bond orders and valences from ab initio wave functions

The definition and properties of the bond order and valence indices calculated from ab initio wave functions are summarized. Their physical interpretation relationships to the exchange effects in bonding and generalization to correlated wave functions are also discussed. Some examples with typical bond order and valence values are shown.     

对结构化学中价键理论教学的若干思考

通过追踪原始文献,分析结构化学中价键理论部分的教学内容,特别是对氧气分子基态电子结构的处理,发现价键理论不仅能够正确解释或预测分子结构,而且对芳香性、铁磁性等化学键本质的描述表现更优.     

经典价键理论的从头算计算方法

价键理论是两大现代化学键理论之一,广泛应用于化学键本质和化学反应机理的研究。由于计算困难,价键理论应用局限于定性的讨论而无法有效地开展从头计算研究。现代经典价键理论在经典价键理论的理论基础上,引入合理有效的计算方法,提高了价键计算的效率。本文回顾近年来经典价键理论从头算方法在提高计算精度和拓展研究范围方面的发展,并简要展望价键理论方法的发展趋势。     

Intrinsic minimal atomic basis representation of molecular electronic wavefunctions

The problem of finding an effective minimal atomic basis that spans the exact occupied wavefunctions of a mean‐field theory at a given molecular geometry, which has a number of special properties, is studied and a new general procedure is developed that (1) solves for a raw minimal set of strongly atom‐centered functions—products of spherical harmonics and molecule‐optimized radial parts—that approximately span the occupied molecular wavefunctions and minimize the sum of their energies, (2) uses projection operators to get a new set of deformed atom‐centered functions that exactly span the occupied space and fall into core and valence subsets, (3) applies a new zero‐bond‐dipole orthogonalization scheme to the core‐orthogonalized valence subset so that for each two‐center product of these functions the projection of its dipole moment along the line going through the two centers is zero. The resulting effective minimal atomic basis is intrinsic to the molecular problem and does not need a free‐atoms input. Some interesting features of the zero‐bond‐dipole orthogonalization are showing up in the atomic population analysis of a diverse set of molecules. The new procedure may be useful for the interpretation of electronic structure, for the construction of model Hamiltonians in terms of transferable molecular integrals, and for the definition of active valence space in the treatment of electron correlation. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Variational optimization of effective atom centered potentials for molecular properties

In plane wave based electronic structure calculations the interaction of core and valence electrons is usually represented by atomic effective core potentials. They are constructed in such a way that the shape of the atomic valence orbitals outside a certain core radius is reproduced correctly with respect to the corresponding all-electron calculations. Here we present a method which, in conjunction with density functional perturbation theory, allows to optimize effective core potentials in order to reproduce ground-state molecular properties from arbitrarily accurate reference calculations within standard density functional calculations. We demonstrate the wide range of possible applications in theoretical chemistry of such optimized effective core potentials (OECPs) by means of two examples. We first use OECPs to tackle the link atom problem in quantum mechanics/molecular mechanics (QM/MM) schemes proposing a fully automatized procedure for the design of link OECPs, which are designed in such a way that they minimally perturb the electronic structure in the QM region. In the second application, we use OECPs in two sample molecules (water and acetic acid) such as to reproduce electronic densities and derived molecular properties of hybrid (B3LYP) quality within general gradient approximated (BLYP) density functional calculations.     

价键理论新进展

概要介绍了现代价键理论的几个主要方法,并讨论了它们各自的特点及其发展现状,并重点介绍了键表方法的基本理论、计算程序及一些应用。     

The application of molecular mechanics to the structures of carbohydrates

A study is reported of the accuracy with which the geometries of pyranose and methyl pyranoside molecules are predicted by molecular mechanics. Calculations of the conformational energies of the model compounds dihydroxymethane, methoxymethanol, and dimethoxymethane, made with the program MMI, produced results that compare well with previous ab initio molecular orbital calculations. This indicates that MMI gives a satisfactory account of the energetic and conformational aspects of the anomeric effect, a conclusion further supported by calculations on 2-methoxytetrahydropyran. The prediction of the observed preferred conformations of the primary alcohol group in aldohexopyranoses appears to be less satisfactory. MMI-CARB, a version of MMI with changes in some of the equilibrium C? O bond lengths of the program, has been used to calculate the geometries of 13 pyranose and methyl pyranoside molecules, the crystal structures of which have been studied by neutron diffraction. When the C? C? O? H torsion angles are constrained to approximately the values observed in the crystal structures, good agreement is obtained between the theoretical and experimental molecular geometries. The rms deviation for C? C and C? O bonds, excluding those significantly affected by thermal motion in the crystal structure determinations, is 0.005 Å. Corresponding figures for the valence angles that do not involve hydrogen atoms and for the ring torsion angles are 1.2° and 2.0°, respectively. The Cremer and Pople puckering parameters for the pyranose rings are reproduced within 0.026 Å in Q and 5.4° in θ.     

Comment on “A stationary‐wave model of enzyme catalysis” by Carlo Canepa

Energy barriers for enzyme‐catalyzed reactions calculated with quantum mechanics/molecular mechanics (QM/MM) and empirical valence bond (EVB) methods can be in excellent agreement with activation energies derived from experiments, supporting the applicability of transition state theory for enzymic reactions. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Combined valence bond-molecular mechanics potential-energy surface and direct dynamics study of rate constants and kinetic isotope effects for the H + C2H6 reaction

This article presents a multifaceted study of the reaction H+C(2)H(6)-->H(2)+C(2)H(5) and three of its deuterium-substituted isotopologs. First we present high-level electronic structure calculations by the W1, G3SX, MCG3-MPWB, CBS-APNO, and MC-QCISD/3 methods that lead to a best estimate of the barrier height of 11.8+/-0.5 kcal/mol. Then we obtain a specific reaction parameter for the MPW density functional in order that it reproduces the best estimate of the barrier height; this yields the MPW54 functional. The MPW54 functional, as well as the MPW60 functional that was previously parametrized for the H+CH(4) reaction, is used with canonical variational theory with small-curvature tunneling to calculate the rate constants for all four ethane reactions from 200 to 2000 K. The final MPW54 calculations are based on curvilinear-coordinate generalized-normal-mode analysis along the reaction path, and they include scaled frequencies and an anharmonic C-C bond torsion. They agree with experiment within 31% for 467-826 K except for a 38% deviation at 748 K; the results for the isotopologs are predictions since these rate constants have never been measured. The kinetic isotope effects (KIEs) are analyzed to reveal the contributions from subsets of vibrational partition functions and from tunneling, which conspire to yield a nonmonotonic temperature dependence for one of the KIEs. The stationary points and reaction-path potential of the MPW54 potential-energy surface are then used to parametrize a new kind of analytical potential-energy surface that combines a semiempirical valence bond formalism for the reactive part of the molecule with a standard molecular mechanics force field for the rest; this may be considered to be either an extension of molecular mechanics to treat a reactive potential-energy surface or a new kind of combined quantum-mechanical/molecular mechanical (QM/MM) method in which the QM part is semiempirical valence bond theory; that is, the new potential-energy surface is a combined valence bond molecular mechanics (CVBMM) surface. Rate constants calculated with the CVBMM surface agree with the MPW54 rate constants within 12% for 534-2000 K and within 23% for 200-491 K. The full CVBMM potential-energy surface is now available for use in variety of dynamics calculations, and it provides a prototype for developing CVBMM potential-energy surfaces for other reactions.     

High-pressure studies of the hydrogen bond networks in molecular crystals

This article gives some examples of using high-pressure techniques to study hydrogen bond networks in molecular crystals.     

Retrieval of crystallographically-derived molecular geometry information

The crystallographically determined bond length, valence angle, and torsion angle information in the Cambridge Structural Database (CSD) has many uses. However, accessing it by means of conventional substructure searching requires nontrivial user intervention. In consequence, these valuable data have been underutilized and have not been directly accessible to client applications. The situation has been remedied by development of a new program (Mogul) for automated retrieval of molecular geometry data from the CSD. The program uses a system of keys to encode the chemical environments of fragments (bonds, valence angles, and acyclic torsions) from CSD structures. Fragments with identical keys are deemed to be chemically identical and are grouped together, and the distribution of the appropriate geometrical parameter (bond length, valence angle, or torsion angle) is computed and stored. Use of a search tree indexed on key values, together with a novel similarity calculation, then enables the distribution matching any given query fragment (or the distributions most closely matching, if an adequate exact match is unavailable) to be found easily and with no user intervention. Validation experiments indicate that, with rare exceptions, search results afford precise and unbiased estimates of molecular geometrical preferences. Such estimates may be used, for example, to validate the geometries of libraries of modeled molecules or of newly determined crystal structures or to assist structure solution from low-resolution (e.g. powder diffraction) X-ray data.     

An ab initio and molecular mechanical investigation of ureas and amide derivatives

Ab initio molecular orbital theory with the 6-31G* basis set has been used to investigate the geometries and preferred conformations for urea, derivatives of urea, and a few complicated amide derivatives. The results from the ab initio calculations provide insight into the gas-phase rotational barrier about the C? N bond and have been used to generate parameters for the MM2(87) molecular mechanics program. When applicable, theoretical structures are compared with corresponding previously reported experimental geometries. Urea is predicted to be nonplanar with pyramidal amino groups.     

Structural forms of green fluorescent protein by quantum mechanics/molecular mechanics calculations

The molecular modeling of structural forms of the green fluorescent protein (GFP) with the Ser65Thr single-site mutation was performed by the quantum mechanics/molecular mechanics (QM/MM) method. Two model systems were constructed based on the crystallographic structure from the Protein Data Bank (PDB entry code 1EMA.) The model systems differ in the initial protonation state of the side chain of the amino acid residue Glu222 near the chromophore. The atomic coordinates of the protein macromolecule corresponding to the equilibrium geometric configurations were determined by total energy minimization using the QM/MM method within the density functional theory approximation PBE0/cc-pVDZ for the quantum subsystem that consists of the chromophore, a water molecule, and the side chains of Arg96, Glu222, and Ser205, and with the parameters of the AMBER force field for the molecular mechanics subsystem. In the analysis of the results, particular attention was given to the hydrogen bond redistribution in the chromophore-containing region of the protein caused by a change in the protonation state of the chromophore. The results obtained from the model containing the initially protonated side chain of Glu222 suggest a new interpretation of the photophysical processes in the green fluorescent protein.     

The ellipsoidal Gaussian basis in molecular orbital theory

The ellipsoidal Gaussian basis function used in a minimal valence atomic orbital representation is compared with the double-zeta spherical Gaussian basis orbital representation for some seventeen molecules made up of first row atoms and hydrogen. Except for acetylene the double-zeta basis gives consistently better total electronic energies and generally better property values than the optimized ellipsoidal single zeta basis. Difference molecular density contour maps comparing the two basis sets, as well as other one-electron property values, indicate that the ellipsoidal basis exaggerates the transfer of charge from the atomic regions to the interatomic and lone pair regions of molecules. Apparently, the forced complete elliptization of the valence atomic orbital in the single-zeta representation does not allow the basis set sufficient flexibility to simultaneously represent both the basically spherical atomic part of these orbitals and the non-spherical molecular bond formation. Other properties and aspects of the ellipsoidal Gaussian basis are also discussed.     

Implementation of molecular symmetry in valence bond calculation

A novel strategy for the construction of many-electron symmetry-adapted wave function is proposed for ab initio valence bond (VB) calculations and is implemented for valence bond self-consistent filed (VBSCF) and breathing orbital valence bond (BOVB) methods with various orbital optimization algorithms. Symmetry-adapted VB functions are constructed by the projection operator of symmetry group. The many-electron symmetry-adapted wave function is expressed in terms of symmetry-adapted VB functions, and thus the VB calculations can be performed with the molecular symmetry restriction. Test results show that molecular symmetry reduces the computational cost of both the iteration numbers and CPU time. Furthermore, excited states with specific symmetry can be conveniently obtained in VB calculations by using symmetry-adapted VB functions.     

Theories of the chemical bond and its true nature

Two different models for chemical bond were developed almost simultaneously after the Schrödinger formulation of quantum theory. These are known as the valence bond (VB) and molecular orbital (MO) theories. Initially chemists preferred the VB theory and ignored the MO theory. Now the VB theory is almost dropped out of currency. The context of discovery and Linus Pauling’s overpowering influence gave the VB theory its initial advantage. The current universal acceptance of the MO theory is due to its ability to provide direct interpretation of many different types of experiments now being pursued. In current research both localized bonds and delocalized charge distributions play important roles and the MO theory has been successful in giving a good account of both.     

Crystal and molecular structures of diastereomeric 2-phosphoryl-, 2-thiophosphoryl-, and 2-selenophosphoryl-substituted 1,3-dithianes

The crystal and molecular structures of five pairs of diastereomeric cis- and trans-2-phosphoryl-, 2-thiophosphoryl-, and 2-selenophosphoryl-5-t-butyl-1,3-dithianes have been determined. For all the examined compounds, all of the basic geometrical parameters, such as bond lengths, bond and torsion angles, and the deformation of a chair conformation of the six-membered heterocyclic rings, have been established. The differences in corresponding bond lengths and valence angles in diastereomeric cis- and trans-2-P-substituted 1,3-dithianes are discussed.