Quality of approximate electron densities and internal consistency of molecular alignment algorithms in molecular quantum similarity

The calculation of molecular quantum similarity measures using the molecular electron density requires the electron density and molecular alignment between two molecules. To obtain meaningful quantum similarity matrices, the electron density should be calculated efficiently and accurately and the alignment should be internally consistent. The internal consistency of the alignment for a series of molecules is investigated through distance geometry concepts. The calculation of the quantum similarity matrix requires the calculation of a quadratic number of similarity integrals, and a scheme to obtain these efficiently is developed. Both the alignment procedure and the ASA method for approximate molecular electron densities are tested for a set of steroid molecules.     

Double Bond Migration Mechanism in Allyl Systems Involving the Hydroxide Ion. 3. Supermolecular Approach

The mechanism of a proton transfer in an allyl system involving the hydroxide ion was investigated by the RHF/6-31+G* and MP2/6-31+G* methods with one, two, and four water molecules (water regarded as a solvent) included in the calculation; in the fourth model, the reactant system and two H₂O molecules were placed into continuum. A possible mechanism of intramolecular proton transfer involving easy exchange of water molecules between the first and second coordination spheres of the propenide ion is considered. The results are compared with those obtained with gas-phase and polarizable continuum models.     

“Crystal” conformations of 2-methyl-2,4-pentanediol: Dipole moment calculations and molecular structure optimizations

The structures of eight symmetrically independent molecules of 2-methyl-2,4-pentanediol (MPD) in six crystal substances are studied based on the data retrieved from the Cambridge Structural Database (CSD). Coordinates of the most part of hydrogen atoms in MPD molecules were not determined experimentally or not presented in CSD, however, O...O distances provide the conclusion about the formation of intramolecular hydrogen bonds in four molecules. To perform quantum chemical calculations the absent hydrogen atoms were added. The choice of H atomic positions in hydroxyl groups are based on the analysis of possible formation of intra- and intermolecular hydrogen bonds by MPD molecules in the respective crystals. The DFT method with the B3PW91 functional and the 6-31G(d,p) basis set is used to carry out for the first time: 1) the calculation of dipole moments and energies for MPD molecules in “crystal” conformations; 2) the optimization of the structure of these molecules with the calculation of dipole moments for the conformations corresponding to the local energy minima. It is found that among the molecules with the experimental geometric parameters one of the conformations without intramolecular hydrogen bonds is most favorable (μ = 0.56 D). As a result of the energy minimization of eight “crystal” conformations in vacuum, five energetically different conformers are obtained. Among them the conformer with the intramolecular hydrogen bond has the lowest energy (μ = 3.53 D). Four variants of the molecular structure correspond to it in the considered crystals, out of which two are R-enantiomers and two S-enantiomers.     

Ab initio calculation of the first order term of the intermolecular energy near the van der Waals minimum

The first order term of the intermolecular energies between two hydrogen molecules and between Li⁺ and H₂ has been computed by three different methods: two of them are based on a perturbative procedure, including or neglecting the overlap between the orbitals of the interacting molecules or atoms in the calculation of the electrostatic and exchange terms. We can then study the effect of the overlap on each of these terms. The third method is the SCF supermolecule treatment which provides results in very good agreement with the perturbative procedure including the overlap. TheT configuration in the case of two hydrogen molecules and theC _2v configuration for Li⁺+H₂ are stable with respect to the first order term.     

Electronic structure of the pyrimidine and purine components of nucleic acids in their ground and lower excited singlet and triplet states

Quantum-chemical calculation of the energies of the electronic transitions and the electronic structures of the neutral and ionic species of the nucleic acids components in their ground and lower excited singlet and triplet ππ* and nπ* states has been carried out in the all-valence-electron approximation CNDO /S . The results of the calculation allow one to identify the most photoreactive sites of the molecules and to consider the dependence of the location of these sites on the ionic state of the molecules. The calculated data are compared with our previous results obtained in a π-electron approximation. The individual absorption spectra of various ionic and tautomeric species of the nucleic acids components obtained by us earlier have been decomposed into bands corresponding to separate electronic transitions. As a rule, there is a good agreement between the calculated data in the two approximations and the experimental results.     

Time-dependent approach to electronically excited states of molecules with the multiconfiguration time-dependent Hartree-Fock method

In this paper the authors show how the multiconfiguration time-dependent Hartree-Fock (MCTDHF) method can be used for the calculation of electronic properties of molecules associated with the population of excited states. In contrast to other methods for correlated electron dynamics, such as configuration interaction, MCTDHF does not rely on a solution of the electronic Schrodinger equation prior to the propagation. The authors apply this approach to the calculation of vertical excitation energies, transition dipole moments, and oscillator strengths for two test molecules, lithium hydride and methane.     

Nitrile and thiocyanate IR probes: quantum chemistry calculation studies and multivariate least-square fitting analysis

Hydration effects on the C[Triple Bond]N stretching mode frequencies of MeCN and MeSCN are investigated by carrying out ab initio calculations for a number of MeCN-water and MeSCN-water complexes with varying number of water molecules. It is found that the CN frequency shift induced by the hydrogen-bonding interactions with water molecules originate from two different ways to form hydrogen bonds with the nitrogen atom of the CN group. Considering the MeCN- and MeSCN-water cluster calculation results as databases, we first examined the validity of vibrational Stark effect relationship between the CN frequency and the electric field component parallel to the CN bond and found no strong correlation between the two. However, taking into account of additional electric field vector components is a simple way to generalize the vibrational Stark theory for the nitrile chromophore. Also, the electrostatic potential calculation method has been proposed and examined in detail. It turned out that the interactions of water molecules with nitrogen atom's lone pair orbital and with nitrile pi orbitals can be well described by the electrostatic potential calculation method. The present computational results will be of use to quantitatively simulate various linear and nonlinear vibrational spectra of nitrile compounds in solutions.     

Theoretical study on solvation effects in chemical reactions: A vibrational coupling model

A vibrational coupling model to treat the solvation effects in chemical reaction rate calculations is proposed and applied to the intramolecular hydrogen transfer reaction CH₃O· → ·CH₂OH in the condensed phase. The effect of solvation is taken into account in two ways: (1) the solvent effect on the activation energy of the reaction is simulated by including 39 surrounding water molecules, represented by fractional charges at the assumed atomic positions, in the potential energy surface calculation; and (2) the vibrational couplings between the 10 nearest solvent molecules and the molecules constituting the reaction system are explicitly included in a vibrational frequency calculation. RRKM theory with Miller's tunneling correction included is employed to calculate the rate constants. The effect of solvation causes a significant change in the chemical reaction rate, mainly through a lowering of the activation energy. The vibrational coupling causes a slight increase of the rate constant in the tunneling region by perturbing the vibrational frequencies of the reactant and transition states, which appear in the rate-constant expression, but has little effect at higher temperatures.     

Light scattering study of solubilization of organic molecules by block copolymer micelles in aqueous media

Block copolymers, when dissolved in a selective solvent, form spherical micelles. These micelles can selectively solubilize organic molecules otherwise insoluble in the pure solvent. In this study, we report solubilization of organic molecules by styrene-methacrylic acid block copolymer micelles in aqueous buffers. A light scattering technique was developed to determine the extent of micellar solubilization. Our results indicate that the extent of micellar solubilization depends on the chemical nature of organic molecules, specifically, on the interactions between the organic compound and polystyrene. A thermodynamic model has been developed to describe micellar solubilization. The theoretical calculation agrees reasonably well with the experimental results for two micellar samples examined. ©1995 John Wiley & Sons, Inc.     

Anharmonic oscillator model of overtone spectra for D3h symmetry molecules

The bond stretching vibrations of XF₅ molecules with D_3h symmetry are treated computationally on the Morse oscillator model in which the bond oscillators are coupled harmonically. Each calculation involves four parameters for two types of Morse potential and three parameters for the kinetic-energy, potential coupling terms. The eigenvalue formula for overtone and combination states up to three are presented and can be used to predict all the vibrational energy levels from local mode molecules through normal mode molecules. For PF₅, AsF₅ and VF₅, the coupled Morse oscillator model gives a prediction in good agreement with the experimental data.     

Calculation of the ground states of molecules with closed shells via Feynman diagrams

A Feynman-diagram calculation is performed for the ground-state energies of molecules of the XY_p type with closed electron shells. The first two orders in perturbation theory are considered.We are indebted to Dr. V. V. Tolmachev for proposing the topic and for substantial assistance in deriving the results, and also to Dr. U. I. Safronova for constant interest.     

Hypervirial SCF treatment for vibrational energy levels of triatomic molecules

The SCF method for the calculation of energy levels of triatomic molecules is applied using the hypervirial perturbative procedure for solving the coupled equations. This treatment allows to obtain in a recursive way the energy corrections and the expectation values required in the SCF treatment, avoiding the explicit calculation of the wave functions. A numerical application is made to the SO₂ and O₃ molecules, comparing our results with those obtained by other methods.     

基态NS、SiF的旋轨耦合常数的非经验计算

分子的自旋轨道耦合常数对分析分子光谱的精细结构有重要意义。Richards等^[1]自七十年代起利用Hartree-Fock波函数,非经验地计算了一些分子的旋轨耦合常数,获得了与实验值吻合的结果。本文报导利用我们发展的计算程序,对两个基态分子NS(X²Π),SiF(X²Π)进行了旋轨耦合常数的计算,其结果与实验符合良好。     

The change in the dressed potential of a polyatomic molecule in intense photon fields: Simple rules based on the nuclear charge-mass ratio

An explicit expression for the dressed potential of a polyatomic molecule, in the adiabatic approximation, is derived. This expression clearly shows the importance of the nuclear charge-mass ratio (NCMR ) for the change of potential due to photon fields. It is found from a simple calculation that the ¹H atom is the only atom having an abnormal NCMR value; all other atoms have similar, or the same, values. This means that only those molecules containing a ¹H atom should be strongly affected by fields. On the basis of this new physical insight, we postulate two rules, which enable us to classify molecules, with respect to their response to intense photon fields, into three classes: high-sensitive, low-sensitive, and insensitive molecules. Qualitative verification is also given by using water isotopes.     

A new method of calculation of internuclear distances in molecules and crystals

It was shown that the earlier derived equation for calculation of the lattice energy of ionic crystals contains a term that can characterize the radius of the overlap region of the electron clouds of interacting atoms. On this basis, simple and rather exact formulas were derived for the calculation of internuclear distances in crystals and molecules. The error of calculation R ₁₂ is from 1.2% (for crystalline Group IA metal halides) to 3.8–5.7% (for various gaseous molecules). The coordination of ions was shown to be essential for determining internuclear distances. The adequacy of the Stuart-Briegleb model of molecular structure was confirmed.     

Calculation of atomic integration data

The calculation of average properties of atoms in molecules and interatomic surfaces is a difficult problem that requires the evaluation of two‐ and three‐dimensional integrals over regions with nontrivial borders. A mathematical formalism is presented that maps these regions onto the whole of ℝ² and/or ℝ³ and allows the construction of efficient and reliable numerical methods for the calculation of these integrals. These methods, which will be part of a forthcoming program package, are described and examples are given. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1040–1048, 2000     

Application of the AMYR calculating method on quinoxaline, 3-chloroquinoxaline,and 3-methylquinoxaline in the interaction with n water molecules (n varies from 1 to 6)

AMYR is a computer program for the calculation of molecular associations using Fraga’s pairwise atomatom potential. The interaction energy is evaluated through a 1/R expansion. A pairwise dispersion energy term is included in the potential and corrected by a damping function. The program carries out energy minimizations through variable metric methods. The new version allows for the stationary point analysis of the intermolecular potential by means of the Hessian eigenvalues. AMYR model is used for the first time in a calculation of quinoxaline, 3-chloroquinoxaline, and 3-methylquinoxaline molecules interacting with some water molecules. Intermolecular interaction energies are obtained and the stable conformation is determined in each case. The change conformation was considered at α ? (CNC) angle when the solute molecules are surrounded by n water molecules (1 ≤ n ≤ 6).     

Floating s and p-type gaussian orbitals

The advantages of including a small number of p-type gaussian functions in a floating spherical gaussian orbital calculation are pointed out and illustrated by calculations on molecules which previously have proved to be troublesome. These include molecules such as F₂ with multiple lone pairs and C₂H₂ with multiple bonds. A feature of the results is the excellent correlation between the orbital energies and those of a double zeta calculation reported by Snyder and Basch.     

An approximate method for calculating transfer integrals based on the ZINDO Hamiltonian

In this article, we discuss a method for calculating transfer integrals for pairs of molecules based on Zerner's Independent Neglect of Differential Overlap Hamiltonian which requires only a single self‐consistent field calculation on an isolated molecule to be performed to determine the transfer integral for a pair of molecules. This method is compared with results obtained by projection of the pair of molecules' molecular orbitals onto the vector space defined by the molecular orbitals of each isolated molecule. The two methods are found to be in good agreement using three compounds as model systems: pentacene, ethylene, and hexabenzocoronene. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008