Approximate calculation of the matrix elements of Coulomb and exchange operators for the “core” electrons of the atoms Li through Ar

A method is described which allows to approximate with a few parameters the Coulomb and exchange integrals employed in valence-electron-only SCF calculations. The necessary parameters for atoms from Li to Ar are given. Very good transferability from atomic to molecular systems and near coincidence with all-electron calculations are found for LiH, HF and HC1 molecules. Extension to other atoms is in progress.     

Unrestricted Hartree-Fock instabilities in semiempirical CNDO/S and INDO/S calculations of spin-spin coupling constants

It is shown that non-convergent calculations of the Fermi contact term of spin-spin coupling constants within the self-consistent and finite perturbation schemes used to solve the coupled Hartree-Fock equations, are originated in non-singlet Hartree-Fock instabilities of the closed-shell restricted Hartree-Fock wavefunction. In CNDO/S and INDO/S wavefunctions, where the electronic system response has been successfully reproduced, all investigated molecules containing MOs were found to be unstable. Results of spin-spin coupling constants are given and compared with experimental as well as FP and SOS INDO values.Part of a Ph.D. thesis (G.E.S.) to be presented to the University of Buenos Aires.Comisión de Investigaciones Científicas (CIC, Pcia. de Bs. As.) fellow.     

Protolytic properties of cyanic and thiocyanic acids and their isoforms

The electronic structure of HOCN, HSCN, HNCO, and HNCS molecules and [OCN]^? and [SCN]^? anions has been studied by ab initio calculations at HF/6-31G(d), HF/6-31G(d, p), MP2/6-31G(d)//HF/6-31G(d), and MP2/6-31G(d, p)//HF/6-31G(d, p) levels of theory. The HNCO and HNCS molecules are shown to have higher thermodynamic stability than HOCN and HSCN, respectively. The protolyte strength series are substantiated: HSCN > HOCN, HNCS > HNCO, HOCN > HNCO, HSCN > HNCS. Computations including electron correlation [MP2/6-31G(d)//HF/6-31G(d) and MP2/6-31G(d, p)//HF/6-31G (d, p)] reproduce the general sequence of proton-donor properties: HSCN > HOCN > HNCS > HNCO, which coincides with the hydrophobicity series for the compounds. The relative proton-donor capacity of these acids in water solutions is generally governed by the electronic structure and by the size of their molecules and [OCN]^? and [SCN]^? anions, but not by medium effects.     

The calculation of electron localization and delocalization indices at the Hartree–Fock, density functional and post-Hartree–Fock levels of theory

 Localization, λ(A), and delocalization indices, δ(A,B), as defined in the atoms in molecules theory, are a convenient tool for the analysis of molecular electronic structure from an electron-pair perspective. These indices can be calculated at any level of theory, provided that first- and second-order electron densities are available. In particular, calculations at the Hartree–Fock (HF) and configuration interaction (CI) levels have been previously reported for many molecules. However, λ(A) and δ(A,B) cannot be calculated exactly in the framework of Kohn–Sham (KS) density functional theory (DFT), where the electron-pair density is not defined. As a practical workaround, one can derive a HF-like electron-pair density from the KS orbitals and calculate approximate localization and delocalization indices at the DFT level. Recently, several calculations using this approach have been reported. Here we present HF, CI and approximate DFT calculations of λ(A) and δ(A,B) values for a number of molecules. Furthermore, we also perform approximate CI calculations using the HF formalism to obtain the electron-pair density. In general, the approximate DFT and CI results are closer to the HF results than to the CI ones. Indeed, the approximate calculations take into account Coulomb electron correlation effects on the first-order electron density but not on the electron-pair density. In summary, approximate DFT and CI localization and delocalization indices are easy to calculate and can be useful in the analysis of molecular electronic structure; however, one should take into account that this approximation increases systematically the delocalization between covalently bonded atoms, with respect to the exact CI results. Received: 13 February 2002 / Accepted: 24 April 2002 / Published online: 18 June 2002     

Vibrational spectroscopic and density functional theory studies of chloranil-imidazole interaction

The present work reports vibrational spectra and density functional theory calculations for chloranil, imidazole and their complexes. The experimentally observed infrared and Raman bands have been assigned with the help of calculated vibrational frequencies and potential energy distribution analysis. Some bands of chloranil and imidazole have been found to shift on the complex formation due to partial electronic charge transfer from imidazole to chloranil. The charge transfer between these molecules is also corroborated by the electronic absorption spectroscopy and calculations. The theoretical values of the interaction energy of various possible chloranil-imidazole interactions suggest that the two molecules interact preferably via N and H atoms of imidazole and CO group of chloranil with their molecular planes almost perpendicular to each other.     

Self-consistent-field – Hartree–Fock method with finite nuclear mass corrections

We have upgraded a Self-consistent-field – Hartree–Fock routine to include a finite nuclear mass correction for molecules developed in our laboratory. The new routine can handle isotopomers without calculating any nuclear kinetic energy matrix element. Tests on H₂, LiH, HF, F₂, and H₂O isotopomers indicate the equivalence of our correction to the standard diagonal adiabatic correction. A further original application to C₂H₆ illustrates the usefulness of the method for polyatomic molecules. The resulting molecular orbitals carry the nuclear mass signature, exemplified with Koopmans ionization potentials.From the Proceedings of the 28th Congreso de Químicos Teóricos de Expresión Latina (QUITEL 2002)     

Theoretical studies on the S-N interactions in sulfoximine

The potential energy surface of sulfoximines has been searched using ab initio MO and Density Functional Calculations. The electronic structures of the isomers of sulfoximine have been studied using HF/6-31+G*, MP2(full)/6-31+G* and B3LYP/6-31+G* levels. Final energies of these molecules have been calculated at the high accuracy G2 and CBS-Q levels. Though a formal SN double bond is generally considered between sulfur and nitrogen in these systems, theoretical studies do not show any π interaction between them. S-N rotational barriers, bond dissociation energies, atomic charge analysis, and NBO analysis all indicate only a single bond across S-N with a very strong ionic interaction.     

Quantum Monte Carlo Calculation of Correlation Effects on Bond Orders

We present a computational approach, using quantum Monte Carlo, that provides some insight into the effect of electron correlation on chemical bonding between individual pairs of atoms. Our approach rests upon a recently suggested relation between the bond order and charge fluctuations with respect to atomic domains. Within the present implementation we have taken a compromise between conceptual rigour and computational simplicity. In a first step atomic domains were obtained from Hartree-Fock (HF) densities, using Bader’s definition of atoms in molecules. These domains were used in a second step in quantum Monte Carlo calculations to determine bond orders for pairs of atoms. Correlation effects have been studied by comparison of HF bond orders with those obtained from pure diffusion quantum Monte Carlo calculations. We illustrate this concept for C–O and C–S bonds in different molecular environments. Our results suggest an approximate linear relation between bond order and bond length for these kinds of bonds.     

Potential curves for proton motion in H-bonded systems: HF and H2O polymers

The presence of long range coupling between hydrogen atoms is shown for the HF and H₂O hydrogen bonded systems. The coupling of H atoms critically depends on the spatial orientation of the H atoms being considered. Explicit calculations of the potential curves of the protons are performed using as a model a ring of six HF, or H₂O, molecules. The method of calculation is the CNDO/2. The strong similarities of the results for H₂O and HF polymers supports the conclusion that the coupling is essentially due to factors such as the asymmetric equilibrium position of the H atoms, the high electronic polarizability of the system, etc.     

Intermediate Electrostatic Field for the Generalized Elongation Method

An intermediate electrostatic field is introduced to improve the accuracy of fragment‐based quantum‐chemical computational methods by including long‐range polarizations of biomolecules. The point charge distribution of the intermediate field is generated by a charge sensitivity analysis that is parameterized for five different population analyses, namely, atoms‐in‐molecules, Hirshfeld, Mulliken, natural orbital, and Voronoi population analysis. Two model systems are chosen to demonstrate the performance of the generalized elongation method (ELG) combined with the intermediate electrostatic field. The calculations are performed for the STO‐3G, 6‐31G, and 6‐31G(d) basis sets and compared with reference Hartree–Fock calculations. It is shown that the error in the total energy is reduced by one order of magnitude, independently of the population analyses used. This demonstrates the importance of long‐range polarization in electronic‐structure calculations by fragmentation techniques.     

Near ab initio quality molecular electrostatic potential maps using hybridization displacement charges at PM3 level and effects of geometrical changes in amino groups

Charge distributions, dipole moments, and molecular electrostatic potentials (MEP) around several molecules consisting of carbon, nitrogen, oxygen, fluorine, sulfur, and chlorine atoms were studied using the PM3 semiempirical method and the results compared with those obtained using ab initio calculations at the RHF/6‐31G** level. Thus it is shown that relative MEP values near different atoms can be obtained using hybridization displacement charges (HDC) obtained by employing PM3 density matrices that usually agree quite satisfactorily with the ab initio ones. Further, positions of ab initio MEP minima are correctly located and the corresponding relative MEP values usually correctly predicted using the PM3(HDC) charges distributed continuously in three dimensions according to the forms of squares of valence s atomic orbitals. The necessary parameters for HDC calculations using the PM3 method were optimized. It is shown how within the frameworks of both PM3 and AM1 methods the π electrons or lone pairs associated with amino group nitrogen atoms and ring atoms can be satisfactorily treated in different situations. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 82: 299–312, 2001     

Modeling properties of the HF dimer in argon clusters

We compare geometry configurations, vibrational properties, and electronic structures of (HF)₂ in a free state and inside argon atom shells Ar_n. For the first stage, molecular dynamics calculations for the (HF)₂ · Ar₆₂ heterocluster are performed with the help of model potentials HF(SINGLE BOND)HF, Ar(SINGLE BOND)Ar, and Ar(SINGLE BOND)HF. Then, ab initio quantum chemistry analysis is carried out for the smaller systems (HF)₂ · Ar₁₅ and (HF)₂ · Ar₆ when keeping the argon atoms closest to the trapped dimer. We conclude that the hydrogen-bonded complex (HF)₂ gains some extra stability inside the argon shells, originating primarily from a decrease of intermolecular distance R_FF. Electronic structure calculations are in accord with the changes in dynamical properties, namely, a noticeable increase in the vibrational frequency assigned to the F(SINGLE BOND)F stretching mode (+25 cm⁻¹) and decrease in rms deviations for the corresponding coordinate δ_FF. In addition to these changes, the argon atoms of the nearest solvent shell donate a small fraction of electron charge which is spent for an increase of population of the antibonding orbital σ^* of the free monomer unit and shift orbital energies primarily of the lone-pair fluorine species. These shifts are greater than the changes due to geometry alterations and the possible inaccuracies of the calculation scheme. © 1997 John Wiley & Sons, Inc.     

Reevaluation of Bruice’s proximity orientation

Ab initio molecular orbital calculations at HF/6-31G, HF/6-31G (d,p) and DFT at B3LYP/6-31G (d,p) levels and molecular mechanics calculations of thermodynamic and kinetic parameters for Bruice’s systems 1-6 indicate that the remarkable acceleration in the cyclization of di-carboxylic semi-esters 1-6 is solely the result of a strain effect and not proximity orientation stemming from the ‘reactive rotamer effect’.     

Interplay between Molecular Recognition and Redox Properties: A Theoretical Study of the Inclusion Complexation of β-Cyclodextrin with Phenothiazine and its Radical Cation

The PM3 molecular orbital method was employed in the conformational analysis of the inclusion complexation of -cyclodextrin with phenothiazine and its radical cation from a complete and unrestricted geometry optimization. Ab initio calculations at the level of HF/3-21G(d) and B3LYP/3-21G(d) were utilized to determine the electronic structures of the host, guest and their complexes. The results indicated that the complexation of -cyclodextrin with the phenothiazineradical cation was significantly more favorable than that with the neutral one, in good agreement with the experimental observation. The charge-transfer interaction was proposed as a physical reason for such behavior. It is suggested that caution should be given when extrapolating one oxidation state behavior to the supramolecular systems in their other oxidation states.     

Electrostatic field-adapted molecular fractionation with conjugated caps for energy calculations of charged biomolecules

An electrostatic field-adapted molecular fractionation with conjugated caps (EFA-MFCC) approach is implemented for treating macromolecules with several charge centers. The molecular fragmentation is performed in an "electrostatic field," which is described by putting point charges on charge centers, directly affecting the Hamiltonians of both fragments and conjugated caps. So the present method does not need truncation during the calculation of electrostatic interactions. Our test calculations on a series of charged model systems and biological macromolecules using the HF and B3LYP methods have demonstrated that this approach is capable of describing the electronic structure with accuracy comparable to other fragment-based methods. The EFA-MFCC approach is an alternative way for predicting the total energies of charged macromolecules with acyclic, loop, and intersectional loop structures and interaction energies between two molecules.     

Interaction of low-energy ions and atoms of light elements with a fluorinated carbon molecular lattice

The mechanism of interaction of low-energy atoms and ions of light elements (H, H+, He, Li, the kinetic energy of the particles 2-40 eV) with C6H6, C6F12, C60, and C60F48 molecules was studied by ab initio MD simulations and quantum-chemical calculations. It was shown that starting from 6 A from the carbon skeleton for the "C6H6 + proton" and "C60 + proton" systems, the electronic charge transfer from the aromatic molecule to H+ occurs with a probability close to 1. The process transforms the H+ to a hydrogen atom and the neutral C6H6 and C60 molecules to cation radicals. The mechanism of interaction of low-energy protons with C6F12 and C60F48 molecules has a substantially different character and can be considered qualitatively as the interaction between a neutral molecule and a point charge. The Coulomb perturbation of the system arising from the interaction of the uncompensated proton charge with the Mulliken charges of fluorine atoms results in an inversion of the energies of the electronic states localized on the proton and on the C6F12 and C60F48 molecules and makes the electronic charge transfer energetically unfavorable. On the different levels of theory, the barriers of the proton penetration for the C6F12 and C60F48 molecules are from two to four times lower than those for the corresponding parent systems (C6H6 and C60). The penetration barriers of the He atom and Li+ ion depend mainly on the effective radii of the bombarding particles. The theoretical penetration and escaped barriers for the "Li+ + C60" process qualitatively explain the experimental conditions of synthesis of the Li@C60 complex.     

Charge transfer in systems of conjugated bonds in cyanobiphenyl molecules: Quantum-chemical calculations of the structure and vibrational spectra

Quantum-chemical calculations of the IR absorption spectra and geometric and electronic structure of cyanobiphenyl molecules

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(I) were performed for various angles between benzene ring planes by the B3LYP/6-31+G** method. It was shown that the stablest conformation of I (X=OCH₃, OC₃H₇) should be the twist conformation with α= 37°, which was in agreement with the gas-phase experimental data. Rotation of benzene rings with respect to each other changed the relative orientation of the interacting π orbitals of the bridge ring carbon atoms and caused charge redistribution over molecule atoms, in particular, over terminal X and CN group atoms. The calculated period of charge oscillations on the alkyl and nitro groups coincided with the period of reversible charge transfer (～5–10 fs) between the conjugated subsystems (benzene ring + substituent) observed as the α angle changed. The rate of charge transfer between the electron donor and electron acceptor groups was calculated to be (3–6)×10⁵ m/s. Charge oscillations on benzene ring carbon atoms and donor and acceptor groups did not cause similar dipole moment oscillations and vibrations in the IR spectrum. The dipole moment of the molecule decreases as the angle between benzene ring planes increases, and the passage to the “perpendicular” conformation should increase the C≡N stretching vibration frequency by ～5 cm^?1 and decrease the intensity of the IR band by ～2 times. The elongation of the aliphatic chain in the X group did not cause noticeable changes in the geometric and electronic structure of the molecule.

     

Density functional calculation of conformations and potentials of internal rotation in polychlorinated biphenyls

Full geometry optimization for all 209 isomers of polychlorinated biphenyls (PCBs) and calculations of internal rotation potentials for 154 isomers have been performed by density functional method B3LYP/6-31G(d, p). Conformations and internal rotation barriers in PCBs were proved to depend on a number of chlorine atoms in ortho-positions and, less, the presence of chlorine atoms in adjacent meta-positions. Subject to the number of chlorine atoms in ortho-and adjacent meta-positions, 209 PCB isomers were classified into 18 groups, within each of them molecules having very close conformations and potentials of internal rotation. It makes possible to evaluate with high accuracy the potential functions of the last 55 PCB molecules for which potential curve calculations have not been made.     

Calculations of molecules,clusters, and solids with a simplified LCAO-DFT-LDA scheme

A simplified LCAO-DFT-LDA scheme for calculations of structure and electronic structure of large molecules, clusters, and solids is presented. Forces on the atoms are calculated in a semiempirical way considering the electronic states. The small computational effort of this treatment allows one to perform molecular dynamics (MD ) simulations of molecules and clusters up to a few hundred atoms as well as corresponding simulations of condensed systems within the Born-Oppenheimer approximation. The accuracy of the method is illustrated by the results of calculations for a series of small molecules and clusters. © 1996 John Wiley & Sons, Inc.