Showing papers in "Journal of Molecular Structure-theochem in 1996"

Gaussian basis sets for use in correlated molecular calculations. VI. Sextuple zeta correlation consistent basis sets for boron through neon

Abstract: The family of correlation consistent polarized valence basis sets (cc-pVXZ) has been extended to include sextuple zeta sets (cc-pV6Z) for the atoms boron through neon. Potential energy functions have been calculated with these sets for the electronic ground states of N2 and HF using a number of correlated wave functions: MP2, MP3, MP4, CCSD, CCSD(T) and CAS+1+2. Spectroscopic constants have been calculated for each level of theory and have been compared with experiment. Combining these results with those of prior studies, complete basis set limits have been estimated for Ee, De and re. It is found that the cc-pV6Z basis sets yield dissociation energies that are within 0.6–0.8 kcal mol−1 (N2) and 0.1 kcal mol−1 (HF) of the estimated CBS limits. Adding core-core and core-valence contributions to the CCSD(T) CBS limits yields De's that are within 0.1 kcal mol−1 of the experimental values.

Thermodynamical properties of solids from microscopic theory : applications to mgf2 and al2o3

Abstract: We have recently developed a non-empirical Debye-like model for the inclusion of thermal effects in the equation of state (EOS) of solids. This model allows the calculation of many thermodynamical properties from the E-V relationship. We report the results of a theoretical investigation that explores the EOS of two ionic solids: MgF2 and Al2O3. The interionic interactions are modelized using either the ab initio Perturbed Ion (aiPI) method or the electron gas formalism along with aiPI electronic wavefunctions, which are allowed to relax with crystal strains. Our EOS results are in overall good agreement with experimental data. Other thermodynamic properties behave in the same way, although Gruneisen constant and related quantities have significant errors. This may be caused by numerical inaccuracies on the high order derivatives needed for its calculation.

Applications of level shift corrected perturbation theory in electronic spectroscopy

Abstract: Multiconfigurational second-order perturbation theory (CASPT2) with a level shift technique used to reduce the effect of intruder states has been tested for applications in electronic spectroscopy. The following molecules have been studied: formamide, adenine, stilbene, Ni(CO) 4 , and a model compound for the active site in the blue copper protein plastocyanin, Cu(Im) 2 (SH)(SH 2 ) + . The results show that the level shift technique can be used to remove the effects of the intruder states in all these molecules. In some cases a drift in the energies as a function of the level shift is observed, which however is small enough that the normal error bar for CASPT2 excitation energies (≈ 0.3 eV ) still holds.

Calculation of energy barriers for bond rupture in some energetic molecules

Abstract: A calculation of the energy for bond rupture for a number of energetic molecules using MNDO/3 indicates that the weakest bond is generally that between the NO 2 and the remainder of the molecule. A calculation of the energy barrier against RNO 2 scission in 26 molecules shows that there is correlation between the size of the energy barrier and the susceptibility to high-rate exothermic reaction (detonation). The correlation seems to be independent of bond type (CN, NN, ON) and thus independent of chemical family. The results suggest that RNO 2 rupture may be the rate-controlling step in the initiation of detonation of many energetic molecules.

Force field representation of the UO22+ cation from free energy MD simulations in water. Tests on its 18-crown-6 and NO3− adducts, and on its calix[6]arene6− and CMPO complexes

Abstract: We report a theoretical study of the UO22+ cation in aqueous solution, using an empirical 1-6-12 representation of the nonbonded interaction energies. Based on free energy perturbation FEP calculations, we first derive new parameters for UO22+ which account for its hydration free energy, compared with the Sr2+ cation (ΔG = 13.6 kcal mol−1). With the new parameters, we simulate the UO22+-2NO3− salt and the UO22+.18-crown-6 adduct which both dissociate in water, and the CMPO.UO2(NO3)2 complexes of 1:1 and 1:2 stoichiometries in which the ligand remains bound to UO22+. The complex of UO22+ with the calix[6]arene6− hexanion remains inclusive, and predicted by free energy simulations to be more stable than the Sr2+ complex.

Theoretical studies of the methyl rotational barrier in toluene

Abstract: We report computations of the rotational barrier of the methyl group in toluene. The computations are based on the use of the gaussian 92 Program Package with the 6-311G∗∗ basis set. The results are 2.69 wavenumbers at the HF level of approximation and 5.02 wavenumbers at the MP2 level. These results compare favorably with the experimental value of 4.9 wavenumbers. It is shown that inclusion of the vibrational zero-point energy in the calculations is necessary for obtaining satisfactory results.

Cooperative effects in water trimers. The performance of density functional approaches

Abstract: The performance of B-LYP, B3-LYP, B3-P86 and B3-PW91 density functional to describe cooperative effects in water trimer was investigated. The geometries and vibrational frequencies of the monomer, the dimer and the trimer were obtained using a 6-31+G(d,p) basis set, while the final energies were calculated at the 6-311++G(3df,2p) level. Our results show that B3-LYP and B-LYP functionals seem to be a good alternative to ab initio calculations to account for cooperative or non-pairwise effects, either if these effects are measured in terms of additive interaction energies or in terms of the so-called cooperativity factors.

Some Properties of the Coupling Coefficients of Real Spherical Harmonics and Their Relation to Gaunt Coefficients

Abstract: Spherical harmonics are of considerable importance for computations involving basis functions corresponding to large values of the angular momentum quantum number l. Their use allows efficient coding of programs involving such basis functions because the formulae of the coupling coefficients are simple. The choice of real spherical harmonics allows one to avoid the use of complex quantities in computer programs that increase storage and CPU time requirements. In this paper, certain properties of the coupling coefficients for real spherical harmonics are derived that are necessary for an efficient computation of coupling terms.

The evaluation of nitrogen containing bond dissociation energies using the ab initio and density functional methods

Abstract: The NH, NN, and CN bond dissociation energies of amines and hydrazines are computed using the ab initio (ROHF and MP2) and the density functional theory (DFT) methods (BHandH, BHandHLYP, Becke3LYP, Becke3P86, BLYP and BP86) with the 6-31 + G(d) basis set. The computed energies are compared to the experimental results and the suitability of the DFT methods, for the computational study of these systems, is discussed.

A theoretical study of CO2 adsorption on TiO2

Abstract: This paper presents a theoretical study of the interaction of CO2 with the rutile TiO2 surface. The calculations are performed using the periodic Hartree-Fock crystal program. Several modes for the adsorption are investigated. On the bare surface at θ = 1 2 , the best adsorption mode is obtained when the CO2 molecule is vertically adsorbed over a titanium atom; at saturation, the CO2 molecules are tilted toward the surface; then, the adsorption mode is also controlled by the adsorbate-adsorbate interactions. Another adsorption mode, competitive with the first one, corresponds to a parallel CO2 molecule over two titanium atoms. The adsorption over an oxygen atom of the oxide is weak. On the hydrated surface, the presence of hydroxyl groups favors the CO2 adsorption and leads to the formation of adsorbed bicarbonate ions.

Theoretical study on pyrolysis and sensitivity of energetic compounds. (2) Nitro derivatives of benzene

Abstract: The UHF-SCF-AM1 method has been employed to study the pyrolysis mechanism and impact sensitivity of nitro derivatives of benzene. Potential energy curves, transition states and activation energies of seven pyrolysis initiation reactions (homolysis of CNO2 bond into radicals) have been obtained here first. The molecular geometries of reactants, transition states and products of the seven reactions were fully optimized. It is found that there is a good linear relationship between the activation energies and bond orders of the weakest bond CNO2 in the molecule of each reactant. The linear correlation coefficient is 0.996. This result gives “the principle of the smallest bond order” powerful support and shows that the activation energy can also be used as a dynamic criterion of impact sensitivity.

The density functional theory investigation of the equilibrium structures of OOF, FOOF, OOF2, and FOOOF

Abstract: The structures of oxygen-fluoride molecules that are known to be problematic for computation were studied using the density functional theory (DFT) methods. The Local (SVWN), hybrid (BECKE3LYP, BECKE3P86), and nonlocal (BLYP, BP86) DFT methods were used with the 6-311++G(2d) Gaussian type basis set. The structures were compared with those generated using the ab initio calculations, and when possible the experimental data. The suitability of the DFT methods for the theoretical study of these molecules is discussed.

Spin-orbit coupling constants of transition metal atoms and ions in density functional theory

Abstract: Spin-orbit coupling constants for various orbitals of first-, second- and third-row transition metal atoms and ions have been calculated using a quasi-relativistic density functional method reported earlier by us. Our results are comparable with the fully relativistic Dirac-Hartree-Fock method and with available experimental values.

Computation of structures of phosphorus fluorides with ab initio and density functional methods

Abstract: Extensive ab initio and density functional theory (DFT) calculations were performed on phosphorous fluorides in order to obtain a reliable theoretical model to reproduce their experimentally determined structures and dissociation energies. ROHF and MP2 were used as ab initio methods while from DFT calculations, a set of local, hybrid, and non-local methods were utilized. To assure a valid comparison, all calculations were performed with 6-311G(d) as a middle-size basis set. Advantages and disadvantages of DFT methods for computation of these systems are presented.

Density functional theory and ab initio study of bond dissociation energy for peroxonitrous acid and peroxyacetyl nitrate

Abstract: Geometries and energies of two nitro peroxides, HOONO2 and CH3COOONO2 are calculated by two common ab initio (ROHF and MP2), local (SVWN), four hybrid (BHandH, BHandHLYP, Becke3LYP, and Becke3P86) and two non-local (BLYP and BP86) density functional theory (DFT) methods. In all calculations standard GAUSSIAN-type basis sets [6-31+G(d) and 6-311++G(3df,3pd)] are used. Based on the comparison of computed and experimental values both Becke3LYP hybrid and BLYP non-local DFT methods generate energies that are in excellent agreement with experimental values. The suitability of other methods for computing these and similar molecules are discussed.

An ab initio study of the molecular properties of the acetylene-HX hydrogen complexes

Abstract: MP2/6–311++G∗∗ ab initio molecular orbital calculations indicate that larger ΔQcorr intermolecular charge transfer values are associated with stronger hydrogen bonds in the acetylene-HX complexes where X is F, Cl, CN, NC or CCH. The MP2/6–311++G∗∗ H-bond lengths are in very good agreement with the corresponding experimental values. The HX stretching frequency is shifted downward upon H-bond formation. Its displacement shows an excellent linear correlation with the intermolecular charge transfer, in agreement with the experimental behaviour previously observed in such complexes. As expected, the more pronounced effect on the IR intensities occurs with the HX stretching intensity, and it is much enhanced after complexation owing to the charge-flux term. The new low-frequency vibrational modes arising from complexation show several interesting features and their normal modes are schematically described herein.

Pseudorotation in heterocyclic five-membered rings : tetrahydrofuran and pyrrolidine

Abstract: Using the 6-31G ∗∗ basis set, the HF-SCF and Moller-Plesset second-order (MP2) perturbation calculations have been carried out for tetrahydrofuran (THF) and pyrrolidine (PY) with the symmetries given by pseudorotation. On the whole, the MP2 calculations give better results on the puckered structures and energetics of both molecules, which are consistent with diffraction and spectroscopic results. From the MP2/6-31G ∗∗ calculations, the twist conformation 4 T 3 is found to be the most stable one for THF, and the twist 1 T 2 ( ax ) and the envelope 1 E( ax ) forms appear to be energetically identical and most feasible for PY. We investigate the correlation between the puckering amplitudes and the sum of deviations of endocyclic bond angles from the standard value. The better correlation may support that the revised pseudorotation model proposed here is more appropriate to describe the puckering of non-equilateral five-membered rings than earlier models.

Quantum-chemical evaluation of energy quantities governing electron transfer kinetics: applications to intramolecular processes

Abstract: Important energy quantities governing electron transfer (ET) kinetics in polar solutions (reorganization energy, Er, and net free energy change, ΔU) are evaluated on the basis of quantum-chemical self-consistent reaction-field (SCRF) models. Either self-consistent field (SCF) or configuration interaction (CI) wavefunctions are used for the solute, which occupies a molecular cavity of realistic shape in a dielectric continuum. A classical SCRF model together with unrestricted Hartree-Fock SCF wavefunctions based on the semiempirical PM3 Hamiltonian is applied to the calculation of the solvent portion of Er (denoted Es) for two different series of radical ion ET systems: radical cations and anions of biphenylyl/naphthyl donor/acceptor ( D A ) pairs linked by cyclohexane-based spacer groups and trans-staggered radical anions of the type (CH2)2m, m = 2–5. Results for Es based on two-configurational CI wavefunctions and an alternative reaction field (the so-called Born-Oppenheimer model, which recognizes the fast timescales of solvent electrons relative to those involved in ET) are also noted. Results for inner-sphere (i.e. intra-solute) reorganization, Ei, and for ΔU are also reported. The semiempirical Es results are quite similar to corresponding ab initio results and display the form of the two-sphere Marcus model for Es as a function of D A separation. Nevertheless, in the one case where direct comparison is possible, the calculated Es result is more than twice the magnitude of the estimate based on experimental ET kinetic data. To reconcile this situation, a generalized SCRF model is proposed, which assigns different effective solute cavity sizes to the optical and inertial components of the solvent response, using ideas based on non-local solvation models.

Hyperconjugation as it affects conformational analysis

Abstract: A primer for the qualitative identification and quantitative analysis of hyperconjugative delocalization is presented. The particular focus is upon the influence of hyperconjugation as it affects conformational analysis. Computational methodologies are illustrated within the context of several diverse molecular systems: anomeric and reverse anomeric effects in 2-tetrahydropyranosylammonium, generalized anomeric effects in phosphorus-stabilized carbanions, and hyperconjugative effects in phosphorus- and silicon-based trigonal bipyramids. Hyperconjugation is shown to compete with apicophilicity in the final examples. Although the latter influence has long been accounted for in traditional conformational analysis of trigonal bipyramidal systems, the former has been less appreciated.

Solvent and counterion effects on Na+Cs+ complexation selectivity by conformationally locked calix[4]-bis-crown ligands: Molecular Dynamics and Free Energy Perturbation studies in water and methanol, acetonitrile and chloroform solutions

Abstract: Calix[4]arene-bis-crown ligands (L), conformationally locked in the 1,3-alternate conformation, display remarkable ionophoric properties with respect to alkali cations (M + ). Of particular interest is the large Cs + Na + binding selectivity displayed by calix[4]-bis-crown-6, in separating radioactive Cs + from nuclear waste. Based on Molecular Dynamics and Free Energy Perturbation simulations, we report a consistent comparison of Na + , K + , Rb + and Cs + complexes in four different solvents (water, methanol, acetonitrile and chloroform) and in the gas phase, in order to elucidate solvent effects on structures and stabilities of these complexes. We predict that Cs + is complexed by calix[4]-bis-crown-6 better than Na + in water and methanol and acetonitrile solutions, whereas in chloroform and in the gas phase, Na + is preferred. Also, calix[4]-bis-crown-5 hosts are predicted to bind selectively Na + in chloroform, but K + or Rb + in methanol. Additionally, our studies on calix[4]-bis-crown-6 involve: 1. (i) the effect of a picrate counterion on structures and selectivities; 2. (ii) the role played by the hydrophobic p-t-butyl substituents; 3. (iii) modelling of ditopic bis-cation 2M + complexes.

An ab initio study of terminal SiOH and bridging Si(OH)Al groups in zeolites and their interaction with carbon monoxide

Abstract: Ab initio calculations have been performed at both levels SCF and second-order Moller-Plesset theory, using double-zeta plus polarization basis set, to investigate the complexes formed between CO and both terminal and bridging OH groups in zeolites. These are mimicked by H-saturated minimal-size clusters, H3SiOH (SIL) and H3SiOHAlH3 (BRO), respectively. Interaction is considered through both the carbon and oxygen ends of CO. The SCF treatment yields unreliable energies of interaction: in contrast with experiment, C-bound complexes are less stable than those O-bound. Semi-quantitative agreement with experiment is instead reached for the vibrational features. Electron correlation considerably stabilizes bonding via the C-end and yields vibrational frequencies in better agreement with experiment. Complexes with BRO are much more stable than with SIL: accordingly, the calculated frequency shifts for OH and CO stretching vibrations are much larger for complexes with BRO than for SIL. The in-plane and out-of-plane O H bending vibrations are sensitive to complex formation, as is the OH stretching vibration. This latter has been studied both in the harmonic and anharmonic approximations, by numerically solving the related Schrodinger equation, for both free and CO-interacting SIL and BRO species. Unpublished experimental data are reported concerning the change in anharmonicity brought about in SiOH and Si(OH)Al by CO complexation. In full agreement with experiment, interaction does not cause any change of anharmonicity with SIL, and a moderate increase with BRO.

Molecular modeling methodology of β-cyclodextrin inclusion complexes

Abstract: A docking approach for molecular mechanics optimization of β-cyclodextrin complexes is described Because of the specific geometry of the cyclodextrins and the class of guests (relatives of tert-butyl benzene), the guest molecule is moved along a vector going through the middle of the cavity This vector is perpendicular to the mean plane of the acetal oxygen atoms that link the glucose units At each step along this vector, the geometry of the bimolecular assembly was optimized to give a minimum in the molecular mechanics steric energy As expected, the energy decreases as the guest molecule enters the cyclodextrin cavity, and again increases as the guest exits from the other side of the cavity Rotation of the guest within the cavity prior to energy minimization did not result in lower energies; the minimization process found the best rotational orientation of the guest On the other hand, it was necessary to drive the guest along the vector; the energy minimization process did not pull the guest into an optimal depth of penetration into the cavity The binding energies calculated at two different dielectric constants were almost identical, indicating that the complex formation is stabilized by dispersive or Van der Waals forces and not electrostatic (dipole-dipole or hydrogen bonding) forces

Comparison of density functional calculations of CNO2, NNO2 and CNF2 dissociation energies

Abstract: We compare the effectiveness of three exchange/correlation functional combinations (Becke/Lee, Yang and Parr; Becke-3/Lee, Yang and Parr; Becke-3/Perdew-Wang 91) for computing CNO 2 , NNO 2 and CNF 2 bond lengths and dissociation energies. The Becke-3/Perdew-Wang 91 is found to give the best results, although for CNF 2 bonds the differences are less important than for CNO 2 and NNO 2 . The presence of NO 2 and NF 2 on the same carbon considerably weakens the bond to each.

Peptide models XIX: Side-chain conformational energy surface and amide I vibrational frequencies of N-formyl-l-phenylalaninamide (For-Phe-NH2) in its γL or γinv or C7eq backbone conformation

Abstract: In a study of cross sections of the E = ƒ(χ1,χ2) side-chain conformational potential energy surface of the γL or c7eq backbone conformation of For-l-Phe-NH2, it was found that there are three conformations (g +, a and g −) due to rotation about the Cαχ1 Cβ bond. It should be emphasised that the γL backbone conformation is conserved during rotation about χ1. However, there is only one unique conformation along the rotation about the Cβχ2 Ph bond. The CH2Ph group showed greater stabilisation, with respect to hydrogen (Gly), than the CH3 (Ala) or CH2OH (Ser) substituents. The hydrogen-bonded CO (amide 1) vibrational frequency is split into two bands due to the coupling of the CO stretching and NH2 scissoring modes of motion. The other carbonyl, not involved in hydrogen bonding, has a characteristic single IR band with a relatively high frequency. The orientation of the Ph group has no appreciable effect on these vibrational frequencies.

A pseudrotation model and ring-puckering of cyclopentane

Abstract: We propose a pseudorotation model for a five-membered ring with the amplitude of the puckering angles and the phase angle. This model is appropriate for constructing the accurate geometry of cyclopentane with the specified puckering parameters and constrained endocyclic bond lengths. In order to evaluate the propriety of this model, conformational analysis for cyclopentane was extensively carried out using the molecular mechanics, semiempirical, and ab initio methods and the results were compared with those of previous studies. The puckering amplitude, given by puckering angles, appears to be linearly proportional to the amplitudes of Cremer-Pople and Altona and co-workers. Our results on the puckering amplitudes of low energy conformations and the barriers to conformational changes for cyclopentane are consistent with those of experiment.

Systematic search in conformational analysis

Abstract: The coupling of conformation to activity and reactivity is a widely accepted concept, and as such has driven the development of tools which execute conformational searches in rapid and robust fashion [T.F. Havel, Prog. Biophys. Molec. Biol., 56 (1991) 43–78; A.R. Leach, In Rev. Comput. Chem.; K.B. Lipkowitz and D.B. Boyd, Ed.; VCH Publishers, Inc.: New York, N.Y., 1991, Vol. II, pp. 1–55]. Among the aims of these methods are the determination of a complete set of local minima from which the global energy minimum can be identified, or the generation of conformations consistent with constraints derived from SAR or structural studies. Most methods fall into two broad categories: those which are random or stochastic, and those which are systematic. Yet another group consists of those which are based on heuristics and artificial intelligence [A.R. Leach, K. Prout, D.P. Dolata, J. Comput. Chem. 11 (1990) 680–693]. The first category is typified by molecular dynamics [W.F. van Gunsteren and H.J.C. Berendsen, Angew. Chem. Int. Ed. Eng., 29 (1990) 992–1023], Monte Carlo [M.P. Alien and D.J. Tildesley, Computer Simulation of Liquids, Oxford Science Publications, 1989], distance geometry [J.M. Blaney and J.S. Dixon, in K.B. Lipkowitz and D.B. Boyd (Eds.), Reviews in Computational Chemistry, VCH, New York, Vol. 5, pp. 299–335, 1994], and other approaches [M. Saunders, J. Comput. Chem., 10 (1989) 203–208] in which the path by which conformational space is examined is ideally completely random, but bounded by the geometries of covalent bond lengths and angles. In traditional systematic searches, the variable to be examined, e.g. torsion angles, is divided into a regular grid. Each and every grid point is evaluated in a systematic fashion to determine its validity. The path through the grid points is regular and defined. In principle, systematic search can, within the resolution of the grid, identify all sterically allowed conformations of a molecule. Consequently, systematic search is an ideal tool for conformational analysis because it is not path dependent and cannot become entrapped in local minima. In this article we review some of the basics of systematic search, algorithmic improvements that have enhanced its speed, and new developments that have increased its accuracy by moving away from the limitations of a fixed torsional grid.

Modelling the vibrational behaviour of the cyclic carboxylic acid dimer. SQM force field of the formic acid dimer

Abstract: The vibrational behaviour of the cyclic carboxylic acid dimer is modelled through the scaled quantum mechanical (SQM) force field of the cyclic formic acid dimer. The results indicate that the SQM force field technique is very well applicable to hydrogen bonded molecules. The frequency shifts observed on hydrogen bonding can be related to the shifts observed on lowering the temperature. This study also confirms that a clear distinction between cyclic carboxylic acid dimers and catamers can be made through the difference between infrared and Raman frequencies, and it is proved here that these conditions are also valid for weaker hydrogen bonded cyclic carboxylic acid dimers.

Electron correlation effects in position and momentum space: the atoms Li through Ar

Abstract: Electron correlation effects on the electronic structure of atoms were investigated by means of a variety of position and momentum space related properties such as radial one-electron densities and radial electron momentum densities, Compton profiles and radial electron pair distributions. The results were obtained from MR-SDCI wavefunctions utilizing very large basis sets and are discussed in a comparative manner, analysing characteristic features and trends.