Ab Initio 6-31G Research Articles

The computation of the potential energy surface for H2 + OH → H2O + H using ab initio and density functional theory methods

The reaction energy profile for H2 + OH → H + H2O was computed using HF, MP2, MP4, QCISD, G1, G2, and G2MP2 ab initio methods. In addition, the B3LYP, B3P86, B3PW91, BLYP, BP291, and SVWN density functional theory (DFT) methods were also used. All the ab initio methods, with the exception of the G series, produced much higher activation barriers and heats of reaction than the experimental values. On the other hand, the DFT methods produced negative forward and reverse barriers which were too low, with the exception of the hybrid DFT methods. The G2 ab initio method generated energies which deviated from the experimental values by ∼ 1 kcal/mol and therefore should be considered a very accurate computational method. The hybrid DFT methods produced positive forward reaction barriers with energies that were 2–4 kcal/mol lower than the experimental values. The geometries of the transition state and energies computed by the ab initio and DFT methods were compared. These results suggest that, in the hybrid exchange functional, the portion of the Slater exchange term should be increased. This may be the reason why the computed energies were too low. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 62: 639–644, 1997

The computation of the potential energy surface for H2 + OH ? H2O + H using ab initio and density functional theory methods

The reaction energy profile for H2 + OH H + H2O was computed using HF, MP2, MP4, QCISD, G1, G2, and G2MP2 ab initio methods. In addition, the B3LYP, B3P86, B3PW91, BLYP, BP291, and SVWN density functional theory (DFT) methods were also used. All the ab initio methods, with the exception of the G series, produced much higher activation barriers and heats of reaction than the experimental values. On the other hand, the DFT methods produced negative forward and reverse barriers which were too low, with the exception of the hybrid DFT methods. The G2 ab initio method generated energies which deviated from the experimental values by ∼ 1 kcal/mol and therefore should be considered a very accurate computational method. The hybrid DFT methods produced positive forward reaction barriers with energies that were 2–4 kcal/mol lower than the experimental values. The geometries of the transition state and energies computed by the ab initio and DFT methods were compared. These results suggest that, in the hybrid exchange functional, the portion of the Slater exchange term should be increased. This may be the reason why the computed energies were too low. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 62: 639–644, 1997

Molecular structure of S-ethylthioacrylate Combined vibrational spectroscopic and ab initioSCF-MO study

Ab initio 6-31G* SCF-MO calculations have been carried out on S-ethyl thioacrylate [CH2CHC(O)SCH2CH3]. Fully optimized geometries, relative stabilities, dipole moments and harmonic force fields for several conformers of this molecule have been determined and the results compared with those for similar molecules. Together with FTIR and Raman spectroscopic data, the theoretical results demonstrate that S-ethyl thioacrylate exists in two different conformations about the Cα–C bond (the s-cis and s-trans forms, with CC–CO dihedral angles equal to 0° and 180°, respectively); the s-cis conformation being more stable than the s-trans form by ca. 6 kJ mol-1 for the isolated molecule. Comparison of the experimental and theoretical vibrational spectra confirms that, as concluded from our previous study on the analogous trans-S-ethyl thiocrotonate molecule (R. Fausto, P. J. Tonge and P. R. Carey, J. Chem. Soc., FaradayTrans., 1994, 90, 3491), the presence of the s-trans isomer of an α,β-unsaturated thioester can be successfully monitored by the IR band at ca. 1170 cm-1, ascribed to the Cα–C stretching mode of this form. In addition, we were also able to identify some IR bands sensitive to the conformation of the ethyl group that may be used as spectroscopic probes to study conformational equilibria associated with this internal degree of freedom in more complex S-ethyl thioesters.

NMR spectroscopic and theoretical structural analysis of 5,5-disubstituted hydantoins in solution

The 1H, 13C and (partly) the 15N NMR spectra of a number of 5,5-disubstituted hydantoins were recorded and assigned by the various methods of 1D and 2D NMR spectroscopy. Employing the NMR parameters, thus obtained, the NOEs between the different protons within the molecules and the results of accompanying semiempirical (AM1 and PM3, respectively) and ab initio (3-21G and, when sulfur atom is present, 3-21G∗) quantum chemical calculations the tautomerism, the acidity, the stereochemistry and the π-electron density distribution along the hydantoin molecule was studied.

Crystal structure determination and ab initio molecular structure prediction for exo,exo-α-P4Se3(CN)2 , the first phosphorus selenide cyanide

Bicyclic exo,exo-α-P 4 Se 3 (CN) 2 1 was made by reaction of α-P 4 Se 3 I 2 with AgCN, and its crystal structure determined from X-ray data collected at 160 K. Molecular structures were predicted for exo,exo-α-P 4 Se 3 (CN) 2 , exo,exo-α-P 4 S 3 (CN) 2 and P 2 Se 5 2 by restricted Hartree–Fock ab initio molecular-orbital calculations using STO-3G, 3-21G* and LanL2DZ(d) ECP basis sets, and for P 2 Se 5 additionally using Ahlrichs’ split-valence and triple-zeta valence basis sets. Comparisons with the crystal structure of exo,exo-α-P 4 Se 3 (CN) 2 and with a previously published crystal structure of P 2 Se 5 showed that the 3-21G* basis sets gave sufficiently good predictions for most bond angles that the effects on them of intermolecular interactions in the crystals could be discussed.

An accurate evaluation of activation barriers for hydrogen abstraction reactions with Becke's 88 density functional theory and high-level G1 and G2 ab initio methods

The activation barriers for computationally difficult radical abstraction reactions with small radicals were studied with Becke's 88 density functional theory (DFT) and G1 and G2 ab initio methods. Although many DFT methods produced negative activation barriers, Becke's 88 DFT methods generated activation barriers which are even closer to experimental values than are ones computed by the G2 ab initio method. Therefore, it was suggested that HFB/6-311G(2d, 2p) should be the method of choice for the DFT study of hydrogen radical abstraction reactions with small radicals. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 65: 75–82, 1997

An accurate evaluation of activation barriers for hydrogen abstraction reactions with Becke's 88 density functional theory and high‐level G1 and G2 ab initio methods

The activation barriers for computationally difficult radical abstraction reactions with small radicals were studied with Becke's 88 density functional theory (DFT) and G1 and G2 ab initio methods. Although many DFT methods produced negative activation barriers, Becke's 88 DFT methods generated activation barriers which are even closer to experimental values than are ones computed by the G2 ab initio method. Therefore, it was suggested that HFB/6-311G(2d, 2p) should be the method of choice for the DFT study of hydrogen radical abstraction reactions with small radicals. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 65: 75–82, 1997

Theoretical Modelling of Mass Spectrometric Behaviour of Peptides: Singly and Doubly Protonated Tetraglycine

Neutral, singly- and doubly protonated tetraglycines have been studied by semiempirical (MNDO) and ab initio (3-21G) methods to model the mass spectral behaviour of singly- and doubly protonated oligopeptides. The favourable bond cleavages in the ions were investigated by using bond orders and energy partitioning values. The most favourable protonation site in singly charged tetraglycine is the N-terminal amine nitrogen. In the doubly protonated forms, protonation at the N- and C-terminal residues is the most favourable energetically, minimizing Coulombic repulsion. Protonation at the amide nitrogen results in a significant weakening of the corresponding amide bond, leading to b+ ion formation from the singly protonated forms, and y+ and b+ or alternatively b2+ ion (ion nomenclature according to P. Roepstorff and J. Fohlman, Biomed. Environ. Mass Spectrom., 11, 601 (1984)) formation from the doubly protonated forms. The critical energy of fragmentation is much lower in the doubly protonated species compared to the singly protonated ones showing the effect of charge repulsion. The relative positions of the two protonated sites also influences the bond cleavages. Most surprisingly, the extended beta-sheet structure, in which the distance between charges is maximized, is not stable, and collapses into a folded conformation, where internal solvation competes successfully with charge repulsion. This suggests that multiply protonated peptides may, generally, have folded and not extended ("linear') structures in the gas phase.

Theoretical Modelling of Mass Spectrometric Behaviour of Peptides: Singly and Doubly Protonated Tetraglycine

Neutral, singly- and doubly protonated tetraglycines have been studied by semiempirical (MNDO) and ab initio (3-21G) methods to model the mass spectral behaviour of singly- and doubly protonated oligopeptides. The favourable bond cleavages in the ions were investigated by using bond orders and energy partitioning values. The most favourable protonation site in singly charged tetraglycine is the N-terminal amine nitrogen. In the doubly protonated forms, protonation at the N- and C-terminal residues is the most favourable energetically, minimizing Coulombic repulsion. Protonation at the amide nitrogen results in a significant weakening of the corresponding amide bond, leading to b+ ion formation from the singly protonated forms, and y+ and b+ or alternatively b2+ ion (ion nomenclature according to P. Roepstorff and J. Fohlman, Biomed. Environ. Mass Spectrom., 11, 601 (1984)) formation from the doubly protonated forms. The critical energy of fragmentation is much lower in the doubly protonated species compared to the singly protonated ones showing the effect of charge repulsion. The relative positions of the two protonated sites also influences the bond cleavages. Most surprisingly, the extended beta-sheet structure, in which the distance between charges is maximized, is not stable, and collapses into a folded conformation, where internal solvation competes successfully with charge repulsion. This suggests that multiply protonated peptides may, generally, have folded and not extended (linear') structures in the gas phase.

Quantum Molecular Modeling of the Interaction Between Guanine and Alkylating Agents - 2 - Nitrogen Mustard

The alkylation mechanism of guanine by nitrogen mustard (HN2) was studied by using a supermolecular modeling at the ab initio 6-31G level. Our computations show that interaction of guanine with the aziridinium form of HN2 necessitates a transition state for the N7 alkylation route. The pathway of N7-guanine alkylation by nitrogen and sulfur mustards is discussed on the basis of the Molecular Electrostatic Potential and HOMO-LUMO properties of these molecules.

Extension of MST/SCRF method to organic solvents:Ab initio and semiempirical parametrization for neutral solutes in CCl4

The self-consistent reaction field (SCRF) method proposed by Miertus, Scrocco, and Tomasi (MST) was extended to solutions of neutral solutes in CCl4. A detailed parametrization of the solute/solvent interface and of the “hardness” atomic parameters determining the van der Waals interactions was performed from comparison with experimental data and Monte Carlo simulations. The parametrization was carried out at both ab initio (6-31G*) and semiempirical (MNDO, AM1, PM3) levels. The MST/SCRF optimized versions provide accurate estimates of the free energy of solvation in CCl4 for the series of molecules studied. Furthermore, a precise description of the solvent effect on different chemical processes in CCl4 solution supports the reliability of the parametrization. © 1996 by John Wiley & Sons, Inc.

Optimization of the Lennard-Jones parameters for a combinedab initio quantum mechanical and molecular mechanical potential using the 3-21G basis set

A combined ab initio quantum mechanical and molecular mechanical (AI-QM/MM) potential for use in molecular modeling and simulation has been described. In this article, we summarize a procedure for deriving the empirical parameters embedded in a combined QM/MM model and suggest a set of Lennard-Jones parameters for the combined ab initio 3-21G and MM OPLS-TIP3P (AI-3/MM) potential. Interaction energies and geometrical parameters predicted with the AI-3/MM model for over 80 hydrogen-bonded complexes of organic compounds with water were found to be in good accord with ab initio 6-31G(d) results. We anticipate that the AI-3/MM potential should be reasonable for use in condensed phase simulations. © 1996 by John Wiley & Sons, Inc.

Diels-Alder Reactivity of a Keto Vinylphosphonate. Empirical and Theoretical Observations. Application to the Syntheses of Phosphonate Analogues of Myo-Inositol

Abstract The Diels-Alder reactivity of the keto vinylphosphonate 1 with furan, cyclopentadiene and E-1-acetoxy-1,3-butadiene was investigated with and without Lewis acid assistance. The acetyl group directed in each case. LUMO molecular orbital coefficients were obtained via ab initio (3-21G*) calculations, and support the experimental data. The Diels-Alder products from the reactions with furan and 1-acetoxybutadiene are being carried on to phosphonate analogs of inositols.

Electron Attachment to the Lowest Unoccupied Orbitals in Linear and Branched Permethylated Polysilanes and Hexamethyldigermane and -distannane

The peculiar properties of polysilanes have stimulated many studies of their electronic structure. While the nature and ordering of the filled MOs have been studied in some detail, the theoretical predictions for the empty counterparts have never been tested experimentally. Here the electron transmission spectra of Me(SiMe2)nMe (with Me = CH3 and n = 1−4), MeSi(SiMe3)3, Si(SiMe3)4, Ge2Me6, and Sn2Me6 are presented and the energies of the observed resonances allow assignment of the lowest unoccupied levels. With the change from monomers to dimers, the presence of a heteroatom−heteroatom bond causes a large electron affinity increase; the LUMO is ascribed to a σ* MO essentially heteroatom in character, whereas the lowest σ*C-heteroatom MOs lie at about 1.5 eV higher energy. The spectra of the linear trimer and tetramer of silicon show that the energy separation between the lowest-lying empty orbitals is even larger than that observed in their filled counterparts. The lowest-lying empty MOs are thus well delocalized on the silicon skeleton but not on the substituents. The resonance energies are also compared with the unoccupied orbital energies calculated by means of ab initio 3-21G* and MNDO methods. The results presented here do not support the previously proposed π* model based upon ab initio calculations.

Experimental and theoretical study of the intramolecular interactions determining the conformation of β-carbonyl sulfoxides

Information on the geometrical and electronic structures of α-methylsulfinylacetophenone, C6H5C(O)CH2S(O)CH3 2, have been obtained from X-ray diffraction analysis, UV photoelectron spectroscopy and ab initio 6-31G** calculations. A comparison of the results with those obtained from the spectra and the computations on α-methylthioacetophenone, C6H5C(O)CH2SCH3 1 and α-methylsulfonylacetophenone, C6H5C(O)CH2SO2CH3 3, together with previous results on β-keto sulfides and β-keto sulfones indicates that the CH2–S(O) bond in 2 is quasi-cis to the carbonyl group in the gas and solid phase, at variance with the other β-carbonyl thioderivatives which adopt a gauche conformation. Eigenvector analysis, electron charge distribution at various atoms and/or groups and geometric parameters indicate that the cis conformation of 2 is stabilized by a strong non-bonded interaction between the negatively charged carbonyl oxygen and the positively charged sulfur atom from which it is separated by a distance (2.8–2.9 A) much shorter than the sum of the van der Waals radii. The predominant charge transfer interaction in 3 and related sulfones occurs in the opposite direction (OSO2→ CCO). The inversion of the direction of the charge transfer (and the change of the cis/gauche orientation of the thio group) from sulfone to sulfoxide is associated with an increase of electron affinity of the thio group in the latter, and could explain its smaller thermal stability. Ab initio 3-21G* calculations on several conformations of the bis-thioderivatives C6H5C(O)CH(SCH3)S(O)CH3 4, C6H5C(O)CH(SR)SO2R (R = Me 5 and Ph 6) and C6H5C(O)CH(SOCH3)SO2CH3 7, together with X-ray diffraction (4, 6 and 7) and photoelectron spectroscopy (4) analyses confirmed the cis(SOR) and gauche(SR and SO2R) preferred orientation of the thio groups with respect to the carbonyl group as observed in the monosubstituted derivatives. In 4 and 7 the SSO atom is about 30° out of the cis plane [O(1)–C(2)–C(3)].

Solvent Effects in Chloroform Solution: Parametrization of the MST/SCRF Continuum Model

The suitability of the self-consistent reaction field (SCRF) strategy for the study of solutes in chloroform solution has been examined. The SCRF method developed by Miertus, Scrocco and Tomasi (MST) has been parametrized at both ab initio 6-31G* and semiempirical AM1, MNDO, and PM3 levels. The reliability of the MST/SCRF model has been assessed from the comparison with results derived from classical Monte Carlo−free energy perturbation simulations and from mixed Monte Carlo−quantum mechanical/molecular mechanical computations, as well as with experimental data. The parametrized MST/SCRF method estimates the free energy of solvation with a root-mean-square deviation of 0.4 kcal/mol from the experimental value for the molecules studied. Further confidence in the optimized method stems from its ability to reproduce the tautomeric change of 2- and 4-pyridone upon transfer from gas phase to chloroform and the partition coefficient for compounds not considered in the parametrization. The results indicate the suitability of the MST/SCRF model for the study of solvent effects in dilute chloroform solutions.

Theoretical study of C 24N 4 molecule

Both ab initio 6-31G, 3-21G and STO-3G basis sets and semiempirical PM3 and AM1 molecular orbital calculations are carried out on the C 24N 4 molecule of the T d symmetry group. Results on the fully optimized structure which constrained T d symmetry, molecular orbitals and vibrational frequency were obtained by both ab initio and semiempirical methods. The binding energy and various thermodynamic properties were also calculated via the PM3 and AM1 semiempirical methods. All the evidence of this work proves that the C 24N 4 molecule is stable and that its four six-membered rings with a remarkable delocalized C…C bond are similar to the related rings in the C 60 buckminsterfullerene structure.

Influence of Benzoannulation on the Molecular and Electronic Structures of Tetracyanoquinodimethanes

The molecular and electronic structures of TCNQ and its π-extended derivatives benzo-TCNQ and TCAQ have been investigated using the semiempirical PM3 method and ab initio 6-31G* calculations. The steric hindrance introduced by lateral benzoannulation determines the loss of planarity of the TCNQ moiety for benzo-TCNQ and TCAQ. For both molecules, the most stable conformation corresponds to a butterfly-type structure, in which the TCNQ ring adopts a boat conformation and the lateral benzene rings remain planar. This structure lies, at the 6-31G* level, 33.45 kcal/mol below the fully planar conformation and 17.50 kcal/mol below a second local minimum for TCAQ, while it only lies 3.35 kcal/mol below the planar structure for benzo-TCNQ. The geometries of the anions and dianions have been also optimized at the semiempirical and ab initio levels. Although reduction induces the aromatization of the TCNQ moiety, the anions of benzo-TCNQ and TCAQ remain nonplanar. The stability of the anions with respect to the neutral systems is thus calculated to decrease along the series TCNQ > benzo-TCNQ > TCAQ, thus explaining the decrease of the electron-acceptor properties along this series. For the dianions, the polycyclic skeleton is fully planar and the C(CN)2 groups are twisted out of the molecular plane. While the first two extra electrons are mostly incorporated into the C(CN)2 groups, the third electron added to form the trianion is shown to enter the central polyacenic unit for TCAQ. This result explains the formation of relatively stable trianions and tetraanions for TCAQ. PM3 calculations have been especially useful in characterizing the stationary structures located for each compound and have been used as a guide for 6-31G* calculations. PM3-optimized geometries are in good agreement with experimental X-ray data and 6-31G* results.

Halon Thermochemistry: Calculated Enthalpies of Formation of Chlorofluoromethanes

The ab initio G2, G2(MP2), CBS-4, CBS-Q, and BAC-MP4 methods have been used to calculate the enthalpies of formation of the series of four chloromethanes and six chlorofluoromethanes [CHxFyCl4-x-y, x = 0−3, y = 0−3]. Calculated values of ΔfH° using the first four ab initio methods exhibit comparatively large systematic negative errors compared with experimental values, up to −50 kJ/mol, which are nearly linearly dependent upon the number of C−F and C−Cl bonds in the molecule. It is found for the chlorofluoromethanes that the application of bond additivity corrections (BAC's) to the ab initio enthalpies effectively removes systematic errors in the calculations and yields values that are in close agreement with experimentally derived heats. The rms deviations of the corrected calculated enthalpies from the experimental values are 2.4, 2.6, 3.4, 4.7, and 3.8 kJ/mol for the G2(MP2), G2, CBS-Q, CBS-4, and BAC-MP4 methods, respectively. These deviations are lower than the rms errors (6.9 kJ/mol) in the experimental enthalpies. Therefore, it is concluded that any of these calculational procedures, together with bond additivity corrections to remove systematic error, may profitably be used to obtain accurate enthalpies of formation in chlorofluorocarbon species.

Molecular electronic properties of a series of 4-quinolinecarbinolamines define antimalarial activity profile.

A detailed computational study on a series of 4-quinolinecarbinolamine antimalarials was performed using the semiempirical Austin model 1 (AM1) quantum chemical method to correlate the electronic features with antimalarial activity and to illuminate more completely the fundamental molecular level forces that affect the function and utility of the compounds. Ab initio (3-21G level) calculations were performed on mefloquine, the lead compound in this series, to check the reliability of the AM1 method. Electron density in specific regions of the molecules appears to play the pivotal role toward activity. A large laterally extended negative potential in the frontal portion of the nitrogen atom of the quinoline ring and the absence of negative potential over the molecular plane are crucial for the potent antimalarials. These electrostatic features are likely to be the modulator of hydrophobicity or lipophilicity of the compounds and, hence, determine their activities. The magnitude of the positive potential located by the hydroxyl hydrogen atom also correlates with potent antimalarial activity. Two negative potential regions occur near the hydroxyl oxygen and piperidyl nitrogen atoms. The two negative potential regions and the positive potential located by the hydroxyl hydrogen atom are consistent with intermolecular hydrogen bonding with the cellular effectors. The present modeling study should aid in efficient designing of this class of antimalarial agents.