Ab initioSTO-3G optimization of planar,perpendicular, and twisted molecular structures of biphenyl

The complete molecular structure of biphenyl, characterized by 12 independent parameters, has been derived by ab initio gradient techniques using a STO -3G basis set for coplanar, perpendicular, and minimum energy conformations with the constraint of planar phenyl ring units and a C₂ symmetry axis along the CC interring bond. The minimum torsional angle obtained was ? = 38.63° with torsional energy barriers of 8.59 and 10.04 kJ/mol for ? = 0° and ? = 90°, respectively.     

The 6-31G++ basis set: An economical basis set for correlated wavefunctions

The 6-31G ⁺⁺ basis set is described. This basis set is very similar to the existing 6-31G ^** set but is somewhat smaller through the use of five (rather than six) second-order Gaussians (d functions) and has polarization function exponents optimized for correlated rather than Hartree–Fock wavefunctions. The performance of 6-31G ⁺⁺ is compared with that of the 6-31G ^** and 6-31G ^** basis sets through calculation of the geometries and atomization energies for the set of molecules LiH, FH, H₂O, NH₃, CH₄, N₂, CO, HCN, and HCCH.     

The performance of the new 6-31G(##) basis set: molecular structures and vibrational frequencies of transition metal carbonyls

The performance of the newly proposed 6-31G(##) basis set for calculating the equilibrium structure and vibrational frequencies of transition metal carbonyl complexes has been studied at the HF and DFT levels of theory. The 6-31G(##) basis set has been constructed by augmentation of the 6-31G basis set by diffuse and polarization functions, which are generated from the corresponding 6-31G basis AOs response functions obtained in the frame of propagator approach. The predicted values of bond distances and vibrational frequencies for the title compounds are in good agreement with the experimental data. The relative energies and HOMO-LUMO gaps were also estimated for the series of MCO complexes.     

Optimization of the Lennard-Jones parameters for a combined ab 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.     

The 3-21G(N*) basis set: An economical polarized basis set for ab initio studies on nitrogen-containing molecules

The 3-21G basis set shares with its older cousin, the 4-31G basis set, a tendency to overestimate valence angles at nitrogen atoms and to underestimate seriously barriers to inversion at such atoms. The 6-31G* basis set generally yields greatly improved results in these respects. It is here shown that, for a variety of molecules, supplementation of the 3-21G basis set at three- or two-coordinate nitrogen atoms with a set of six d-functions having exponent 1.0 leads to optimized geometries and inversion barriers at such nitrogen centers in good agreement with results obtained with the 6-31G* basis set. This supplemented basis set, designated as 3-21G(N*), also leads to calculated vibrational frequencies in good agreement with those calculated with the 6-31G* basis set. The 3-21G(N*) basis set offers an economical alternative to the 6-31G* basis set, particularly for molecules containing several first-row atoms other than nitrogen.     

Dynamical properties of liquid water from ab initio molecular dynamics performed in the complete basis set limit

Dynamical properties of liquid water were studied using Car-Parrinello [Phys. Rev. Lett. 55, 2471 (1985)] ab initio molecular dynamics (AIMD) simulations within the Kohn-Sham (KS) density functional theory employing the Becke-Lee-Yang-Parr exchange-correlation functional for the electronic structure. The KS orbitals were expanded in a discrete variable representation basis set, wherein the complete basis set limit can be easily reached and which, therefore, provides complete convergence of ionic forces. In order to minimize possible nonergodic behavior of the simulated water system in a constant energy (NVE) ensemble, a long equilibration run (30 ps) preceded a 60 ps long production run. The temperature drift during the entire 60 ps trajectory was found to be minimal. The diffusion coefficient [0.055 A2/ps] obtained from the present work for 32 D2O molecules is a factor of 4 smaller than the most up to date experimental value, but significantly larger than those of other recent AIMD studies. Adjusting the experimental result so as to match the finite-sized system used in the present study brings the comparison between theory and experiment to within a factor of 3. More importantly, the system is not observed to become "glassy" as has been reported in previous AIMD studies. The computed infrared spectrum is in good agreement with experimental data, especially in the low frequency regime where the translational and librational motions of water are manifested. The long simulation length also made it possible to perform detailed studies of hydrogen bond dynamics. The relaxation dynamics of hydrogen bonds observed in the present AIMD simulation is slower than those of popular force fields, such as the TIP4P potential, but comparable to that of the TIP5P potential.     

On the ab initio geometry optimization of molecular solutes

We present several variants of methods for the automatic search of optimum geometries of solutes via ab initio SCF procedures. The physical meaning of geometry optimization in solution is discussed. Advantages and disadvantages of the different variants are shown making use of calculations on the HF dimer with different basis sets, supplemented by information on the computational times. Suggestions for the most convenient strategies (which in part depend on the nature of the solute) are also done.     

Structure of liquid water at ambient temperature from ab initio molecular dynamics performed in the complete basis set limit

Structural properties of liquid water at ambient temperature were studied using Car-Parrinello [Phys. Rev. Lett. 55, 2471 (1985)] ab initio molecular dynamics (CPAIMD) simulations combined with the Kohn-Sham (KS) density functional theory and the BLYP exchange-correlation functional for the electronic structure. Unlike other recent work on the same subject, where plane-wave (PW) or hybrid Gaussian/plane-wave basis sets were employed, in the present paper, a discrete variable representation (DVR) basis set is used to expand the KS orbitals, so that with the real-space grid adapted in the present work, the properties of liquid water could be obtained very near the complete basis set limit. Structural properties of liquid water were extracted from a 30 ps CPAIMD-BLYP/DVR trajectory at 300 K. The radial distribution functions (RDFs), spatial distribution functions, and hydrogen bond geometry obtained from the CPAIMD-BLYP/DVR simulation are generally in good agreement with the most up to date experimental measurements. Compared to recent ab initio MD simulations based on PW basis sets, less significant overstructuring was found in the RDFs and the distributions of hydrogen bond angles, suggesting that previous plane-wave and Gaussian basis set calculations have exaggerated the tendency toward overstructuring.     

Ab initio study of the structures of polythionylphosphazene molecular mimics with H,Cl, and CH3 side groups: 3-21G* and 6-31G* Basis sets comparison

The stable structures of substituted polythionylphosphazene single chains have been modeled with small molecular compounds consisting of one repeat unit of the polymer. The geometrical parameters of the nonplanar “trans-cis” conformations of these molecular models are obtained using the ab initio molecular orbital theory. The substituents studies include hydrogen and chlorine atoms and methyl groups. Two basis sets, 3-21G * and 6-31G *, were used in the computations. We have found a very good agreement between the molecular geometries obtained from the two basis sets computations for the methyl-substituted model compounds. The agreement is not as good for the hydrogenated and especially for the chlorinated model compounds. The comparison seems to indicate that the 6-31G * is an essential basis set for the chlorinated compounds. The magnitude of the total dipole moments for these compounds ranges between 3.7 and 7.9 Debye. © 1995 John Wiley & Sons, Inc.     

Molecular conformations of methyl formate and methyl vinyl ether from ab initio molecular orbital calculations

Ab initio molecular orbital theory with minimal and extended basis sets and a flexible rotor geometric model has been used to investigate the rotational potential surfaces of methyl formate and methyl vinyl ether. For both molecules, the most stable structures (IA and IIA, respectively) are planar cis; additional potential minima are found which correspond to planar trans structures (IB and IIB). The latter lie respectively about 4—8 and 1—2 kcal mol^?1 above the corresponding cis rotational isomers. Methyl rotational barriers have been determined for cis and trans structures of each molecule. For trans methyl formate, there is a slight but unexpected preference for an eclipsed arrangement of the methyl group.     

Application of the ab initio Hartree-Fock-Slater method to the calculation of molecular conformations: Ozone and thiozone

The total statistical energy as provided by the ab initio Hartree-Fock-Slater method is tested as a measure of molecular conformation for ozone and thiozone. Comparison is made with single determinant Hartree-Fock calculations for the same molecules.     

Vibrational spectroscopic studies, conformations and ab initio calculations of 3,3,3-trifluoropropyltrichlorosilane

Infrared spectra of 3,3,3-trifluoropropyltrichlorosilane (CF3CH2CH2SiCl3) were obtained in the vapour, amorphous and crystalline solid phases in the range 4000-50 cm-1. Additional spectra in argon matrices at 5.0 K were recorded before and after annealing to 20-36 K. Raman spectra of the compound as a liquid were recorded at various temperatures between 298 and 210 K and spectra of the amorphous and crystalline solids were obtained. The spectra suggested the existence of two conformers (anti and gauche) in the fluid phases and in the matrix. When the vapour was shock-frozen on a cold finger at 80 K and subsequently annealed to 120-150 K, six weak or very weak Raman bands vanished in the crystal. Similar variations were observed in the corresponding infrared spectra after annealing and four very weak IR bands disappeared after crystallization. From intensity variations between 298 and 210 K of three Raman band pairs an average value Delta(conf)H degrees (gauche-anti)=6.1+/-0.5 kJmol-1 was obtained in the liquid. Annealing experiments indicate that the anti conformer also has a lower energy in the argon matrices. The conformational equilibrium is highly shifted towards anti in the liquid, and the low energy conformer also forms the crystal. The spectra of the abundant anti conformer and the few bands ascribed to the gauche conformer have been interpreted. Ab initio calculations at the HF/6-311G(**) and B3LYP/6-311G(**) gave optimized geometries, infrared and Raman intensities and vibrational frequencies for the anti and gauche conformers. The conformational energy differences derived were 11.8 and 9.2 kJmol-1 from the HF and the B3LYP calculations, respectively.     

An ab initio study of the structures and energetics of the planar ground and 90°‐twisted excited states of substituted ethylenes

Ab initio molecular orbital calculations are performed on the planar ground states (S₀), the 90°‐twisted triplet (T₁), and pyramidalized singlet (S₁) excited states of ethylene, methaniminium cation (MC), monocyano‐ (MCE), 1,1‐dicyano‐ (DCE), 1,1‐dihydroxy‐ (DHE), and 1,1‐dicyano‐2,2‐dihydroxy (DCHE) ethylenes. Equilibrium geometries are optimized at the Hartree–Fock (HF) level with the 6‐31G* basis set. Electron correlation corrections are estimated by optimizing the HF/6‐31G* geometries at the (U)MP2/6‐31G* level and then by carrying out single‐point calculations at the fourth‐order Møller–Plesset perturbation theory ((U)MP4/6‐311G**//MP2/6‐31G*). The effects of various types of perturbations on the structures, energetics, dipole moments, and state ordering of S₀, S₁, and T₁ are carefully investigated. “Positive” S₁–T₁ splittings are estimated at the HF level for all studied molecules, while “negative” S₁–T₁ splittings are obtained at the MP2 level for MC, DHE, and DCHE. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 82: 242–254, 2001     

Complete basis set ab initio computational study of three-dimensional aromaticity in highly symmetric hydrogen clusters

The aromaticity of planar and highly symmetric three-dimensional hydrogen clusters were evaluated with the complete basis set ab initio computational method. The energy of formation of the hydrogen clusters from the hydrogen molecule and hydrogen molecular ions were used in comparison to their relative stabilities. The aromaticity of planar hydrogen clusters, as well as hydrogen clusters in the three dimensions, arranged as highly symmetric regular polyhedra (Plato's polyhedras), were discussed with respect to the Hückel and Möbius aromatic rules.     

Gas-phase molecular structures of third row transition-metal hexafluorides WF6, ReF6, OsF6, IrF6, and PtF6. An electron-diffraction and ab initio study

The molecular structures of WF6, ReF6, OsF6, IrF6, and PtF6 have been measured by electron diffraction from the gases, the last from both PtF6 itself and from a vapor assumed to consist of a mixture of O2 and PtF6 obtained by heating the salt O2PtF6. For models of Oh symmetry the bond lengths in the first three members of the series are essentially identical, but the Ir-F and Pt-F bonds are respectively about 0.01 and 0.02 A longer. Models of D4h symmetry were also tested for ReF6, OsF6, and IrF6 in which operation of the Jahn-Teller effect is thought possible. For these models the same trend was seen in the average bond-length values. The effect of three-atom multiple scattering was also investigated, and experimental estimates of the effects of vibrational averaging ("shrinkage") on the distances were obtained. Normal-coordinate analyses based on the observed wavenumbers yielded stretching force constants consistent with the usual inverse bond-length/force-constant relationship. Ab initio molecular orbital optimizations of the molecules constrained to Oh symmetry were carried out at several levels of theory and basis-set size. Less extensive optimizations of ReF6, OsF6, and IrF6 with D4h symmetry were also carried out. The best overall agreement with both the experimental values and the distance trend for Oh symmetry was obtained with the Hay-Wadt (n+1)VDZ basis on the metals and the aug-cc-pVTZ on the fluorines at the MP2 level, but these bases with B3P86 and B3PW91 density functional theory were nearly as good and with B3LYP only slightly worse. The D4h structures for ReF6, OsF6, and IrF6 with the cited bases at the B3P86 level were slightly more stable (respectively 0.8, 2.6, and 1.4 kcal/mol) with the axial bonds shorter by about 0.04 A in ReF6 and 0.07 A in OsF6, but about 0.05 A longer in IrF6. The significance of these values is uncertain. The experimental bond lengths (rg/A) with estimated 2sigma uncertainties for the models of Oh symmetry are W-F = 1.829(2), Re-F = 1.829(2), Os-F = 1.828(2), Ir-F = 1.839(2), and Pt-F = 1.852(2); the Pt-F value from the O2PtF6 sample was 1.851(2) A. Although the experimental data neither confirm nor refute the existence of the Jahn-Teller effect in ReF6, OsF6, and IrF6, they ensure that if present the distortion from Oh symmetry must be small.     

Controlling the shape and flexibility of arylamides: a combined ab initio, ab initio molecular dynamics, and classical molecular dynamics study

Using quantum chemistry plus ab initio molecular dynamics and classical molecular dynamics methods, we address the relationship between molecular conformation and the biomedical function of arylamide polymers. Specifically, we have developed new torsional parameters for a class of these polymers and applied them in a study of the interaction between a representative arylamide and one of its biomedical targets, the anticoagulant drug heparin. Our main finding is that the torsional barrier of a C(aromatic)-C(carbonyl) bond increases significantly upon addition of an o-OCH2CH2NH3+ substituent on the benzene ring. Our molecular dynamics studies that are based on the original general AMBER force field (GAFF) and GAFF modified to include our newly developed torsional parameters show that the binding mechanism between the arylamide and heparin is very sensitive to the choice of torsional potentials. Ab initio molecular dynamics simulation of the arylamide independently confirms the degree of flexibility we obtain by classical molecular dynamics when newly developed torsional potentials are used.     

Dependence of approximate ab initio molecular loge sizes on the quality of basis functions

Size and shape parameters for the core, bonding, and lone electron pairs of the ten-electron hydrides (CH₄, NH₃, H₂O, HF) were determined from ab initio MO wave functions using various Gaussian basis sets. The fundamental features of approximate electron pair loge representation are somewhat more sensitive to the quality of the basis functions than the molecular total energy. The total size of the molecular electron distribution is less affected by basis set variations than its components: the core, bonding, and lone pair sizes. There is an apparent tendency to “preserve” the total size of molecular distribution.     

Correlation of 2-, 3-, 4- and disubstituted pyridine gas-phase proton affinities with ab initio calculated energies at the sto-3g basis set level

Total energies of 2-, 3-, 4- and disubstituted pyridines were calculated for the salt and the free base using ab initio molecular orbital calculations at the STO-3G basis set level [2]. In each set, the difference in energy, ΔE_H, between the salt and the free base was calculated and plotted against experimentally derived gas-phase proton affinities. The correlation was very good for each of the substituent categories listed. All of the energies and proton affinities were then plotted together on the same graph. The result was an excellent correlation with r = 0.97. The linear equation for gas phase proton affinity, PA_B = 28.51 + 435.45ΔE_H kcal/mole, was derived from this plot and was used to calculate proton affinities for all of the thirty-one compounds used in this study as well as for a series of dicyanopyridines for which values of proton affinity are not available at this time.