The determination of the equilibrium structures of oxygen,ozone, and hydrogen peroxide using the ab initio and density functional theory methods

The geometries and energies of small oxygen containing molecules are studied by both the ab initio and density functional theory (DFT) methods. The RHF, MP2, and QCISD(T) ab initio methods, BHandH, BHandHLYP, BeckeSLYP, Becke3P86 DFT hybrid methods, BLYP, and the BP86 non-local DFT methods with the 3-21G¹, 6-31G(d,p), 6-311 + G(2d,2p) and 6-311 + + G(3df,3pd) basis sets were used for the computational study. The obtained results from the different methods were compared to the experimental values. The suitability of the DFT methods for reproducing experimental data were discussed.     

A theoretical study of the Si-O bond in disiloxane and related molecules

Summary A comparison of semi-empirical (MNDO) and ab initio (GAUSSIAN) calculations for disiloxane and related molecules is given. The STO-3G^* basis set well reproduced the observed geometries of disiloxane (*), DZP, TZVP) gave much poorer agreement with the observed geometries.Comparison of the STO-3G^* and the STO-3G basis sets demonstrates the necessity of including d-orbitals on the silicon. However, the semi-empirical MNDO program gave, despite the absence of d-orbitals, a better approximation to the molecular geometry than the complex ab initio basis sets.Force field parameters have been calculated for k_SiOSi, k_OSiO, 0.089 and 0.73 mdyneÅ/rad², and the SiOSiO torsion which has a V₁ potential of –0.68 kcal/mol. In addition, the HSiOH torsion is shown to have a three-fold potential of 0.78 kcal/mol. These are profoundly different from the analogous carbon-oxygen force constants, demonstrating that C-O parameters cannot be transferred to the corresponding Si-O systems.     

Infrared and raman spectra,vibrational assignments,normal coordinate analysis,and ab initio calculations of methyltrifluoromethyldisulfide and bis(trifluoromethyl)disulfide

The infrared and Raman (3500-35 cm^–1) spectra of gaseous and solid methyltrifluoromethyldisulfide, CF₃SSCH₃, and bis(trifluoromethyl)disulfide, CF₃SSCF₃, have been recorded. Additionally, the Raman spectra of the neat liquids have been obtained and qualitative depolarization values have been measured. These vibrational data have been interpreted, for both molecules, on the basis that the C-S-S-C dihedral angle is approximately 90°. Vibrational assignments are given for both molecules and are supported by normal coordinate calculations utilizing ab initio Hartree-Fock gradient calculations with the 3-21G^* basis set to obtain the frequencies for the normal modes and potential energy distributions. The CH₃ and CF₃ torsional modes have been observed at 140 and 48 cm^–1, respectively, for CF₃SSCH₃, from which periodic barriers of 485 cm^–1 (1.39 kcal mol^–1) and 853 cm^–1 (2.44 kcal mol^–1), respectively, have been calculated. Complete equilibrium geometries have been determined for both molecules by ab initio calculations employing both 3–21G and 6–31G basis sets. The structural parameters for bis(trifluoromethyl)disulfide are compared to those suggested from electron diffraction studies. The results are compared to corresponding quantities obtained for some similar molecules.Taken in part from the thesis of M. M. Bergana which will be submitted to the Department of Chemistry in partial fulfillment of the Ph.D. degree.     

Ab initio and density functional theory study of the enthalpies of formation of F2SOx and FClSOx (x=1, 2)

Enthalpies of formation of F₂SO, F₂SO₂, FClSO and FClSO₂ molecules have been determined using ab initio molecular orbital theory and density functional theory (DFT) calculations. Different DFT approaches and levels of the Gaussian-3 and the complete basis set (CBS) ab initio model chemistries have been employed to calculate enthalpies of formation from both total atomization energies and isodesmic reaction schemes. The best values at 298 K for F₂SO, F₂SO₂, FClSO and FClSO₂ as derived from an average of G3, G3B3, CBS-Q and CBS-QB3 isodesmic energies are −140.6, −181.1, −92.6 and −132.3 kcal mol⁻¹, respectively. The results obtained suggest that the accumulated small component errors found in the DFT-based methods are significantly reduced at the ab initio levels employed. Structural properties, harmonic vibrational frequencies, mode assignations and infrared intensities derived from B3LYP and mPW1PW91 functional with the 6-311+G(3df) basis set are presented.     

Electron density properties and metallophilic interactions of gold halides AuX2 and Au2X (X = F–I): Ab Initio calculations

We present ab initio calculations of the electron density properties and metallophilic interactions of the gold halide series, AuX₂ and Au₂X (X = F–I) as well as their anions performed at MP2 theoretical level with extended basis sets. The gold halide's structure, stability, and interactions with alkali metal atoms were investigated. The mechanisms of metallophilic interactions were explored by natural bond orbital analyses, electron localization function, electron density deformation, atoms in molecules, and reduced density gradient analyses. © 2016 Wiley Periodicals, Inc.     

Vibrational circular dichroism,absolute configuration and predominant conformations of volatile anesthetics: 1,2,2,2-tetrafluoroethyl methyl ether

Vibrational absorption and circular dichroism spectra of (−)-1,2,2,2-tetrafluoroethyl methyl ether have been measured in CCl₄ solution in the 2000–900 cm⁻¹ region. These spectra are compared with the ab initio predictions of absorption and VCD spectra obtained with density functional theory using B3LYP/6-31G* and B3PW91/6-311G(2d) basis sets for different conformers of (R)-1,2,2,2-tetrafluoroethyl methyl ether. The results suggest that the trans-conformer of 1,2,2,2-tetrafluoroethyl methyl ether is predominant in the solution phase and that the (−)-enantiomer has the R-configuration.     

Theoretical study of the changes in the electronic structure of benzonitrile accompanying its conversion into a radical anion

The electronic structure of benzonitrile and its radical anion have been investigated at different levels of ab initio MO theory: STO-3G, 6-31G and 6-31G^**. The changes in the electronic structure of the neutral molecule accompanying its conversion into the corresponding radical anion have been estimated. It was established that the radicalization leads to significant changes in the bond lengths with double and triple bond character expressed in the conjugated system. The distribution of the total atomic charges on transition from the neutral molecule to the corresponding radical anion have been investigated using the Mulliken population analysis. The distribution of the odd electron density in the radical anion was estimated at the different basis sets: STO-3G, 6-31G and 6-31G^**. The ab initio calculations suggest that the quinoid structure is preferred for the radical anion.     

A computational mechanistic study of the deamination reaction of melamine

A detailed computational study of the deamination reaction of melamine by OH^–, n H₂O/OH^–, n H₂O (where n = 1, 2, 3), and protonated melamine with H₂O, has been carried out using density functional theory and ab initio calculations. All structures were optimized at M06/6‐31G(d) level of theory, as well as with the B3LYP functional with each of the basis sets: 6‐31G(d), 6‐31 + G(d), 6‐31G(2df,p), and 6‐311++G(3df,3pd). B3LYP, M06, and ω B97XD calculations with 6‐31 + G(d,p) have also been performed. All structures were optimized at B3LYP/6‐31 + G(d,p) level of theory for deamination simulations in an aqueous medium, using both the polarizable continuum solvation model and the solvation model based on solute electron density. Composite method calculations have been conducted at G4MP2 and CBS‐QB3. Fifteen different mechanistic pathways were explored. Most pathways consisted of two key steps: formation of a tetrahedral intermediate and in the final step, an intermediate that dissociates to products via a 1,3‐proton shift. The lowest overall activation energy, 111 kJ mol^?1 at G4MP2, was obtained for the deamination of melamine with 3H₂O/OH^?.     

Comparative studies on the structures,infrared spectrum,and thermodynamic properties of phthalocyanine using ab initio Hartree–Fock and density functional theory methods

The molecular structure, vibrational spectrum, standard thermodynamic functions, and enthalpy of formation of free base phthalocyanine (Pc) have been studied using the density functional theory B3LYP procedure, as well as the ab initio Hartree–Fock method. Various basis sets 3‐21G, 6‐31G*, and LANL2DZ have been employed. The results obtained at various levels are discussed and compared with each other and with the available experimental data. It is shown that calculations performed at the Hartree–Fock level cannot produce a reliable geometry and related properties such as the dipole moment of Pc and similar porphyrin‐based systems. Electron correlation must be included in the calculations. The basis set has comparatively less effect on the calculated results. The results derived at the B3LYP level using the smaller 3‐21G and LANL2DZ basis sets are very close to those produced using the medium 6‐31G* basis set. The geometry of Pc obtained at the B3LYP level has D_2h symmetry and the diameter of the central macrocycle is about 4 Å. The enthalpy of formation of Pc in the gas phase has been predicted to be 1518.50 kJ/mol at the B3LYP/6‐311G(2d,2p)//B3LYP/6‐31G* level via an isodesmic reaction. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Cooperative atomic migrations in the associates of formic acid molecule with H2O...X systems (X=CH3OH,NH2OH,H2O2, HOF,and H2O)

The pathways and activation barriers of cooperative biproton migrations in the associates of the formic acid molecule with H₂O and X molecules (X=CH₃OH, NH₂OH, H₂O₂, FOH, and H₂O) are calculated by an ab initio method (3-21G and 6-31G^** basis sets). A cooperative triproton transfer occurs in the system with X=H₂O. The activation barriers of this transfer calculated in the 3-21G and 6-31G^** basis sets are 6.94 and 27.29 (through the structure of C₂ symmetry) or 7.99 and 26.08 kcal/mole (through the structure of C_s symmetry), respectively. In the systems with X=H₃COH, HOOH, and FOH, the biproton transfer is accompanied by synchronous shifts of two hydroxyl groups and overcomes high activation barriers (>40 kcal/mole), which is accounted for by poor stereochemical similarity for the low-barrier cooperative processes in the given molecular associates. Scientific Research Institute of Physical and Organic Chemistry, Rostov State University. Translated fromZhurnal Strukturnoi Khimii, Vol. 37, No. 5, pp. 845–858, September–October, 1996. Translated by I. Izvekova     

A theoretical study of the force field for carbon trioxide

Geometries force constants and harmonic frequencies are calculated for the cyclic (dioxirane) structure of CO₃ by ab initio SCF methods using the 3-21G, 3-21G(*). 6-31G and 6-31G* bases calculated frequency shifts for isotopomeric species agree with experiment and lend support to the vibrational assignments of Jacox and Milligan. Earlier arguments for and against the cyclic, cyclic and open structures of CO₃, based upon the “physical reasonableness” of valence force constants are shown to be invalid owing to the dependence of conventional “rigid” force constants upon the choice of valence coordinates. The use of “relaxed” force constants as a basis for meaningful comparison of force fields for molecules described by different sets of redundant valence coordinates is demonstrated.     

X-Ray spectral determination of the effective charges on phosphorus,sulfur, and chlorine atoms in chemical compounds with a nonempirical charge scale

Linear dependence between the experimental K_a line shifts and Mulliken atomic charges obtained by SCF ab initio calculations with 4-31G, 4-31G*, and 4-31G** basis sets for the P, S, and Cl atoms have been found. The electron density redistribution of PCl₃ and SPCl₃ free ligands on their complexation with AlBr₃ has been investigated. It has been shown that a significant transfer of the total ligand electron density to the acceptor is absent, but there is an essential growth of the ionicity of all bonds on complexation. The P = S and P S bond ionicities are found to increase linearly with the growth of the positive charge on the central phosphorus atom. © John Wiley & Sons, Inc.     

Ab initio molecular orbital study on the gas phase SN2 reaction F + CH3Cl → CH3F + Cl

Ab-initio molecular orbital (MO) and direct ab initio dynamics calculations have been applied to the gas phase S_N2 reaction F⁻ + CH₃Cl → CH₃F + Cl⁻. Several basis sets were examined in order to select the most convenient and best fitted basis set to that of high-quality calculations. The Hartree–Fock (HF) 3−21+G(d) calculation reasonably represents a potential energy surface calculated at the MP2/6−311++G(2df,2pd) level. A direct ab initio dynamics calculation at the HF/3−21+G(d) level was carried out for the S_N2 reaction. A full dimensional ab initio potential energy surface including all degrees of freedom was used in the dynamics calculation. Total energies and gradients were calculated at each time step. Two initial configurations at time zero were examined in the direct dynamics calculations: one is a near collinear collision, and the other is a side-attack collision. It was found that in the near collinear collision almost all total available energy is partitioned into two modes: the relative translational mode between the products (40%) and the C − F stretching mode (60%). The other internal modes of CH₃F were still in the ground state. The lifetimes of the early- and late-complexes F⁻ … CH₃Cl and FCH₃ … Cl⁻ are significantly short enough to dissociate directly to the products. On the other hand, in the side-attack collision, the relative translation energy was about 20% of total available energy.     

Toward similarity measures for macromolecular bodies: Medla test calculations for substituted benzene systems

A new method is proposed for the evaluation of numerical similarity measures for large molecules, defined in terms of their electron density (ED) distributions. The technique is based on the Molecular Electron Density Lego Assembler (MEDLA) approach, proposed earlier for the generation of ab initio quality electron densities for proteins and other macromolecules. The reliability of the approach is tested using a family of 13 substituted aromatic systems for which both standard ab initio electron density computations and the MEDLA technique are applicable. These tests also provide additional examples for evaluating the accuracy of the MEDLA technique. Electron densities for a series of 13 substituted benzenes were calculated using the standard ab initio method with STO-3G, 3-21G, and 6-31G** basis sets as well as the MEDLA approach with a 6-31G** database of electron density fragments. For each type of calculation, pairwise similarity measures of these compounds were calculated using a point-by-point numerical comparison of the EDs. From these results, 2D similarity maps were constructed, serving as an aid for quick visual comparisons for the entire molecular family. The MEDLA approach is shown to give virtually equivalent numerical similarity measures and similarity maps as the standard ab initio method using a 6-31G** basis set. By contrast, significant differences are found between the standard ab initio 6-31G** results and the standard ab initio results obtained with smaller STO-3G and 3-21G basis sets. These tests indicate that the MEDLA-based similarity measures faithfully mimic the actual, standard ab initio 6-31G** similarity measures, suggesting the MEDLA method as a reliable technique to assess the shape similarities of proteins and other macromolecules. The speed of the MEDLA computations allows rapid, pairwise comparisons of the actual EDs for a series of molecules, requiring no more computer time than other simplified, less detailed representations of molecular shape. The MEDLA method also reduces the need to store large volumes of numerical density data on disk, as these densities can be quickly recomputed when needed. For these reasons, the proposed MEDLA similarity analysis technique is likely to become a useful tool in computational drug design. © 1995 John Wiley & Sons, Inc.     

Ab initio and DFT investigation of the structures and properties of chloromethyl and chlorofluoromethyl peroxyl radicals

Ab initio and Density Functional Theory (DFT) calculations were performed to determine the equilibrium geometries, charge distributions, spin density distributions, dipole moments, electron affinities (EAs), and C–O bond dissociation energies (BDEs) of CH₂ClO₂^? CHCl₂O₂^?, CCl₃O₂^?, CF₂ClO₂^?, CFCl₂O₂^?, and CHFClO₂^? peroxyl radicals. The C–H BDEs of the parent methanes were calculated using the same levels of theories. Both MP2(full) and B3LYP methods, using the 6‐31G(d,p) basis set, were found to be capable of accurately predicting the geometries of peroxyl radicals. The B3LYP/6‐31G(d,p) method was found to be comparable to high ab initio levels in predicting C–O BDEs of studied peroxyl radicals and C–H BDEs of the parent alkanes. The progressive chlorine substitution of hydrogen atoms in methyl peroxyl radicals results in an increase (decrease) of the spin density on the terminal (inner) oxygen, a decrease in dipole moments, and an increase in electron affinities. The substitution of fluorine by chlorine in the series CF₃O₂^? – CCl₃O₂^? was found to lengthen (destabilize) the C–O bonds. Both C–O BDEs and EAs of peroxyl radicals (RO₂^?) were found to correlate well with Taft σ* substituent constants for the R groups. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Computational studies of bond dissociation energies, ionization potentials, and heat of formation for NH and NH+. Are hybrid density functional theory methods as accurate as quadratic complete basis set and Gaussian-2 ab initio methods?

Ionization potentials, bond dissociation energies, and heat of formation for NH and NH⁺ molecular species as well as for their elements were computed with highly reliable quadratic complete basis set and Gaussian-2 ab initio methods. The results are compared with experimental results and the assurance of these ab initio approaches is assessed. The same studies were also performed with three hybrid density functional methods (B3LYP, B3P86, and B3PW91) in combination with variously sized basis sets. The computational results are discussed in light of density functional theory reliability for exploring the potential energy of small polar molecular systems. Received: 21 July 1997 / Accepted: 8 December 1997     

In cation interactions with some organics: ab initio molecular orbital and density functional theory

Ab initio molecular orbital and density functional theory studies were undertaken to investigate the structural and energetic characteristics of complexes of In⁺ with several different organic molecules for the first time. HF, MP2, QCISD, and CCD levels of theory in ab initio MO as well as B3LYP, B3PW91 hybrid functionals in density functional theory were used. A valence TZ+P basis set with relativistic effective core potentials was used for the In atom while the 6-311++G(3d, 2p) basis set was utilized for all other atoms. Both closed-shell (H₂O, CH₄, CH₃OH, and C₆H₆) and open-shell (CH₃ and C₂H₃) molecules were considered for complexation with In⁺. In⁺ affinities of 21.5, 24.8, 28.6, 18.4, and 23.0 kcal/mol were obtained with the B3PW91 hybrid functional for H₂O, CH₃OH, C₆H₆, CH₃, and C₂H₃, respectively. The large values for the calculated affinities indicate the validity of our recent experimental detection of In⁺ ion attachment to some organic molecules.     

Theoretical study of the isomerism of stepwise-hydrogenated b-doped aluminum clusters BAl12H− 2n (n = 1-6) with the [B@Al12]t- framework

The structure, energy, vibrational, and magnetic characteristics of stepwise-hydrogenated borondoped aluminum clusters B@A₁₂H _2n ^t- (n = 1–6) have been calculated by ab initio density functional theory B3LYP method with the basis sets 6-31G* and 6-311+G*. The results are compared with those of analogous calculations of the related series Al@A₁₂H _2n ^t- . The substitution of boron for the endohedral aluminum atom sharply changes the structure of isomers, their arrangement on the energy scale, and their stability toward the elimination of H₂ molecules. Differences in the behavior of these properties on varying n in the Al@A₁₂H _2n ^t- and B@A₁₂H _2n ^t- families are traced, and the effect of the dopant on these properties is examined.     

The influence of basis sets on wave function tails

Wave function tails are analyzed quantitatively by investigating the dependence of exterior electron density (EED ) on basis sets; the EED is defined as the integrated electron density outside the repulsive molecular surface. Ab initio MO calculations with large scale basis sets were performed to establish the benchmark order of EED values for valence orbitals of some simple molecules. It is found that very popular basis sets, such as 4-31G, which are determined by energy optimization, are inferior in describing the wave function tails to some similar size basis sets, such as MIDI -4, which are obtained by least-squares fit to near Hartree-Fock atomic functions. Further the EED values for atomic 2s functions are shown to be unfavorably smaller than those for atomic 2p functions when the same value is used for the exponent α in the GTO basis sets. This indicates that the frequently used constraint α_s = α_p is not appropriate for describing wave function tails with medium-size basis sets. Deficiencies in the energy-optimized basis sets are found to become more serious for molecules including heavier atoms.     

Study of locally dense and locally saturated basis sets in localized molecular orbital calculations of nuclear shielding: Ab initio LORG calculations for 13C and 17O in norbornenone

This study demonstrates the use of uneven atomic basis sets for ab initio calculations of NMR shielding in the localized orbital/local origin (LORG) approach with norbornenone as the test case. We distinguish between locally dense sets (extended basis on target atom only) and locally saturated sets (extended bases on target atom and atoms in its first bonding sphere), using 6-311G ** and 6-31G sets to describe the high and low level of function sets. It is shown that the use of these uneven sets can simulate high basis set level calculations of shieldings for ¹H and for all the ¹³C nuclei in this molecule and, hence, allows quite accurate ab initio calculations of shielding properties of these nuclei in large molecules using relatively modest computational facilities. The shielding of the double-bonded ¹⁷O nucleus is apparently sensitive to basis-set quality beyond the first bonding sphere. © 1996 John Wiley & Sons, Inc.