The structure of 1-chlorosilatrane: An ab initio molecular orbital and a density functional theory study

The molecular geometries of the 1-chloro-, 1-fluoro-, 1-methyl-, and 1-hydrogenosilatranes were fully optimized by the restricted Hartree-Fock (HF) method supplemented with 3-21G, 3-21G(d), 6-31G(d), and CEP-31G(d) basis sets; by MP2 calculations using 6-31G(d) and CEP-31G(d) basis sets; and by GGA-DFT calculations using 6-31G(d5) basis set with the aim of locating the positions of the local minima on the energy hypersurface. The HF/6-31G(d) calculations predict long (>254 pm) and the MP2/CEP calculations predicted short (∼225 pm) equilibrium Si(SINGLE BOND)N distances. The present GGA-DFT calculations reproduce the available gas phase experimental Si(SINGLE BOND)N distances correctly. The solid phase experimental results predict that the Si(SINGLE BOND)N distance is shorter in 1-chlorosilatrane than in 1-fluorosilatrane. In this respect the HF results show a strong basis set dependence, the MP2/CEP results contradict the experiment, and the GGA-DFT results in electrolytic medium agree with the experiment. The latter calculations predict that 1-chlorosilatrane is more polarizable than 1-fluorosilatrane and also support a general Si(SINGLE BOND)N distance shortening trend for silatranes during the transition from gas phase to polar liquid or solid phase. The calculations predict that the ethoxy links of the silatrane skeleton are flexible. Consequently, it is difficult to measure experimentally the related bond lengths and bond and torsion angles. This is the probable origin of the surprisingly large differences for the experimental structural parameters. On the basis of experimental analogies, ab initio calculations, and density functional theory (DFT) calculations, a gas phase equilibrium (r_e) geometry is predicted for 1-chlorosilatrane. The semiempirical methods predict a so-called exo minimum (at above 310 pm Si(SINGLE BOND)N distance); however, the ab initio and GGA-DFT calculations suggest that this form is nonexistent. The GGA-DFT geometry optima were characterized by frequency analysis. © 1996 by John Wiley & Sons, Inc.     

Ab initio calculations of the geometry and polarizabilities of bisphenyls having aliphatic substituents

Ab initio geometry optimization and polarizability calculations of a series of bisphenyls, which are the model compounds of chemically different polycarbonates using HF/6‐31G and 6‐31G** basis sets are presented. Calculated absolute value of the conformationally averaged optical anisotropy (〈γ²〉) of diphenyl propane, a model analog of bisphenol A polycarbonate, is higher than the corresponding experimental value in the dilute solution phase. The calculations have reproduced the relative trend in the optical anisotropy for the different bisphenyl model compounds in a manner similar to those using semiclassical approach, by incorporation of the condensed phase polarizabilities and quantum chemically calculated geometry structure into the valence optical scheme. Individual contributions to the gas phase polarizability and optical anisotropy of the model compounds for various dihedral conformers, because of the presence of different aliphatic chemical groups, are correctly predicted by the calculations here. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Performance of theoretical methods and basis sets on the molecular structure, atomisation and ionisation energies, electron affinity, and vibrational spectrum of silylene

This work compares the performance of theoretical methods and basis sets on the molecular structure, atomisation and ionisation energies, electron affinity, and vibrational spectrum of silylene. Silylene, its cation and anion have been studied in ¹ A ₁, ² A ₁ and ² B ₁ states, respectively, in the gas phase and C_2v symmetry. The methods considered are second-order Møller-Plesset perturbation theory (MP2), the density functional theory (DFT), Gaussian-2 (G2) and complete basis set methods (CBS-4M and CBS-Q). The basis sets used are 6-31G(d,p), 6-311G(d,p), 6-31++G(d,p) and 6-311++G(d,p). The functional used for the DFT method is B3LYP. Silylene and its cation and anion have been optimised using the MP2 and DFT methods and the named basis sets. Single-point energy calculations (G2, CBS-4M and CBS-Q) were performed using MP2/6-311++G(d,p) structures and these energies have been used to calculate atomisation energy, ionisation energy and adiabatic electron affinity. Frequency calculations were also done and the raw vibrational frequencies were assigned. It is interesting to note the close similarity between the predicted parameters and some of the available literature values. The results obtained are consistent and converge with different basis sets with improved size and quality. However, the parameters obtained are very much method dependent.     

Proton affinity correlations for alkyl chlorides

Ab initio SCF calculations with minimal STO-3G and extended 44-31G basis sets have been performed on the simple alkyl chlorides, HCl to t-BuCl, and their protonated analogs. MINDO/3 calculations are also reported for these species and a variety of cyclic and bicyclic chlorides. The much closer agreement with experiment for STO-3G proton affinities than for 44-31G values is in sharp contrast to the results for first-row bases. An excellent correlation is found between both the STO-3G and MINDO/3 proton affinities and the charge on the CIH fragment in RCIH⁺. For the acyclic chlorides, correlations of PA's with the polar substituent constant, σ*, and IP's are also reasonable. In addition, the calculated carbonium ion-HCl interaction energy for t-BuClH⁺ indicates that protonated tertiary chlorides are no more than marginally stable in the gas phase.     

Application of Density Functional Theory for evaluation of standard two-electron reduction potentials in some quinone derivatives

In this research, two-electron reduction potentials are calculated for a set of eight quinones using Density Functional Theory (DFT) at B1B95/6-31G^** and B1B95/6-311++G^** levels in aqueous solution. Two different mechanisms, direct and indirect, which have been presented before, are employed for these calculations. DPCM and CPCM models of solvation are carried out to include solution phase contribution. The results show that CPCM is properly matched with DFT method at the B1B95 level in both direct and indirect mechanisms. It is found that direct mechanism gives more accurate two-electron reduction potentials in comparison to indirect mechanism. Mean Absolute Deviation (MAD) obtained through indirect mechanism and CPCM model of solvation are about 0.041 and 0.022 V for 6-31G^** and 6-311++G^**, respectively. The MAD values of direct mechanism are about 0.024 and 0.018 V for 6-31G^** and 6-311++G^** basis sets, respectively. The calculated MAD for both direct and indirect mechanisms is comparable with MAD previously reported at MP3 level for this set of molecules.     

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     

Ab initio studies of RO− … HOR′ complexes. Solvent effects on the relative acidities of water and methanol

Ab initio molecular orbital calculations are reported for complexes of hydroxide and methoxide anions with water and methanol. The basis set dependence of the results is carefully considered for HO^? ? H₂O. 4-31G and 6-31G* calculations yield similar geometrical predictions; however, the 6-31G* basis set is superior for computing dissociation energies. Further extension to the 6-31G** level provides little change. The dissociation energies for the complexes range from 25 to 37 kcal/mole with hydroxide ion and methanol acting as the strongest base and acid. The difference in gas phase acidities of water and methanol is halved by the introduction of one solvent molecule.     

Ab initio calculations of tautomer equilibrium and protonation enthalpy of 4- and 5-methylimidazole in the gas phase: Basis set and correlation effects

Ab initio calculations are performed to evaluate molecular properties of 4- and 5-methylimidazole (MeIm) and the protonated form (MeImH⁺) with extended basis sets ranging from 6-31G¹ to 6-311 + +G⁷ at Hartree-Fock, Møller-Plesset perturbation (MP2, MP3, MP4) and density functional (BLYP, B3LYP, B3PW91) levels. Optimized geometry structures, energies and thermochemical properties are carefully analysed. The geometries are not particularly sensitive to the basis set employed, but change appreciably when correlation effects are included. The tautomer equilibrium constant and the protonation energy are, in contrast, much more sensitive to both basis set and correlation effects, although good results are obtained at the simple MP2 level. The computationally less costly density functional (DF) method leads to results similar to those from MP2. The gas phase tautomer equilibrium constant and the protonation enthalpy of 4- and 5-MeIm are calculated at all levels. The results obtained with the 6-31+G¹, 6-311+G¹ and 6-311++G⁷ basis sets at MP2 and DF levels are in excellent agreement with available experimental values.     

Theoretical studies on the effects of methods and parameterization on the calculated free energy of hydration for small molecules

Free energies of hydration (FEH) have been computed for 13 neutral and nine ionic species as a difference of theoretically calculated Gibbs free energies in solution and in the gas phase. In‐solution calculations have been performed using both SCIPCM and PCM polarizable continuum models at the density functional theory (DFT)/B3LYP and ab initio Hartree–Fock levels with two basis sets (6‐31G* and 6‐311++G**). Good linear correlation has been obtained for calculated and experimental gas‐phase dipole moments, with an increase by ～30% upon solvation due to solute polarization. The geometry distortion in solution turns out to be small, whereas solute polarization energies are up to 3 kcal/mol for neutral molecules. Calculation of free energies of hydration with PCM provides a balanced set of values with 6‐31G* and 6‐311++G** basis sets for neutral molecules and ionic species, respectively. Explicit solvent calculations within Monte Carlo simulations applying free energy perturbation methods have been considered for 12 neutral molecules. Four different partial atomic charge sets have been studied, obtained by a fit to the gas‐phase and in‐solution molecular electrostatic potentials at in‐solution optimized geometries. Calculated FEH values depend on the charge set and the atom model used. Results indicate a preference for the all‐atom model and partial charges obtained by a fit to the molecular electrostatic potential of the solute computed at the SCIPCM/B3LYP/6‐31G* level. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Potential energy surface of the reaction of imidazole with peroxynitrite: Density functional theory study

This article presents a theoretical investigation of the reaction mechanism of imidazole nitration by peroxynitrite using density functional theory calculations. Understanding this reaction mechanism will help in elucidating the mechanism of guanine nitration by peroxynitrite, which is one of the assumed chemical pathways for damaging DNA in cells. This work focuses on the analysis of the potential energy surface (PES) for this reaction in the gas phase. Calculations were carried out using Hartree–Fock (HF) and density functional theory (DFT) Hamiltonians with double‐zeta basis sets ranging from 6‐31G(d) to 6‐31++G(d,p), and the triple‐zeta basis set 6‐311G(d). The computational results reveal that the reaction of imidazole with peroxynitrite in gas phase produces the following species: (i) hydroxide ion and 2‐nitroimidazole, (ii) hydrogen superoxide ion and 2‐nitrosoimidazole, and (iii) water and 2‐nitroimidazolide. The rate‐determining step is the formation of a short‐lived intermediate in which the imidazole C₂ carbon is covalently bonded to peroxynitrite nitrogen. Three short‐lived intermediates were found in the reaction path. These intermediates are involved in a proton‐hopping transport from C₂ carbon to the terminal oxygen of the ? O? O moiety of peroxynitrite via the nitroso (ON? ) oxygen. Both HF and DFT calculations (using the Becke3–Lee–Yang–Parr functional) lead to similar reaction paths for proton transport, but the landscape details of the PES for HF and DFT calculations differ. This investigation shows that the reaction of imidazole with peroxynitrite produces essentially the same types of products (nitro‐ and nitroso‐) as observed experimentally in the reaction of guanine with peroxynitrite, which makes the former reaction a good model to study by computation the essential characteristics of the latter reaction. Nevertheless, the computationally determined activation energy for imidazole nitration by peroxynitrite in the gas phase is 84.1 kcal/mol (calculated at the B3LYP/6‐31++G(d,p) level), too large for an enzymatic reaction. Exploratory calculations on imidazole nitration in solution, and on the reaction of 9‐methylguanine with peroxynitrite in the gas phase and solution, show that solvation increases the activation energy for both imidazole and guanine, and that the modest decrease (15 kcal mol^?1) in the activation energy, due to the adjacent six member ring of guanine, is counterbalanced by solvation. These results lead to the speculation that proton tunneling may be at the origin of experimentally observed high reaction rate of guanine nitration by peroxynitrite in solution. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Determination and characterization of a transition structure for water–formaldehyde addition

Quantum mechanical calculations of the geometric, energetic, electronic, and vibrational features of a transition structure for gas-phase water–formaldehyde addition (FW1?) are described, and a new transition-structure search algorithm is presented. Basis-set-dependent effects are assessed by comparisons of computed properties obtained from self-consistent field (SCF) molecular orbital (MO) calculations with STO-3G, 4-31G, and 6-31G^** basis sets in the absence of electron correlation. The results obtained suggest that STO-3G-level calculations may be sufficiently reliable for the prediction of the transition structure of FW1? and for the transition structures of related carbonyl addition reactions. Moreover, the calculated activation energy for formation of FW1? from water and formaldehyde (?44 kcal mol^?1) is very similar in all three basis sets. However, the energy of formaldehyde hydration predicted by STO-3G (? ?45 kcal mol^?1) is about three times larger than that predicted by the other two basis sets, with the activation energy for dihydroxymethane dehydration also being too large in STO-3G. Calculated force constants in all three basis sets are generally too large, leading to vibrational frequencies that are also too large. However, uniformly scaled force constants (in internal coordinates) give much better agreement with experimental frequencies, scaled 4-31G force constants being slightly superior to scaled STO-3G force constants.     

Geometry of intramolecular silicon complexes: an ab initio estimation of the sensitivity to the effect of medium. (Aroyloxymethyl)trifluorosilanes

The effect of medium on the geometry of the (benzoyloxymethyl)trifluorosilane (1) molecule was studied by the HF and MP2 methods with the 6-31G(d), 6-311G(d), and 6-311+G(d,p) basis sets, as well as using the Onsager SCRF model, the PCM approach, and the data of X-ray diffraction study. Molecule 1 has a low complexation energy (5.4 kcal mol^–1 according to MP2(Full)/6-31G(d)+ZPE calculations and 6.8 kcal mol^–1 according to IR spectroscopy data), while its geometric parameters are the least sensitive to the effects of medium among all hypervalent silicon compounds studied to date. Nevertheless, the results obtained revealed a pronounced deformation of the SiO coordination bond in 1 on going from the gas phase to the polar solution and crystal. This serves as a theoretical substantiation of the hypothesis that substantial changes in the IR and NMR spectral characteristics of the (O—Si)-chelate (aroyloxymethyl)trifluorosilanes upon variation of external factors are due to geometric reasons. Analysis of the electron density distribution according to Bader indicates that the SiO bond in molecule 1 can be treated as a covalent bond of high polarity.     

A quantum mechanical approach to the kinetics of the hydrogen abstraction reaction H2O2 + •OH → HO2 + H2O

The kinetics of the hydrogen abstraction from H₂O₂ by ^?OH has been modeled with MP2/6‐31G*//MP2/6‐31G*, MP2‐SAC//MP2/6‐31G*, MP2/6‐31+G**//MP2/6‐31+G**, MP2‐SAC// MP2/6‐31+G**, MP4(SDTQ)/6‐311G**//MP2/6‐31G*, CCSD(T)/6‐31G*//CCSD(T)/6‐31G*, CCSD(T)/6‐31G**//CCSD(T)/6‐31G**, CCSD(T)/6‐311++G**//MP2/6‐31G* in the gas phase. MD simulations have been used to generate initial geometries for the stationary points along the potential energy surface for hydrogen abstraction from H₂O₂. The effective fragment potential (EFP) has been used to optimize the relevant structures in solution. Furthermore, the IEFPCM model has been used for the supermolecules generated via MD calculations. IEFPCM/MP2/6‐31G* and IEFPCM/CCSD(T)/6‐31G* calculations have also been performed for structures without explicit water molecules. Experimentally, the rate constant for hydrogen abstraction by ^?OH drops from 1.75 × 10^?12 cm³ molecule^?1 s^?1 in the gas phase to 4.48 × 10^?14 cm³ molecule^?1 s^?1 in solution. The same trend has been reproduced best with MP4 (SDTQ)/6‐311G**//MP2/6‐31G* in the gas phase (0.415 × 10^?12 cm³ molecule^?1 s^?1) and with EFP (UHF/6‐31G*) in solution (3.23 × 10^?14 cm³ molecule^?1 s^?1). © 2005 Wiley Periodicals, Inc. Int J Chem Kinet 37: 502–514, 2005     

Infrared spectrum of potassium‐cationized triethylphosphate generated using tandem mass spectrometry and infrared multiple photon dissociation

Tandem mass spectrometry and wavelength‐selective infrared photodissociation were used to generate an infrared spectrum of gas‐phase triethylphosphate cationized by attachment of K⁺. Prominent absorptions were observed in the region of 900 to 1300 cm^?1 that are characteristic of phosphate P?O and P? O? R stretches. The relative positions and intensities of the IR absorptions were reproduced well by density functional theory (DFT) calculations performed using the B3LYP functional and the 6‐31+G(d), 6‐311+G(d,p) and 6‐311++G(3df,2pd) basis sets. Because of good correspondence between experiment and theory for the cation, DFT was then used to generate a theoretical spectrum for neutral triethylphosphate, which in turn accurately reproduces the IR spectrum of the neat liquid when solvent effects are included in the calculations. Copyright © 2009 John Wiley & Sons, Ltd.     

Laser Raman spectroscopy of polyacrylamide

The Raman spectra of polyacrylamide and its covalently crosslinked gel (with N,N′-methylenebis-acrylamide as the crosslinking agent) in the region of 200–3600 cm^?1 are discussed. The vibrational band assignments for polyacrylamide are made on the basis of a comparison with the spectra of acrylamide, acrylic acid, polyacrylic acid, poly(vinyl alcohol), and other vinyl polymers. The Raman spectra of polyacrylamide in the solid phase and in aqueous solution have similar spectral features. The Raman spectra of gels with low crosslink content and of polyacrylamide in aqueous solution are comparable except that one new band, predominantly due to the residual monomer, appears in the gel phase. An analysis based on polarized Raman, infrared and NMR spectra, model building, and group theoretical calculations suggests a structure dominated by isotactic species.     

Potential energy surfaces for the molecular and free radical dissociations of H2CS,F2CS and Cl2CS: An ab initio SCF MO study

Energies along the planar symmetric (C_2v) and planar assymetric (C_s paths to molecular dissociation of the ground state thiocarbonyl halides, F₂CS and Cl₂CS, together with their transition state geometries, have been calculated by ab initio SCF MO methods using the STO-3G and 4-31G basis sets. For comparison, results on H₂CS at similar levels of calculation are also included in this report. In addition, the 4-31G^** basis set has been employed to predict the geometries of the ground state species and the endothermicities of their free radical dissociations. The results of experiments in which the lowest excited singlet states of these molecules have been photoexcited are interpreted in light of these calculations. Thermodynamic data for both molecular and free radical dissociations are evaluated and discussed.     

An ab initio quantum chemical study of reaction mechanisms in the C2H2/CH3OH/KOH/DMSO system

An ab initio quantum chemical study (MP2/6-311++G**//B3LYP/6-31+G*) of a number of possible interactions is performed for the gas phase system of acetylene—potassium hydroxide-dimethylsulfoxide(DMSO)—methanol and with regard to the solvent effect within the continuum model. Key structures in the vinylation reaction are shown to be methoxide ion complexes with the alkali metal hydroxide and acetylene molecules. The formation of these complexes results in the activation of the acetylene molecule and an increase in the nucleophilicity of the methoxide ion. In the C₂H₂/CH₃OH/KOH/DMSO reaction system, a proton exchange between the acetylene molecule and the anionic nucleophile ([OH]^- and [CH₃O]^-) is freely performed with the formation of systems with ethynideions, whereas the thermodynamically preferable formation of vinyl alcohol or methyl vinyl ether is determined by a barrier of 20 kcal/mol.     

Conformational stability of trivinylborane from vibrational spectra and ab initio calculations

The conformational stability, barriers to internal rotation and vibrational frequencies of trivinylborane have been determined from the vibrational spectra and ab initio calculations. The ab initio calculations have been carried out utilizing the RHF/3-21G, RHF/6-31G*, and MP2/6-31G* basis sets and support the vibrational data that there are two stable conformations in the fluid phases separated by a relatively small energy difference. One of the conformations is a near-planar form which has the three vinyl groups twisted out of the BC₃ plane and belongs to the C₃ point group. The other conformer has a non-planar structure and belongs to the C₁ point group. These and other calculated results are compared to the corresponding quantities obtained from the experiment.     

Solvent effects on dimeric self-association of 2-pyrrolidinone: An ab initio study

Full geometry optimizations were carried out for 2-pyrrolidinone (2-Py) and its dimer structures at the DFT (B3LYP) and HF levels in the gas phase and in solution. Additionally, single-point MP2/6-31G^** calculations were performed on the HF/6-31G^** optimized geometries. The self-association of 2-Py in 1,4-dioxane (=2.21) and in water (=78.54) were studied using the self-consistent reaction field (SCRF) theory. The calculated relative free energies (G) for the dimerization processes predict the cyclic dimer (CD) to be more stable than the open dimer (OD) at all levels of theory in the gas phase and in solution. The results show that, at least for the properties of the hydrogen-bonded systems studied in this work, the B3LYP/6-31G^** calculations give better results than the HF and MP2 calculations with the same basis set. The data obtained from this study were compared with the corresponding experimental results when available.     

A quantum chemical study of reactions of DNA bases with sulphur mustard: a chemical warfare agent

Reactions of the sulphonium ion of sulphur mustard (SM⁺¹) at the N7, N3 and O6 sites of guanine, N7, N3 and N1 sites of adenine, O2 and N3 sites of cytosine and O2 and O4 sites of thymine were studied theoretically in gas phase and aqueous media employing density functional theory (DFT) and second order Møller–Plesset perturbation (MP2) theory. The B3LYP, B3PW91 and B1B95 functionals of DFT and the 6-31+G* and AUG-cc-pVDZ basis sets were used in the calculations. Basis set superposition error was treated using the counterpoise method by single point energy calculations at the B3LYP/6-31+G* level in gas phase. The present study explains the mechanism of alkylation of the DNA bases and shows that SM⁺¹ would form stable adducts at the endocyclic nitrogen sites of the DNA bases, and at the O6 site of guanine and the O2 site of cytosine. Formation of adducts at the N7 site of guanine and N3 site of adenine are found to be most favored and next most favored respectively, which agrees with experimental observations.