Correlated ab initio quantum chemical calculations of di- and trisaccharide conformations

High level correlated quantum chemical calculations, using MP2 and local MP2 theory, have been performed for conformations of the disaccharide, beta-maltose, and the trisaccharide, 3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranose. For beta-maltose, MP2 and local MP2 calculations using the 6-311++G** basis set are in good agreement, predicting a global minimum gas-phase conformation with a counterclockwise hydrogen bond network and the experimentally-observed intersaccharide hydrogen bonding arrangement. For conformations of 3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranose, MP2/6-311++G**, and local MP2/6-311++G** calculations do not provide a consensus prediction of relative energetics, with the MP2 method finding large differences in stability between extended and folded trisaccharide conformations. Local MP2 calculations, less susceptible to intramolecular basis set superposition errors, predict a narrower range of trisaccharide energetics, in line with estimates from Hartree-Fock theory and B3LYP and BP86 density functionals. All levels of theory predict compact, highly hydrogen-bonded conformations as lowest in energy on the in vacuo potential energy surface of the trisaccharide. These high level, correlated local MP2/6-311++G** calculations of di- and trisaccharide energetics constitute potential reference data in the development and testing of improved empirical and semiempirical potentials for modeling of carbohydrates in the condensed phase.     

方酸构象和振动光谱的从头算研究

在6-31G^*^*水平上对方酸(3, 4-二羟基-3-环丁烯-1, 2-二酮)三种构象异构体进行了SCF计算。结果表明ZZ型异构体最稳定, ZE型次之。用等键反应能量分析方酸的稳定性, 并与苯作比较, 讨论方酸的芳香性。在6-31G水平上计算了方酸三种构象的振动频率。     

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.     

Matrix isolation infrared and ab initio study of the conformations of 2,2-dimethoxypropane

Conformations of 2,2-dimethoxypropane (DMP) were studied using matrix isolation infrared spectroscopy. An effusive source maintained at different temperatures (298, 388 and 430 K) was used to deposit DMP in a nitrogen matrix. As a result of these experiments, spectrally resolved infrared features of the ground and first higher energy conformer of DMP have been recorded, for the first time. The experimental studies were supported by ab initio computations performed at B3LYP/6-31++G** level. Computationally, four minima were identified corresponding to conformers with G+/-G-/+, TG+/-, G+/-G+/- and TT structures. The computed frequencies at the B3LYP level were found to compare well with the experimental matrix isolation frequencies, leading to a definitive assignment of the infrared features of DMP, for the G+/-G-/+ and TG+/- conformers. At the B3LYP/6-31++G** level, the energy difference between the G+/-G-/+ and TG+/- conformers was computed to be 3.25 kcal x mol(-1). The barrier for conformation interconversion, TG+/--->G+/-G-/+, was calculated to be 1.29 kcal x mol(-1). The magnitude of this barrier is consistent with the experimental observation that the spectral features due to the TG+/- decreased considerably in intensity when the matrix was annealed.     

Size-expanded yDNA bases: an ab initio study

xDNA and yDNA are new classes of synthetic nucleic acids characterized by having base-pairs with one of the bases larger than the natural congeners. Here these larger bases are called x- and y-bases. We recently investigated and reported the structural and electronic properties of the x-bases (Fuentes-Cabrera et al. J. Phys. Chem. B 2005, 109, 21135-21139). Here we extend this study by investigating the structure and electronic properties of the y-bases. These studies are framed within our interest that xDNA and yDNA could function as nanowires, for they could have smaller HOMO-LUMO gaps than natural DNA. The limited amount of experimental structural data in these synthetic duplexes makes it necessary to first understand smaller models and, subsequently, to use that information to build larger models. In this paper, we report the results on the chemical and electronic structure of the y-bases. In particular, we predict that the y-bases have smaller HOMO-LUMO gaps than their natural congeners, which is an encouraging result for it indicates that yDNA could have a smaller HOMO-LUMO gap than natural DNA. Also, we predict that the y-bases are less planar than the natural ones. Particularly interesting are our results corresponding to yG. Our studies show that yG is unstable because it is less aromatic and has a Coulombic repulsion that involves the amino group, as compared with a more stable tautomer. However, yG has a very small HOMO-LUMO gap, the smallest of all the size-expanded bases we have considered. The results of this study provide useful information that may allow the synthesis of an yG-mimic that is stable and has a small HOMO-LUMO gap.     

The surface of ordered mesoporous benzene-silica hybrid material: an infrared and ab initio molecular modeling study

Joint IR and computational results allow a detailed characterization of the surface properties of a mesoporous benzene-silica hybrid material with crystal-like wall structure. After outgassing at 450 degrees C, hydroxyl species mainly consist of noninteracting silanols, with both O-H and Si-O stretching modes at lower frequencies than those of SiOH in silica. Interaction with several probe molecules, followed both by experiment and calculus, shows that the aryl group in the coordination sphere of Si imparts a lesser acidity with respect to the isolated silanol in silica. In contrast, adsorption isotherms indicate that the interaction with acetone is stronger with benzene-silica than with silica: this is interpreted in terms of secondary interactions taking place between the slightly acidic CH in acetone and the electronic cloud in benzene-like rings. This suggests that both the inorganic component and the organic one play a role in dictating the surface behavior.     

SurfKin: An ab initio kinetic code for modeling surface reactions

In this article, we describe a C/C++ program called SurfKin (Surface Kinetics) to construct microkinetic mechanisms for modeling gas–surface reactions. Thermodynamic properties of reaction species are estimated based on density functional theory calculations and statistical mechanics. Rate constants for elementary steps (including adsorption, desorption, and chemical reactions on surfaces) are calculated using the classical collision theory and transition state theory. Methane decomposition and water–gas shift reaction on Ni(111) surface were chosen as test cases to validate the code implementations. The good agreement with literature data suggests this is a powerful tool to facilitate the analysis of complex reactions on surfaces, and thus it helps to effectively construct detailed microkinetic mechanisms for such surface reactions. SurfKin also opens a possibility for designing nanoscale model catalysts. © 2014 Wiley Periodicals, Inc.     

Thermal decomposition of decalin: an ab initio study

Density functional theory calculations (B3LYP and BH&HLYP functionals) of the potential energy surface have been performed to investigate the mechanisms of decalin breakdown, and the Rice-Ramsperger-Kassel-Marcus and transition state theory methods have been used to compute the high-pressure limit thermal rate constants for the new reaction pathways. The new pathways connect decalin to five primary monoaromatic species: benzene, toluene, styrene, ethylbenzene, and xylene. The reactions used for the new routes are carbon-carbon bond cleavage reaction, dissociation reaction, and hydrogen abstraction and addition reactions. A kinetic analysis was performed for pyrolytic conditions, and benzene, toluene, and xylene were identified as major products.     

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.     

Eclipsed and staggered conformations of (SIH3)2F+: An ab initio study

Ab initio calculations at 6–31G**, 6–31++G**, and MP2/6–31G** levels were performed on disilyl–fluoronium, (SiH₃)₂F⁺, with the SiH₃ group eclipsed or staggered. Optimized geometries, total energies, dipole moments, atomic charges, electronic density, and vibrational frequencies were computed. The results were compared with calculated structural parameters and vibrational frequencies of H₃SiF, H₂SiF⁺, H₂SiF^?, and H₄SiF⁺ ions. The basis-set effects were studied. Several thermochemistry parameters—ZPE, thermal energy, rotational constants, and entropies—were also calculated. © 1994 John Wiley & Sons, Inc.     

Resonance and aromaticity: an ab initio valence bond approach

Resonance energy is one of the criteria to measure aromaticity. The effect of the use of different orbital models is investigated in the calculated resonance energies of cyclic conjugated hydrocarbons within the framework of the ab initio Valence Bond Self-Consistent Field (VBSCF) method. The VB wave function for each system was constructed using a linear combination of the VB structures (spin functions), which closely resemble the Kekulé valence structures, and two types of orbitals, that is, strictly atomic (local) and delocalized atomic (delocal) p-orbitals, were used to describe the π-system. It is found that the Pauling-Wheland's resonance energy with nonorthogonal structures decreases, while the same with orthogonalized structures and the total mean resonance energy (the sum of the weighted off-diagonal contributions in the Hamiltonian matrix of orthogonalized structures) increase when delocal orbitals are used as compared to local p-orbitals. Analysis of the interactions between the different structures of a system shows that the resonance in the 6π electrons conjugated circuits have the largest contributions to the resonance energy. The VBSCF calculations also show that the extra stability of phenanthrene, a kinked benzenoid, as compared to its linear counterpart, anthracene, is a consequence of the resonance in the π-system rather than the H-H interaction in the bay region as suggested previously. Finally, the empirical parameters for the resonance interactions between different 4n+2 or 4n π electrons conjugated circuits, used in Randi?'s conjugated circuits theory or Herdon's semi-emprical VB approach, are quantified. These parameters have to be scaled by the structure coefficients (weights) of the contributing structures.     

Vibrational spectra and conformations of 1,4-cyclohexadiene and its oxygen analogues: ab initio and density functional calculations

The vibrational spectra and ring-puckering potential energy functions of 1,4-cyclohexadiene, 4H-pyran and 1,4-dioxin have been examined using a density functional theory (DFT) method as well as the Hartree–Fock (HF) and second-order Møller–Plesset (MP2) methods. The calculated vibrational frequencies and potential energy functions of those molecules have been compared with previously reported experimental data and MM3 results. For all three molecules, the DFT method using Becke's three-parameter functional (B3LYP) has led to the prediction of more accurate vibrational frequencies than the HF and MP2 methods. The enlargement of the basis set at the B3LYP levels has improved the accuracy of calculated vibrational frequencies. In particular, the C–O–C=C torsional force field parameters obtained from the B3LYP method have correctly predicted the ring-puckering potential energy functions of the oxygen-containing analogues, 4H-pyran and 1,4-dioxin, which could not be done by the MM3 method.     

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.     

Wheland intermediates: an ab initio valence bond study

The traditional resonance model for electrophilic attacks on substituted aromatic rings is revisited using high level valence bond (VB) calculations. A large π-donation is found in the X = NH(2) case and a weaker one for the X = Cl case, not only for ortho and para isomers but also for the meta case, which can be explained by considering five (not three) fundamental VB structures. No substantial π-effect is found in the X = NO(2) case, generally viewed as π-attractive.     

AsH3 ultraviolet photochemistry: an ab initio view

Multireference configuration interaction calculations have been carried out for low-lying electronic states of AsH(3). Bending potentials for the nine lowest states of AsH(3) are obtained in C(3v) symmetry for As-H distances fixed at the ground state equilibrium value of 2.850 a(0), as well as for the minimum energy path constrained to R(1) = R(2) = R(3). The calculated equilibrium geometry and bond energy for the X (1)A(1) ground state agree very well with the previous experimental and theoretical data. It is shown that the lowest excited singlet state belongs to the (1)A(1) symmetry (in C(3v)), in contradiction to the previous calculations. This state is characterized by a planar equilibrium geometry. Asymmetric stretch potential energy surface (PES) cuts along the H(2)As-H recoil coordinate (at R(1) = R(2) = 2.850 a(0), θ = 123.9° and 90°) for numerous excited states and two-dimensional PESs for the X and ? states up to the dissociation limits are obtained for the first time. The ? (1)A(1), B(1)E-X (1)A(1) transition moments are calculated as well and used together with the PES data for the analysis of possible photodecay channels of arsine in its first absorption band.     

Pseudorotation motion in tetrahydrofuran: an ab initio study

The use of different models based on experimental information about the observed level splitings, rotational constants, and far-infrared transition frequencies leads to different predictions on the equilibrium geometry for tetrahydrofuran. High-level ab initio calculations [coupled cluster singles, doubles (triples)/complete basis set (second order Moller-Plesset triple, quadrupole, quintuple)+zero-point energy(anharmonic)] suggest that the equilibrium conformation of tetrahydrofuran is an envelope C(s) structure. The theoretical geometrical parameters might be helpful to plan further microwave spectroscopic studies in order to get a physical interpretation of the measurements.     

Towards SiC surface functionalization: an ab initio study

We present a microscopic model of the interaction and adsorption mechanism of simple organic molecules on SiC surfaces as obtained from ab initio molecular-dynamics simulations. Our results open the way to functionalization of silicon carbide, a leading candidate material for biocompatible devices.     

Photodissociation of 1,3,5-triazine: an ab initio and RRKM study

The ab initio/Rice-Ramsperger-Kassel-Marcus (RRKM) approach has been applied to investigate the photodissociation mechanism of 1,3,5-triazine at different wavelengths of the absorbed photon. Reaction pathways leading to various decomposition products have been mapped out at the G3(MP2,CC)//B3LYP level, and then the RRKM and microcanonical variational transition state theories have been applied to compute rate constants for individual reaction steps. Relative product yields (branching ratios) for the dissociation products have been calculated using the steady-state approach. The results show that, after being excited by 275, 248, or 193 nm photons, the triazine molecule isomerizes to an opened-ring structure on the first singlet excited-state potential energy surface (PES), which is followed by relaxation into the ground electronic state via internal conversion. On the contrary, excitation by 285 and 295 nm photons cannot initiate the ring-opening reaction on the excited-state PES, and the molecule relaxes into the energized ring isomer in the ground electronic state. The dissociation reaction starting from the ring isomer is calculated to have branching ratios of various reaction channels significantly different from those for the reaction initiating from the opened-ring structure. The existence of two distinct mechanisms of 1,3,5-triazine photodissociation can explain the inconsistency in the translational energy distributions of HCN moieties at different wavelengths observed experimentally.     

Vibrational predissociation dynamics of methane-Ar: an ab initio approach

We calculated the cross sections for vibrational predissociation of methane-Ar induced by excitation of the methane nu 3 mode with the aid of an ab initio CH4-Ar potential depending explicitly on the nu 3 and nu 1 normal coordinates of the CH4 monomer. We found that dissociation into CH4 fragments excited in the nu 1 mode, a V-->V' process with very low kinetic energy release, strongly dominates over direct dissociation into Ar and ground state CH4, and is responsible for the line broadening observed experimentally. The (observed and calculated) strong variation of the line widths for the Van der Waals levels excited in combination with the nu 3 mode (giving states of A, F and E symmetry) is related to the opening up of appropriate nu 1 dissociation channels and the occurrence of rotational resonances in the nu 1 continuum in the energy range of the quasi-bound nu 3 levels.