Direct ab initio MD study on the hydrogen abstraction reaction of triplet state acetone from methanol molecule

Solvent re-orientation process of triplet acetone/methanol complex and intermolecular hydrogen atom abstraction reaction on the triplet state energy surface, (CH₃)₂C=O (T₁) + CH₃OH → (CH₃)₂C–OH + CH₂OH in gas phase, have been investigated by means of density functional theory (DFT) and direct ab initio molecular dynamics (MD) methods. The static DFT calculation of hydrogen abstraction reaction at the T₁ state showed that the transition state is 16.4 and 30.9 kcal/mol lower than the energy levels of S₁ and S₂ states, respectively, and 9.2 kcal/mol higher than the bottom of T₁ state. The product state, (CH₃)₂C–OH⋯CH₂OH, is 8.4 kcal/mol lower in energy than the level of T₁ state. The direct ab initio MD calculation showed that the product is rapidly formed within 150 fs and the separated products (CH₃)₂C–OH + CH₂OH were formed. The mechanism of reaction dynamics of the triplet acetone/methanol complex was discussed on the basis of theoretical results.     

High-level ab initio studies of unimolecular dissociation of the ground-state N3 radical

A comprehensive study of the unimolecular dissociation of the N(3) radical on the ground doublet and excited quartet potential energy surfaces has been carried out with multireference single and double excitation configuration interaction and second-order multireference perturbation methods. Two forms of the N(3) radical have been located in the linear and cyclic region of the lowest doublet potential energy surface with an isomerization barrier of 62.2 kcal/mol above the linear N(3). Three equivalent C(2v) minima of cyclic N(3) are connected by low barrier, meaning the molecule is free to undergo pseudorotation. The cyclic N(3) is metastable with respect to ground state products, N((4)S)+N(2), and dissociation must occur via intersystem crossing to a quartet potential energy surface. Minima on the seams of crossing between the doublet and quartet potential surfaces are found to lie substantially higher in energy than the cyclic N(3) minima. This strongly suggests that cyclic N(3) possesses a long collision-free lifetime even if formed with substantial internal excitation.     

Ab initio studies on hydrogen-transfer tunneling for Cl + HCl abstraction hydrogen reaction

This article presents a treatment scheme of the tunneling of hydrogen between two molecular centers (Cl…Cl). The purpose is to calculate the tunneling probabilities of hydrogen atom transfer from the initial (the proceeding complex) to the final-state energy minima (the succeeding complex) in two anharmonic vibrational states (0 → 0 and 1 → 1) in terms of the time-dependent perturbation theory expression and to see whether spectroscopic signatures of tunneling persist in the form of splittings of the vibrational modes. The analysis uses the realistic potential energy function calculated at the HF/6−31 + G** self-consistent-field basis-set level for the interaction between transferred hydrogen and its molecular skeleton (Cl…H…Cl). This potential energy surface is calibrated by comparing its properties with those from sf-POLCI and the LEPS potential-energy surfaces. The anharmonic vibrational state is characterized by the corrected vibrational energy levels and a set of linear combination coefficients obtained via perturbation theory. The tunneling probabilities for two transitions (0 → 0 and 1 → 1) were calculated and compared with those from Gamow's equation. Applicability of the time-dependent perturbation theory expression and Gamow's equation to the [Cl BOND H…Cl] system is discussed. The vibrational splitting energies are obtained, and a spectroscopic signature caused by tunneling is expected and should be observable. © 1996 John Wiley & Sons, Inc.     

High-level ab initio studies of the electronic excited states of the hydroxyl radical and water-hydroxyl complex

The lowest-energy electronic transitions in the hydroxyl radical and the hydrogen bound complex H(2)O.HO have been studied using ab initio methods. We have used the complete active-space self-consistent field and multireference configuration interaction (MRCI) methods to calculate vertical excitation energies and oscillator strengths. At the MRCI level the lowest-lying (2)Sigma(+)<--(2)Pi electronic transition is redshifted by about 2500 cm(-1) upon formation of the H(2)O.HO complex. We propose that this transition could be used to identify the complex in the gas phase, which in turn could be used to examine the role of H(2)O.HO in atmospheric reactions.     

High-level ab initio studies of the structure, vibrational spectra, and energetics of S3

Observation of mass-dependent and non-mass-dependent sulfur isotope fractionations in elemental sulfur is providing new insight into the nature of the sulfur cycle in the atmosphere. Interpretation of the experimental isotope data requires estimation of the energetics for the reaction S+S2-->S3 (isoelectronic with O+O2-->O3). Key molecular properties of the S3 potential-energy surface, such as vibrational frequencies and isotopic shifts, are presented that can be used to assess the mass-dependent fractionation effect. Ab initio results are compared to the available experimental results for S2 to evaluate the reliability of the computational results for S3. The S-S bond dissociation energy for S3 is determined to be 60.9+/-1 kcal mol(-1).     

Kinetic Monte Carlo studies of hydrogen abstraction from graphite

We present Monte Carlo simulations on Eley-Rideal abstraction reactions of atomic hydrogen chemisorbed on graphite. The results are obtained via a hybrid approach where energy barriers derived from density functional theory calculations are used as input to Monte Carlo simulations. By comparing with experimental data, we discriminate between contributions from different Eley-Rideal mechanisms. A combination of two different mechanisms yields good quantitative and qualitative agreement between the experimentally derived and the simulated Eley-Rideal abstraction cross sections and surface configurations. These two mechanisms include a direct Eley-Rideal reaction with fast diffusing H atoms and a dimer mediated Eley-Rideal mechanism with increased cross section at low coverage. Such a dimer mediated Eley-Rideal mechanism has not previously been proposed and serves as an alternative explanation to the steering behavior often given as the cause of the coverage dependence observed in Eley-Rideal reaction cross sections.     

Site specificity of alpha-H abstraction reaction among secondary structure motif--an ab initio study

The initial step of protein oxidation is studied through alpha-H abstraction by an OH radical with various secondary structure motifs of proteins. It is found that there exist preferential alpha-Hs in this kind of abstractions. The typical abstraction mechanism involves three steps: forming a pre-reactive complex before abstraction, the abstraction reaction, and the H(2)O detachment from a post-reactive complex to form the product, C(alpha)-center radical. Using the stability of the pre-reactive complex and the reaction barrier, we provide some explanation for this site preference. The feasibility of alpha-H abstraction by OH radical depends not only on the types of secondary structure, but also on the reaction condition, such as in aqueous or in gas phase. Moreover, the reactivity of the abstraction also depends on the location of alpha-H in the secondary structure motifs. The preferential alpha-Hs to be abstracted in beta-sheet are those immediate to the amide or carbonyl group, and without involving hydrogen bonding, whereas in reverse turns, the preferential alpha-Hs are near the C-terminal of type I and near the N-terminal of type II. In general, the alpha-Hs in alpha-helix are more difficult to be abstracted than those in beta-sheet and polypeptide in linear form. It is consistent with the trend of their bond dissociation energies. Our theoretical rate constant of N-acetyldiglycin-methylamide (Ac(Gly)(2)NHCH(3)) in aqueous solution (6.75 x 10(8) M(-1) s(-1)) is close to the experimental observation of N-acetyldiglycinamide (Ac(Gly)(2)NH(2)) (8.6 x 10(8) M(-1) s(-1)).     

Photoelectron spectra of hydrogen peroxide and hydrogen disulphide: ab initio calculations

Koopmans' theorem ionization potentials from ab initio gaussian basis set calculations on cis, trans and skew forms of HOOH and HSSH are compared with experimental values from photoelectron spectroscopy.     

High-level ab initio potential energy surfaces and vibrational energies of H2CS

Six-dimensional (6D) potential energy surfaces (PESs) of H(2)CS have been generated ab initio using the recently proposed explicitly correlated (F12) singles and doubles coupled cluster method including a perturbational estimate of connected triple excitations, CCSD(T)-F12b [T. B. Adler, G. Knizia, and H.-J. Werner, J. Chem. Phys. 127, 221106 (2007)] in conjunction with F12-optimized correlation consistent basis sets. Core-electron correlation, high-order correlation, scalar relativistic, and diagonal Born-Oppenheimer terms were included as additive high-level (HL) corrections. The resulting 6D PESs were represented by analytical functions which were used in variational calculations of the vibrational term values below 5000 cm(-1). The best PESs obtained with and without the HL corrections, VQZ-F12(*HL) and VQZ-F12?, reproduce the fundamental vibrational wavenumbers with mean absolute deviations of 1.13 and 1.22 cm(-1), respectively. A detailed analysis of the effects of the HL corrections shows how the VQZ-F12 results benefit from error cancellation. The present purely ab initio PESs will be useful as starting points for empirical refinements towards an accurate "spectroscopic" PES of H(2)CS.     

壳聚糖－戊二醛的量子化学从头算

采用量子化学从头算方法研究了壳聚糖-戊二醛交联膜的稳定结构,研究了壳聚糖和戊二醛通过氨醛缩合形成阳离子膜的几何构型、键能、键序和电子迁移,讨论了膜的成键形式和稳定性．     

An ab initio potential surface describing abstraction and exchange for H+CH4

We report an ab initio-based global potential energy surface for H+CH4 that describes the abstraction and exchange reactions. The PES, which is invariant with respect to any permutation of five H atoms, is a fit to 20,728 electronic energies calculated using the partially spin-restricted coupled-cluster method (RCCSD(T)) with a moderately large basis (aug-cc-pVTZ). A first set of quasiclassical trajectory calculations using this PES are reported for the H+CD4-->HD+CD3 reaction at collision energies of 0.65 and 1.52 eV and are compared to experiment and recent direct dynamics calculations done with density functional theory.     

An ab initio benchmark study of hydrogen bonded formamide dimers

The five singly and doubly hydrogen bonded dimers of formamide are calculated at the correlated level by using resolution of identity M?ller-Plesset second-order perturbation theory (RIMP2) and the coupled cluster with singles, doubles, and perturbative triples [CCSD(T)] method. All structures are optimized with the Dunning aug-cc-pVTZ and aug-cc-pVQZ basis sets. The binding energies are extrapolated to the complete basis set (CBS) limit by using the aug-cc-pVXZ (X = D, T, Q) basis set series. The effect of extending the basis set to aug-cc-pV5Z on the geometries and binding energies is studied for the centrosymmetric doubly N-H...O bonded dimer FA1 and the doubly C-H...O bonded dimer FA5. The MP2 CBS limits range from -5.19 kcal/mol for FA5 to -14.80 kcal/mol for the FA1 dimer. The DeltaCCSD(T) corrections to the MP2 CBS limit binding energies calculated with the 6-31+G(d,p), aug-cc-pVDZ, and aug-cc-pVTZ basis sets are mutually consistent to within < or =0.03 kcal/mol. The DeltaCCSD(T) correction increases the binding energy of the C-H...O bonded FA5 dimer by 0.4 kcal/mol or approximately 9% over the distance range +/-0.5 Angstrom relative to the potential minimum. This implies that the ubiquitous long-range C-H...O interactions in proteins are stronger than hitherto calculated.     

Vibrational spectroscopic studies and ab initio calculations of sulfanilamide

FT-Raman and FT-IR spectra of sulfanilamide were recorded and analyzed. The vibrational frequencies of the compound have been computed using the Hartree-Fock/6-21G(*) basis and compared with the experimental values. The assignments of the observed bands were made on the basis of available literature.     

Hydrogen abstraction from n-butanol by the methyl radical: high level ab initio study of abstraction pathways and the importance of low energy rotational conformers

Hydrogen abstraction reactions by the methyl radical from n-butanol have been investigated at the ROCBS-QB3 level of theory. Reaction energies and product geometries for the most stable conformer of n-butanol (ROH) have been computed, the reaction energies order α < γ < β < δ < OH. The preference for n-butane to favour H-abstraction at C(β) and C(γ) while, in contrast, n-butanol favours radical reactions at the C(α) carbon is rationalised. Transition state (TS) barriers and geometries for the most stable conformer of n-butanol are presented, and discussed with respect to the Hammond postulate. The reaction barriers order as α < OH < γ < β < δ. This relative ordering is not consistent with product radical stability, C-H bond dissociation energies or previous studies using O[combining dot above]H and HO[combining dot above](2) radicals. We provide a molecular orbital based rationalisation for this ordering and answer two related questions: Why is the γ-channel more stable than the β-channel? Why do the two C(γ)-H H-abstraction TS differ in energy? The method and basis set dependence of the TS barriers is investigated. The Boltzmann probability distribution for the n-butanol conformers suggests that low energy conformers are present in approximately equal proportions to the most stable conformer at combustion temperatures where ?H(3) radicals are present. Thus, the relative significance of the various H-abstraction channels has been assessed for a selection of higher energy conformers (ROH'). Key results include finding that higher energy n-butanol conformers (E(ROH') > E(ROH)) can generate lower energy product radicals, E(ROH') < E(ROH). Moreover, higher energy conformers can also have a globally competitive TS energy for H-abstraction.     

High-level ab initio thermochemical data for halides of chromium, manganese, and iron

The thermochemistry of the transition-metal fluorides and chlorides MF(n)() and MCl(n)() (M = Cr, Mn, Fe; n = 1, 2) has been characterized by high-level ab initio electronic structure methods. Geometries and harmonic vibrational frequencies were computed at the B3LYP level of theory using triple-zeta basis sets including diffuse and polarization functions. Heats of formation were computed from isogyric reaction energies at the CCSD(T) level using high-quality basis sets, including corrections for core-valence correlation and scalar relativistic effects. To investigate the possible linearity of the ground states of CrCl(2) and CrF(2), we performed geometry optimizations for these species at the CCSD(T) level using large basis sets. In both cases, a bent ((5)B(2)) minimum structure was located, but the bent structure is only slightly below the linear form, which was found to be a transition state. For all of the investigated halides, polynomial fits were carried out for the heat capacity and the standard enthalpy and entropy in the 300-3000 K temperature range.     

Infrared and ab initio studies of hydrogen bonding and proton transfer in the complexes formed by pyrazoles

The results of experimental studies and quantum mechanical calculations of vibrational spectra and structure of hydrogen bonded complexes formed by pyrazole (P) and 3,5-dimethylpyrazole (DMP) are presented. IR spectra of pyrazoles in solutions, gas phase, and solid state have been investigated in wide range of concentrations and temperatures. It has been found that in the gas phase both P and DMP reveal the equilibrium between monomers, dimers, and trimers. In solutions the equilibrium between monomers and trimers dominates, no bands, which can be attributed to dimers were detected. DMP retains the trimer structure in solid state, while in the case of pyrazole P, formation of the crystal provides another type of association. Geometrical and spectral characteristics of dimers and trimers, obtained by ab initio calculations, are presented and compared with experimental data.

IR spectra of solutions containing P and DMP with a number of acids (acetic and trifluoroacetic acids, pentachlorophenol, HBr) have been studied in parallel with ab initio calculations. It has been found that pentachlorophenol forms with pyrazoles complexes with one strong hydrogen bond O–HN, while NH pyrazole group remains unbonded. With carboxylic acids DMP forms 1:1 cyclic complexes with two hydrogen bonds. In the case of acetic acid, the complex in CH₂Cl₂ solution reveals molecular structure with OHN and C=OHN bonds, in accordance with results of the calculations. For trifluoroacetic acid, the calculations predict the molecular structure to be energetically more stable in the case of the isolated binary complex (in gas phase), while the experimental spectrum of CH₂Cl₂ solution gives an evidence of the proton transfer with formation of the cyclic ionic pair with two NH⁺O⁻ bonds. The agreement with experimental results can be improved by taking into account the influence of environment in the framework of Onsager or Tomasi models. The shape of proton potential function of the complexes and medium effect on its parameters, resulted from experimental data and calculations, are discussed. It has been found that the number of potential minima and their relative depth depend strongly on the method of calculations and the basic set. Under excess of trifluoroacetic acid, the formation of 2:1 acid–DMP complex has been detected. Spectral characteristics and results of calculations point to the cyclic structure of this complex, which includes homoconjugated bis-trifluoroacetate anion and DMPH⁺ cation. With HBr both studied pyrazoles were found to form ionic complexes including one or two pyrazole molecules per one acid molecule and correspondingly monocation or homoconjugated cation BHB⁺.     

Properties of phosphorothioate DNA analogs. An ab initio study of prototype model linkages derived from dimethyl-phosphate anion

Ab initio HF and MP2 calculations on prototype model linkages of phosphorothioate DNA backbones illuminate the effects of phosphorothioation on electronic and structural properties of DNA backbone. The replacement of a bridging oxygen atom by sulfur in the phosphodiester linkage is energetically favored over that of replacement of a non-bridging oxygen atom. In phosphorothioate derivatives containing the P(OS)_nb moiety, the non-bridging oxygen atom always bears a higher negative charge than the non-bridging sulfur. Additional calculations on protonated (neutral) adducts suggest that phosphorothioation of the phosphodiester linkage lowers its proton affinity. Moreover, protonation of the non-bridging oxygen atom at phosphorous is favored over the protonation of the non-bridging sulfur atom for linkages containing the P(OS)_nb moiety. The ab initio calculated structural parameters are compared to the available crystallographic data of small phosphorothioate molecules and phosphorothioate oligodeoxynucleotides. These results have implications upon the biological activity of phosphorothioate DNA analogs.     

Quantum wavepacket ab initio molecular dynamics for extended systems

In this paper, we introduce a symmetry-adapted quantum nuclear propagation technique that utilizes distributed approximating functionals for quantum wavepacket dynamics in extended condensed-phase systems. The approach is developed with a goal for implementation in quantum-classical methods such as the recently developed quantum wavepacket ab intio molecular dynamics (QWAIMD) to facilitate the study of extended systems. The method has been numerically benchmarked for extended electronic systems as well as protonic conducting systems that benefit from quantum nuclear treatment. Vibrational properties are computed for the case of the protonic systems through use of a novel velocity-flux correlation function. The treatment is found to be numerically accurate and efficient.     

Note on the ab initio PUHF treatment of open-shell systems

Ab initio projected-unrestricted Hartree-Fock calculations have been carried out on a number of excited and ionic states of the water molecule. Results have been compared with large-scale CI calculations, with IVO calculations, and with those of Mrozek and Golebiewski obtained by the 2 × 2 rotation method applied to orbitals. It is concluded that the PUHF method may provide the most useful alternative to large-scale CI for calculating properties of open-shell systems. But it will not be generally useful for calculating spectral transition energies.