Theoretical study on the β−-decay effect in mono-tritiated two hydrogen bonded systems: proton transfer along the hydrogen bond direction

The effect of tritium β^?-decay on the “two” hydrogen bonds in mono-tritiated formamide dimer (A), formic acid dimer (B), and acetic acid-formic acid (C) was studied with ab initio MO calculations. The tritium β^?-decay in (A) and (B) is expected to result in spontaneous transfer of one proton along the hydrogen bond direction: no proton transfer takes place in (C).     

Ab initio molecular dynamics with discrete variable representation basis sets: techniques and application to liquid water

Finite temperature ab initio molecular dynamics (AIMD), in which forces are obtained from "on-the-fly" electronic structure calculations, is a widely used technique for studying structural and dynamical properties of chemically active systems. Recently, we introduced an AIMD scheme based on discrete variable representation (DVR) basis sets, which was shown to have improved convergence properties over the conventional plane wave (PW) basis set [Liu,Y.; et al. Phys. Rev. B 2003, 68, 125110]. In the present work, the numerical algorithms for the DVR based AIMD scheme (DVR/AIMD) are provided in detail, and the latest developments of the approach are presented. The accuracy and stability of the current implementation of the DVR/AIMD scheme are tested by performing a simulation of liquid water at ambient conditions. The structural information obtained from the present work is in good agreement with the result of recent AIMD simulations with a PW basis set (PW/AIMD). Advantages of using the DVR/AIMD scheme over the PW/AIMD method are discussed. In particular, it is shown that a DVR/AIMD simulation of liquid water in the complete basis set limit is possible with a relatively small number of grid points.     

A Theoretical Analysis on the Oxidation and Water Dissociation Resistance on Group-IV Phosphide Monolayers

Group-IV phosphide monolayers (MP, M=C, Si, Ge and Sn) provide a versatile platform for photocatalysts, as well as optoelectronic and nanoelectronic devices. Herein, comprehensive first-principles calculations and ab initio molecular dynamics (AIMD) simulations were performed to explore their stabilities in the air. We identified that the MP monolayers have excellent mechanical properties and their carrier mobilities are higher than that of phosphorene. The MP monolayers were predicted to possess superior oxidation resistance than the boron phosphide (BP) monolayer based on the proposed donation–backdonation theory. It was observed that the dissociation and chemisorption of a water molecule on the monolayers are kinetically difficult both in the water and in oxygen–water environments involving energy barriers of 1.28–3.48 eV. We also performed AIMD simulations at 300, 1000, 1200 and 1500 K. It is noteworthy that only the carbon phosphide (CP) monolayer can retain an intact structure at 1500 K, while the other three monolayers can just sustain to 1200 K. These results provide a guidance for their practical application and experimental fabrication.     

Hydration shell structure and dynamics of curium(III) in aqueous solution: first principles and empirical studies

Results of ab initio molecular dynamics (AIMD), quantum mechanics/molecular mechanics (QM/MM), and classical molecular dynamics (CMD) simulations of Cm(3+) in liquid water at a temperature of 300 K are reported. The AIMD simulation was based on the Car-Parrinello MD scheme and GGA-PBE formulation of density functional theory. Two QM/MM simulations were performed by treating Cm(3+) and the water molecules in the first shell quantum mechanically using the PBE (QM/MM-PBE) and the hybrid PBE0 density functionals (QM/MM-PBE0). Two CMD simulations were carried out using ab initio derived pair plus three-body potentials (CMD-3B) and empirical Lennard-Jones pair potential (CMD-LJ). The AIMD and QM/MM-PBE simulations predict average first shell hydration numbers of 8, both of which disagree with recent experimental EXAFS and TRLFS value of 9. On the other hand, the average first shell hydration numbers obtained in the QM/MM-PBE0 and CMD simulations was 9, which agrees with experiment. All the simulations predicted an average first shell and second shell Cm-O bond distance of 2.49-2.53 ? and 4.67-4.75 ? respectively, both of which are in fair agreement with corresponding experimental values of 2.45-2.48 and 4.65 ?. The geometric arrangement of the 8-fold and 9-fold coordinated first shell structures corresponded to the square antiprism and tricapped trigonal prisms, respectively. The second shell hydration number for AIMD QM/MM-PBE, QM/MM-PBE0, CMD-3B, and CMD-LJ, were 15.8, 17.2, 17.7, 17.4, and 16.4 respectively, which indicates second hydration shell overcoordination compared to a recent EXAFS experimental value of 13. Save the EXAFS spectra CMD-LJ simulation, all the computed EXAFS spectra agree fairly well with experiment and a clear distinction could not be made between configurations with 8-fold and 9-fold coordinated first shells. The mechanisms responsible for the first shell associative and dissociative ligand exchange in the classical simulations have been analyzed. The first shell mean residence time was predicted to be on the nanosecond time scale. The computed diffusion constants of Cm(3+) and water are in good agreement with experimental data.     

稀醋酸/水溶液中单个醋酸与水分子的氢键结构

在醋酸/水体系的工业分离中,溶液中的氢键对分离效率有很大影响.本文采用两种第一性原理方法,即从头算分子动力学模拟(AIMD)和量子化学计算(QCC),对由单个醋酸和不同水分子所组成聚合体的氢键相互作用进行了研究,采用极化统一模型和自洽反应场模型计算得到了聚合体在水溶液中的热力学数据.从QCC计算的气相和水溶液中的聚合自由能表明六元环在两种状态下都为最优结构,热力学数据反映出的各种结构的相对稳定性与AIMD模拟的环分布符合得相当一致.研究表明,由于存在醋酸和水分子间的氢键作用,稀醋酸/水溶液中的醋酸分离要比在浓醋酸溶液中困难得多.     

Aggregation of acetic and propionic acid in argon matrices--a matrix isolation and computational study

Monomeric acetic acid MA and propionic acid MP were isolated in argon matrices at 10K by using a pulse deposition technique. The dimerization of the monomers was induced by warming the matrices from 10 to 40 K. Under these conditions the diffusion of small trapped molecules is rapid and the dimerization could be monitored directly by IR spectroscopy. Both carboxylic acids form the symmetrical dimers B with two strong C=O...HO hydrogen bridges as the thermodynamically most stable dimers. With acetic acid a less stable dimer AA could be obtained if high concentrations of acetic acid in argon were used during the deposition of the matrix. On annealing this dimer rearranges to the more stable BA. In contrast, propionic acid does not form a corresponding less stable dimer under any experimental condition. These observations are rationalized on the basis of DFT and ab initio calculations.     

Conformations of trimethoxymethylsilane: matrix isolation infrared and ab initio studies

Conformations of trimethoxymethylsilane were studied using matrix isolation infrared spectroscopy and ab initio computations. Trimethoxymethylsilane was trapped in both argon and nitrogen matrixes using heated nozzle effusive sources and a supersonic jet source, in an effort to alter the conformational population in the matrix. Ab initio calculations were carried out at the HF and B3LYP level using 6-31++G basis set to support our experimental observations. The frequencies computed at the B3LYP level was found to fit well with our experimental data. A conformer with a C1(g(+/-)g(+/-)t) structure was predicted by our computations to be the ground state conformer.     

Infrared laser spectroscopy of imidazole complexes in helium nanodroplets: monomer, dimer, and binary water complexes

Infrared laser spectroscopy has been used to characterize imidazole (IM), imidazole dimer (IMD), and imidazole-water (IMW) binary systems formed in helium nanodroplets. The experimental results are compared with ab initio calculations reported here. Vibrational transition moment angles provide conclusive assignments for the various complexes studied here, including IM, one isomer of IMD, and two isomers of the IMW binary complexes.     

Molecular orbital propagation to accelerate self-consistent-field convergence in an ab initio molecular dynamics simulation

Based on the idea of molecular orbital (MO) propagation, we propose a novel effective method for predicting initial guesses for the self-consistent-field calculations in direct ab initio molecular dynamics (AIMD) simulations. This method, called LIMO, adopts the Lagrange interpolation (LI) polynomial technique and predicts initial MO coefficients at the next AIMD step by using several previous results. Taking into account the crossing and/or mixing of MOs leads to orbital invariant formulas for the LIMO method. We also propose a simple method for determining the optimal degree of the LI polynomial, which corresponds to the number of previous steps. Numerical tests confirm that this proposed method is both effective and feasible.     

Ab initio ground and excited state potential energy surfaces for NO-Kr complex and dynamics of Kr solids with NO impurity

The intermolecular potentials for the NO(X 2Pi)-Kr and NO(A 2Sigma+)-Kr systems have been calculated using highly accurate ab initio calculations. The spin-restricted coupled cluster method for the ground 1 2A' state [NO(X 2Pi)-Kr] and the multireference singles and doubles configuration interaction method for the excited 2 2A' state [NO(A 2Sigma+)-Kr], respectively, were used. The potential energy surfaces (PESs) show two linear wells and one that is almost in the perpendicular position. An analytical representation of the PESs has been constructed for the triatomic systems and used to carry out molecular dynamics (MD) simulations of the NO-doped krypton matrix response after excitation of NO. MD results are shown comparatively for three sets of potentials: (1) anisotropic ab initio potentials [NO molecule direction fixed during the dynamics and considered as a point (its center of mass)], (2) isotropic ab initio potentials (isotropic part in a Legendre polynomial expansion of the PESs), and (3) fitted Kr-NO potentials to the spectroscopic data. An important finding of this work is that the anisotropic and isotropic ab initio potentials calculated for the Kr-NO triatomic system are not suitable for describing the dynamics of structural relaxation upon Rydberg excitation of a NO impurity in the crystal. However, the isotropic ab initio potential in the ground state almost overlaps the published experimental potential, being almost independent of the angle asymmetry. This fact is also manifested in the radial distribution function around NO. However, in the case of the excited state the isotropic ab initio potential differs from the fitted potentials, which indicates that the Kr-NO interaction in the matrix is quite different because of the presence of the surrounding Kr atoms acting on the NO molecule. MD simulations for isotropic potentials reasonably reproduce the experimental observables for the femtosecond response and the bubble size but do not match spectroscopic results. A general overall view of the results suggests that, when the Kr-NO interaction takes place inside the matrix, potentials are rather symmetric and less repulsive than those for the triatomic system.     

Free energy perturbation study of water dimer dissociation kinetics

An efficient approach is described for using accurate ab initio calculations to determine the rates of elementary condensation and evaporation processes that lead to nucleation of aqueous aerosols. The feasibility of the method is demonstrated in an application to evaporation rates of water dimer at 230 K. The method, known as ABC-FEP (ab initio/classical free energy perturbation), begins with a calculation of the potential of mean force for the dissociation (evaporation) of small water clusters using a molecular dynamics (MD) simulation with a model potential. The free energy perturbation is used to calculate how changing from the model potential to a potential calculated from ab initio methods would alter the potential of mean force. The difference in free energy is the Boltzmann-weighted average of the difference between the ab initio and classical potential energies, with the average taken over a sample of configurations from the MD simulation. In principle, the method does not require a highly accurate model potential, though more accurate potentials require fewer configurations to achieve a small sampling error in the free energy perturbation step. To test the feasibility of obtaining accurate potentials of mean force from ab initio calculations at a modest number of configurations, the free energy perturbation method has been used to correct the errors when some standard models for bulk water (SPC, TIP4P, and TIP4PFQ) are applied to water dimer. To allow a thorough exploration of sampling issues, a highly accurate fit to results of accurate ab initio calculations, known as SAPT-5s, as been used a proxy for the ab initio calculations. It is shown that accurate values for a point on the potential of mean force can be obtained from any of the water models using ab initio calculations at only 50 configurations. Thus, this method allows accurate simulations of small clusters without the need to develop water models specifically for clusters.     

Dissolution nature of cesium fluoride by water molecules

The structures, stabilities, thermodynamic quantities, dissociation energies, infrared spectra, and electronic properties of CsF hydrated by water molecules are investigated by using density functional theory, M?ller-Plesset second-order perturbation theory (MP2), coupled cluster theory with singles, doubles, and perturbative triples excitations (CCSD(T)), and ab initio molecular dynamic (AIMD) simulations. It is revealed that at 0 K three water molecules (as a global minimum structure) begin to half-dissociate the Cs-F, and six water molecules (though not a global minimum energy structure) can dissociate it. By the combination of the accurate CCSD(T) conformational energies for Cs(H2O)6 at 0 K with the AIMD thermal energy contribution, it reveals that the half-dissociated structure is the most stable at 0 K, but this structure (which is still the most stable) changes to the dissociated structure above 50 K. The spectra of CsF(H2O)(1-6) from MP2 calculations and the power spectra of CsF(H2O)6 from 50 and 100 K AIMD simulations are also reported.     

Dimerization of thymol blue in solution: Theoretical evidence

The possibility of dimerization of thymol blue was addressed by ab initio and force field calculations. In agreement with experimental information, a dimer forming symmetrical chemical environments for hydrogen bond formation was determined. This dimer is stable in vacuum and aqueous media and corresponds to the same protonated state proposed by the experiment. A comparison of the CVFF and MM3 force fields and ab initio results shows the suitability of CVFF to qualitatively describe this system.     

A single transition state serves two mechanisms. The branching ratio for CH2O*- + CH3Cl on improved potential energy surfaces

The reaction of formaldehyde radical anion with methyl chloride, CH2O*- + CH3Cl, is an example in which a single transition state leads to two products: substitution at carbon (Sub(C), CH3CH2O* + Cl-) and electron transfer (ET, CH2O + CH3* + Cl-). The branching ratio for this reaction has been studied by ab initio molecular dynamics (AIMD). The energies of transition states and intermediates were computed at a variety of levels of theory and compared to accurate energetics calculated by the G3 and CBS-QB3 methods. A bond additivity correction has been constructed to improve the Hartree-Fock potential energy surface (BAC-UHF). A satisfactory balance between good energetics and affordable AIMD calculations can be achieved with BH&HLYP/6-31G(d) and BAC-UHF/6-31G(d) calculations. Approximately 200 ab initio classical trajectories were calculated for each level of theory with initial conditions sampled from a thermal distribution at 298 K at the transition state. Three types of trajectories were distinguished: trajectories that go directly to ET product, trajectories that go to Sub(C) product, and trajectories that initially go into the Sub(C) valley and then dissociate to ET products. The BH&HLYP/6-31G(d) calculations overestimate the number of nonreactive and direct ET trajectories because the transition state is too early. For the BH&HLYP and BAC-UHF methods, about one-third of the trajectories that initially go into the Sub(C) valley dissociate to ET products, compared to just over half with UHF/6-31G(d) in the earlier study. This difference can be attributed to a better value for the calculated energy release from the initial transition state and to an improved Sub(C) --> ET barrier height with the BH&HLYP and BAC-UHF methods.     

Ab initio potential and dipole moment surfaces for water. II. Local-monomer calculations of the infrared spectra of water clusters

We employ recent flexible ab initio potential energy and dipole surfaces [Y. Wang, X. Huang, B. C. Shepler, B. J. Braams, and J. M. Bowman, J. Chem. Phys. 134, 094509 (2011)] to the calculation of IR spectra of the intramolecular modes of water clusters. We use a quantum approach that begins with a partitioned normal-mode analysis of perturbed monomers, and then obtains solutions of the corresponding Schro?dinger equations for the fully coupled intramolecular modes of each perturbed monomer. For water clusters, these modes are the two stretches and the bend. This approach is tested against benchmark calculations for the water dimer and trimer and then applied to the water clusters (H(2)O)(n) for n = 6-10 and n = 20. Comparisons of the spectra are made with previous ab initio harmonic and empirical potential calculations and available experiments.     

Quantitative determination of magnetization exchange rate constants from a series of two-dimensional exchange NMR spectra

A method for quantitative determination of magnetization exchange rate constants (cross-relaxation and chemical exchange) from a series of two-dimensional exchange spectra is presented. The method, the least error matrix analysis (LEMA), combines a series of full matrix calculations at different mixing times in a least-squares manner. LEMA embodies the principal advantages of full-relaxation matrix analysis (FMA) and initial rate buildup (BU) analysis. Like FMA, it takes into account all the relations among the spectral matrix elements and in analogy to BU makes use of their time evolution. By means of calculations, simulations, and experiments, we have shown that LEMA provides the dynamic matrix from a given set of experimental data with errors that are smaller than in either FMA or BU calculations.     

Magnitude and orientation dependence of intermolecular interaction of perfluoropropane dimer studied by high-level ab initio calculations: comparison with propane dimer

Intermolecular interaction energies of 12 orientations of C(3)F(8) dimers were calculated with electron correlation correction by the second-order M?ller-Plesset perturbation method. The antiparallel C(2h) dimer has the largest interaction energy (-1.45 kcal/mol). Electron correlation correction increases the attraction considerably. Electrostatic energy is not large. Dispersion is mainly responsible for the attraction. Orientation dependence of the interaction energy of the C(3)F(8) dimer is substantially smaller than that of the C(3)H(8) dimer. The calculated interaction energy of the C(3)F(8) dimer at the potential minimum is 78% of that of the C(3)H(8) dimer (-1.85 kcal/mol), whereas the interaction energies of the CF(4) and C(2)F(6) dimers are larger than those of the CH(4) and C(2)H(6) dimers. The intermolecular separation in the C(3)F(8) dimer at the potential minimum is substantially larger than that in the C(3)H(8) dimer. The larger intermolecular separation due to the steric repulsion between fluorine atoms is the cause of the smaller interaction energy of the C(3)F(8) dimer at the potential minimum. The calculated intermolecular interaction energy potentials of the C(3)F(8) dimers using an all atom model OPLS-AA (OPLS all atom model) force field and a united atom model force field were compared with the ab initio calculations. Although the two force fields well reproduces the experimental vapor and liquid properties of perfluoroalkenes, the comparison shows that the united atom model underestimates the potential depth and orientation dependence of the interaction energy. The potentials obtained by the OPLS-AA force field are close to those obtained by the ab initio calculations.     

Accurate equilibrium structures obtained from gas-phase electron diffraction data: sodium chloride

A novel method has been developed to allow the accurate determination of equilibrium gas-phase structures from experimental data, thus allowing direct comparison with theory. This new method is illustrated through the example of sodium chloride vapor at 943 K. Using this approach the equilibrium structures of the monomer (NaCl) and the dimer (Na(2)Cl(2)), together with the fraction of vapor existing as dimer, have been determined by gas-phase electron diffraction supplemented with data from microwave spectroscopy and ab initio calculations. Root-mean-square amplitudes of vibration (u) and distance corrections (r(a) - r(e)) have been calculated explicitly from the ab initio potential-energy surfaces corresponding to the vibrational modes of the monomer and dimer. These u and (r(a) - r(e)) values essentially include all of the effects associated with large-amplitude modes of vibration and anharmonicity; using them we have been able to relate the ra distances from a gas-phase electron diffraction experiment directly to the re distances from ab initio calculations. Vibrational amplitudes and distance corrections are compared with those obtained by previous methods using both purely harmonic force fields and those including cubic anharmonic contributions, and the differences are discussed. The gas-phase equilibrium structural parameters are r(e)(Na-Cl)(monomer) = 236.0794(4) pm; r(e)(Na-Cl)(dimer) = 253.4(9) pm; and <(e)ClNaCl = 102.7(11) degrees. These results are found to be in good agreement with high-level ab initio calculations and are substantially more precise than those obtained in previous structural studies.