Molecular dynamics and metadynamics simulations of [2 + 2] photocycloaddition

Triplet state mechanism of [2 + 2] photocycloaddition forming a cyclobutane ring from two ethylenes is investigated in the context of photocatalysis. High‐level ab initio calculations are combined with ab initio adiabatic molecular dynamics and ab initio metadynamics for rare events modeling. In a photocatalytic scheme, a reactant reaches the triplet state either via intersystem crossing (ISC) or triplet sensitization. The model system adopts a biradical structure, which represents energy intersection with the ground state. The system either completes cyclization or undergoes fragmentation into two olefinic units. The potential and free energy surfaces of the cyclobutane/ethylenes system are mapped with multireference approaches describing possible reaction pathways. To obtain a full picture of a double bond photoreactivity, ab initio adiabatic dynamical calculations were used to estimate reaction yields and to model the effects of excess energy. The potential use of density functional theory based approaches for [2 + 2] photocycloaddition was investigated for future simulations and design of realistic photocatalytic systems. Dynamical aspects of [2 + 2] photocycloaddition via a triplet state manifold are investigated by combining ab initio multireference methods and ab initio molecular dynamics and metadynamics. The reaction pathways are studied for a model system of two ethylenes forming a cyclobutane ring to provide a basis for further studies on design of photocatalytic systems.     

HN2(2A') electronic manifold. I. A global ab initio study of first two states

A detailed ab initio multireference configuration interaction calculation with a standard aug-cc-pVTZ basis set is reported for the 1(2)A' and 2(2)A' states of the title system. The aim is to establish the dissociation scheme of all channels, while revealing the 2(2)A'/3(2)A' seam of conical intersections consistent with the crossings in the diatomic fragments. An ab initio mapping of linear NNH and T-shaped and linear NHN loci of conical intersections is also reported, jointly with a discussion of the topological features associated to a newly reported 2(2)A'/3(2)A' crossing seam.     

Theory, measurements, and modeling of OH and HO2 formation in the reaction of cyclohexyl radicals with O2

The production of OH and HO(2) in Cl-initiated oxidation of cyclohexane has been measured using pulsed-laser photolytic initiation and continuous-laser absorption detection. The experimental data are modeled by master equation calculations that employ new G2(MP2)-like ab initio characterizations of important stationary points on the cyclo-C(6)H(11)O(2) surface. These ab initio calculations are a substantial expansion on previously published characterizations, including explicit consideration of conformational changes (chair-boat, axial-equatorial) and torsional potentials. The rate constants for the decomposition and ring-opening of cyclohexyl radical are also computed with ab initio based transition state theory calculations. Comparison of kinetic simulations based on the master equation results with the present experimental data and with literature determinations of branching fractions suggests adjustment of several transition state energies below their ab initio values. Simulations with the adjusted values agree well with the body of experimental data. The results once again emphasize the importance of both direct and indirect components of the kinetics for the production of both HO(2) and OH in radical + O(2) reactions.     

Peptide/TiO2 surface interaction: a theoretical and experimental study on the structure of adsorbed ALA-GLU and ALA-LYS

The adsorption on the TiO(2) surface of two dipeptides AE (L-alanine-L-glutamic acid) and AK (L-alanine-L-lysine), that are "building blocks" of the more complex oligopeptide EAK16, has been investigated both theoretically and experimentally. Classical molecular dynamics simulations have been used to study the adsorption of H-Ala-Glu-NH(2) and H-Ala-Lys-NH(2) dipeptides onto a rutile TiO(2) (110) surface in water solution. Several peptide conformers have been considered simultaneously upon the surface. The most probable contact points between the molecules and the surface have been identified. Carbonyl oxygens as well as nitrogen atoms are possible Ti coordination points. Local effects are responsible for adsorption and desorption events. Self-interaction effects can induce molecular reorientations giving less strongly adsorbed species. The chemical structure and composition of thin films of the two dipeptides AE and AK on TiO(2) were investigated by XPS (X-ray photoelectron spectroscopy) measurements at both O and N K-edges. Theoretical ab initio calculations (DeltaSCF) were also performed to simulate the spectra, allowing for a direct comparison between experiment and theory.     

Accuracy of recent potential energy surfaces for the He-N2 interaction. I. Virial and bulk transport coefficients

A new exchange-Coulomb semiempirical model potential energy surface for the He-N2 interaction has been developed. Together with two recent high-level ab initio potential energy surfaces, it has been tested for the reliability of its predictions of second-virial coefficients and bulk transport phenomena in binary mixtures of He and N2. The agreement with the relevant available measurements is generally within experimental uncertainty for the exchange-Coulomb surface and the ab initio surface of Patel et al. [J. Chem. Phys. 119, 909 (2003)], but with slightly poorer agreement for the earlier ab initio surface of Hu and Thakkar [J. Chem. Phys. 104, 2541 (1996)].     

Dynamics of the F2+CH3SCH3 reaction: a molecule-molecule reaction without entrance barrier

The F(2)+CH(3)SCH(3) reaction was studied with crossed molecular beam techniques and high level ab initio calculations. Significant reactivity was observed even at low collision energies, consistent with the negligible barrier height obtained from the ab initio calculations. All experimental findings are consistent with a weakly bound reaction intermediate of F-F-S(CH(3))(2) structure, which possesses a special type of three-center four-electron bonding. Analogous intermediates can also explain the reactions of F(2) with CH(3)SH and CH(3)SSCH(3).     

Potential energy surface and MULTIMODE vibrational analysis of C2H3+

A full dimensional, ab initio-based semiglobal potential energy surface for C(2)H(3) (+) is reported. The ab initio electronic energies for this molecule are calculated using the spin-restricted, coupled cluster method restricted to single and double excitations with triples corrections [RCCSD(T)]. The RCCSD(T) method is used with the correlation-consistent polarized valence triple-zeta basis augmented with diffuse functions (aug-cc-pVTZ). The ab initio potential energy surface is represented by a many-body (cluster) expansion, each term of which uses functions that are fully invariant under permutations of like nuclei. The fitted potential energy surface is validated by comparing normal mode frequencies at the global minimum and secondary minimum with previous and new direct ab initio frequencies. The potential surface is used in vibrational analysis using the "single-reference" and "reaction-path" versions of the code MULTIMODE.     

精密从头算与ABEEM/MM模型对水团簇(H2O)11 9种低能结构的计算

用精密从头算方法研究了(H2O)11的9种低能异构体的性质, 包括优化的几何结构、结合能、偶极矩和氢键个数等, 并且得出了515-a是(H2O)11的全局最低能结构. 同时, 也用ABEEM/MM(atom bond electronegativity equalization method/molecular mechanics) 模型研究了这些性质, 与从头算的结果进行了比较, 得到了相符合的结果. 这显示了ABEEM/MM模型在描述中等大小的水分子团簇结构上是成功的.     

Vibrational assignment of the normal modes of 2-phenyl-4-(4-methoxy benzylidene)-2-oxazolin-5-one via FTIR and Raman spectra, and ab inito calculations

Raman and FTIR spectra of 2-phenyl-4-(4-methoxy benzylidene)-2-oxazolin-5-one were recorded in the regions, 100-3300 and 400-4000 cm(-1), respectively. Vibrational frequencies and intensities of the fundamental modes of this hetrocyclic organic molecule were computed using ab initio as well as AM1 semiempirical molecular orbital methods. Ab initio calculations were carried out with basis set up to RHF/6-311G. Conformational studies regarding the effect of moving the methoxy group in the 2-phenyl-4-(4-methoxy benzylidene)-2-oxazolin-5-one molecule to a different position on the ring was also carried out. Observed vibrational wavenumbers were found to be mostly consistent with ab initio values. The most intense mode of vibration observed at 1250 cm(-1) in Raman spectra, also observed as a strong band in FTIR, was assigned as C-O stretching vibration in the methoxy group. Asymmetric stretching vibrations between CC and CN bonds was predicted as most intense mode by our ab initio calculation.     

Separation of CO2 and N2 by adsorption in C168 schwarzite: a combination of quantum mechanics and molecular simulation study

Using a hierarchical multiscale approach combining quantum mechanics and molecular simulation, we have investigated the adsorption of pure CO(2) and N(2) and their mixture at room temperature in C(168) schwarzite, as a model for nanoporous carbons. First, the adsorbate-adsorbent interaction potential is determined using ab initio quantum mechanics computations, and then the adsorption is predicted using full atomistic Monte Carlo simulations. The extents of adsorption, adsorption energies, and isosteric heats of pure CO(2) and N(2) simulated with the ab initio potential are found to be higher than those with the empirical Steele potential that had been developed from gas adsorption on planar graphite. The inclusion of the electric quadrupole moment of adsorbate in simulation has no discernible effect on N(2) adsorption but results in a larger extent of CO(2) adsorption at high coverages. The selectivity of CO(2) over N(2) in the C(168) schwarzite from a model flue gas is predicted to be significantly larger with the ab initio potential than with the Steele potential. This illustrates the importance of an accurate adsorbate-adsorbent interaction potential in determining gas adsorption and suggests that nanoporous carbons might be useful for the separation of flue gases. As a comparison, the adsorption and selectivity of CO(2) and N(2) in ZSM-5 zeolites are also simulated with the experimentally validated potential parameters. The selectivity in the C(168) schwarzite predicted with the ab initio or Steele potential is found to be larger than the selectivity in all-silica ZSM-5, but less than that in Na-exchanged ZSM-5 zeolites.     

Microwave spectra and molecular structures of (Z)-pent-2-en-4-ynenitrile and maleonitrile.

Accurate equilibrium structures have been determined for (Z)-pent-2-en-4-ynenitrile (8) and maleonitrile (9) by combining microwave spectroscopy data and ab initio quantum chemistry calculations. The microwave spectra of 10 isotopomers of 8 and 5 isotopomers of 9 were obtained using a pulsed nozzle Fourier transform microwave spectrometer. The ground-state rotational constants were adjusted for vibration-rotation interaction effects calculated from force fields obtained from ab initio calculations. The resultant equilibrium rotational constants were used to determine structures that are in very good agreement with those obtained from high-level ab initio calculations (CCSD(T)/cc-pVTZ). The geometric parameters in 8 and 9 are very similar; they also do not differ significantly from the all-carbon analogue, (Z)-hex-3-ene-1,5-diyne (7), the parent molecule for the Bergman cyclization. A small deviation from linearity about the alkyne and cyano linkages is observed for 7-9 and several related species where accurate equilibrium parameters are available. The data on 7-9 should be of interest to radioastronomy and may provide insights on the formation and interstellar chemistry of unsaturated species such as the cyanopolyynes.     

Calculating geochemical reaction pathways--exploration of the inner-sphere water exchange mechanism in Al(H2O)6(3+)(aq) + nH2O with ab Initio calculations and molecular dynamics

We have simulated exchange of inner-sphere and bulk water molecules for different sizes of Al3+(aq) clusters, Al(H2O)63+ + nH2O for n = 0, 1, 6, or 12, with ab initio and molecular dynamics simulations, in order to understand how robust the ab initio method is for identifying hydrolytic reaction pathways of particular importance to geochemistry. In contrast to many interfacial reactions, this particular elementary reaction is particularly simple and well-constrained by experiment. Nevertheless, we find that a rich array of parallel reaction pathways depend sensitively on the details of the solvation sphere and structure and that larger clusters are not necessarily better. Inner-sphere water exchange in Al3+(aq) may occur through two Langford-Gray dissociative pathways, one in which the incoming and outgoing waters are cis, the other in which they are trans to one another. A large majority of exchanges in the molecular dynamics simulations occurred via the trans mechanism, in contrast to the predictions of the ab initio method. In Al(H2O)63+ + H2O, the cis mechanism has a transition state of 84.3 kJ/mol, which is in good agreement with previous experimental and ab initio results, while the trans mechanism has only a saddle point with two negative frequencies, not a transition state, at 89.7 kJ/mol. In addition to the exchange mechanisms, dissociation pathways could be identified that were considerably lower in energy than experiment and varied considerably between 60 and 100 kJ/mol, depending on the particular geometry and cluster size, with no clear relation between the two. Ab initio calculations using large clusters with full second coordination spheres (n = 12) were unable to find dissociation or exchange transition states because the network of hydrogen bonds in the second coordination sphere was too rigid to accommodate the outgoing inner-sphere water. Our results indicate that caution should surround ab initio simulation of complicated dynamic processes such as hydrolysis, ion exchange, and interfacial reactions that involve several steps. Dynamic methods of simulation need to accompany static methods such as ab initio calculation, and it is best to consider simulated pathways as hypotheses to be tested experimentally rather than definitive properties of the reaction.     

A hierarchical construction scheme for accurate potential energy surface generation: an application to the F+H2 reaction

We present a hierarchical construction scheme for accurate ab initio potential energy surface generation. The scheme is based on the observation that when molecular configuration changes, the variation in the potential energy difference between different ab initio methods is much smaller than the variation for potential energy itself. This means that it is easier to numerically represent energy difference to achieve a desired accuracy. Because the computational cost for ab initio calculations increases very rapidly with the accuracy, one can gain substantial saving in computational time by constructing a high accurate potential energy surface as a sum of a low accurate surface based on extensive ab initio data points and an energy difference surface for high and low accuracy ab initio methods based on much fewer data points. The new scheme was applied to construct an accurate ground potential energy surface for the FH(2) system using the coupled-cluster method and a very large basis set. The constructed potential energy surface is found to be more accurate on describing the resonance states in the FH(2) and FHD systems than the existing surfaces.     

Photodissociation spectroscopy of Zn+(H2O) and Zn+(D2O)

We report on a study of the photodissociation spectroscopy of weakly bound Zn+(H2O) and Zn+(D2O) complexes. The work is supported by ab initio electronic structure calculations of the ground and low-lying excited energy surfaces. We assign two molecular absorption bands in the near UV correlating to Zn+ (4s-4p)-based transitions, and identify vibrational progressions associated with both intermolecular and intramolecular vibrational modes of the cluster. Partially resolved rotational structure is consistent with a C(2V) equilibrium complex geometry. Experimental spectroscopic constants are in very good agreement with ab initio theoretical predictions. Results are compared with previous work on main group and transition metal ion-H2O clusters.     

X–NO2 rotational energy barriers: Local density functional calculations

The X–NO₂ rotational energy barriers of nitromethane, nitroethylene, nitrobenzene, and a group of nitramines have been computed using a local density functional (LDF ) procedure, using ab initio Hartree–Fock (HF )-optimized structures of the ground and rotational transition states. The results have been discussed in relation to HF and some correlated ab initio values and the available experimental data. Our LDF barriers are overall quite reasonable, in generally satisfactory agreement with the experimental and correlated ab initio results. © 1993 John Wiley & Sons, Inc.     

Heavy atom nitroxyl radicals. V. An experimental and ab initio study of the previously unknown H2PS free radical

The B?(2)A(')-X?(2)A(') transition of the prototypical thiophosphoryl radical, H(2)PS, was observed for the first time using laser-induced fluorescence and single vibronic level emission spectroscopy. H(2)PS and its deuterated isotopologues, D(2)PS and HDPS, were produced in a pulsed supersonic discharge jet from a precursor mixture of Cl(3)PS and H(2) or D(2) or an H(2)/D(2) mixture in high-pressure argon. High level ab initio calculations of the lowest three doublet electronic states helped in the definitive assignment of the B?-X? transition, which involves electron promotion from the π to the π? orbital. Vibrational frequencies were determined for several modes of each isotopologue in the X? and B? states and found to be in accord with theoretical predictions. Although a line-by-line rotational analysis was not possible, the observed band contours are consistent with the geometries obtained from our ab initio calculations. Theory indicates that PS bond length increases upon electronic excitation, while the pyramidalization of the radical does not change significantly.     

Interpolating moving least-squares methods for fitting potential energy surfaces: an application to the H2CN unimolecular reaction

Classical trajectories have been used to compute rates for the unimolecular reaction H2CN-->H+HCN on a fitted ab initio potential energy surface (PES). The ab initio energies were obtained from CCSD(T)/aug-cc-pvtz electronic structure calculations. The ab initio energies were fitted by the interpolating moving least-squares (IMLS) method. This work continues the development of the IMLS method for producing ab initio PESs for use in molecular dynamics simulations of many-atom systems. A dual-level scheme was used in which the preliminary selection of data points was done using a low-level theory and the points used for fitting the final PES were obtained at the desired higher level of theory. Classical trajectories were used on various low-level IMLS fits to tune the fit to the unimolecular reaction under study. Procedures for efficiently picking data points, selecting basis functions, and defining cutoff limits to exclude distant points were investigated. The accuracy of the fitted PES was assessed by comparing interpolated values of quantities to the corresponding ab initio values. With as little as 330 ab initio points classical trajectory rate constants were converged to 5%-10% and the rms error over the six-dimensional region sampled by the trajectories was a few tenths of a kcal/mol.     

Theoretical study of O2-H2O: potential energy surface, molecular vibrations, and equilibrium constant at atmospheric temperatures

The intermolecular potential energy surface of O(2)-H(2)O was investigated at ab initio MP2 and MRSDCI levels using the aug-cc-pVTZ basis set. The vibrational levels were evaluated by numerically solving the Schr?dinger equations for the nuclear motions with the ab initio potential functions using one- to three-dimensional finite-element methods. On the basis of the calculated partition functions, the equilibrium constant of the complex, K(p), was studied. The K(p) values at atmospheric temperatures of 200-300 K were found to be 1-2 orders of magnitude less than previous estimates from the harmonic oscillator approximation.     

Ab initio studies on vibrational spectra of XSO_2NCO (X=F,Cl):harmonic force fields and frequency assignments

ＴｈｅｆｌｕｏｒｏｓｕｌｆｏｎｙｌｉｓｏｃｙａｎａｔｅａｎｄｃｈｌｏｒｏｓｕｌｆｏｎｙｌｉｓｏｃｙａｎａｔｅｍｏｌｅｃｕｌｅｓａｒｅｔｈｅｍｏｓｔｒｅａｃｔｉｖｅｍｏｌｅｃｕｌｅｓｆｏｒｔｈｅｔｒａｎｓｆｅｒｅｎｃｅｏｆｔｈｅＮＣＯｇｒｏｕｐａｎｄａｒｅｖｅｒｙｉｍｐｏｒｔａｎｔｉｎｓｙｎｔｈｅｔｉｃｃｈｅｍｉｓｔｒｙ.Ｄｕｅｔｏｔｈｅｉｒｖｅｒｓａｔｉｌｉｔｙｉｎｃｈｅｍｉｃａｌｒｅａｃｔｉｏｎｓ,ｔｈｅｙｈａｖｅａｌｓｏｂｅｃｏｍｅｔｈｅｓｕｂｊｅｃｔｏｆｍａｎｙｓｔｒｕｃｔｕｒａｌｓｔｕｄｉ…     

High level ab initio study of the structure and vibrational spectra of HO(2)NO(2)

A high-level ab initio study has been performed on the conformational structure and vibrational spectra of HO(2)NO(2). Calculations carried out with coupled-cluster methods using a series of Pople and Dunning basis sets reveal that there is a significant basis set dependence on the predicted ab initio structure. Higher angular momentum basis sets are shown to be necessary in order to bring the calculated structure into agreement with experimental rotational constants. Harmonic vibrational frequencies of HO(2)NO(2) are computed at the CCSD(T)/aug-cc-pVTZ level of theory while the corresponding vibrational anharmonicities are calculated at the MP2/cc-pVTZ level. In addition, the absorption cross sections of OH stretching overtones in HO(2)NO(2) are calculated using a dipole function computed at the QCISD level of theory and found to be in good agreement with the available experimental data.