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.     

Photodissociation of acetic acid in the gas phase: an ab initio study

Photodissociation of acetic acid in the gas phase was investigated using ab initio molecular orbital methods. The stationary structures on the ground-state potential energy surfaces were mainly optimized at the MP2 level of theory, while those on the excited-state surfaces were determined by complete active space SCF calculations with a correlation-consistent basis set of cc-pVDZ. The reaction pathways leading to different photoproducts are characterized on the basis of the computed potential energy surfaces and surface crossing points. The calculations reproduce the experimental results well and provide additional insight into the mechanism of the ultraviolet photodissociation of acetic acid and related compounds.     

Product branching ratios in photodissociation of phenyl radical: a theoretical ab initio/Rice-Ramsperger-Kassel-Marcus study

Ab initio CCSD(T)/CBS//B3LYP/6-311G** calculations of the potential energy surface for possible dissociation channels of the phenyl radical are combined with microcanonical Rice-Ramsperger-Kassel-Marcus calculations of reaction rate constants in order to predict statistical product branching ratios in photodissociation of c-C(6)H(5) at various wavelengths. The results indicate that at 248 nm the photodissociation process is dominated by the production of ortho-benzyne via direct elimination of a hydrogen atom from the phenyl radical. At 193 nm, the statistical branching ratios are computed to be 63.4%, 21.1%, and 14.4% for the o-C(6)H(4) + H, l-C(6)H(4) ((Z)-hexa-3-ene-1,5-diyne) + H, and n-C(4)H(3) + C(2)H(2) products, respectively, in a contradiction with recent experimental measurements, which showed C(4)H(3) + C(2)H(2) as the major product. Although two lower energy pathways to the i-C(4)H(3) + C(2)H(2) products are identified, they appeared to be kinetically unfavorable and the computed statistical branching ratio of i-C(4)H(3) + C(2)H(2) does not exceed 1%. To explain the disagreement with experiment, we optimized conical intersections between the ground and the first excited electronic states of C(6)H(5) and, based on their structures and energies, suggested the following photodissociation mechanism at 193 nm: c-C(6)H(5) 1 → absorption of a photon → electronically excited 1 → internal conversion to the lowest excited state → conversion to the ground electronic state via conical intersections at CI-2 or CI-3 → non-statistical decay of the vibrationally excited radical favoring the formation of the n-C(4)H(3) + C(2)H(2) products. This scenario can be attained if the intramolecular vibrational redistribution in the CI-2 or CI-3 structures in the ground electronic state is slower than their dissociation to n-C(4)H(3) + C(2)H(2) driven by the dynamical preference.     

Photodissociation of azulene at 193 nm: ab initio and RRKM study

The ab initio/Rice-Ramsperger-Kassel-Marcus (RRKM) approach has been applied to investigate the photodissociation mechanism of azulene at 6.4 eV (the laser wavelength of 193 nm) upon absorption of one UV photon followed by internal conversion into the ground electronic state. 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 photoexcited azulene can readily isomerize to naphthalene and the major dissociation channel is elimination of an H-atom from naphthalene. The branching ratio of this channel decreases with an increase of the photon energy. Acetylene elimination is the second probable reaction channel and its branching ratio rises as the photon energy increases. The main C8H6 fragments at 193 nm are phenylacetylene and pentalene and the yield of the latter grows fast with the increasing excitation energy.     

Unimolecular decomposition of ethyl hydroperoxide: ab initio/Rice-Ramsperger-Kassel-Marcus theoretical prediction of rate constants

Alkyl hydroperoxides are found to be important intermediates in the combustion and oxidation processes of hydrocarbons. However, studies of ethyl hydroperoxide (CH(3)CH(2)OOH) are limited. In this work, kinetics and mechanisms for unimolecular decomposition of CH(3)CH(2)OOH have been investigated. The potential energy surface of decomposition reactions have first been predicted at the CCSD(T)/6-311+G(3df,2p)//B3LYP/6-311G(d,p) level. The results show that the formation of CH(3)CH(2)O + OH via O-O direct bond dissociation is dominant, the branching ratio of which is over 99% in the whole temperature range from 300 to 1000 K, and its rate constant can be expressed as k1 = 9.26 × 10(52)T(-11.91)exp(-26879/T) s(-1) at 1 atm. The rate constants of the reaction CH(3)CH(2)OOH → CH(3)CH(2)O + OH at different temperatures and pressures have been calculated, which can help us to comprehend the reactions of CH(3)CH(2)OOH at experimental conditions.     

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.     

A comparative ab initio study of ethylene,acetylene and benzene

Ground state properties have been calculated by use of a medium-sized Gaussian basis set and comparison with other bases has been made. Contraction to double-zeta of a comparatively small basis is found to be superior to a large set of primitive Gaussians contracted to minimal basis. Molecular optimization is not important for double-zeta bases. Inclusion of a balanced set of polarization functions is essential in all cases studied. Population analysis gives a certain insight in molecular properties but contour maps are found to be significantly superior. This is demonstrated on bonding properties of corresponding orbitals within the series. In case of benzene Slater's energyband plot is shown to be useful for classifying bonding properties.     

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.     

Photodissociation of warm water: ab initio calculations of the room-temperature absorption spectrum

This Letter presents cross sections of water in the second absorption band obtained from quantum mechanical calculations. A Monte-Carlo sampling over the initial rotational state is applied in order to calculate the cross section for water at a temperature of 300 K (warm water). This makes a fair comparison with the experimental spectrum, only available for water at room temperature, possible. The overall rotation of the water molecule is treated exactly. The inclusion of initial rotational motion, which reduces the resonance structure in the spectrum, significantly improves the agreement between theory and experiment.     

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.     

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.     

Towards highly accurate ab initio thermochemistry of larger systems: benzene

The high accuracy extrapolated ab initio thermochemistry (HEAT) protocol is applied to compute the total atomization energy (TAE) and the heat of formation of benzene. Large-scale coupled-cluster calculations with more than 1500 basis functions and 42 correlated electrons as well as zero-point energies based on full cubic and (semi)diagonal quartic force fields obtained with the coupled-cluster singles and doubles with perturbative treatment of the triples method and atomic natural orbital (ANO) triple- and quadruple-zeta basis sets are presented. The performance of modifications to the HEAT scheme and the scaling properties of its contributions with respect to the system size are investigated. A purely quantum-chemical TAE and associated conservative error bar of 5463.0 ± 3.1 kJ mol(-1) are obtained, while the corresponding 95% confidence interval, based on a statistical analysis of HEAT results for other and related molecules, is ± 1.8 kJ mol(-1). The heat of formation of benzene is determined to be 101.5 ± 2.0 kJ mol(-1) and 83.9 ± 2.1 kJ mol(-1) at 0 K and 298.15 K, respectively.     

Accurate ab initio binding energies of the benzene dimer

Accurate binding energies of the benzene dimer at the T and parallel displaced (PD) configurations were determined using the single- and double-coupled cluster method with perturbative triple correction (CCSD(T)) with correlation-consistent basis sets and an effective basis set extrapolation scheme recently devised. The difference between the estimated CCSD(T) basis set limit electronic binding energies for the T and PD shapes appears to amount to more than 0.3 kcal/mol, indicating the PD shape is a more stable configuration than the T shape for this dimer in the gas phase. This conclusion is further strengthened when a vibrational zero-point correction to the electronic binding energies of this dimer is made, which increases the difference between the two configurations to 0.4-0.5 kcal/mol. The binding energies of 2.4 and 2.8 kcal/mol for the T and PD configurations are in good accord with the previous experimental result from ionization potential measurement.     

Electron attachment in ice-HCl clusters: an ab initio study

Experimental work has shown that small amounts of HCl strongly enhance electron capture in ice films. The purpose of the present study was to investigate the effect of adsorbed HCl on the interaction of electrons with small clusters of water. Studies were made with clusters of 6 and 12 water molecules with various geometries both with and without one HCl attached. A number of distinct HCl coordination motifs were examined. All of the neutral structures with HCl exhibited zero thresholds for electron attachment and formed dipole bound anionic states (DBS). The relaxation processes for these "initial DBS" depended on the number of H(2)O (n) and on the number and type of H-bonds to the HCl (x). The initial DBS of systems with only O-H...Cl H-binding underwent dissociative electron attachment (DEA), forming H atoms. Relaxation for systems with ClH...OH(2) bonds was more complex. For the two layer n = 12 systems with x = 2 or 3 the HCl proton moved to the nearest oxygen to form H(3)O(+). Then rearrangement of the proton network occurred, and the Cl(-) became solvated by three HO-H...Cl(-) bonds. The presence of Cl(-) and H(3)O(+) increases the dipole moment and the electron binding energy (EBE) of the network. Further stabilization is achieved by decay into deeper DBS electron traps and/or by reaction of the excess electron with H(3)O(+) to form H(*) atoms. The HCl(H(2)O)(6) clusters with a single Cl-H...OH(2) bond behaved differently. They increased their stability by becoming more linear. This raised the dipole moment and the EBE therefore increased, reducing the total energy. None of these species showed any signs of increasing the number of H-bonds to Cl. The implication of these observations for the interpretation of the results of the experiments with 0.2 monolayer of HCl on 5 monolayer of H(2)O at 20 K, and on the possible role of cosmic ray-induced ionization in polar stratospheric clouds in ozone depletion is discussed.     

Current rectification by asymmetric molecules: an ab initio study

Current rectification effect in an asymmetric molecule HCOO-C6H4-(CH2)n sandwiched between two aluminum electrodes has been studied using an ab initio nonequilibrium Green's function method. The conductance of the system decreases exponentially with the increasing number n of CH2. The phenomenon of current rectification is observed such that a very small current appears at negative bias and a sharp negative differential resistance at a critical positive bias when n>or=2. The rectification effect arises from the asymmetric structure of the molecule and the molecule-electrode couplings. A significant rectification ratio of approximately 38 can be achieved when n=5.     

Glycine interaction with carbon nanotubes: an ab initio study

The interaction of the glycine radical on the side walls of both armchair and zigzag single walled carbon nanotubes is investigated by density functional theory. It is found that the interaction potential of the N-centered glycine radical with the tubes has a minimum of 16.9 (armchair) and 20.2 (zigzag) kcal/mol with respect to the dissociation products. In contrast, the C-centered radical, which is 22.7 kcal/mol lower in energy than the N-centered radical, does not form stable complexes with both types of carbon nanotubes.     

Lithium hydroxide phase transition under high pressure: an ab initio molecular dynamics study.

The high-pressure phase transition in the deuterated lithium hydroxide crystalline state has been studied by Car-Parrinello molecular dynamics simulations, in the constant-pressure, constant-temperature ensemble. The recently developed metadynamics approach has been applied to encourage the system to transform into different phases in an affordable simulation time. A previously not completely characterized high-pressure phase has been obtained. The structural and spectroscopic properties have been studied and compared with the neutron scattering, infrared and Raman measurements. It has been found that the calculated structure differs slightly from the experimental hypothesis, and that the presence of strong hydrogen bonds is the source of the red shift and of the characteristic features of the OD-stretching bands in both IR and Raman spectra.     

Ultrafast transformation of graphite to diamond: an ab initio study of graphite under shock compression

We report herein ab initio molecular dynamics simulations of graphite under shock compression in conjunction with the multiscale shock technique. Our simulations reveal that a novel short-lived layered diamond intermediate is formed within a few hundred of femtoseconds upon shock loading at a shock velocity of 12 kms (longitudinal stress>130 GPa), followed by formation of cubic diamond. The layered diamond state differs from the experimentally observed hexagonal diamond intermediate found at lower pressures and previous hydrostatic calculations in that a rapid buckling of the graphitic planes produces a mixture of hexagonal and cubic diamond (layered diamond). Direct calculation of the x-ray absorption spectra in our simulations reveals that the electronic structure of the final state closely resembles that of compressed cubic diamond.     

Addition of anions to carbonyl compounds: an ab initio study

Energies for the addition of anionic nucleophiles, Z(-), to carbonyl compounds, XYCO, are calculated at the G2(MP2) level of theory. The substituents X, Y, and Z are taken from the set {H, CH3, NH2, OH, F, CF3, CHCH2, CHO, CCH, and CN}. The basicity and, to a lesser extent, ionization potential of Z(-) were found to correlate with the enthalpy of addition of Z(-) to H2CO. The enthalpy of addition of Z(-) to XYCO relative to H2CO is largely independent of Z. The ordering of the enthalpies of addition for the series of XYCO's is rationalized. By using a thermodynamic cycle, the independence of this ordering from Z is attributed to the additivity of the inductive stabilization of XYZCO(-) by X and Y versus H2ZCO(-). A method for estimating the enthalpy of addition for nucleophile/carbonyl combinations not studied above is described and shown to give good results on a model system.