The infrared spectrum of N-phenylpyrrole (PP) was measured in the gas phase and in an argon matrix, and the Raman spectrum was obtained in a single crystal. The measured matrix shifts are found to be small: many bands are not split, and the shifts from the gas phase values are less than 1%. Splitting to two sub-bands is observed for some bands, indicating the presence of two major trapping sites, in agreement with previous predictions. The spectra are analyzed with the help of harmonic calculations on the free molecule and on its adduct with one or two argon atoms, and anharmonic frequency calculations on the free molecule. Harmonic frequencies were obtained at the MP2/cc-pVDZ and DFT-B3LYP/cc-pVDZ levels. Anharmonic frequencies were obtained by the correlation-corrected vibrational self-consistent field (CC-VSCF) method with a variant of the PM3 semiempirical electronic structure method, calibrated for much improved spectroscopic accuracy. The potential surfaces used in the CC-VSCF calculation obtained by adjusting standard PM3 surfaces so that they provide harmonic frequencies that are comparable to those obtained at the DFT-B3LYP/cc-pVDZ level. Agreement between the experimental and theoretical results is in general very good, allowing the assignments of most bands. The harmonic frequency calculations of PP-Ar clusters, at the MP2/cc-pVDZ level show that the environment can greatly affect the intensities of some of the transitions, which is in accord with experiment. (c) 2007 Elsevier B.V. All rights reserved.

The results of anharmonic frequency calculations on neutral imidazole (C3N2H4, Im), protonated imidazole (ImH(+)), and its complexes with water (ImH(+))(H2O)(n), are presented and compared to gas phase infrared photodissociation spectroscopy (IRPD) data. Anharmonic frequencies are obtained via ab initio vibrational self-consistent field (VSCF) calculations taking into account pairwise interactions between the normal modes. The key results are: (1) Prediction of anharmonic vibrational frequencies on an MP2 ab initio potential energy surface show excellent agreement with experiment and outstanding improvement over the harmonic frequencies. For example, the ab initio calculated anharmonic frequency for (ImH(+))(H2O)N-2 exhibits an overall average percentage error of 0.6% from experiment. (2) Anharmonic vibrational frequencies calculated on a semiempirical potential energy surface fitted to ab initio harmonic data represents spectroscopy well, particularly for water complexes. As an example, anharmonic frequencies for (ImH(+))H2O and (ImH(+))(H2O)(2) show an overall average deviation of 1.02% and 1.05% from experiment, respectively. This agreement between theory and experiment also supports the validity and use of the pairwise approximation used in the calculations. (3) Anharmonic coupling due to hydration effects is found to significantly reduce the vibrational frequencies for the NH stretch modes. The frequency of the NH stretch is observed to increase with the removal of a water molecule or replacement of water with N-2. This result also indicates the ability of the VSCF method to predict accurate frequencies in a matrix environment. The calculation provides insights into the nature of anharmonic effects in the potential surface. Analysis of percentage anharmoncity in neutral Im and ImH(+) shows a higher percentage anharmonicity in the NH and CH stretch modes of neutral Im. Also, we observe that anharmonicity in the NH stretch modes of ImH(+) have some contribution from coupling effects, while that of neutral Im has no contribution whatsoever from mode-mode coupling. It is concluded that the incorporation of anharmonic effects in the calculation brings theory and experiment into much closer agreement for these systems.

The vibrational spectroscopy of (SO(4)(2-))center dot(H(2)O)(n) is studied by theoretical calculations for n=1-5, and the results are compared with experiments for n=3-5. The calculations use both ab initio MP2 and DFT/B3LYP potential energy surfaces. Both harmonic and anharmonic calculations are reported, the latter with the CC-VSCF method. The main findings are the following: (1) With one exception (H(2)O bending mode), the anharmonicity of the observed transitions, all in the experimental window of 540-1850 cm(-1), is negligible. The computed anharmonic coupling suggests that intramolecular vibrational redistribution does not play any role for the observed linewidths. (2) Comparison with experiment at the harmonic level of computed fundamental frequencies indicates that MP2 is significantly more accurate than DFT/B3LYP for these systems. (3) Strong anharmonic effects are, however, calculated for numerous transitions of these systems, which are outside the present observation window. These include fundamentals as well as combination modes. (4) Combination modes for the n=1 and n=2 clusters are computed. Several relatively strong combination transitions are predicted. These show strong anharmonic effects. (5) An interesting effect of the zero point energy (ZPE) on structure is found for (SO(4)(2-))center dot(H(2)O)(5): The global minimum of the potential energy corresponds to a C(s) structure, but with incorporation of ZPE the lowest energy structure is C(2v), in accordance with experiment. (6) No stable structures were found for (OH(-))center dot(HSO(4)(-))center dot(H(2)O)(n), for n <= 5. (C) 2007 American Institute of Physics.

One-photon and two-photon ionization dynamics of tryptophan is studied by classical trajectory simulations using the semiempirical parametric method number 3 (PM3) potential surface in ‘‘on the fly’’ calculations. The tryptophan conformer is assumed to be in the vibrational ground state prior to ionization. Initial conditions for the trajectories are weighted according to the Wigner distribution function computed for that state. Vertical ionization in the spirit of the classical Franck-Condon principle is assumed. For the two-photon ionization process the ionization is assumed to go resonantively through the first excited state. Most trajectories are computed, and the analysis is carried out for the first 10 ps. A range of interesting effects are observed. The main findings are as follows: (1) Multiple conformational transitions are observed in most of the trajectories within the ultrafast duration of 10 ps. (2) Hydrogen transfer from the carboxyl group to the amino group and back has been observed. A zwitterion is formed as a transient state. (3) Two new isomers are formed during the dynamics, which have apparently not been previously observed. (4) Fast energy flow between the ring modes and the amino acid backbone is observed for both one- and two-photon ionization. However, the effective vibrational temperatures only approach the same value after 90 ps. The conformation transition dynamics, the proton-transfer processes and the vibrational energy flow are discussed and analyzed.

The dynamics of long timescale evolution of conformational changes in small biological molecules is described by a hybrid molecular dynamics/RRK algorithm. The approach employs classical trajectories for transitions between adjacent structures separated by a low barrier, and the classical statistical RRK approximation when the barrier involved is high. In determining the long-time dynamics from an initial structure to a final structure of interest, an algorithm is introduced for determining the most efficient pathways (sequence of the intermediate conformers). This method uses the Dijkstra algorithm for finding optimal paths on networks. Three applications of the method using an AMBER force field are presented: a detailed study of conformational transitions in a blocked valine dipeptide; a multiple reaction path study of the blocked valine tripeptide; and the evolution in time from the beta hairpin to alpha helix structure of a blocked alanine hexapeptide. Advantages and limitations of the method are discussed in light of the results.

Ab initio calculations predict the existence of the compounds Ng(- C CH)(4) and Ng(- C CH)(6), where Ng=Xe or Kr. Presently known organic noble gas compounds have a coordination number of two at most. The Ng(- C CH)(4) molecules have D-4h symmetry, and Ng(- C CH)(6) molecules have O-h symmetry. The bonding in all these compounds is partly ionic and partly covalent, with significant contributions from both types of bonding. The relatively high vibrational frequencies and the substantial Ng-(C CH) binding energy in these species indicate that these compounds should be fairly stable, at least in cryogenic conditions. These compounds could be a very interesting addition to the range of known organic noble gas compounds. Suggestions are made on possible approaches to their preparation. (c) 2006 American Institute of Physics.

Although heterogeneous chemistry on surfaces in the troposphere is known to be important, there are currently only a few techniques available for studying the nature of surface-adsorbed species as well as their chemistry and photochemistry under atmospheric conditions of 1 atm pressure and in the presence of water vapor. We report here a new laboratory approach using a combination of long path Fourier transform infrared spectroscopy ( FTIR) and attenuated total reflectance (ATR) FTIR that allows the simultaneous observation and measurement of gases and surface species. Theory is used to identify the surface-adsorbed intermediates and products, and to estimate their relative concentrations. At intermediate relative humidities typical of the tropospheric boundary layer, the nitric acid formed during NO2 heterogeneous hydrolysis is shown to exist both as nitrate ions from the dissociation of nitric acid formed on the surface and as molecular nitric acid. In both cases, the ions and HNO3 are complexed to water molecules. Upon pumping, water is selectively removed, shifting the NO3-HNO3(H2O)(y) equilibria toward more dehydrated forms of HNO3 and ultimately to nitric acid dimers. Irradiation of the nitric acid-water film using 300-400 nm radiation generates gaseous NO, while irradiation at 254 nm generates both NO and HONO, resulting in conversion of surface-adsorbed nitrogen oxides into photochemically active NOx. These studies suggest that the assumption that deposition or formation of nitric acid provides a permanent removal mechanism from the atmosphere may not be correct. Furthermore, a potential role of surface-adsorbed nitric acid and other species formed during the heterogeneous hydrolysis of NO2 in the oxidation of organics on surfaces, and in the generation of gas-phase HONO on local to global scales, should be considered.

The diacetylides of Xe and Kr, HCCXeCCH and HCCKrCCH, are predicted to exist as metastable, chemically-bound compounds. The electronic structure, properties of the potential energy surfaces and decomposition paths are computed and analyzed. MP2, MCSCF and CASPT2 ab initio methods are used, as appropriate for each of the properties studied. Using transition state theory and the computed barrier for decomposition, the lifetime of HCCXeCCH is calculated as a function of temperature. The molecule is predicted to be stable well above the cryogenic range, with a lifetime of 24 h at 200 K. The implications for organic chemistry of the noble gases are discussed.

Photochemical processes in HNO3, HNO3-H2O, and cis- and trans-HONO following overtone excitation of the OH stretching mode are studied by classical trajectory simulations. Initial conditions for the trajectories are sampled according to the initially prepared vibrational wave function. Semiempirical potential energy surfaces are used in ‘‘on-the-fly’’ simulations. Several tests indicate at least semiquantitative validity of the potential surfaces employed. A number of interesting new processes and intermediate species are found. The main results include the following: (1) In excitation of HNO3 to the fifth and sixth OH-stretch overtone, hopping of the H atom between the oxygen atoms is found to take place in nearly all trajectories, and can persist for many picoseconds. H-atom hopping events have a higher yield and a faster time scale than the photodissociation of HNO3 into OH and NO2. (2) A fraction of the trajectories for HNO3 show isomerization into HOONO, which in a few cases dissociates into HOO and NO. (3) For high overtone excitation of HONO. isomerization into the weakly bound species HOON is seen in all trajectories, in part of the events as an intermediate step on the way to dissociation into OH + NO. This process has not been reported previously. Well-established processes for HONO, including cis-trans isomerization and H hopping are also observed. (4) Only low overtone levels of HNO3-H2O have sufficiently long liftimes to be spectrocopically relevant. Excitation of these CH stretching overtones is found to result in the dissociation of the cluster H hopping, or dissociation of HNO3 does not take place. The results demonstrate the richness of processes induced by overtone excitation of HNOx species, with evidence for new phenomena. Possible relevance of the results to atmospheric processes is discussed.

Photodissociation of I-2 in the I2Ar17 cluster is studied by quantum wavepacket simulations, using time-dependent mean-field potentials. It is found that: (a) Initial energy transfer from the 12 is Mostly to three cluster modes, which undergo multiquantum excitation. Several other modes undergo single-quantum excitation. (b) Coherent phase transfer from the 12 to specific cluster modes is found. (c) Energy transfer from initially-excited modes to the other modes becomes large after 0.6 ps. Phase space interpretation is provided by computed Wigner distributions in time. (c) 2006 Elsevier B.V. All rights reserved.

Calculations at B3LYP level predict the existence of three carbon chain oligomers containing HXeC C - branches: C7H8Xe2, C11H12Xe3, and C15H16Xe4. The geometries and NBO charges of the HXeC C - groups in the species are similar to those of the experimental known HXeC CH molecule, and are insensitive to the length of the carbon chain. The structures of the xenon oligomers are very similar to their hydrocarbon precursors. The energetics for C11H12Xe3 is calculated to assess the stability of these polymers. Similar to HXeCCH, C11H12Xe3 is kinetically stable and protected by a high barrier of 2.47 eV against dissociation to C11H12Xe2+Xe, and is energetically more stable by 1.30 eV than the C11H11Xe2+Xe+H products, which strongly supports the existence of the molecule. Extrapolation of the results for the oligomers suggests the existence of an extended [-CH2CH(C CXeH)-](n) polymer. A strategy for preparation is proposed. (c) 2006 American Institute of Physics.

Dynamics of glycine chemisorbed on the surface of a silicon cluster is studied for a process that involves single-photon ionization, followed by recombination with the electron after a selected time delay. The process is studied by ‘‘on-the-fly’’ molecular dynamics simulations, using the semiempirical parametric method number 3 (PM3) potential energy surface. The system is taken to be in the ground state prior to photoionization, and time delays from 5 to 50 fs before the recombination are considered. The time evolution is computed over 10 ps. The main findings are (1) the positive charge after ionization is initially mostly distributed on the silicon cluster. (2) After ionization the major structural changes are on the silicon cluster. These include Si-Si bond breaking and formation and hydrogen transfer between different silicon atoms. (3) The transient ionization event gives rise to dynamical behavior that depends sensitively on the ion state lifetime. Subsequent to 45 fs evolution in the charged state, the glycine molecule starts to rotate on the silicon cluster. Implications of the results to various processes that are induced by transient transition to a charged state are discussed. These include inelastic tunneling in molecular devices, photochemistry on conducting surfaces, and electron-molecule scattering. (c) 2005 American Institute of Physics.

Electronic structure calculations predict the existence of a novel type of a chemically bound noble gas compound. The predicted species is an extended linear and periodic polymer, made of the repeat unit -(XeCC)-, where CC is the acetylenic group. The polymer has a strong partly ionic nature, with positive partial charge on the xenon atoms and a negative one on the CC groups. High energy barriers are found for the removal of a Xe atom from the chain, indicating high stability. This is the first polymer with a noble-gas-containing building block. 2005 American Institute of Physics.

Vibrational frequencies are computed for the fundamental, OH stretching overtone and combination transitions of HNO(3), HNO(4) and the HNO(3)-H(2)O complex. The frequencies are computed directly from ab initio MP2 potential surface points, using the correlation corrected vibrational self-consistent field (CC-VSCF) method, which includes anharmonic effects. The results are compared with experimental data. The computed fundamental transitions are in accord with experiment. The main improvement over the harmonic approximation is for the OH stretching frequencies. The OH overtone excitations (up to the 3rd overtone) of HNO(3), HNO(4) are also in good accord with experiment. For overtone levels near the dissociation threshold, the deviations from experiment are larger, as the VSCF method is unsatisfactory for the extremely large anharmonicities in these cases. Finally, very satisfactory results are obtained for the combination mode transitions. The main conclusions are (1) CC-VSCF seems to work well also for low overtone excitations and for combination transitions. (2) The MP2/TZP potential surfaces, used in the CC-VSCF calculations, are by the test of spectroscopy adequate for these species. The results are encouraging for VSCF calculations of larger, related systems such as HNO(3)-(H(2)O)(n) 17 > 1. (c) 2005 Elsevier B.V. All rights reserved.

The results of harmonic and anharmonic frequency calculations on a guanine-cytosine complex with an enolic structure (a tautomeric form with cytosine in the enol form and with a hydrogen at the 7-position on guanine) are presented and compared to gas-phase IR-UV double resonance spectral data. Harmonic frequencies were obtained at the RI-MP2/cc-pVDZ, RI-MP2/TZVPP, and semiempirical PM3 levels of electronic structure theory. Anharmonic frequencies were obtained by the CC-VSCF method with improved PM3 potential surfaces; the improved PM3 potential surfaces are obtained from standard PM3 theory by coordinate scaling such that the improved PM3 harmonic frequencies are the same as those computed at the RI-MP2/cc-pVDZ level. Comparison of the data with experimental results indicates that the average absolute percentage deviation for the methods is 2.6% for harmonic RI-MP2/cc-pVDZ (3.0% with the inclusion of a 0.956 scaling factor that compensates for anharmonicity), 2.5% for harmonic RI-MP2/TZVPP (2.9% with a 0.956 anharmonicity factor included), and 2.3% for adapted PM3 CC-VSCF; the empirical scaling factor for the ab initio harmonic calculations improves the stretching frequencies but decreases the accuracy of the other mode frequencies. The agreement with experiment supports the adequacy of the improved PM3 potentials for describing the anharmonic force field of the G(...)C base pair in the spectroscopically probed region. These results may be useful for the prediction of the pathways of vibrational energy flow upon excitation of this system. The anharmonic calculations indicate that anharnionicity along single mode coordinates can be significant for simple stretching modes. For several other cases, coupling between different vibrational modes provides the main contribution to anharmonicity. Examples of strongly anharmonically coupled modes are the symmetric stretch and group torsion of the hydrogen-bonded NH2 group on guanine, the OH stretch and torsion of the enol group on cytosine, and the NH stretch and NH out-of-plane bend of the non-hydrogen-bonded NH group on guanine.