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.

Progress in the study of a new class of chemically bound compounds of noble-gas atoms is reviewed. The focus is on rare-gas molecules of the form HNgY, where Ng is a noble-gas atom and Y is an electronegative group, prepared by photolysis of HY in the rare-gas matrix. Other related types of new molecules of noble-gas atoms are discussed as well. Topics discussed in this review include: (a) The nature of bonding and the energetic stability of the compounds. (b) The vibrational spectroscopy of the molecules, and its role in identification of the species. (c) The mechanism and dynamics of photochemical formation of HNgY in the matrix, and the pathways for thermal and infrared (IR)-induced decomposition. Specifically, attention is given to the issue of ``direct'' formation following photolysis of HY versus ``delayed'' formation involving H atom diffusion. (d) Molecules of the lighter rare gases Ar, Ne, and He, focusing on the experimentally prepared HArF and on theoretical predictions suggesting the existence of other molecules. (e) The most-recently discovered photochemically induced insertion compounds of Ng into hydrocarbons, such as HXeCCH. (f) Clusters of HNgY with other molecules. The possible existence of neat aggregates and crystals of HNgY The reviewed state-of-the-art suggests this field is at an early stage of development with major open questions bearing on the surprising properties of the molecules and on the formation mechanisms. These are part of the challenge for the future.

Photodissociation experiments were carried out at 193 nm for single HCl molecules which are adsorbed on the surface. of large Ar-n clusters and small (HCl)(m) complexes which are embedded in the interior of these clusters. For the surface case the size dependence is measured for the average sizes =140-1000. No cage exit events are observed in, agreement with the substitutional position, of the molecule deeply buried in. the outermost shell. This result is confirmed by a molecular dynamics simulation of the pickup process under realistic conditions concerning the experiment and the interaction potentials. The calculations of the dissociation process employ the surface hopping model., For the embedded case the average sizes covered are =3 and 6 and =8-248. The kinetic energy of the H atom fragments is measured exhibiting peaks at zero and around 2.0 eV which mark completely caged and unperturbed fragments, respectively. The ratio of theses peaks strongly depends on the cluster size and agrees well with theoretical predictions for one and two closed icosahedral shells, in which the nonadiabatic coupling of all states was accounted for. (C) 2004 American Institute of Physics.

Single photon ionization dynamics of glycine is studied by classical trajectory simulations using the semiempirical PM3 potential surface in ``on the fly'' calculations. The glycine 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. The main findings are as follows: (1) The photoionization triggers a fast internal rotation about the C-C bond, with the NH(2) group rotating in one direction, and the COOH group rotating in the opposite direction. For the trajectories where the fast rotation occurs, it persists till the end of the simulation (10 ps). The yield for this process is about 6%, suggesting it may be experimentally observable. (2) For many of the trajectories, the photoproduced glycine ion exhibits ``hops'' between two conformer structures. The rates computed from the dynamics for these conformational transitions differ considerably from RRK predictions. (3) Different behavior of vibrational energy flow is found for different types of modes. There is no significant approach to statistical distribution of the energy throughout the first 10 picoseconds. (4) The preferred dissociation channel is the C-C bond cleavage. Indeed, fragmentation is observed for a few trajectories, one of them shows H atom hopping from the amino group to the carbonyl group prior to dissociation. Another trajectory shows only this hydrogen transfer and the transfer back. Possible experimental implications of some of the findings are briefly discussed.

A modification of the semi-empirical PM3 electronic structure method is proposed. It employs a coordinate scaling procedure, such that the harmonic frequencies from the modified PM3 potentials for lower-energy conformers of glycine (conformer 1), alanine (conformers I and 11) and proline (conformer 11), fit more closely with ab initio (MP2/DZP) harmonic frequencies. The anharmonic frequencies are then calculated using the modified PM3 surfaces with the Vibrational Self-Consistent Field (VSCF) and Correlation-Corrected VSCF (CC-VSCF) methods. The computed anharmonic frequencies are in very good accord with spectroscopic experiments for the three amino acids. The results are much superior to those obtained from standard (unscaled) PM3 potentials, indicating that the modified PM3 potentials may be used as high quality potentials for biological molecules, at least in the configuration ranges pertinent to vibrational spectroscopy. The scaling parameters computed for the lowest energy conformers listed above were tested for transferability: they were used in computing the anharmonic spectra of two other conformers (glycine 11 and proline 1). The good agreement of the resulting frequencies with observed frequencies, indicates the transferability of the scaling parameters. It is concluded from this study that the improved PM3 potentials offer accurate and computationally efficient force fields for vibrational spectroscopy calculations of biological molecules. Possible additional applications of the new potentials are discussed.

The UV absorption spectra of neat water clusters (H2O)(n) of sizes in the range of n = 8-50 are computed. The simple model used for the excited states includes the dependence of the excitonic interactions on both the intermolecular and intramolecular coordinates. For a cluster (H2O)(n), n excitonic potential energy surfaces are computed for geometries in the Franck-Condon region. The Coker-Watts potential is used to describe the interactions in the electronic ground state, and molecular dynamics simulations are performed to sample geometries for the classical Franck-Condon calculations. There are numerous crossings of different excitonic potential surfaces for (H2O)(n) in the range of the geometries sampled. The main findings are (i) the main absorption peak of (H2O)(n) shifts to the blue and increases in width as the cluster size n is increased; (ii) the widths of the absorption bands increase with temperature, e.g., for (H2O)(20), the width is 1.2 eV at 80 K and 1.6 eV at 220 K; (iii) several well-resolved peaks within the absorption band are found for some of the systems at certain temperatures, and in such cases, each of the peaks generally results from absorption into different excitonic states; (iv) although the absorption peaks are strongly shifted to the blue, with respect to the (H2O) monomer, for some cluster sizes, a weak absorption tail to the red side is also observed as the temperature increases.

We report anharmonic vibrational spectra (fundamentals, first overtones) for the F(-)(H(2)O) and F(-)(H(2)O)(2) clusters computed at the MP2 and CCSD(T) levels of theory with basis sets of triple-zeta quality. Anharmonic corrections were estimated via the correlation-corrected vibrational self-consistent field (CC-VSCF) method. The CC-VSCF anharmonic spectra obtained on the potential energy surfaces evaluated at the CCSD(T) level of theory are the first ones reported at a correlated level beyond MP2. We have found that the average basis set effect (TZP vs aug-cc-pVTZ) is on the order of 30-40 cm(-1), whereas the effects of different levels of electron correlation [MP2 vs CCSD(T)] are smaller, 20-30 cm(-1). However, the basis set effect is much larger in the case of the H-bonded O-H stretch of the F(-)(H(2)O) cluster amounting to 100 cm(-1) for the fundamentals and 200 cm(-1) for the first overtones. Our calculations are in agreement with the limited available set of experimental data for the F(-)(H(2)O) and F(-)(H(2)O)(2) systems and provide additional information that can guide further experimental studies.

Argon is an extremely chemically inert element. HArF is presently the only experimentally known neutral molecule containing a chemically bound argon atom. Ab initio calculations at the MP2 and CCSD(T) levels presented here suggest, however, the existence of whole families of additional molecules. Explicitly predicted are FArCCH, with an argon-carbon bond, and FArSiF(3), with an argon-silicon bond. These metastable compounds are found to be protected from decomposition by relatively high energy barriers. Other organo-argon and organo-silicon molecules derived from the above should be equally stable. The results may open the way to a substantial field of ``argon chemistry.'' (C) 2003 American Institute of Physics.

Collisions of the gaseous hydroxyl (OH) radical and ozone (O-3) with the surfaces of sodium chloride or iodide solutions, as well as with the surface of neat water, were investigated by molecular dynamics simulations. The principal intent was to answer atmospherically relevant questions concerning the trapping and accommodation of the OH and O-3 species at the surface and their uptake into the bulk solution. Although trapping is substantial for both species, OH adsorbs and absorbs significantly better than O-3. Most of the trapped O-3 molecules desorb from the surface within 50 ps, whereas a significant fraction of OH radicals remains at the interface for time intervals exceeding 100 ps. The aqueous surface has also an orientational effect on the OH species, favoring geometries with the H atom pointing toward the aqueous bulk. The effect of the dissolved salt on the trapping efficiency is minor; therefore, most likely, atomic ions solvated in aqueous aerosols do not act as strong scavengers of reactive gases in the atmosphere. However, frequent and relatively long contacts between the adsorbed molecules and halide anions do occur, allowing for heterogeneous atmospheric chemistry in the interfacial layer.

We report the production in the gas phase of ionically bound HXeI molecules. The molecules are generated by the photodissociation of HI molecules in large Xe-n clusters and are identified from the asymmetry of the detected H atom fragments arising from the dissociation of oriented HXeI. The orientation, resulting from a synergistic action of a pulsed laser field with a weak electrostatic field, is quite pronounced, due to a large ratio of the polarizability anisotropy to the rotational constant of HXeI. (C) 2003 American Institute of Physics.

The role of vibrational spectroscopy in the testing of force fields of biological molecules and in the determination of improved force fields is discussed. Analysis shows that quantitative testing of potential energy surfaces by comparison with spectroscopic data generally requires calculations that include anharmonic couplings between different vibrational modes. Applications of the vibrational self-consistent field (VSCF) method to calculations of spectroscopy of biological molecules are presented, and comparison with experiment is used to determine the merits and flaws of various types of force fields. The main conclusions include the following: (1) Potential surfaces from ab initio methods at the level of MP2 yield very satisfactory agreement with spectroscopic experimental data. (2) By the test of spectroscopy, ab initio force fields are considerably superior to the standard versions of force fields such as AMBER or OPLS. (3) Much of the spectroscopic weakness of AMBER and OPLS is due to incorrect description of anharmonic coupling, between different vibrational modes. (4) Potential surfaces of the QM/MM (Quantum Mechanics/Molecular Mechanics) type, and potentials based on improved versions of semi-empirical electronic structure theory, which are feasible for large biological molecules, yield encouraging results by the test of vibrational spectroscopy. (C) 2003 Wiley Periodicals, Inc.

HArF and HKrF are chemically bound rare-gas compounds that have been produced by photolysis of HF and subsequent thermal annealing in the respective rare-gas matrices. In this paper we present a computational study of the delayed, thermally induced formation of these molecules in the matrix. Using realistic potentials for the molecular and guest-host interactions, the potential energy along the minimum energy paths for formation is evaluated, and thermal transition rates are computed using a Monte Carlo transition state method. A closely packed, dissociated configuration of the molecular fragments is found to play an important role, both as the possible trapping site of the photolyzed fragments, and as an intermediate structure for diffusion-controlled formation. The computed threshold temperatures of formation for the HArF and HKrF molecules at different matrix sites are in good agreement with experimental findings and with previous site assignments for these molecules. (C) 2003 American Institute of Physics.