Selective reactivity of glycosyl cation stereoisomers: the role of intramolecular hydrogen bonding.

The impact of the stereochemistry of the glycosyl cation species upon its dynamic properties is examined together with their vibrational spectra in order to gain insight into the effects of configurational isomerism on conformer dynamics and proton mobility. Ab initio molecular dynamics (AIMD) simulations and infrared multiple photon dissociation (IRMPD) spectroscopy explore the conformational and reactive dynamics of two pairs of glycosyl cation isomers: (1) protonated α- and ß- anomers of methyl-D-galactopyranoside and (2) the oxocarbenium ions of the D-aldohexose C2 epimers galactose and talose. Analysis of these simulations together with experimental spectroscopy, interpreted by anharmonic calculations, points to the key role played by the intramolecular hydrogen bonds which are present in a unique pattern and extent in each isomer. We find that the reactivity of galactoside stereoisomers toward acid-catalyzed nucleophilic substitution, as gauged by the ability to form free oxocarbenium ions, differs markedly in a way that agrees with experimental measurements in the condensed phase. Other properties such as conformer stability and vibrational transitions were also found to reflect the characteristic hydrogen bonding interactions present in each isomer. In both systems, the stereochemistry is shown to determine the strength of intramolecular hydrogen bonding as well as between which substituents proton transfer is possible. We expect that the critical impact of non-covalent interactions on stereoisomer selectivity may be a widely found phenomenon whose effects should be further investigated.

Gas phase dynamics, conformational transitions and spectroscopy of charged saccharides: the oxocarbenium ion, protonated anhydrogalactose and protonated methyl galactopyranoside.

Protonated intermediates are postulated to be involved in the rate determining step of many sugar reactions. This paper presents a study of protonated sugar species, isolated in the gas phase, using a combination of infrared multiple photon dissociation (IRMPD) spectroscopy, classical ab initio molecular dynamics (AIMD) and quantum mechanical vibrational self-consistent field (VSCF) calculations. It provides a likely identification of the reactive intermediate oxocarbenium ion structure in a d-galactosyl system as well as the saccharide pyrolysis product anhydrogalactose (that suggests oxocarbenium ion stabilization), along with the spectrum of the protonated parent species: methyl d-galactopyranoside-H+. Its vibrational fingerprint indicates intramolecular proton sharing. Classical AIMD simulations for galactosyl oxocarbenium ions, conducted in the temperature range ∼300-350 K (using B3LYP potentials on-the-fly) reveal efficient transitions on the picosecond timescale. Multiple conformers are likely to exist under the experimental conditions and along with static VSCF calculations, they have facilitated the identification of the individual structural motifs of the galactosyl oxocarbenium ion and protonated anhydrogalactose ion conformers that contribute to the observed experimental spectra. These results demonstrate the power of experimental IRMPD spectroscopy combined with dynamics simulations and with computational spectroscopy at the anharmonic level to unravel conformer structures of protonated saccharides, and to provide information on their lifetimes.

Understanding interactions of organic nitrates with the surface and bulk of organic films: implications for particle growth in the atmosphere.

Understanding impacts of secondary organic aerosol (SOA) in air requires a molecular-level understanding of particle growth via interactions between gases and particle surfaces. The interactions of three gaseous organic nitrates with selected organic substrates were measured at 296 K using attenuated total reflection Fourier transform infrared spectroscopy. The organic substrates included a long chain alkane (triacontane, TC), a keto-acid (pinonic acid, PA), an amorphous ester oligomer (poly(ethylene adipate) di-hydroxy terminated, PEA), and laboratory-generated SOA from α-pinene ozonolysis. There was no uptake of the organic nitrates on the non-polar TC substrate, but significant uptake occurred on PEA, PA, and α-pinene SOA. Net uptake coefficients (γ) at the shortest reaction times accessible in these experiments ranged from 3 × 10-4 to 9 × 10-6 and partition coefficients (K) from 1 × 107 to 9 × 104. Trends in γ did not quantitatively follow trends in K, suggesting that the intermolecular forces involved in gas-surface interactions are not the same as those in the bulk, which is supported by theoretical calculations. Kinetic modeling showed that nitrates diffused throughout the organic films over several minutes, and that the bulk diffusion coefficients evolved as uptake/desorption occurred. A plasticizing effect occurred upon incorporation of the organic nitrates, whereas desorption caused decreases in diffusion coefficients in the upper layers, suggesting a crusting effect. Accurate predictions of particle growth in the atmosphere will require knowledge of uptake coefficients, which are likely to be several orders of magnitude less than one, and of the intermolecular interactions of gases with particle surfaces as well as with the particle bulk.

Concerted transfer of multiple protons in acid-water clusters: [(HCl)(H2O)]2 and [(HF)(H2O)]4.

Molecular dynamics simulations using directly ab initio potentials are carried out for the ionically bonded clusters [(Cl-)(H3O+)]2 and [(F-)(H3O+)]4 to explore their transitions to the hydrogen-bonded [(HCl)(H2O)]2 and [(HF)(H2O)]4 structures during the first picosecond of simulation. Both the ionic and the H-bonded structures that are formed are highly symmetric. It is found that proton transfers are concerted in all trajectories for [(Cl-)(H3O+)]2. For [(F-)(H3O+)]4, the fully concerted mechanism is dominant but partially concerted transfers of two or three protons at the same time also occur. The concerted mechanism also holds for the reverse process of ionization of neutral acid molecules. It is suggested that the high symmetry of the ionic and the H-bonded structures plays a role in the preference for concerted transfers. Possible implications of the results for proton transfers in other systems are discussed.

Ionization of acids on the quasi-liquid layer of ice.

The ice quasi-liquid layer (QLL) forms on ice surfaces below the bulk ice melting temperature. It is abundant in the atmosphere, and its importance for atmospheric chemistry is recognized. In the present work, we have studied the microscopic mechanisms of acid ionization on the QLL using ab initio molecular dynamics. The model system QLL is established by nanosecond time scale simulations with empirical force fields, while the reactivity of the QLL is studied using ab initio molecular dynamics. Our ab initio simulations reveal that QLL is reactive, exhibiting stable crystalline point defects, which contribute to efficient acid solvation, ionization, and proton transfer. We study in detail deuterated hydrogen iodide (DI) and nitric acid (DNO3). Ionization in both cases benefits from the abundance of weakly bonded hydrogen-bond single-acceptor double-donor water molecular species available on the QLL in high relative concentration. Picosecond time scale ionization is demonstrated for both molecular species. Our results suggest efficient reactivity of acid ionization and proton transfer at temperature ranges appropriate for the upper troposphere and lower stratosphere.

Ab initio and semi-empirical Molecular Dynamics simulations of chemical reactions in isolated molecules and in clusters.

Recent progress in "on-the-fly" trajectory simulations of molecular reactions, using different electronic structure methods is discussed, with analysis of the insights that such calculations can provide and of the strengths and limitations of the algorithms available. New developments in the use of both ab initio and semi-empirical electronic structure algorithms are described. The emphasis is on: (i) calculations of electronic properties along the reactive trajectories and the unique insights this can contribute to the processes; (ii) electronic structure methods recently introduced to this topic to improve accuracy, extend applicability or enhance computational efficiency. The methods are presented with examples, including new results, of reactions of both isolated molecules and of molecules in media, mostly clusters. Possible future directions for this fast growing field are suggested.

Ionization of Nitric Acid on Crystalline Ice: The Role of Defects and Collective Proton Movement.

Ionization of nitric acid (HNO3) on a model ice surface is studied using ab initio molecular dynamics at temperatures of 200 and 40 K with a surface slab model that consists of the ideal ice basal plane with locally optimized and annealed defects. Pico- and subpicosecond ionization of nitric acid can be achieved in the defect sites. Key features of the rapid ionization are (a) the efficient solvation of the polyatomic nitrate anion, by stealing hydrogen bonds from the weakened hydrogen bonds at defect sites, (b) formation of contact ion pairs to stable "presolvated" molecular species that are present at the defects,

Ultrafast photochemistry of methyl hydroperoxide on ice particles.

Simulations show that photodissociation of methyl hydroperoxide, CH(3)OOH, on water clusters produces a surprisingly wide range of products on a subpicosecond time scale, pointing to the possibility of complex photodegradation pathways for organic peroxides on aerosols and water droplets. Dynamics are computed at several excitation energies at 50 K using a semiempirical PM3 potential surface. CH(3)OOH is found to prefer the exterior of the cluster, with the CH(3)O group sticking out and the OH group immersed within the cluster. At atmospherically relevant photodissociation wavelengths the OH and CH(3)O photofragments remain at the surface of the cluster or embedded within it. However, none of the 25 completed trajectories carried out at the atmospherically relevant photodissociation energies led to recombination of OH and CH(3)O to form CH(3)OOH. Within the limited statistics of the available trajectories the predicted yield for the recombination is zero. Instead, various reactions involving the initial fragments and water promptly form a wide range of stable molecular products such as CH(2)O, H(2)O, H(2), CO, CH(3)OH, and H(2)O(2).

Anharmonic vibrational spectroscopy calculations for proton-bound amino acid dimers.

Results of anharmonic frequency calculations carried out for GlysLysH(+) and GlyGlyH(+) are presented and compared to gas phase electrospray ionization (ESI) spectroscopy experiments. Anharmonic frequencies are obtained via correlation-corrected vibrational self-consistent field (CC-VSCF) calculations. The potential used is based on the PM3 semiempirical electronic structure method, but improved by fitting to ab initio MP2 calculations at the harmonic level. The key results are as follows: (1) Hydrogens acting as intermolecular bridges have very anharmonic stretches whose frequencies cannot be reliably predicted by the harmonic approximation. An example is the carboxylate bound NH(3)(+) stretch. (2) The computed anharmonic vibrational frequencies are in good agreement with experiment and provides a very large improvement over harmonic frequencies especially for OH and NH stretches. For example the calculated CC-VSCF frequencies of GlysLysH(+) and GlyGlyH(+) have overall average deviations of 1.35% and 1.48% only, respectively, from experiment. (3) The harmonic OH bond stretching frequency deviates by 6.64% from experiments. The CC-VSCF calculations reduce this deviation by more than an order of magnitude to 0.56%. The anharmonicity of the OH stretch is intrinsic, rather than due to coupling with other modes. (4) Anharmonic coupling between the NH(3)(+) stretch and several other normal modes is strong, and provide the main contribution for the anharmonicity of this mode. Properties of the potential energy surfaces of the proton-bound complexes are briefly discussed in light of the results.

Mid-IR spectra of different conformers of phenylalanine in the gas phase.

The experimental mid- and far-IR spectra of six conformers of phenylalanine in the gas phase are presented. The experimental spectra are compared to spectra calculated at the B3LYP and at the MP2 level. The differences between B3LYP and MP2 IR spectra are found to be small. The agreement between experiment and theory is generally found to be very good, however strong discrepancies exist when -NH2 out-of-plane vibrations are involved. The relative energies of the minima as well as of some transition states connecting the minima are explored at the CCSD(T) level. Most transition states are found to be less than 2000 cm(-1) above the lowest energy structure. A simple model to describe the observed conformer abundances based on quasi-equilibria near the barriers is presented and it appears to describe the experimental observation reasonably well. In addition, the vibrations of one of the conformers are investigated using the correlation-corrected vibrational self-consistent field method.

Dynamics of electronic states and spin-flip for photodissociation of dihalogens in matrices: experiment and semiclassical surface-hopping and quantum model simulations for F2 and ClF in solid Ar.

Three approaches are combined to study the electronic states' dynamics in the photodissociation of F(2) and ClF in solid argon. These include (a) semiclassical surface-hopping simulations of the nonadiabatic processes involved. These simulations are carried out for the F(2) molecule in a slab of 255 argon atoms with periodic boundary conditions at the ends. The full manifold of 36 electronic states relevant to the process is included. (b) The second approach involves quantum mechanical reduced-dimensionality models for the initial processes induced by a pump laser pulse, which involve wavepacket propagation for the preoriented ClF in the frozen argon lattice and incorporate the important electronic states. The focus is on the study of quantum coherence effects. (c) The final approach is femtosecond laser pump-probe experiments for ClF in Ar. The combined results for the different systems shed light on general properties of the nonadiabatic processes involved, including the singlet to triplet and intertriplet transition dynamics. The main findings are (1) that the system remains in the initially excited-state only for a very brief, subpicosecond, time period. Thereafter, most of the population is transferred by nonadiabatic transitions to other states, with different time constants depending on the systems. (2) Another finding is that the dynamics is selective with regard to the electronic quantum numbers, including the Lambda and Omega quantum numbers, and the spin of the states. (3) The semiclassical simulations show that prior to the first "collision" of the photodissociated F atom with an Ar atom, the argon atoms can be held frozen, without affecting the process. This justifies the rigid-lattice reduced-dimensionality quantum model for a brief initial time interval. (4) Finally, degeneracies between triplets and singlets are fairly localized, but intertriplet degeneracies and near degeneracies can span an extensive range. The importance of quantum effects in photochemistry of matrix-isolated molecules is discussed in light of the results.

New experimental and theoretical approach to the heterogeneous hydrolysis of NO2: key role of molecular nitric acid and its complexes.

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 NO(3-)-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 NO(x). 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.

Photochemical processes induced by vibrational overtone excitations: dynamics simulations for cis-HONO, trans-HONO, HNO3, and HNO3-H2O.

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 OH 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 HNO(x) species, with evidence for new phenomena. Possible relevance of the results to atmospheric processes is discussed.

Different chemical dynamics for different conformers of biological molecules: photoionization of glycine.

Single-photon ionization dynamics of two conformers of glycine is studied by classical trajectory simulations using the semiempirical PM3 potential surface in "on the fly" calculations. Initial conditions for the trajectories are weighted according to the Wigner distribution function computed for the initial vibrational ground state. Vertical ionization in the spirit of the classical Franck-Condon principle is assumed. The dynamics of the two conformers are compared during the first 10 ps. The comparison shows very different dynamical behavior for the two conformers. In particular, the chemical fragmentation pathways differ in part. Also, one of the conformers gives much higher rates of conformational transitions, while the other conformer gives larger chemical fragmentation yields. The example shows significantly different chemical dynamics for two conformers close in energy and separated by a low barrier.

Ab initio vibrational calculations for H2SO4 and H2SO4 x H2O: spectroscopy and the nature of the anharmonic couplings.

Vibrational frequencies for fundamental, overtone, and combination excitations of sulfuric acid (H2SO4) and of sulfuric acid monohydrate cluster (H2SO4 x H2O) are computed directly from ab initio MP2/TZP potential surface points using the correlation-corrected vibrational self-consistent field (CC-VSCF) method, which includes anharmonic effects. The results are compared with experiment. The computed transitions show in nearly all cases good agreement with experimental data and consistent improvement over the harmonic approximation. The CC-VSCF improvements over the harmonic approximation are largest for the overtone and combination excitations and for the OH stretching fundamental. The agreement between the calculations and experiment also supports the validity of the MP2/TZP potential surfaces. Anharmonic coupling between different vibrational modes is found to significantly affect the vibrational frequencies. Analysis of the mean magnitude of the anharmonic coupling interactions between different pairs of normal modes is carried out. The results suggest possible mechanisms for the internal flow of vibrational energy in H2SO4 and H2SO4 x H2O.

Formation of novel rare-gas molecules in low-temperature matrices.

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.

Vibrational spectroscopy and the development of new force fields for biological molecules.

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.

Ultrafast solvent-induced spin-flip and nonadiabatic coupling: ClF in argon solids.

Femtosecond pump-probe spectra show direct evidence for ultrafast solvent-induced spin flip in photodissociation-recombination events of ClF, a light diatomic molecule, for which the spin-orbit coupling is weak. The bound triplet states ((3)Pi) of ClF are probed and the dynamics for excitation to the singlet state ((1)Pi(1)) is compared with excitation to the triplet state B((3)Pi(0)). The population initially excited to the singlet state (1)Pi(1) is transferred to the bound triplet states (3)Pi within tau(f)=0.5 ps. Oscillations in the spectra indicate wave packet dynamics with the triplet state period of 300 to 400 fs in both cases. According to simulations of F(2)/Ar, most of the initially excited singlet state population is converted to repulsive and weakly bound triplet states within approximately 60 fs. In the first ps, 40% of the triplet population accumulates in the weakly bound (3)Pi states, in good accord with the experiment.

Formation of novel rare-gas-containing molecules by molecular photodissociation in clusters.

Recent work by Räsänen and coworkers showed that photolysis of hydrides in rare-gas matrices results in part in formation of novel, rare-gas-containing molecules. Thus, photolysis of HCl in Xe and of H2O in Xe result respectively in formation of HXeCl and HXeOH in the Xe matrices. Ab initio calculations show that the compounds HRgY so formed are stable in isolation, and that by the strength and nature of the bonding these are molecules, very different from the corresponding weakly bound clusters Rg...HY. This paper presents a study of the formation mechanism of HRgY following the photolysis of HY in clusters Rgn(HY). Calculations are described for HXeCl, as a representative example. Potential energy surfaces that govern the formation of HXeCl in the photolysis of HCl in xenon clusters are obtained, and the dynamics on these surfaces is analyzed, partly with insight from trajectories of molecular dynamics simulations. The potential surfaces are obtained by a new variant of the DIM (diatomics in molecules) and DIIS (diatomics in ionic systems) models. Non-adiabatic couplings are also obtained. The main results are: (1) Properties of HXeCl predicted by the DIM-DIIS model are in reasonable accord with results of ab initio calculations. (2) The potential along the isomerization path HXeCl-->Xe...HCl predicted by DIM is in semiquantitative accord with the ab initio results. (3) Surface-hopping molecular dynamics simulations of the process in clusters, with "on the fly" calculations of the DIM-DIIS potentials and non-adiabatic couplings are computationally feasible. (4) Formation of HXeCl, following photolysis of HCl in Xe54(HCl), requires cage-exit of the H atom as a precondition. The H atom and the Cl can then attack the same Xe atom on opposite sides, leading to charge transfer and production of the ionic HXeCl. (5) Non-adiabatic processes play an important role, both in the reagent configurations, and at the charge-transfer stage. The results open the way to predictions of the formation of new HRgY species.