Observation of a simple vibrational wavepacket in a polyatomic molecule via time-resolved photoelectron velocity-map imaging: a prototype for time-resolved IVR studies

We have prepared a coherent superposition of the two components of a Fermi resonance in the S1 state of toluene at approximately 460 cm(-1) with a approximately 1 ps laser pulse and monitored time-resolved photoelectron velocity-map images. The photoelectron intensities oscillate with time in a manner that depends on their kinetic energy, even though full vibrational resolution in the cation is not achieved. Analysis of the time-dependent photoelectron spectra enables information on the composition of the S1 wavepacket to be deduced. Such an experiment, in which a whole set of partially dispersed cation vibrational states are detected simultaneously, suggests an efficient method of studying intramolecular vibrational energy redistribution processes in excited states.     

Size evolution of the vibrational predissociation process in Br2...Nen clusters: simulation and kinetic study

A hybrid quantum-classical simulation of the vibrational predissociation of Br2...Nen, (n = 2-11) clusters in the B electronic state is carried out. The time-evolution of the reactants, products, and intermediates is analyzed by a kinetic mechanism consisting of three elementary steps: direct vibrational predissociation (VP), intramolecular vibrational redistribution (IVR), and evaporative cooling (EC). The importance of intramolecular vibrational redistribution followed by evaporative cooling relative to direct vibrational predissociation is shown to increase rapidly with increasing cluster size. Final product state distributions reveal that only one or less Br2 stretching quantum per neon atom is required in order to achieve complete dissociation (n quanta for n < or = 9 and n - 1 for n = 10 and 11). The proportion of available energy going into translation is proposed as a parameter to study the statistical behavior of the Van der Waals clusters. It is shown to depend only on the number of remaining degrees of freedom, a characteristic of a statistical behavior, for n > or = 3.     

Theoretical characterization of four distinct isomer types in hydrated-electron clusters, and proposed assignments for photoelectron spectra of water cluster anions

Water cluster anions, (H(2)O)(N)(-), are examined using mixed quantum/classical molecular dynamics based on a one-electron pseudopotential model that incorporates many-body polarization and predicts vertical electron detachment energies (VDEs) with an accuracy of ~0.1 eV. By varying the initial conditions under which the clusters are formed, we are able to identify four distinct isomer types that exhibit different size-dependent VDEs. On the basis of a strong correlation between the electron's radius of gyration and its optical absorption maximum, and extrapolating to the bulk limit (N → ∞), our analysis supports the assignment of the "isomer Ib" data series, observed in photoelectron spectra of very cold clusters, as arising from cavity-bound (H(2)O)(N)(-) cluster isomers. The "isomer I" data reported in warmer experiments are assigned to surface-bound isomers in smaller clusters, transitioning to partially embedded isomers in larger clusters. The partially embedded isomers are characterized by a partially formed solvent cavity at the cluster surface, and they are spectroscopically quite similar to internalized cavity isomers. These assignments are consistent with various experimental data, and our theoretical characterization of these isomers sheds new light on a long-standing assignment problem.     

Lactic acid in solution: investigations of lactic acid self-aggregation and hydrogen bonding interactions with water and methanol using vibrational absorption and vibrational circular dichroism spectroscopies

The infrared vibrational absorption (VA) and vibrational circular dichroism (VCD) spectral features of L-(+)-lactic acid (LA) in CDCl3 solution are concentration dependent, showing evidence of oligomerization with increasing concentrations. To understand the observed spectra, geometry optimizations, vibrational frequencies, and VA and VCD intensities were evaluated for (LA)n with n=1-4 using density functional theory calculations at the B3LYP6-311++G(d,p), B3LYP/cc-pVTZ, and in some cases, B3LYP/aug-cc-pVTZ levels of theory. Comparisons with the experimental spectra indicate that the lowest energy LA dimer (AA), formed by two C Double Bond O...HO hydrogen bonds, is one of the dominating species in solution at room temperature. Possible contributions from the LA trimer and tetramer are also discussed. To model the VA and VCD spectra of LA in water and in methanol, both implicit polarizable continuum model and explicit hydrogen bonding considerations were used. For explicit hydrogen bonding, geometry optimizations of the AA-(water)n and AA-(methanol)n complexes, with n=2,4,6, were performed, and the corresponding VA and VCD spectra were simulated. Comparisons of the calculated and experimental VA and VCD spectra in the range of 1000-1800 cm(-1) show that AA-(water)n with n=6 best reproduces the experimental spectra in water. On the other hand, AA-(methanol)n with n=2 reproduces well the experimental results taken in methanol solution. In addition, we found evidence of chirality transfer, i.e., some vibrational bands of the achiral water subunits gain VCD strength upon complexation with the chiral LA solute. The study is the first to use VCD spectroscopy to probe the structures of LA aggregates and hydrogen bonding solvation clusters in the solution phase.     

Molecular analysis of water clusters: Calculation of the cluster structures and vibrational spectrum using density functional theory

Density functional theory (DFT) is applied to obtain absorption spectra at THz frequencies for molecular clusters of H₂O. The vibrational modes of the clusters are calculated. Coupling among molecular vibrational modes explains their spectral features associated with THz excitation. THz excitation is associated with vibrational frequencies which are here calculated within the DFT approximation of electronic states. This is done for both isolated molecules and collections of molecules in a cluster. The principal result of the paper is that a crystal-like cluster of 38 water molecules together with a continuum solvent background is sufficient to replicate well the experimental vibrational frequencies.     

Identification of two distinct electron binding motifs in the anionic water clusters: a vibrational spectroscopic study of the (H2O)6- isomers

Photoelectron spectroscopy of the water cluster anions, (H2O)n-, has revealed that several isomeric forms are present for most sizes, and here, we use vibrational spectroscopy to address the structure of the (H2O)6- isomer that more weakly binds the extra electron. To overcome the severe line broadening that occurs in the OH stretching region of this isomer caused by fast electron autodetachment, we concentrate on the low-energy bending modes of the perdeutero isotopomer. Sharp spectroscopic signatures are recovered for two isomers using argon predissociation spectroscopy, and the resulting bands are heavily overlapped. To extract their independent contributions to the observed spectra, we exploit the substantial dependence of their relative populations on the number of attached argon atoms in the (D2O)6-.Ar(m) clusters, determined by photoelectron spectroscopy. The vibrational spectra of each isomer can then be isolated by spectral subtraction, which is implemented with a covariance mapping approach. The resulting band patterns establish that the more weakly binding isomer does not display the characteristic electron-binding motif common to the more strongly bound isomer class. Whereas the strongly binding isomer features a single water molecule pointing toward the excess electron cloud with both of its hydrogen atoms, the spectrum of the more weakly binding isomer suggests a structure where the electron is bound by a number of dangling OH groups corresponding to water molecules in acceptor-donor binding sites.     

Photoelectron spectroscopy of S1 toluene: II. Intramolecular dynamics of selected vibrational levels in S1 toluene studied by nanosecond and picosecond time-resolved photoelectron spectroscopies

We present results which suggest that the photophysics of S(1) toluene is significantly more complicated than that of the related molecules p-fluorotoluene or p-difluorobenzene. We have measured a range of photoelectron spectra for a number of S(1) internal energies, on different time scales and at different temperatures, in an attempt to unravel the competing processes, but the final conclusion remains outstanding.     

Proton and deuteron position preferences in water clusters: an ab initio study

In order to explore the effect of H-to-D substitution on the zero-point energy (ZPE) of water clusters, Hessians were computed for a database of 53 optimized (H2O)n clusters, 5 < or = n < or = 21, at the B3LYP6-311 + + G** level. The 53 clusters contained 1524 protons, which were sorted into 18 categories according to the type of their donor O and (if not free) acceptor O. Letting deltaZPE[H]* denote the change in ZPE when the proton H* is replaced by D, mean values for deltaZPE[H*] for the H-bonded categories ranged from -2172 cal mol(-1) for H* in a DDAA-DDAA bond to -2118 for H* in a DAA-DDA bond. Mean value for H* free on DAA (respectively, DA) was -2018 (respectively, -1969). For DAA-DDA bonds, and for short H bonds in general, there was a strong inverse correlation between /deltaZPE[H*]/ and the O-H* distance. deltaZPE for multiple H-to-D substitutions was additive, except for a cooperativity effect of -13.7 to -19.7 cal mol(-1) when two substituted protons were in the same H2O unit and a much smaller cooperativity when one proton's donor was the other's acceptor. Implications of these data include a relative preference for D to occupy H bonded rather than free positions in finite water clusters, a value of 3.82 for the disproportionation equilibrium constant of mixed ice at 150 K, increased occupation by H at surface positions of mixed ice, and a larger average coordination number for liquid D2O than for liquid H2O.     

Synchrotron radiation photoelectron studies for primary radiation effects using a liquid water jet in vacuum: Total and partial photoelectron yields for liquid water near the oxygen -edge

A new spectroscopy to identify the hydration structure playing important role in liquid-phase radiation damage is in progress using a laminar liquid water jet sample in vacuum in combination with soft X-ray synchrotron radiation. We present the total and partial electron yields for liquid water using a photoelectron spectroscopy. Partial electron yields for the K^-11b₁1b₁ Auger transition are obtained for the first time by measuring the electrostatically dispersed electron kinetic energy spectra as a function of photon energy of synchrotron radiation.     

Probing the structures and chemical bonding of boron-boronyl clusters using photoelectron spectroscopy and computational chemistry: B(4)(BO)(n) (-) (n = 1-3)

The electronic and structural properties of a series of boron oxide clusters, B(5)O(-), B(6)O(2) (-), and B(7)O(3) (-), are studied using photoelectron spectroscopy and density functional calculations. Vibrationally resolved photoelectron spectra are obtained, yielding electron affinities of 3.45, 3.54, and 4.94 eV for the corresponding neutrals, B(5)O, B(6)O(2), and B(7)O(3), respectively. Structural optimizations show that these oxide clusters can be formulated as B(4)(BO)(n) (-) (n = 1-3), which involve boronyls coordinated to a planar rhombic B(4) cluster. Chemical bonding analyses indicate that the B(4)(BO)(n) (-) clusters are all aromatic species with two π electrons.     

Tuning of the internal energy and isomer distribution in small protonated water clusters H(+)(H2O)(4-8): an application of the inert gas messenger technique

Infrared spectroscopy of gas-phase hydrated clusters provides us much information on structures and dynamics of water networks. However, interpretation of spectra is often difficult because of high internal energy (vibrational temperature) of clusters and coexistence of many isomers. Here we report an approach to vary these factors by using the inert gas (so-called "messenger")-mediated cooling technique. Protonated water clusters with a messenger (M), H(+)(H(2)O)(4-8)·M (M = Ne, Ar, (H(2))(2)), are formed in a molecular beam and probed with infrared photodissociation spectroscopy in the OH stretch region. Observed spectra are compared with each other and with bare H(+)(H(2)O)(n). They show clear messenger dependence in their bandwidths and relative band intensities, reflecting different internal energy and isomer distribution, respectively. It is shown that the internal energy follows the order H(+)(H(2)O)(n) > H(+)(H(2)O)(n)·(H(2))(2) > H(+)(H(2)O)(n)·Ar > H(+)(H(2)O)(n)·Ne, while the isomer-selectivity, which changes the isomer distribution in the bare system, follows the order H(+)(H(2)O)(n)·Ar > H(+)(H(2)O)(n)·(H(2))(2) > H(+)(H(2)O)(n)·Ne ~ (H(+)(H(2)O)(n)). Although the origin of the isomer-selectivity is unclear, comparison among spectra measured with different messengers is very powerful in spectral analyses and makes it possible to easily assign spectral features of each isomer.     

Hydration process of Na2- in small water clusters: photoelectron spectroscopy and theoretical study of Na2- (H2O)n

Photoelectron spectroscopy (PES) of Na2- (H2O)n (n < or = 6) was investigated to examine the solvation of sodium aggregates in small water clusters. The PES bands for the transitions from the anion to the neutral ground and first excited states derived from Na2 (1(1)Sigmag+) and Na2 (1(3)Sigmau+) shifted gradually to the blue, and those to the higher-excited states correlated to the 3(2)S + 3(2)P asymptote dropped down rapidly to the red and almost degenerated on the 1(3)Sigmau+-type band at n = 4. Quantum chemical calculations for n up to 3 showed that the spectra can be ascribed to structures where one of the Na atoms is selectively hydrated. From the electron distributions, it is found that the Na- -Na+(H2O)n- -type electronic state grows with increasing cluster size, which can be regarded as a sign of the solvation of Na2- with ionization of the hydrated Na.     

The vibrational predissociation spectra of the H5O2 +RGn(RG = Ar,Ne) clusters: correlation of the solvent perturbations in the free OH and shared proton transitions of the Zundel ion

Predissociation spectra of the H(5)O(2) (+)RG(n)(RG = Ar,Ne) cluster ions are reported in energy regions corresponding to both the OH stretching (3350-3850 cm(-1)) and shared proton (850-1950 cm(-1)) vibrations. The two free OH stretching bands displayed by the Ne complex are quite close to the band origins identified earlier in bare H(5)O(2) (+) [L. I. Yeh, M. Okumura, J. D. Myers, J. M. Price, and Y. T. Lee, J. Chem. Phys. 91, 7319 (1989)], indicating that the symmetrical H(5)O(2) (+) "Zundel" ion remains largely intact in H(5)O(2) (+)Ne. The low-energy spectrum of the Ne complex is simpler than that observed previously for H(5)O(2) (+)Ar, and is dominated by two sharp transitions at 928 and 1047 cm(-1), with a weaker feature at 1763 cm(-1). The H(5)O(2) (+)Ar(n),n = 1-5 spectra generally exhibit complex band structures reflecting solvent-induced symmetry breaking of the Zundel core ion. The extent of solvent perturbation is evaluated with electronic structure calculations, which predict that the rare gas atoms should attach to the spectator OH groups of H(5)O(2) (+) rather than to the shared proton. In the asymmetric complexes, the shared proton resides closer to the more heavily solvated water molecule, leading to redshifts in the rare gas atom-solvated OH stretches and to blueshifts in the shared proton vibrations. The experimental spectra are compared with recent full-dimensional vibrational calculations (diffusion Monte Carlo and multimode/vibrational configuration interaction) on H(5)O(2) (+). These results are consistent with assignment of the strong low-energy bands in the H(5)O(2) (+)Ne spectrum to the vibration of the shared proton mostly along the O-O axis, with the 1763 cm(-1) band traced primarily to the out-of-phase, intramolecular bending vibrations of the two water molecules.     

Novel water clusters in the crystalline state: structures of a symmetrical,cyclic hexamer and an 'opened-cube' octamer

Six- and eight-membered hydrogen-bonded water clusters of novel structure types have been found in crystalline hydrates.     

Finding important anharmonic terms in the sixth-order potential energy function by the scaled hypersphere search method: an application to vibrational analyses of molecules and clusters

A fitting method of the sixth-order potential energy function is proposed, where ab initio potential energy data for the fitting are sampled in directions containing maximal anharmonic downward distortions detected by the scaled hypersphere search (SHS) method. This technique has been applied to H2O, HCHO, HCOOH, C2H4, CH3OH, CH3CHO, CH3NH2, B2H6, (H2O)2, and (H2O)3, where, without using the symmetry, 176, 904, 1432, 2992, 2520, 2760, 3608, 6232, 768, and 1456 times single-point energy calculations, respectively, were required for obtaining anharmonic terms. Experimental IR peak positions of not only fundamentals but also overtones and combinations in the excitation energy range of 1000-4000 cm(-1) could be reproduced very accurately by the post-vibrational self-consistent field theory employing potential functions obtained by the present SHS based polynomial fitting method.     

Correlation of structure and vibrational spectra of the zwitterion L-alanine in the presence of water: an experimental and density functional analysis

Infrared vibrational spectra were collected along with the vibrational circular dichroism (VCD) spectra for the zwitterions alpha-D-alanine, alpha-L-alanine, alpha-D-mannose and alpha-L-mannose as potassium bromide (KBr) pressed samples. VCD for D- and L-alanine dissolved in water was also measured and compared against the spectra resulting from KBr pressed samples. The experimental data were compared against the ab initio B3LYP/6-31G* optimized geometry. The zwitterion structure of alpha-L-alanine was stabilized by the addition of water molecules. Computationally, beta-L-mannose was studied and resulting expected VCD bands assigned. We present the molecular structures resulting VCD spectra and infrared vibrational spectra from experimentation as compared with the computed results.     

Studies in hydrogen bonding: Association within small clusters of water,methanol, and ammonia molecules using Jorgensen's intermolecular pair potentials

The geometries of the dimer, trimer, and tetramer hydrogen-bonded clusters of water, methanol, and ammonia molecules have been derived using previously published intermolecular pair potentials containing constants optimized from ab initio calculations. The lowest energy forms for the dimers of all three types of molecules have an open structure, while the trimers and tetramers have cyclic structures. The results are compared with those previously described using another empirical potential, EPEN .     

Probing variable amine/amide ligation in Ni(II)N2S2 complexes using sulfur K-edge and nickel L-edge X-ray absorption spectroscopies: implications for the active site of nickel superoxide dismutase

Nickel superoxide dismutase (NiSOD) is a recently discovered metalloenzyme that catalyzes the disproportionation of O2(*-) into O2 and H2O2. In its reduced state, the mononuclear Ni(II) ion is ligated by two cis-cysteinate sulfurs, an amine nitrogen (from the protein N-terminus), and an amide nitrogen (from the peptide backbone). Unlike many small molecule and metallopeptide-based NiN2S2 complexes, S-based oxygenation is not observed in NiSOD. Herein we explore the spectroscopic properties of a series of three Ni(II)N2S2 complexes (bisamine-ligated (bmmp-dmed)Ni(II), amine/amide-ligated (Ni(II)(BEAAM))(-), and bisamide-ligated (Ni(II)(emi))(2-)) with varying amine/amide ligation to determine the origin of the dioxygen stability of NiSOD. Ni L-edge X-ray absorption spectroscopy (XAS) demonstrates that there is a progression in ligand-field strength with (bmmp-dmed)Ni(II) having the weakest ligand field and (Ni(II)(emi))(2-)) having the strongest ligand field. Furthermore, these Ni L-edge XAS studies also show that all three complexes are highly covalent with (Ni(II)(BEEAM))(-) having the highest degree of metal-ligand covalency of the three compounds studied. S K-edge XAS also shows a high degree of Ni-S covalency in all three complexes. The electronic structures of the three complexes were probed using both hybrid-DFT and multiconfigurational SORCI calculations. These calculations demonstrate that the nucleophilic Ni(3d)/S(pi)* HOMO of these NiN2S2 complexes progressively decreases in energy as the amide-nitrogens are replaced with amine nitrogens. This decrease in energy of the HOMO deactivates the Ni-center toward O2 reactivity. Thus, the Ni-S bond is protected from S-based oxygenation explaining the enhanced stability of the NiSOD active-site toward oxygenation by dioxygen.     

Accurate theoretical prediction of vibrational frequencies in an inhomogeneous dynamic environment: a case study of a glutamate molecule in water solution and in a protein-bound form

We propose a hierarchical approach to model vibrational frequencies of a ligand in a strongly fluctuating inhomogeneous environment such as a liquid solution or when bound to a macromolecule, e.g., a protein. Vibrational frequencies typically measured experimentally are ensemble averaged quantities which result (in part) from the influence of the strongly fluctuating solvent. Solvent fluctuations can be sampled effectively by a classical molecular simulation, which in our model serves as the first, low level of the hierarchy. At the second high level of the hierarchy a small subset of system coordinates is used to construct a patch of the potential surface (ab initio) relevant to the vibration in question. This subset of coordinates is under the influence of an instantaneous external force exerted by the environment. The force is calculated at the lower level of the hierarchy. The proposed methodology is applied to model vibrational frequencies of a glutamate in water and when bound to the Glutamate receptor protein and its mutant. Our results are in close agreement with the experimental values and frequency shifts measured by the Jayaraman group by the Fourier transform infrared spectroscopy [Q. Cheng et al., Biochem. 41, 1602 (2002)]. Our methodology proved useful in successfully reproducing vibrational frequencies of a ligand in such a soft, flexible, and strongly inhomogeneous protein as the Glutamate receptor.     

Indirect detection in reversed-phase liquid chromatography: Ion-pair retention models for anionic analytes and mobile phase components on polystyrene polymers using an alkaline mobile phase

Summary Retention models for anionic analytes and mobile phase compounds in reversed-phase ion-pair chromatographic systems have been studied. The solid phase was a polystyrene-divinylbenzene copolymer. The analytes were mono- and divalent anions monitored by indirect detection technique. The mobile phase was highly alkaline and contained a detectable anion, sulfanilic acid.Expressions for the ion-pair retention of solutes and mobile phase components have been developed assuming Langmuir distribution of ion-pairs to a solid phase with one kind of binding site. The validity of the expressions and the origin of system peaks have been confirmed by determination of distribution constants using linear regression.