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Amide I spectroscopy probes the backbone C=O stretch vibrations of peptides and proteins. Amide I spectra are often collected in deuterated water (D2O) since this provides a cleaner background in the amide I frequency range; such data are often referred to as amide I′ spectra since deuteration induces changes in the mode structure, including a roughly ∼10 cm−1 redshift. For biological samples, however, deuteration is often not possible. As amide I frequency maps are increasingly applied to quantitative protein structural analysis, this raises the interesting challenge of drawing direct connections between amide I and amide I′ data. We here analyze amide I and amide I′ peak frequencies for a series of dipeptides and related compounds. Changes in protonation state induce large electrostatic shifts in the peak frequencies, allowing us to amass a sizable library of data points for direct amide I/amide I′ comparison. While we find an excellent linear correlation between amide I and amide I′ peak frequencies, the deuteration-induced shift is smaller for more red-shifted vibrations, indicating different electrostatic tuning rates in the two solvents. H2O/D2O shifts were negligible for proline-containing dipeptides that lack exchangeable amide hydrogens, indicating that the intrinsic properties of the solvent do not strongly influence the H/D shift. These findings indicate that the distinct tuning rates observed for the two vibrations arise from modifications to the intrinsic properties of the amide bond and provide (at least for solvated dipeptides) a simple, linear "map" for translating between amide I and amide I′ frequencies. [ABSTRACT FROM AUTHOR]

We investigate the structure of copper formate and deuterated copper formate clusters using infrared multiple photon dissociation in combination with quantum chemical calculations. Symmetric and asymmetric C–O stretching vibrations along with C–H/C–D stretching vibrations were characterized. Fermi interactions between the C–H stretch and likely a C–O combination band and/or the overtone of a C–H in-plane bending motion have been confirmed by deuteration. The spectra reveal a strong dependence on the monodentate or bidentate binding motif of the formate ligands. Many minima are energetically accessible on the potential energy surface through rotation of the monodentate formate ligands into several almost isoenergetic local minima. While the C–H/C–D stretching vibration is heavily influenced by the charge distribution in the cluster, the C–O vibrations are largely unaffected. The C–H stretch region is not very diagnostic due to a variety of possible Fermi resonances, which also depend on the charge distribution at the formate ligand. Deuteration yields unperturbed spectra in the C–D stretch region and reveals characteristic shifts of the C–D stretching mode for the different binding motifs, with a strong dependence of the band position on the oxidation state of the copper center. The observed bands are compared with formate adsorbed on copper surfaces from the literature. [ABSTRACT FROM AUTHOR]

Glassing matrix deuteration could be a beneficial sample preparation method for 13C dynamic nuclear polarization (DNP) when large electron paramagnetic resonance (EPR) width free radicals are used. However, it could yield the opposite DNP effect when samples are doped with small EPR width free radicals. Herein, we have investigated the influence of solvent deuteration on the 13C nuclear and electron relaxation that go along with the effects on 13C DNP intensities at 3.35 T and 1.2 K. For 13C DNP samples doped with trityl OX063, the 13C DNP signals decreased significantly when the protons are replaced by deuterons in glycerol:water or DMSO:water solvents. Meanwhile, the corresponding solid-state 13C T1 relaxation times of trityl OX063-doped samples generally increased upon solvent deuteration. On the other hand, 13C DNP signals improved by a factor of ∼1.5 to 2 upon solvent deuteration of samples doped with 4-oxo-TEMPO. Despite this 13C DNP increase, there were no significant differences recorded in 13C T1 values of TEMPO-doped samples with nondeuterated or fully deuterated glassing matrices. While solvent deuteration appears to have a negligible effect on the electron T1 relaxation of both free radicals, the electron T2 relaxation times of these two free radicals generally increased upon solvent deuteration. These overall results suggest that while the solid-phase 13C DNP signals are dependent upon the changes in total nuclear Zeeman heat capacity, the 13C relaxation effects are related to 2H/1H nuclear spin diffusion-assisted 13C polarization leakage in addition to the dominant paramagnetic relaxation contribution of free radical centers. [ABSTRACT FROM AUTHOR]

We present the results of experiments demonstrating the spectroscopic detection of Förster resonance energy transfer from NH3 in the X1A1 ground electronic state to helium atoms in 1sns 3S1 Rydberg levels, where n = 37 and n = 40. For these values of n, the 1sns 3S1 →1snp 3PJ transitions in helium lie close to resonance with the ground-state inversion transitions in NH3 and can be tuned through resonance using electric fields of less than 10 V/cm. In the experiments, energy transfer was detected by direct state-selective electric field ionization of the 3S1 and 3PJ Rydberg levels and by monitoring the population of the 3DJ levels following pulsed microwave transfer from the 3PJ levels. Detection by microwave spectroscopic methods represents a highly state selective, low-background approach to probing the collisional energy transfer process and the environment in which the atom-molecule interactions occur. The experimentally observed electric-field dependence of the resonant energy transfer process, probed both by direct electric field ionization and by microwave transfer, agrees well with the results of calculations performed using a simple theoretical model of the energy transfer process. For measurements performed in zero electric field with atoms prepared in the 1s40s 3S1 level, the transition from a regime in which a single energy transfer channel can be isolated for detection to one in which multiple collision channels begin to play a role has been identified as the NH3 density was increased. [ABSTRACT FROM AUTHOR]

Heat capacity measurements were made down to 0.35 K for the isotopic modifications of methanol, CH3-nDnOH, and methyl iodide, CH3-nDnI, (n = 0, 1, 2, 3) to determine the orientation of the partially deuterated methyl group in the solid phase. The mono-deuterated modifications favor the symmetric conformation, whereas the di-deuterated ones favor the asymmetric conformation. Infrared spectroscopy demonstrates that some vibrational modes change in intensity depending on temperature, which supports the energy scheme obtained by calorimetry. Zero-point kinetic energies were obtained by single molecule density functional theory calculations. Although the favorable conformations of CH2DOH and CHD2OH were confirmed, the energy difference between symmetric and asymmetric conformations was twice as large as that determined experimentally, which indicates that intermolecular forces significantly decrease the energy difference. For CHD2OH, the conversion between the two asymmetric conformations becomes very slowat lowtemperature and results in a residual entropy of R ln 2. [ABSTRACT FROM AUTHOR]

¹H nuclear magnetic resonance relaxometry was applied to investigate the dynamics of L-alanine in the solid phase (powder). The experimental studies were carried out in a very broad frequency range, covering four orders of magnitude--from 4 kHz to 40 MHz (referring to the ¹H resonance frequency) in order to probe motional processes of much different time scales by a single experiment. To get access to the dynamics of different proton groups of alanine, the ¹H spin-lattice relaxation measurements were performed for non-deuterated and partially deuterated alanine. The experiments were carried out in the temperature range of 293 K-370 K (non-deuterated alanine) and 318 K-370 K (partially deuterated alanine). As a result of a thorough theoretical analysis of the extensive set of experimental results, three motional processes occurring on different time scales are identified and quantitatively described. The slowest process occurs on a time scale of ºs and it is attributed to the collective dynamics of a 3D hydrogen bond network of alanine, while the intermediate, attributed to the dynamics of the NH3 group, corresponds to the range of tenths of ns. The fast process describes the rotation of the CH3 group. [ABSTRACT FROM AUTHOR]

The IR spectrum of benzyl radical:water clusters was recorded. Benzyl radicals were produced by vacuum flash pyrolysis and trapped in superfluid helium nanodroplets. The infrared spectrum of benzyl radical water aggregates in the range 2585-2820 cm-1 was recorded by subsequent addition of deuterated water. A total of seven peaks are observed at 2766, 2750, 2656, 2638, 2633, 2598, and 2593 cm-1. Based on pressure dependent measurements and comparison to accompanying ab initio calculations, five of these bands are assigned to distinct O-D stretch vibrations of benzyl:water clusters with one and two water molecules. In line with previous experiments on benzene:water clusters, we observe the formation of a water dimer-like motif that is attached to one face of the benzyl radical. [ABSTRACT FROM AUTHOR]

The HNNS radical has been promoted recently as a viable intermediate in the interstellar creation of the spectroscopically elusive nitrogen molecule. Any confirmation of this pathway or utilizing HNNS as a tracer of N2 depends upon the ability to observe the radical intermediate whether in the laboratory or in the interstellar medium. Established and accurate quantum chemical procedures are employed here to produce spectroscopic constants, fundamental vibrational frequencies, and intensities that can be utilized for any possible detection of HNNS. While trans-HNNS is confirmed here to be 3.0 kcal/mol lower in energy than cis-HNNS, the latter will be more readily observed rotationally due to its significantly larger dipole moment. The N-N bond in cis-HNNS is stronger than in trans-HNNS, and earlierwork has suggested that cis-HNNS is more useful in the creation of N2 fromNHand NS. Hence, the detection of cis-HNNS may be of greater value anyway. Furthermore, the N-N stretch in either conformer is also exceptionally bright and will occur in the mid-infrared with nearly 30 cm-1 separating the fundamentals of the two conformers. Finally, the low isomerization barrier can be affected significantly upon deuteration also making ND an interesting consideration as a starting material in the interstellar formation of N2. [ABSTRACT FROM AUTHOR]

We employ the diffusion Monte Carlo (DMC) method in conjunction with the recently developed, ab initio-based MB-pol potential energy surface to characterize the ground states of small (H2O)2-6 clusters and their deuterated isotopomers. Observables, other than the ground state energies, are computed using the descendant weighting approach. Among those are various spatial correlation functions and relative isomer fractions. Interestingly, the ground states of all clusters considered in this study, except for the dimer, are delocalized over at least two conformations that differ by the orientation of one or more water monomers with the relative isomer populations being sensitive to the isotope substitution. Most remarkably, the ground state of the (H2O)6 hexamer is represented by four distinct cage structures, while that of (D2O)6 is dominated by the prism, i.e., the global minimum geometry, with a very small contribution from a prism-book geometry. In addition, for (H2O)6 and (D2O)6, we performed DMC calculations to compute the ground states constrained to the cage and prism geometries. These calculations compared results for three different potentials, MB-pol, TTM3/F, and q-TIP4P/F. [ABSTRACT FROM AUTHOR]

Singly deuterated silylene has been detected and characterized in the gas-phase using high-resolution, two-dimensional, optical spectroscopy. Rotationally resolved lines in the 000X¹A' → A¹A″ band are assigned to both c-type perpendicular transition and additional parallel, axis-switching induced bands. The extracted rotational constants were combined with those for SiH2 and SiD2 to determine an improved equilibrium bond length, rSiH, and bond angle, θ, of 1.5137 ± 0.0003 Å and 92.04? ± 0.05?, and 1.4853 ± 0.0005 Å and 122.48? ± 0.08? for the X¹A' (0,0,0) and A¹A″(0,0,0) state respectively. The dispersed fluorescence consists of a long progression in the A¹A″(0,0,0) →X¹A'(0,ν2,0) emission which was analyzed to produce vibrational parameters. A strong quantum level dependence of the rotationally resolved radiative decay curves is analyzed. [ABSTRACT FROM AUTHOR]

The magnetoelectroluminescence of conjugated organic polymer films is widely accepted to arise from a polaron pair mechanism, but their magnetoconductance is less well understood. Here we derive a new relationship between the experimentally measurable magnetoelectroluminescence and magnetoconductance and the theoretically calculable singlet yield of the polaron pair recombination reaction. This relationship is expected to be valid regardless of the mechanism of the magnetoconductance, provided the mobilities of the free polarons are independent of the applied magnetic field (i.e., provided one discounts the possibility of spin-dependent transport). We also discuss the semiclassical calculation of the singlet yield of the polaron pair recombination reaction for materials such as poly(2,5-dioctyloxy-paraphenylene vinylene) (DOO-PPV), the hyperfine fields in the polarons of which can be extracted from light-induced electron spin resonance measurements. The resulting theory is shown to give good agreement with experimental data for both normal (H-) and deuterated (D-) DOO-PPV over a wide range of magnetic field strengths once singlet-triplet dephasing is taken into account. Without this effect, which has not been included in any previous simulation of magnetoelectroluminescence, it is not possible to reproduce the experimental data for both isotopologues in a consistent fashion. Our results also indicate that the magnetoconductance of DOO-PPV cannot be solely due to the effect of the magnetic field on the dissociation of polaron pairs. [ABSTRACT FROM AUTHOR]

The lattice constants of hydrogenated and deuterated CH4-, CO2-, Xe- (clathrate structure type I) and N2-hydrates (clathrate structure type II) from 10 K up to the stability limit were established in neutron- and synchrotron diffraction experiments and were used to derive the related thermal expansivities. The following results emerge from this analysis: (1) The differences of expansivities of structure type I and II hydrates are fairly small. (2) Despite the larger guest-size of CO2 as compared to methane, CO2-hydrate has the smaller lattice constants at low temperatures, which is ascribed to the larger attractive guest-host interaction of the CO2-water system. (3) The expansivity of CO2-hydrate is larger than for CH4-hydrate which leads to larger lattice constants for the former at temperatures above ~150 K; this is likely due to the higher motional degrees of freedom of the CO2 guest molecules. (4) The cage occupancies of Xe- and CO2-hydrates affect significantly the lattice constants. (5) Similar to ice Ih, the deuterated compounds have generally slightly larger lattice constants which can be ascribed to the somewhat weaker H-bonding. (6) Compared to ice Ih, the high temperature expansivities are about 50% larger; in contrast to ice Ih and the empty hydrate, there is no negative thermal expansion at low temperature. (7) A comparison of the experimental results with lattice dynamical work, with models based on an Einstein oscillator model, and results from inelastic neutron scattering suggest that the contribution of the guest atoms' vibrational energy to thermal expansion is important, most prominently for CO2- and Xe-hydrates. [ABSTRACT FROM AUTHOR]

High-resolution spectra of the S1 ← S0 transition in jet-cooled deuterated benzenes were observed using pulse dye amplification of single-mode laser light and mass-selective resonance enhanced multiphoton ionization (REMPI) detection. The vibrational and rotational structures were accurately analyzed for the vibronic levels in the S1 state. The degenerate 6¹ levels of C6H6 or C6D6 are split into 6a¹ and 6b¹ in many of deuterated benzenes. The rigid-rotor rotational constants were assessed and found to be slightly different between 6a and 6b because of different mean molecular structures. Their rotational levels are significantly shifted by Coriolis interactions. It was found that the Coriolis parameter proportionally changed with the number of substituted D atoms. [ABSTRACT FROM AUTHOR]

A thorough characterization of the γ, β, and glass phases of deuterated 1,1,2,2 tetrachloroethane (C2D2Cl4) via nuclear quadrupole resonance and Molecular Dynamic Simulations (MDSs) is reported. The presence of molecular reorientations was experimentally observed in the glass phase and in the β phase. In the β phase, and from MDS, these reorientations are attributed to two possible movements, i.e., a 180? reorientation around the C2 molecular symmetry axis and a reorientation of the molecule between two non-equivalent positions. In the glass phase, the spin-lattice relaxation time T¹ is of the order of 16 times lower than in the crystalline phase and varies as T-1 below 100 K in good agreement with the strong quadrupolar relaxation observed in amorphous materials and in the glassy state of molecular organic systems. The activation energy of molecular reorientations in the glass phase (19 kJ/mol) is comparable to that observed in the glassy crystal of a "molecular cousin" compound, Freon 112 (C2F2Cl4), for the secondary β-relaxation. Moreover, the on-site orientational motion of tetrachloroethane molecules offers a new indirect evidence of the prominent role of such orientational disorder in glassy dynamics. [ABSTRACT FROM AUTHOR]

The influence of vibrational excitations in the partially deuterated water (HOD) reactant on its bond selective reactions with F is investigated using a full-dimensional quantum wave packet method on an accurate global potential energy surface. Despite the decidedly early barrier of the F + H2O reaction, reactant vibrational excitation in each local stretching mode of HOD is found to significantly enhance the reaction which breaks the excited bond. In the mean time, excitation of the HOD bending mode also enhances the reaction, but with much lower efficacy and weaker bond selectivity. Except for low collision energies, all vibrational modes are more effective in promoting the bond selective reactions than the translational energy. These results are compared with the predictions of the recently proposed sudden vector projection model. [ABSTRACT FROM AUTHOR]

Low-temperature and high-pressure experiments were performed with filled ice Ih structure of methane hydrate under 2.0-77.0 GPa and 30-300 K using diamond anvil cells and a helium-refrigeration cryostat. In situ X-ray diffractometry revealed distinct changes in the compressibility of the axial ratios of the host framework with pressure. Raman spectroscopy showed a split in the C-H vibration modes of the guest methane molecules, which was previously explained by the orientational ordering of the guest molecules. The pressure and temperature conditions at the split of the vibration modes agreed well with those of the compressibility change. The results indicate the following: (i) the orientational ordering of the guest methane molecules from an orientationally disordered state occurred at high pressures and low temperatures; and (ii) this guest ordering led to anisotropic contraction in the host framework. Such guest orientational ordering and subsequent anisotropic contraction of the host framework were similar to that reported previously for filled ice Ic hydrogen hydrate. Since phases with different guest-ordering manners were regarded as different phases, existing regions of the guest disordered-phase and the guest ordered-phase were roughly estimated by the X-ray study. In addition, above the pressure of the guest-ordered phase, another high-pressure phase developed in the low-temperature region. The deuterated-water host samples were also examined, and the influence of isotopic effects on guest ordering and phase transformation was observed. [ABSTRACT FROM AUTHOR]

The HOOO hydridotrioxygen radical and its deuterated analog (DOOO) have been isolated in helium nanodroplets following the in situ association reaction between OH and O2. The infrared spectrum in the 3500-3700 cm-1 region reveals bands that are assigned to the ν1 (OH stretch) fundamental and ν1 + ν6 (OH stretch plus torsion) combination band of the trans-HOOO isomer. The helium droplet spectrum is assigned on the basis of a detailed comparison to the infrared spectrum of HOOO produced in the gas phase [E. L. Derro, T. D. Sechler, C. Murray, and M. I. Lester, J. Chem. Phys. 128, 244313 (2008)]. Despite the characteristic low temperature and rapid cooling of helium nanodroplets, there is no evidence for the formation of a weakly bound OH-O2 van der Waals complex, which implies the absence of a kinetically significant barrier in the entrance channel of the reaction. There is also no spectroscopic evidence for the formation of cis-HOOO, which is predicted by theory to be nearly isoenergetic to the trans isomer. Under conditions that favor the introduction of multiple O2 molecules to the droplets, bands associated with larger H/DOOO-(O2)n clusters are observed shifted ∼1-10 cm-1 to the red of the trans-H/DOOO ν1 bands. [ABSTRACT FROM AUTHOR]

We propose a generalization of the intrinsic reaction coordinate (IRC) for quantum many-body systems described in terms of the mass-weighted ring polymer centroids in the imaginary-time path integral theory. This novel kind of reaction coordinate, which may be called the 'centroid IRC,' corresponds to the minimum free energy path connecting reactant and product states with a least amount of reversible work applied to the center of masses of the quantum nuclei, i.e., the centroids. We provide a numerical procedure to obtain the centroid IRC based on first principles by combining ab initio path integral simulation with the string method. This approach is applied to NH3 molecule and N2H5- ion as well as their deuterated isotopomers to study the importance of nuclear quantum effects in the intramolecular and intermolecular proton transfer reactions. We find that, in the intramolecular proton transfer (inversion) of NH3, the free energy barrier for the centroid variables decreases with an amount of about 20% compared to the classical one at the room temperature. In the intermolecular proton transfer of N2H5-, the centroid IRC is largely deviated from the 'classical' IRC, and the free energy barrier is reduced by the quantum effects even more drastically. [ABSTRACT FROM AUTHOR]

Nuclear motion in the vicinity of conical intersections of the degenerate electronic ground state of fully deuterated triatomic hydrogen, D3, is investigated with the aid of a time-dependent wavepacket approach in hyperspherical coordinates. Vibronic energy level spectra and the eigenfunctions are examined by including, for example, (1) geometric phase (GP) correction, (2) diagonal Born-Huang (BH) correction, and (3) both GP and BH corrections to the Born-Oppenheimer adiabatic Hamiltonian and finally by considering the nonadiabatic coupling between the two electronic surfaces explicitly. It emerges from this study that inclusion of both the GP and BH corrections is insufficient to explain the spectral features observed in the experiment. The latter are recovered by considering the complete two-states coupled Hamiltonian only. This study shows that both the GP and BH corrections constitute a minor part of the surface coupling effects, in particular, on the dynamics of the upper adiabatic sheet. Most importantly, we add that the experimental signature of the GP effect appears only in the observed shift of the eigenlevels of the electronic state when compared to those obtained from a completely Born-Oppenheimer Hamiltonian. The detail fine structure of the observed band of the electronic state is shaped by the off-diagonal derivative coupling elements of the nonadiabatic coupling operator. [ABSTRACT FROM AUTHOR]

The reaction of HOD+ with N2O was studied over the collision energy (Ecol) range from 0.20 eV to 2.88 eV, for HOD+ in its ground state and in each of its fundamental vibrational states: bend (010), OD stretch (100), and OH stretch (001). The dominant reaction at low Ecol is H+ and D+ transfer, but charge transfer becomes dominant for Ecol > 0.5 eV. Increasing Ecol enhances charge transfer only in the threshold region (Ecol < 1 eV), but all modes of HOD+ vibrational excitation enhance this channel over the entire energy range, by up to a factor of three. For reaction of ground state HOD+ the H+ and D+ transfer channels have similar cross sections, enhanced by increasing collision energy for Ecol < 0.3 eV, but suppressed by Ecol at higher energies. OD stretch excitation enhances D+ transfer by over a factor of 2, but has little effect on H+ transfer, except at low Ecol where a modest enhancement is observed. Excitation of the OH stretch enhances H+ transfer by up to a factor of 2.5, but actually suppresses D+ transfer over most of the Ecol range. Excitation of the bend mode results in ∼60% enhancement of both H+ and D+ transfer at low Ecol but has little effect at higher energies. Recoil velocity distributions at high Ecol are strongly backscattered in the center-of-mass frame, indicating direct reaction dominated by large impact parameter collisions. At low Ecol the distributions are compatible with mediation by a short-lived collision complex. Ab initio calculations find several complexes that may be important in this context, and RRKM calculations predict lifetimes and decay branching that is consistent with observations. The recoil velocity distributions show that HOD+ vibrational excitation enhances reactivity in all collisions at low Ecol, while for high Ecol with enhancement comes entirely from the subset of collisions that generate strongly back-scattered product ions. [ABSTRACT FROM AUTHOR]

An aqueous methanol solution (xMeOH = 0.30) has been studied by quasielastic neutron scattering. The single-particle water dynamics were effectively isolated by employing deuterated methanol. A smooth dynamic transition to a sub-Arrhenius temperature dependence has been observed in the relaxation times. We associate this behavior with the formation of small crystallites in the system. These findings are compared with molecular dynamics simulations and previous nuclear magnetic resonance measurements. We discuss possible dynamic signatures of structuring in the mixture. [ABSTRACT FROM AUTHOR]