The method of isotope substitution in neutron spectroscopy is introduced to measure for the rst time the partial vibrational density of states of two network glass forming systems, namely GeSe2 at temperatures of 5, 20 and 292 K and GeO2 at a temperature of 10 K. This work included the development of a new data analysis procedure involving corrections for e.g. beam attenuation, multiple scattering and multiple phonon scattering. The measurements were made using the MARI and MERLIN spectrometers at the ISIS pulsed neutron source where measurements of the elastic lines were used to help deduce the mean squared atomic displacements and Debye-Waller factors. In the case of GeSe2, the latter were found as a function of temperature between 10 and 280 K. The results for GeSe2 glass at temperatures of 5, 20, and 292 K were found to be in good agreement, proving the ecacy of the data correction procedure. For both GeSe2 and GeO2, the results were interpreted with the aid of molecular dynamics simulations to identify the energies corresponding to rocking, bending and stretching motions. The method of in situ high pressure neutron diraction was developed using double toroid sintered diamond anvils in a Paris-Edinburgh press to measure, for the rst time, reliable diraction patterns for GeO2, SiO2 and B2O3 glasses at pressures up to 17.5 GPa. The total pair distribution functions were obtained, allowing the nearest neighbour Ge-O, Si-O or B-O coordination numbers and bond distances to be calculated. The glass networks collapse by two principal mechanisms. The rst mechanism, at lower pressures, involves a rearrangement of the structural motifs on an intermediate range length scale. The second mechanism, above thresholds in pressure of 5, 20 and 9 GPa for GeO2, SiO2 and B2O3, respectively, involves a change in the nature of the structural motifs.

A theoretical approach was developed to model the vibrational dynamics of amorphous, two-dimensional materials. The materials were modeled as continuous random networks (CRN's) comprising an assemblage of planar rings of diverse size. In-plane vibrational modes for symmetric 4-, 5-, 60, 7-, and 8-membered rings were examined. Vibrational states of isolated rings were modified by coupling the rings to a continuous network to represent rings embedded in a CRN. An effective force constant was used to couple the ring vibrations to the network's collective motions. Potentials were approximated with the use of a central force model (bond-stretching force constant) and a valence force model (bond-stretching and bond-angle-bending force constants). Valence force model calculations employed group theory. Mode frequencies were calculated using the method of small oscillations and the normal coordinate treatment. Amorphous carbon was used as a test case for the embedded ring approach. A physically consistent set of force constants for the valence force model was determined by comparing the 6-membered ring E2g mode in graphite. Frequencies for selected ring modes were calculated, resulting in a discrete line spectrum. Calculated frequencies were fitted with gaussian peaks and convoluted into theoretical spectra for comparison with the experimental Raman spectrum of amorphous carbon. Integrated gaussian lineshape intensities were assumed to be directly proportional to the CRN ring statistics. The peaks were convoluted with the peak widths, ring statistics, and number of modes as the adjustable parameters. Parameters consistent with previous research on the structure and dynamics of amorphous carbon provided satisfactory fits to the data. The best fit to the Raman data includes the E2g and A1g modes of 6-membered rings (present in Raman spectra of nanocrystalline graphite), and the Raman active E2' modes of 5- and 7-membered rings. The corresponding ring statistics agree with previous results, supporting the presence of a sizable percentage of 5- and 7- membered rings, but with no 4- or 8-membered rings. This positive result provides verification for the embedded ring approach, and supports a CRN model for amorphous carbon.

Proton-transfer reactions are one of the most fundamental chemical reactions. However, the chemical dynamics of these processes remain elusive due to the difficulty of modeling these reactions. Establishing an experimental model system and using infrared absorption and two-dimensional infrared (2D IR) spectroscopies as means for detection, the chemical dynamics of the protonation states that are involved in a ground-electronic-state proton-transfer reaction in solution can be determined. In this study, experimental models are established with formic acid and nitrogenous bases in a low dielectric solvent. A hydrogen bond forms between the acid and the base, which will allow for the proton to transfer between the two molecules to form the neutral and the ion-pair protonation states. The carbon-deuterium (C-D) stretch and the carbonyl (C=O) stretch of the formic acid molecule are used as the reporter groups for the 2D IR measurements. The results of the C-D stretch demonstrate that there is a high sensitivity to the deprotonation, vibrational coupling, and vibrational dynamics trends that are linked to the solute-solvent interactions. The results of the C=O stretch demonstrate a sensitivity to the deprotonation and conformational disorder in which the position of the C=O changes the dynamics of the protonation state. Although, a proton-transfer is not detected, the experimental model system provides an understanding of the features that govern the chemical dynamics of proton-transfer reactions.

The vibrational dynamics of theOH stretching mode in Ba(ClO4)2 trihydrate are investigated by means of femtosecond infrared spectroscopy. The sample offers plane cyclic water trimers in the solid phase that feature virtually no hydrogen bond interaction between thewater molecules. Selective excitation of the symmetric and asymmetric stretching leads to fast population redistribution, while simultaneous excitation yields quantum beats, which are monitored via a combination tone that dominates the overtone spectrum. The combination of steady-state and time-resolved spectroscopy with quantum chemical simulations and general theoretical considerations gives indication of various aspects of symmetry breakage. The system shows a joint population lifetime of 8 ps and a long-lived coherence between symmetric and asymmetric stretching, which decays with a time constant of 0.6 ps.

Successful enzyme catalysis depends on many noncovalent interactions between the enzyme, cofactors, and substrate that poise the system to access a productive transition state. Motions on a variety of timescales contribute to this, but some controversy exists surrounding the role of ultrafast dynamics on catalysis. Site-specific 2D IR spectroscopy using probes of vibrational dynamics provides the opportunity to explore ultrafast motions in an enzyme active site owing to the technique’s spatial and temporal resolution. In this work, a series of aryl-azide vibrational labels were assessed using a variety of 2D IR techniques for their sensitivity to solvent and energy transfer processes, and their ability to be adapted to experiments in biomacromolecules. One of these labels, 4-azido-N-phenylmaleimide, is a substrate analog for the promiscuous ene-reductase from Pyrococcus horikoshii (PhENR). The label was covalently attached in two orientations in the enzyme active site, occupying the same position as native substrates based on X-ray crystallography and molecular dynamics simulations. FTIR and 2D IR spectroscopy were used to identify close-lying conformational states based on the strong anharmonic coupling of the label, revealing that the active site itself modulates the probe’s internal vibrational coupling. More commonly used analogous aryl-nitrile labels, however, were not sensitive to such small structural and lineshape changes. This demonstrates the importance of thoughtful label design to maximize the amount of information that can be gleaned from 2D IR studies. Using the methods herein—both spectroscopic and biochemical—provides a strategy for probing ultrafast motions that could possibly be catalytically relevant.

Over the past two decades, vibrational sum-frequency generation (VSFG) has been applied as a versatile technique for probing the structure and dynamics of molecules at surfaces and interfaces. The excellent surface specificity of the SFG allows for probing different kinds of liquid interfaces with no or negligible contribution from adjacent and much deeper bulk phase. VSFG spectroscopy has provided evidence that the structure of the water at interfaces is different from the bulk. With the ultrafast pulses, VSFG can also be used as a probe of ultrafast vibrational dynamics at interfaces. However, apart from a few pioneering studies, the extension of VSFG into time domain has not been explored extensively. Here VSFG is used as a probe of ultrafast vibrational dynamics of water at silica interfaces. Silica is an excellent model system for the solid phase where one can systematically vary the surface charge via bulk pH adjustment. The extension of the surface electric field, the interfacial thickness and surface accumulation of ions at a charged silica surface were studied using IR pump-VSFG probe spectroscopy. A vibrational lifetime (T1) of about 250 fs, similar to bulk H2O, was observed for the O-H stretch of H2O/silica interface when the silica surface is negatively charged. At the neutral surface, where the thickness of interfacial water is smaller than at the charged surface, the vibrational lifetime of O-H stretch becomes more than two times longer (T1~ 600 fs) due to the decreased number of neighboring water molecules, probed by SFG. The fast T1 at negatively charged surface begins to slow down by screening of the penetration of surface electric field via adding salt which suggests the primary reason for similar vibrational dynamics of water at charged interface with bulk water is the penetration of electric field. By decoupling of OH of HDO in D2O, a frequency dependent vibrational lifetime is observed with faster T1 at the red compared to the blue side of the hydrogen bond spectral region. This correlates with the redshift of the SFG spectra with increasing charged surface and is consistent with a theoretical model that relates the vibrational lifetime to the strength of the hydrogen bond network. / Chemistry

The distinct structure and dynamics of interfacial water are due to a break in the extended hydrogen bonding network present in bulk water. At solid-aqueous interfaces, the presence of surface charge, which induces a static electric field, and the electrolytes, which are present in most naturally relevant systems, can additionally perturb the hydrogen bonding environment due to polarization. The interplay between the surface-charge-induced electric field and the ions in changing the structure of interfacial water has important consequences in the chemistry of processes ranging from protein-water interactions to mineral-water reactivity in oil recovery. Accessing information about the first few layers of water at buried interfaces is challenging. Vibrational sum-frequency generation (vSFG) spectroscopy is a powerful technique to study exclusively the interfacial region and is used here to investigate the role of interfacial solvent structure on surface reactivity. It is known that the rate of quartz dissolution increases on addition of salt at neat water pH. The reason for this enhancement was hypothesized to be a consequence of perturbations in interfacial water structure. The vSFG spectra, which is a measure of ordering in the interfacial water structure, shows an enhanced effect of salt (NaCl) at neat pH 6~8. The trend in the effect of salt on vSFG spectra versus the bulk pH is remarkably consistent with the enhancement of rate of quartz dissolution, providing the first experimental correlation between interfacial water structure and silica dissolution. If salt alters the structure of interfacial water, it must affect the vibrational energy transfer pathways of water, which is extremely fast in bulk water (~130 fs). Thus far, the role of ions on the vibrational dynamics of water at charged surfaces has been limited to the screening effects and reduction in the depth of the region that contributes to vSFG. Here, we measure the ultrafast vibrational relaxation of the O-H stretch of water at silica at different bulk pH, using time-resolved (TR-vSFG). The fast vibrational dynamics of water (~200 fs) observed at charged silica surfaces (pH 6 and pH 12), slows down (~600 fs) on addition of NaCl only at pH 6 and not at pH 12. On the other hand at pH 2 (neutral surface), the vibrational relaxation shows an acceleration at high ionic strengths (0.5 M NaCl). The TR-vSFG results suggest that there is a surface-charge dependence on the sensitivity of the interfacial dynamics to ions and that reduction in the probe depth of vSFG alone cannot explain the changes in the vibrational lifetime of interfacial O-H. This is further supported by the cation specific effects observed in the TR-vSFG of the silica/water interface. While the vibrational relaxation of O-H stretch slows on addition of all salts (LiCl, NaCl, RbCl, and CsCl), the degree of slowing down is sensitive to the cation identity. The vibrational lifetime of O-H stretch in the presence of different cations follows the order: Li+ < Na+ < Rb+, consistent with previous Hofmeister effect reported in vSFG spectroscopy as well as AFM measurements at silica/water interface. To provide molecular insight on the effect of surface charge density and ionic strength on the changes in interfacial water structure, Molecular Dynamics (MD) simulations were performed on water at different types of surfaces. It was shown that the properties of water near the interface, e.g., a net orientation and the depth to which this persists, depend on the degree of specific adsorption of the counter ions. Our vSFG results, along with the insights from MD simulations, highlight the importance of considering the role of ions on the solvent structure within the electric double layer region, beyond the screening effects predicted by classical electrochemical models. / Chemistry

Doctor of Philosophy / Department of Physics / Uwe Thumm / The time-dependent Schrödinger equation is integrated on a numerical lattice for up to three-dimensional problems. The wave packet propagation technique has been applied to ion – atom collisions in a strong laser field, the vibrational nuclear motion in small homonuclear diatomic molecular ions, and for the scattering of an ion in front of a metallic surface. For laser-assisted proton – hydrogen collisions it is shown, that strong circularly polarized radiation significantly alters the capture and ionization probabilities and results in a dichroism with respect to the helicity. In a pump – control – probe scheme, “stroboscopic” exposure of a nuclear wave packet of the deuterium molecular ion by a single or a series of short and intense laser control pulses may be used to produce an almost stationary distribution of a single vibrational level, where the nodal structure can be tested using the Coulomb explosion imaging technique. Using a pump – probe setup with variable probe delays it is proposed to use Fourier analysis of the time dependence of the Coulomb explosion kinetic energy release spectrum to reveal insight into the initial vibrational state distribution for small diatomic molecules. A last application demonstrates, that resonant charge transfer for scattering of a negative hydrogen anion on a metal surface depends crucially on the position of surface and image states relative to the conduction and valence band, thereby implying different reaction mechanisms for different surface cuts of a metal.

In this thesis, theoretical and computer simulation studies of vibrational phase relaxation in various molecular liquids are presented. That includes liquid nitrogen, both along the coexistence line and the critical isochore, binary liquid mixture and liquid water. The focus of the thesis is to understand the dependence of the vibrational relaxation on the density, temperature, composition and the role of different interactions among the molecules. The density fluctuation of the solute particles in a solvent is studied systematically, where the computer simulation results are compared with the mode coupling theory (MCT). The classical density functional theory (DFT) is used to study the vibrational relaxation dynamics in molecular liquids with an aim to understand the heterogeneous nature of the dynamics commonly observed in experiments. Chapter 1 contains a brief overview of the earlier relevant theories, their successes and shortcomings in the light of the problems discussed in this thesis. This chapter discusses mainly the basic features of the vibrational dynamics of molecular liquids and portrays some of the theoretical frameworks and formalisms which are widely recognized to have contributed to our present understanding. Vibrational dephasing of nitrogen molecules is known to show highly interesting anomalies near its gas–liquid critical point. In Chapter 2, we present the results of extensive computer simulation studies and theoretical analysis of the vibrational phase relaxation of nitrogen molecules both along the critical isochore and the gas–liquid coexistence line. The simulation includes the different contributions (density (ρ), vibration–rotation (VR), and resonant transfer (Rs)) and their cross–correlations. Following Everitt and Skinner, we have included the vibrational coordinate (q) dependence of the inter–atomic potential, which is found to have an important contribution. The simulated results are in good agreement with the experiments. The linewidth (directly proportional to the rate of the vibrational phase relaxation) is found to have a lambda shaped temperature dependence near the critical point. As observed in the experimental studies, the calculated lineshape becomes Gaussian–like as the critical temperature (Tc) is approached while being Lorentzian–like at the temperatures away from Tc. Both the present simulation and a mode coupling theory (MCT) analysis show that the slow decay of the enhanced density fluctuations near the critical point (CP), probed at the sub–picosecond timescales by the vibrational frequency modulation, and an enhanced vibration–rotation coupling, are the main causes of the observed anomalies. Dephasing time (тv) and the root mean square frequency fluctuation (Δ) in the supercritical region are calculated. The principal results are: 1. a crossover from a Lorentzian–like to a Gaussian–like lineshape is observed as the critical point is approached along the critical isochore, 2. the root mean square frequency fluctuation shows a non–monotonic dependence on the temperature along the critical isochore, 3. the temperature dependent linewidth shows a divergence–like (λ–shaped) behavior along the coexistence line and the critical isochore. It is found that the linewidth calculated from the time integral of the normal coordinate time correlation function (CQ(t)) is in good agreement with the known experimental results. The origin of the anomalous temperature dependence of linewidth can be traced to simultaneous effects of several factors, (i) the enhancement of the negative cross–correlations of ρ with VR and Rs and (ii) the large density fluctuations as the critical point (CP) is approached. Due to the negative cross–correlations of ρ with VR and Rs the total decay becomes faster (correlation times are in the femtosecond scale). The reason for the negative cross–correlation between ρ and VR is explored in detail. A mode coupling theory (MCT) analysis shows a slow decay of the enhanced density fluctuations near the critical point. The MCT analysis demonstrates that the large enhancement of VR–coupling near CP may arise from a non–Gaussian behavior of the equilibrium density fluctuations. This enters through a non–zero value of the triplet direct correlation function. Many of the complex systems found in nature and used routinely in industry are multi–component systems. In particular, binary mixtures are highly non–ideal and play an important role in the industry. The dynamic properties are strongly influenced by composition fluctuations which are absent in the one component liquids. In Chapter 3, isothermal–isobaric (NPT) ensemble molecular dynamics simulation studies of vibrational phase relaxation (VPR) in a model system are presented. The model considers strong attractive interaction between the dissimilar species to prevent phase separation. The model reproduces the experimentally observed non–monotonic, nearly symmetric, composition dependence of the dephasing rate. In addition, several other experimentally observed features, such as the maximum of the frequency modulation correlation time (т c) at a mole fraction near 0.5 and the maximum rate enhancement by a factor of about 3 above the pure component value, are also reproduced. The product of the mean square frequency modulation ((Δω2(0))) with тc indicates that the present model is in the intermediate regime of the inhomogeneous broadening. The non–monotonic composition (χ) dependence of тv is found to be primarily due to the non–monotonic χ dependence of тc, rather than due to a similar dependence in the amplitude of (Δω2(0)). The probability distribution of Δω shows a markedly non–Gaussian behavior at intermediate composition (χ - 0.5). We have also calculated the composition dependence of the viscosity (η∗) in order to explore the correlation between the viscosity with that of тv and тc. It is found that both the correlation times essentially follow the nature of the composition dependence of the viscosity. A mode coupling theory (MCT) analysis is presented to include the effects of the composition fluctuations in binary mixture. Water is an interesting and attractive object for research, not only because of its great importance in life processes but also due to its unusual and intriguing properties. Most of the anomalous properties of water are related to the presence of a three–dimensional network of hydrogen bonds, which is constantly changing at ultrafast, sub–picosecond timescales. Vibrational spectroscopy provides the means to study the dynamics of processes involving only certain chemical bonds. The dynamics of hydrogen bonding can be probed via its reflection on molecular vibrations, e.g., the stretching vibrational mode of the O–H bond. Recently developed femtosecond infrared vibrational spectroscopy has proved to be valuable to study water dynamics because of its unique temporal resolution. Recent studies have shown that the vibrational relaxation of the O–H stretch of HDO occurs at an extremely fast timescale with time constant being less than 100 femtosecond. Here, in Chapter 4, we investigate the origin of this ultrafast vibrational dephasing using computer simulation and appropriate theoretical analysis. In addition to the usual fast vibrational dynamics due to the hydrogen bonding excitations, we find two additional reasons: (a) the large amplitude of angular jumps of the water molecules (with 30–40 fs time intervals) provide large contribution to the mean square vibrational frequency and (b) the projected force along the O–H bond due to the solvent molecules, on the oxygen (FO(t)) and hydrogen (FH (t)) atoms of the O–H bond exhibit a large negative cross–correlation (NCC) between FO(t) and FH (t). This NCC is shown to be partly responsible for a weak, non–Arrhenius temperature dependence of the relaxation rate. In the concluding note, Chapter 5 starts with a brief summary of the outcome of this thesis and ends up with suggestions of a few relevant problems that may prove worthwhile to be addressed in the future.

In the first part of the thesis, the molecular structure and electronic properties of phospholipids at the single molecule level and also for a monolayer structure are investigated via ab initio calculations under different degrees of hydration. The focus of the study is on phosphatidylcholines, in particular dipalmitoylphosphatidylcholine (DPPC), which are the most abundant phospholipids in biological membranes. Upon hydration, the phospholipid shape into a sickle-like structure. The hydration dramatically alters the surface potential, dipole and quadrupole moments of the lipids, and probably guides the interactions of the lipids with other molecules and the communication between cells. The vibrational spectrum of DPPC and DPPC-water complexes are completely assigned and it is shown that water hydrating the lipid head groups enables efficient energy transfer across membrane leaflets on sub-picosecond time scales. Moreover, the vibrational modes and lifetimes of pure and hydrated DPPC lipids, at human body temperature, are estimated by performing ab initio molecular dynamics simulations. The vibrational modes of the water molecules close to the head group of DPPC are active in the frequency range between 0.5 - 55 THz, with a peak at 2.80 THz in the energy spectrum. The computed lifetimes for the high-frequency modes agree well with recent data measured at room temperature, where high-order phonon scattering is not negligible. The structure and auto-ionization of water at the water-phospholipid interface are investigated by ab initio molecular dynamics and ab initio Monte Carlo simulations using local density approximation and generalized gradient approximation for the exchange-correlation energy functional. Depending on the lipid head group, strongly enhanced ionization is observed, leading to dissociation of several water molecules into H+ and OH- per lipid. The results can shed light on the phenomena of the high proton conductivity along membranes that has been reported experimentally. In the second part of the thesis, Monte Carlo simulations of the lipid bilayer, on the basis of a coarse grained model, are performed to gain insight into the mechanical properties of planar lipid bilayers. By using a rescaling method, the Poisson's ratio is calculated for different phases. Additional information on the bending rigidity, determined from height fluctuations on the basis of the Helfrich Hamiltonian, allows for calculation of the Young's modulus for each phase. In addition, the free energy barrier for lipid flip-flop process in the fluid and gel phases are estimated. The main rate-limiting step to complete a flip-flop process is related to a free energy barrier that has to be crossed in order to reach the center of the bilayer. The free energy cost for performing a lipid flip-flop in the gel phase is found to be five times greater than in the fluid phase, demonstrating the rarity of such events in the gel phase. Moreover, an energy barrier is estimated for formation of transient water pores that often precedes lipid translocation events and accounts for the rate-limiting step of these pore-associated lipid translocation processes.