Vibrational phase relaxation of O–H stretch in bulk water: Role of large amplitude angular jumps and negative cross-correlations among the forces on the O–H bond

The ultrafast vibrational phase relaxation of O–H stretch in bulk water is investigated in molecular dynamics simulations. The dephasing time (T2) of the O–H stretch in bulk water calculated from the frequency fluctuation time correlation function (Cω(t)) is in the range of 70–80 femtosecond (fs), which is comparable to the characteristic timescale obtained from the vibrational echo peak shift measurements using infrared photon echo [W.P. de Boeij, M.S. Pshenichnikov, D.A. Wiersma, Ann. Rev. Phys. Chem. 49 (1998) 99]. The ultrafast decay of Cω(t) is found to be responsible for the ultrashort T2 in bulk water. Careful analysis reveals the following two interesting reasons for the ultrafast decay of Cω(t). (A) The large amplitude angular jumps of water molecules (within 30–40 fs time duration) provide a large scale contribution to the mean square vibrational frequency fluctuation and gives rise to the rapid spectral diffusion on 100 fs time scale. (B) The projected force, due to all the atoms of the solvent molecules on the oxygen (FO(t)) and hydrogen (FH(t)) atom of the O–H bond exhibit a large negative cross-correlation (NCC). We further find that this NCC is partly responsible for a weak, non-Arrhenius temperature dependence of the dephasing rate.

Multiscale study on hydrogen mobility in metallic fusion divertor material

For achieving efficient fusion energy production, the plasma-facing wall materials of the fusion reactor should ensure long time operation. In the next step fusion device, ITER, the first wall region facing the highest heat and particle load, i.e. the divertor area, will mainly consist of tiles based on tungsten. During the reactor operation, the tungsten material is slowly but inevitably saturated with tritium. Tritium is the relatively short-lived hydrogen isotope used in the fusion reaction. The amount of tritium retained in the wall materials should be minimized and its recycling back to the plasma must be unrestrained, otherwise it cannot be used for fueling the plasma. A very expensive and thus economically not viable solution is to replace the first walls quite often. A better solution is to heat the walls to temperatures where tritium is released. Unfortunately, the exact mechanisms of hydrogen release in tungsten are not known. In this thesis both experimental and computational methods have been used for studying the release and retention of hydrogen in tungsten. The experimental work consists of hydrogen implantations into pure polycrystalline tungsten, the determination of the hydrogen concentrations using ion beam analyses (IBA) and monitoring the out-diffused hydrogen gas with thermodesorption spectrometry (TDS) as the tungsten samples are heated at elevated temperatures. Combining IBA methods with TDS, the retained amount of hydrogen is obtained as well as the temperatures needed for the hydrogen release. With computational methods the hydrogen-defect interactions and implantation-induced irradiation damage can be examined at the atomic level. The method of multiscale modelling combines the results obtained from computational methodologies applicable at different length and time scales. Electron density functional theory calculations were used for determining the energetics of the elementary processes of hydrogen in tungsten, such as diffusivity and trapping to vacancies and surfaces. Results from the energetics of pure tungsten defects were used in the development of an classical bond-order potential for describing the tungsten defects to be used in molecular dynamics simulations. The developed potential was utilized in determination of the defect clustering and annihilation properties. These results were further employed in binary collision and rate theory calculations to determine the evolution of large defect clusters that trap hydrogen in the course of implantation. The computational results for the defect and trapped hydrogen concentrations were successfully compared with the experimental results. With the aforedescribed multiscale analysis the experimental results within this thesis and found in the literature were explained both quantitatively and qualitatively.

Radiation effects in supported nanoparticles

Nanotechnology applications are entering the market in increasing numbers, nanoparticles being among the main classes of materials used. Particles can be used, e.g., for catalysing chemical reactions, such as is done in car exhaust catalysts today. They can also modify the optical and electronic properties of materials or be used as building blocks for thin film coatings on a variety of surfaces. To develop materials for specific applications, an intricate control of the particle properties, structure, size and shape is required. All these depend on a multitude of factors from methods of synthesis and deposition to post-processing. This thesis addresses the control of nanoparticle structure by low-energy cluster beam deposition and post-synthesis ion irradiation. Cluster deposition in high vacuum offers a method for obtaining precisely controlled cluster-assembled materials with minimal contamination. Due to the clusters small size, however, the cluster-surface interaction may drastically change the cluster properties on deposition. In this thesis, the deposition process of metal and alloy clusters on metallic surfaces is modelled using molecular dynamics simulations, and the mechanisms influencing cluster structure are identified. Two mechanisms, mechanical melting upon deposition and thermally activated dislocation motion, are shown to determine whether a deposited cluster will align epitaxially with its support. The semiconductor industry has used ion irradiation as a tool to modify material properties for decades. Irradiation can be used for doping, patterning surfaces, and inducing chemical ordering in alloys, just to give a few examples. The irradiation response of nanoparticles has, however, remained an almost uncharted territory. Although irradiation effects in nanoparticles embedded inside solid matrices have been studied, almost no work has been done on supported particles. In this thesis, the response of supported nanoparticles is studied systematically for heavy and light ion irradiation. The processes leading to damage production are identified and models are developed for both types of irradiation. In recent experiments, helium irradiation has been shown to induce a phase transformation from multiply twinned to single-crystalline nanoparticles in bimetallic alloys, but the nature of the transition has remained unknown. The alloys for which the effect has been observed are CuAu and FePt. It is shown in this thesis that transient amorphization leads to the observed transition and that while CuAu and FePt do not amorphize upon irradiation in bulk or as thin films, they readily do so as nanoparticles. This is the first time such an effect is demonstrated with supported particles, not embedded in a matrix where mixing is always an issue. An understanding of the above physical processes is essential, if nanoparticles are to be used in applications in an optimal way. This thesis clarifies the mechanisms which control particle morphology, and paves way for the synthesis of nanostructured materials tailored for specific applications.

Local structure of water studied by Compton scattering

This thesis presents a novel application of x-ray Compton scattering to structural studies of molecular liquids. Systematic Compton-scattering experiments on water have been carried out with unprecedented accuracy at third-generation synchrotron-radiation laboratories. The experiments focused on temperature effects in water, the water-to-ice phase transition, quantum isotope effects, and ion hydration. The experimental data is interpreted by comparison with both model computations and ab initio molecular-dynamics simulations. Accordingly, Compton scattering is found to provide unique intra- and intermolecular structural information. This thesis thus demonstrates the complementarity of the technique to traditional real-space probes for studies on the local structure of water and, more generally, molecular liquids.

Single-File Diffusion of Confined Water Inside SWNTs: An NMR Study

We report a nuclear magnetic resonance (NMR) study of confined water inside similar to 1.4 nm diameter single-walled carbon nanotubes (SWNTs). We show that the confined water does not freeze even up to 223 K. A pulse field gradient (PFG) NMR method is used to determine the mean squared displacement (MSD) of the water molecules inside the nanotubes at temperatures below 273 K, where the bulk water outside the nanotubes freezes and hence does not contribute to the proton NMR signal. We show that the mean squared displacement varies as the square root of time, predicted for single-file diffusion in a one-dimensional channel. We propose a qualitative understanding of our results based on available molecular dynamics simulations.

Hydration of ions under confinement

Molecular dynamics simulations are used to examine the changes in water density and hydration characteristics of NaCl solutions confined in slit-shaped graphitic pores. Using a structural signature, we define the hydration limit as the salt concentration at which a sharp drop in the hydration number is observed. At small pores (H = 8.0-10 angstrom), confined water does not possess bulk-like features and remains in a layered arrangement between two surfaces. Despite this high degree of confinement, ions are able to form a quasi-2D hydration shell between two surfaces. Our results indicate the strong propensity of ions to form the first hydration shell, even under extremely confined aqueous environments. The hydration of ions is seen to weakly perturb the oxygen density distributions between two surfaces. The hydration number of Na+ reduces to about 4.15 at a pore width of H = 0.8 nm, when compared with the bulk hydration number of 6.25. At larger pore widths, above H = 16 angstrom, where bulk-like water densities are observed in the central regions of the pore, the hydration number is above 6.

Irradiation effects in graphene and related materials

Nanomaterials with a hexagonally ordered atomic structure, e.g., graphene, carbon and boron nitride nanotubes, and white graphene (a monolayer of hexagonal boron nitride) possess many impressive properties. For example, the mechanical stiffness and strength of these materials are unprecedented. Also, the extraordinary electronic properties of graphene and carbon nanotubes suggest that these materials may serve as building blocks of next generation electronics. However, the properties of pristine materials are not always what is needed in applications, but careful manipulation of their atomic structure, e.g., via particle irradiation can be used to tailor the properties. On the other hand, inadvertently introduced defects can deteriorate the useful properties of these materials in radiation hostile environments, such as outer space. In this thesis, defect production via energetic particle bombardment in the aforementioned materials is investigated. The effects of ion irradiation on multi-walled carbon and boron nitride nanotubes are studied experimentally by first conducting controlled irradiation treatments of the samples using an ion accelerator and subsequently characterizing the induced changes by transmission electron microscopy and Raman spectroscopy. The usefulness of the characterization methods is critically evaluated and a damage grading scale is proposed, based on transmission electron microscopy images. Theoretical predictions are made on defect production in graphene and white graphene under particle bombardment. A stochastic model based on first-principles molecular dynamics simulations is used together with electron irradiation experiments for understanding the formation of peculiar triangular defect structures in white graphene. An extensive set of classical molecular dynamics simulations is conducted, in order to study defect production under ion irradiation in graphene and white graphene. In the experimental studies the response of carbon and boron nitride multi-walled nanotubes to irradiation with a wide range of ion types, energies and fluences is explored. The stabilities of these structures under ion irradiation are investigated, as well as the issue of how the mechanism of energy transfer affects the irradiation-induced damage. An irradiation fluence of 5.5x10^15 ions/cm^2 with 40 keV Ar+ ions is established to be sufficient to amorphize a multi-walled nanotube. In the case of 350 keV He+ ion irradiation, where most of the energy transfer happens through inelastic collisions between the ion and the target electrons, an irradiation fluence of 1.4x10^17 ions/cm^2 heavily damages carbon nanotubes, whereas a larger irradiation fluence of 1.2x10^18 ions/cm^2 leaves a boron nitride nanotube in much better condition, indicating that carbon nanotubes might be more susceptible to damage via electronic excitations than their boron nitride counterparts. An elevated temperature was discovered to considerably reduce the accumulated damage created by energetic ions in both carbon and boron nitride nanotubes, attributed to enhanced defect mobility and efficient recombination at high temperatures. Additionally, cobalt nanorods encapsulated inside multi-walled carbon nanotubes were observed to transform into spherical nanoparticles after ion irradiation at an elevated temperature, which can be explained by the inverse Ostwald ripening effect. The simulation studies on ion irradiation of the hexagonal monolayers yielded quantitative estimates on types and abundances of defects produced within a large range of irradiation parameters. He, Ne, Ar, Kr, Xe, and Ga ions were considered in the simulations with kinetic energies ranging from 35 eV to 10 MeV, and the role of the angle of incidence of the ions was studied in detail. A stochastic model was developed for utilizing the large amount of data produced by the molecular dynamics simulations. It was discovered that a high degree of selectivity over the types and abundances of defects can be achieved by carefully selecting the irradiation parameters, which can be of great use when precise pattering of graphene or white graphene using focused ion beams is planned.

Elucidation of the conformational free energy landscape in H.pylori LuxS and its implications to catalysis

Background: One of the major challenges in understanding enzyme catalysis is to identify the different conformations and their populations at detailed molecular level in response to ligand binding/environment. A detail description of the ligand induced conformational changes provides meaningful insights into the mechanism of action of enzymes and thus its function. Results: In this study, we have explored the ligand induced conformational changes in H. pylori LuxS and the associated mechanistic features. LuxS, a dimeric protein, produces the precursor (4,5-dihydroxy-2,3-pentanedione) for autoinducer-2 production which is a signalling molecule for bacterial quorum sensing. We have performed molecular dynamics simulations on H. pylori LuxS in its various ligand bound forms and analyzed the simulation trajectories using various techniques including the structure network analysis, free energy evaluation and water dynamics at the active site. The results bring out the mechanistic details such as co operativity and asymmetry between the two subunits, subtle changes in the conformation as a response to the binding of active and inactive forms of ligands and the population distribution of different conformations in equilibrium. These investigations have enabled us to probe the free energy landscape and identify the corresponding conformations in terms of network parameters. In addition, we have also elucidated the variations in the dynamics of water co-ordination to the Zn2+ ion in LuxS and its relation to the rigidity at the active sites. Conclusions: In this article, we provide details of a novel method for the identification of conformational changes in the different ligand bound states of the protein, evaluation of ligand-induced free energy changes and the biological relevance of our results in the context of LuxS structure-function. The methodology outlined here is highly generalized to illuminate the linkage between structure and function in any protein of known structure.

Tetrahydrofuran Clathrate Hydrate Formation

We report on the formation of tetrahydrofuran clathrate hydrate studied by x-ray Raman scattering measurements at the oxygen K edge. A comparison of x-ray Raman spectra measured from water-tetrahydrofuran mixtures and tetrahydrofuran hydrate at different temperatures supports stochastic hydrate formation models rather than models assuming hydrate precursors. This is confirmed by molecular dynamics simulations and density functional theory calculations of x-ray Raman spectra. In addition, changes in the spectra of tetrahydrofuran hydrate with temperatures close to the hydrate's dissociation temperature were observed and may be connected to changes in hydrate's local structure due to the formation of hydrogen bonds between guest and water molecules.

Influence of non-geometrical factors on intracrystalline diffusion -- Role of sorbate-zeolite interactions

Molecular dynamics simulations on Xe in NaY and Ar in NaCaA zeolite are reported. Rates of cage-to-cage crossovers in the two zeolites exhibit trends which are contrary to that expected from geometrical considerations. The results suggest the important role of the sorbate-zeolite interactions in determining the molecular sieve properties of zeolites for small sized sorbates. The results are explained in terms of the barrier height for cage-to-cage crossover in the two zeolites.

DNA Compaction by a Dendrimer

At physiological pH, a PAMAM dendrimer is positively charged and can effectively bind negatively charged DNA. Currently, there has been great interest in understanding this complexation reaction both for fundamental (as a model for complex biological reactions) as well as for practical (as a gene delivery material and probe for sensing DNA sequence) reasons. Here, we have studied the complexation between double-stranded DNA (dsDNA) and various generations of PAMAM dendrimers (G3-05) through atomistic molecular dynamics simulations in the presence of water and ions. We report the compaction of DNA on a nanosecond time scale. This is remarkable, given the fact that such a short DNA duplex with a length close to 13 nm is otherwise thought to be a rigid rod. Using several nanoseconds long MD simulations, we have observed various binding modes of dsDNA and dendrimers for various generations of PAMAM dendrimers at varying charge ratios, and it confirms some of the binding modes proposed earlier. The binding is driven by the electrostatic interaction, and the larger the dendrimer charge, the stronger the binding affinity. As DNA wraps/binds to the dendrimer, counterions originally condensed onto DNA (Na+) and the dendrimer (Cl-) get released. We calculate the entropy of counterions and show that there is gain in entropy due to counterion release during the complexation. MD simulations demonstrate that, when the charge ratio is greater than 1 (as in the case of the G5 dendrimer), the optimal wrapping of DNA is observed. Calculated binding energies of the complexation follow the trend G5 > 04 > 03, in accordance with the experimental data. For a lower-generation dendrimer, such as G3, and, to some extent, for G4 also, we see considerable deformation in the dendrimer structure due to their flexible nature. We have also calculated the various helicoidal parameters of DNA to study the effect of dendrimer binding on the structure of DNA. The B form of the DNA is well preserved in the complex, as is evident from various helical parameters, justifying the use of the PAMAM dendrimer as a suitable delivery vehicle.

Inherent structures of phase-separating binary mixtures: Nucleation, spinodal decomposition, and pattern formation

An energy landscape view of phase separation and nonideality in binary mixtures is developed by exploring their potential energy landscape (PEL) as functions of temperature and composition. We employ molecular dynamics simulations to study a model that promotes structure breaking in the solute-solvent parent binary liquid, at low temperatures. The PEL of the system captures the potential energy distribution of the inherent structures (IS) of the system and is obtained by removing the kinetic energy (including that of intermolecular vibrations). The broader distribution of the inherent structure energy for structure breaking liquid than that of the structure making liquid demonstrates the larger role of entropy in stabilizing the parent liquid of the structure breaking type of binary mixtures. At high temperature, although the parent structure of the structure breaking binary mixture is homogenous, the corresponding inherent structure is found to be always phase separated, with a density pattern that exhibits marked correlation with the energy of its inherent structure. Over a broad range of intermediate inherent structure energy, bicontinuous phase separation prevails with interpenetrating stripes as signatures of spinodal decomposition. At low inherent structure energy, the structure is largely phase separated with one interface where as at high inherent structure energy we find nucleation type growth. Interestingly, at low temperature, the average inherent structure energy (< EIS >) exhibits a drop with temperature which signals the onset of crystallization in one of the phases while the other remains in the liquid state. The nonideal composition dependence of viscosity is anticorrelated with average inherent structure energy.

Interaction of single-walled carbon nanotubes with poly(propyl ether imine) dendrimers

We study the complexation of nontoxic, native poly(propyl ether imine) dendrimers with single-walled carbon nanotubes (SWNTs). The interaction was monitored by measuring the quenching of inherent fluorescence of the dendrimer. The dendrimer-nanotube binding also resulted in the increased electrical resistance of the hole doped SWNT, due to charge-transfer interaction between dendrimer and nanotube. This charge-transfer interaction was further corroborated by observing a shift in frequency of the tangential Raman modes of SWNT. We also report the effect of acidic and neutral pH conditions on the binding affinities. Experimental studies were supplemented by all atom molecular dynamics simulations to provide a microscopic picture of the dendrimer-nanotube complex. The complexation was achieved through charge transfer and hydrophobic interactions, aided by multitude of oxygen, nitrogen, and n-propyl moieties of the dendrimer. (C) 2011 American Institute of Physics. doi:10.1063/1.3561308]

Collective Effects on Single Particle Orientational Relaxation in Slow Dipolar Liquids

Theoretical and computer simulation studies of orientational relaxation in dense molecular liquids are presented. The emphasis of the study is to understand the effects of collective orientational relaxation on the single-particle orientational dynamics. The theoretical analysis is based on a recently developed molecular hydrodynamic theory which allows a self-consistent description of both the collective and the single-particle orientational relaxation. The molecular hydrodynamic theory can be used to derive a relation between the memory function for the collective orientational correlation function and the frequency-dependent dielectric function. A novel feature of the present work is the demonstration that this collective memory function is significantly different from the single-particle rotational friction. However, a microscopic expression for the single-particle rotational friction can be derived from the molecular hydrodynamic theory where the collective memory function can be used to obtain the single-particle orientational friction. This procedure allows, us to calculate the single-particle orientational correlation function near the alpha-beta transition in the supercooled liquid. The calculated correlation function shows an interesting bimodal decay below the bifurcation temperature as the glass transition is approached from above. Brownian dynamics simulations have been carried out to check the validity of the above procedure of translating the memory function from the dielectric relaxation data. We have also investigated the following two issues important in understanding the orientational relaxation in slow liquids. First, we present an analysis of the ''orientational caging'' of translational motion. The value of the translational friction is found to be altered significantly by the orientational caging. Second, we address the question of the rank dependence of the dielectric friction using both simulation and the molecular hydrodynamic theory.

Orientational relaxation in dipolar systems: How much do we understand the role of correlations

Dipolar systems, both liquids and solids, constitute a class of naturally abundant systems that are important in all branches of natural science. The study of orientational relaxation provides a powerful method to understand the microscopic properties of these systems and, fortunately, there are many experimental tools to study orientational relaxation in the condensed phases. However, even after many years of intense research, our understanding of orientational relaxation in dipolar systems has remained largely imperfect. A major hurdle towards achieving a comprehensive understanding is the long range and complex nature of dipolar interactions which also made reliable theoretical study extremely difficult. These difficulties have led to the development of continuum model based theories, which although they provide simple, elegant expressions for quantities of interest, are mostly unsatisfactory as they totally neglect the molecularity of inter-molecular interactions. The situation has improved in recent years because of renewed studies, led by computer simulations. In this review, we shall address some of the recent advances, with emphasis on the work done in our laboratory at Bangalore. The reasons for the failure of the continuum model, as revealed by the recent Brownian dynamics simulations of the dipolar lattice, are discussed. The main reason is that the continuum model predicts too fast a decay of the torque-torque correlation function. On the other hand, a perturbative calculation, based on Zwanzig's projection operator technique, provides a fairly satisfactory description of the single particle orientational dynamics for not too strongly polar dipolar systems. A recently developed molecular hydrodynamic theory that properly includes the effects of intermolecular orientational pair correlations provides an even better description of the single-particle orientational dynamics. We also discuss the rank dependence of the dielectric friction. The other topics reviewed here includes dielectric relaxation and solvation dynamics, as they are intimately connected with orientational relaxation. Recent molecular dynamics simulations of the dipolar lattice are also discussed. The main theme of the present review is to understand the effects of intermolecular interactions on orientational relaxation. The presence of strong orientational pair correlation leads to a strong coupling between the single particle and the collective dynamics. This coupling can lead to rich dynamical properties, some of which are detailed here, while a major part remains yet unexplored.