Biomolecules function only in aqueous environments and their dynamics are strongly influenced by physiological conditions including the temperature and the presence of co-solutes. The presence of biomolecules in aqueous solutions will change the dynamics and structure of water, and as a response, water will form hydration layers around biomolecules. The dynamics of hydration water, as well as hydrated proteins, lead to translation, rotation, and oscillating dipoles that, in turn, give rise to absorption in the megahertz-to-terahertz frequencies. However, the strong absorption of water in this frequency range leads to a significant challenge in obtaining terahertz dielectric spectra of aqueous biomolecular solutions. In response, I have employed a high sensitivity terahertz frequency-domain spectroscopy to overcome these issues on a large range of frequencies from 10 MHz to 1.12 THz. The high dynamical range of the system combined with a variable-path-length cell allows precise measurement of the complex dielectric response of the solutions. Employing Debye and Lorentzian approximations, I have decomposed contributions of the dielectric response of the solutions. The structure and dynamics of hydration shells and hydrated biomolecules have been identified. Performing experiments on a number of biomolecules have verified the certainty of the methods, thus, enriching the knowledge of the biological science of dynamics and functions of biomolecules. / Doctor of Philosophy / Biomaterials are essential for life, including all elements present in cells and organisms, and contribute to the living biological processes. Biomaterials, consisting of a diverse range of biomolecules, have traditionally been characterized in a wide range of approaching methods based on biological, chemical, and physical methodologies. This study investigates the molecular dynamics of biomolecules in native living environments to explore physics- and mechanics-based insights into their biological functions. Biomaterials together with water molecules perform their functions through molecular translations, rotations, and collective motions. To explore these dynamics, a home-built terahertz spectroscopy with high sensitivity has been utilized to characterize the dynamics of biomolecular aqueous solutions in the frequency range from megahertz to terahertz. The collected complex dielectric responses of the solutions have been examined through physical models to map out structures and dynamics of hydration shells and, then, the dynamics of hydrated biomolecules have been determined. The successfully investigating results in the dynamics of solvents from three different types of proteins and ionic solutions reveal critical information on hydrated biomolecular dynamics and biomolecule–water interactions, which impact the biochemical functions and reactivity of biomolecules.

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Studying dynamics of proteins in their biological milieu such as water is interesting because of their strong absorption in the terahertz range that contain information on their global and sub-global collective vibrational modes (conformational dynamics) and global dynamical correlations among solvent water molecules and proteins. In addition, water molecules dynamics within protein solvation layers play a major role in enzyme activity. However, due to the strong absorption of water in the gigahertz-to-terahertz frequencies, it is challenging to study the properties of the solvent dynamics as well as the conformational changes of protein in water. In response, we have developed a highly sensitive megahertz-to-terahertz dielectric spectroscopy system to probe the hydration shells as well as large-scale dynamics of these biomolecules. Thereby, we have deduced the conformation flexibility of proteins and compare the hydration dynamics around proteins to understand the effects of surface-mediated solvent dynamics, relationships among different measures of interfacial solvent dynamics, and protein-mediated solvent dynamics based on the complex dielectric response from 50 MHz up to 2 THz by using the system we developed. Comparing these assets of various proteins in different classes helps us shed light on the macromolecular dynamics in a biologically relevant water environment. / Doctor of Philosophy / Proteins are complicated biomolecules that exist in all living creatures and they are, mostly, involved in building up structures and cell functions in various biological systems. Not only their existence but also their complex movements and dynamics are vital to cell functions in living beings. Until recently, their chemical functions and dynamics have been extremely challenging to investigate and track in their native environments. Thanks to various efforts by researchers all over the world to learn more about their convoluted behavior, new techniques have arisen to study these properties. We, as a part of this community, have been able to develop highly sensitive megahertz-to-terahertz dielectric spectroscopy system to probe proteins and other biomolecules dynamics in picosecond to microsecond range. Using our benchmark system, we have been able to map the detailed dynamical properties of biomolecules as well as their exclusive hydration shell characterizations. In this work, we gathered details about three well-known proteins and biomolecules by studying their dielectric responses. Thus, we have been able to discuss the movements, relaxation processes and hydration shell properties of these molecules in liquid water as their basic native environment.

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The thesis, which contains nine chapters, reports extensive large scale atomistic molecular dynamics (MD) simulation studies of water structure and dynamics at the surface of an anionic micelle, hydration layer of two proteins, and in the grooves of a 38-base pairs long DNA. Understanding the structure and dynamics of water molecules at the surfaces of self-organized assemblies and complex biological macromolecules has become a subject of intense research in recent times. Chapter 1 contains a brief overview of the biomolecular hydration dynamics. Relevant experimental, computational, and theoretical studies of biomolecular hydration and the time scales associated with the water dynamics are discussed. In Chapters 2 and 3, the structure, environment, energetics, and dynamics of constrained water molecules in the aqueous anionic micelle of cesium perfluorooctanoate (CsPFO) have been studied using large scale atomistic molecular dynamics simulations. Based on the number of hydrogen bond (HB) that interfacial water molecule makes with the polar head group (PHG) oxygen of the micelle, we find the existence of three kinds of water at the interface. We introduce a nomenclature to identify the species as IBW2 (form two HBs with two different PHG), IBW1 (form one HB with PHG), and IFW (no HB with PHG). Despite of possessing two strong w-PHG bonds, the concentration of the IBW2 species is rather low due to entropic effect. The ion solvation dynamics study at the interface shows the presence of a slow component, with a relaxation time 1-2 order of magnitude slower than that in the corresponding bulk solvent in agreement with the experimental results. Both the translational and orientational dynamics of the water molecules near the micellar surface is found to be much slower than those in the bulk. The HB between the PHG of the micelle and the water molecule has almost 13 times longer life time than that in the bulk between two tagged water molecules. In Chapter 4, we present results of extensive atomistic MD simulation studies of the structure and dynamics of aqueous protein solution of the toxic domain of Enterotoxin (1ETN) and the chicken villin headpiece sub-domain containing 36 amino acid residues (HP-36). Reduced water structure and the faster water dynamics around the active site of these proteins have been observed which may have biological significance. Chapter 5 presents an extensive atomistic molecular dynamics simulations study of water dynamics in the hydration layer of a 38 base long hydrated DNA duplex. The computed rotational time correlation function (TCF) of the minor groove water dipoles is found to be markedly non-exponential with a slow component at long time. The constrained water molecule is also found to exhibit anisotropic diffusion in both the major and minor grooves. At short-to-intermediate times, translational motion of water molecules in minor groove is sub-diffusive. Chapter 6 presents the study of water entropy in both the grooves DNA. The average values of the entropy of water at 300K in both the grooves of DNA are found to be significantly lower than that in bulk water. We propose that the configurational entropy of water in the grooves can be used as a measure of the mobility (or micro viscosity) of water molecules in a given domain. In Chapter 7, we study the specific DNA base-water hydrogen bond lifetime (HBLT) dynamics at the major and the minor grooves of a hydrated duplex. The base-water HBLT correlation functions are in general multi-exponential and the average lifetime depends significantly on the specificity of the DNA sequence. The average HBLT is longer in the minor groove than that in the major groove by almost a factor of 2. Chapter 8 presents the solvation dynamics of constituent bases of aqueous DNA duplex. The solvation TCFs of the four individual bases display highly non-exponential decay with time. An interesting negative cross-correlation between water and counterions is observed which makes an important contribution to relaxation at intermediate to longer times. In the concluding note, Chapter 9 presents a brief summary of the outcome of the thesis and suggests several relevant problems that may prove w orthwhile to be addressed in future

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Mit Hilfe von linearer und nichtlinearer Infrarotspektroskopie im Femtosekundenbereich wurden Schwingungsdynamiken von H2PO4- und BH4- Ionen untersucht sowie ein Volumenplasmon in einem Schichtsystem aus Ga-dotiertem ZnO. Phosphatgruppen stellen Hydratisierungsstellen in Biomolekülen wie DNS oder Phospholipiden dar und wechselwirken intensiv mit wässrigen Solvatationsschalen. Die Untersuchung einer isolierten Phosphatgruppe in Wasser, dem Phosphation H2PO4-, hat ergeben, dass Phosphatschwingungen sehr sensitive Sonden für die ausgeprägte Fluktuationsdynamik von Volumenwasser darstellen, was experimentell mit homogen verbreiterten Linienformen nachgewiesen werden konnte. Komplexe Hydride wie NaBH4 werden wegen ihres großen Wasserstoffgehalts als potenzielle Wasserstoff- bzw. Energieträger für mobile Anwendungen diskutiert. Jedoch ist die Wasserstoffabsorption- bzw. emission energieaufwendig. Für ein detailliertes Verständnis der Wasserstoffdynamiken im BH4- Tetraeder wurden die Energieverlustkanäle nach optischer Anregung von B-H Schwingungen untersucht. Es konnte experimentell gezeigt werden, dass eine Energieumverteilung von hoch- zu niederfrequenten B-H Schwingungen stattfindet mit abschließender Dissipation in das umgebende Medium, z.B. ein Lösungsmittel oder ein NaBH4 Festkörper. Volumenplasmonen repräsentieren kollektive, longitudinale Anregungen eines freien Elektronengases in ionischen oder polaren Kristallstrukturen. In einer hoch Ga-dotierten ZnO-Schicht eines speziellen Schichtsystems konnte eine Volumenplasmon in Reflektionsgeometrie optisch angeregt werden. Dabei führte Intrabandanregung von Leitungsbandelektronen zur Erhitzung des Elektronengases und, durch das nichtparabolische ZnO-Leitungsband, zu einer Erhöhung der effektiven Elektronenmasse und damit zu einer Rotverschiebung der Plasmafrequenz auf einer sub-ps Zeitskala. Damit konnte ein Mechanismus aufgezeigt werden, um Plasmafrequenzen von Volumenplasmonen gezielt transient zu kontrollieren. / The vibrational dynamics of H2PO4- and BH4- ions and a bulk plasmon in Ga-doped ZnO were studied with methods of linear and nonlinear infrared spectroscopy in the femtosecond range. Phosphates constitute the major hydration sites of biomolecules such as DNA or phospholipds and, thus, strongly interact with aqueous hydrations shells. The investigation of isolated phosphate ions (H2PO4-) revealed a distinct sensitivity of phosphate vibrations on the fluctuation dynamics of bulk water that could be experimentally shown by homogeneously broadened line shapes of phosphate vibrations. Complex hydrides such as NaBH4 constitute a large hydrogen content and, accordingly, are discussed as energy- and hydrogen carriers for mobile applications. However, hydrogen uptake and release are energetically unfavourable. In order to gain detailed insights into hydrogen dynamics within the BH4- tetrahedrons energy relaxation mechanisms were studied after optical excitation of B-H vibrations. It could be experimentally shown that energy dissipation proceeds from high-frequency to low-frequency B-H vibrations into the heat bath of the environment, such as e.g. a liquid solvent or the solid state NaBH4. Bulk plasmons represent collective, longitudinal excitations of a free electron gas in an ionic or polar crystal. Within a specifically designed system of Ga-doped ZnO layers, a bulk plasmon could be optically excited in a reflection geometry. Intraband excitation of conduction band electrons resulted in a heating of the electron gas. Due to a non-parabolic ZnO conduction band hot electrons exhibit an increased effective electron mass and, thereby, reduce the plasma frequency. A redshift of the bulk plasma frequency that possesses sub-ps dynamics could be experimentally shown which represents a mechanism for the time-dependent control of plasma frequencies.

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