Physics
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Item LINK BETWEEN DYNAMICS AND FUNCTION IN SINGLE AND MULTI-SUBUNIT ENZYMES(2010) Chen, Jie; Thirumalai, Devarajan; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Biopolymers, such as proteins and DNA, are polymers whose three-dimensional conformations dene their biological functions. Current emphasis on structures has greatly advanced our understanding of the functions of biopolymers. However, there is a need to understand the deeper link between biopolymer dynamics and function, because in water and under cellular conditions, everything that biopolymers do can be understood in terms of "the jigglings and wigglings of atoms". These motions arise from thermal noise in the solvent and due to intrinsic motion of the enzymes. In biological systems, the motions are often highly regulated to ensure that cellular processes are executed over the required time scales. For enzymes, which are essentially proteins that catalyze chemical reactions or generate mechanical work, conformational fuctuations are coupled at various stages through interactions with ligands during the catalytic cycle. We have studied two dierent enzymes, dihydrofolate reductase (DHFR), which catalyzes reduction of dihydrofolate to tetrahydrofolate, and RNA polymerase (RNAP from bacteria and Pol II from yeast), which is responsible for RNA synthesis using DNA as a template. In order to study the link between dynamics and function we have developed new methods and extended a variety of computational techniques. For DHFR, we use both evolutionary imprints (SCA) and structure-based perturbation method (SPM) to extract a network of residues that facilitate the transitions between two distinct conformational states (closed and occluded states). The transition kinetics and pathways connecting the closed and occluded states are described using Brownian dynamics (BD) simulation. We found the sliding motion of Met20 loop across helix 2 is involved in the forward and reverse transitions between the closed and occluded states. We also found that cross-linking M16-G121 inhibits both the forward and the reverse transitions. In addition, we showed the transition states of these transitions are broad and resemble high energy states. For RNAP, we focus on the conformational changes of RNAP and DNA in promoter melting process. Using BD, we show that DNA conformation changes in promoter melting occur in three steps. We also show that internal dynamics of RNAP is relevant to facilitate the bending of DNA. For Pol II, the structural transitions between two initiation conformational states and between initiation state and elongation state are studied using SPM and BD. We determine the structural units that regulate structural transitions and describe the transition kinetics. The combination of three dierent methods, SCA, SPM and BD, provide results that are in accord with many experiments. Moreover, our description of the detailed structural transitions in these enzymes lead to new insights and testable predictions in these extraordinarily important enzyme functions.Item INTERFACIAL SOLVATION AND EXCITED STATE PHOTOPHYSICAL PROPERTIES OF 7-AMINOCOUMARINS AT SILICA/LIQUID INTERFACES(2010) Roy, Debjani; Walker, Robert A; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The properties of solutes adsorbed at interfaces can be very different compared to bulk solution limits. This thesis examines how polar, hydrophilic silica surfaces and different solvents systematically change a solute's equilibrium and dynamic solvation environment at solid/liquid interfaces. The primary tools used in these studies are steady state fluorescence spectroscopy and time correlated single photon counting (TCSPC) -a fluorescence method capable resolving fluorescence emission on the picosecond timescale. To sample adsorbed solutes, TCSPC experiments were carried out in total internal reflection (TIR) geometry. These studies used total of six different 7 aminocoumarin dyes to isolate the effects of molecular and electronic structure on solute photophysical behavior. Fluorescence lifetimes measured in the TIR geometry are compared to the lifetimes of coumarins in bulk solution using different solvents to infer interfacial polarity and excited state solute conformation and dynamics. Steady state emission experiments measuring the behavior of the coumarins adsorbed at silica surfaces from bulk methanol solutions show that all coumarins had a similar affinity &delta G ads &sim &minus 25-30 kJ/mole. Despite these similar adsorption energetics solute structure had a very pronounced effect on the tendency of solutes to aggregate and form multilayers. Our finding suggests that hydrogen bonding donating properties of the silica surface plays a dominant role in determining the interfacial behavior of these solutes. The silica surface also had pronounced effects on the time dependent emission of some solutes. In particular, the strong hydrogen bond donating properties of the silica surface inhibit formation of a planar, charge transfer state through hydrogen bond donation to the solute's amine group. A consequence of this interaction is that the time dependent emission from solutes adsorbed at the surface appears to be more similar to emission from solutes in nonpolar solvation environments. To test the role of solvent identity on the photophysical properties of adsorbed solutes, additional experiments were carried out with a nonpolar solvent (decane), a moderately polar solvent (n decanol) and a polar aprotic solvent (acetonitrile). The results from these studies demonstrated that interfacial solvation depends sensitively on a balance of competing forces including those between the solute and substrate, the solute and solvent and the surface and adjacent solvent.Item SCANNING TUNNELING MICROSCOPY / SPECTROSCOPY STUDIES OF BINARY ORGANIC FILMS(2009) Jin, Wei; Reutt-Robey, Janice E; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Multi-component organic molecular films have seen increasing applications in photovoltaic technologies and other organic electronic applications. These applications have been based upon assumptions regarding film structure and electronic properties. This thesis provides an increased understanding of factors that control structure in binary molecular films and begins to establish structure-electronic property relations. In this thesis, three technologically relevant "donor-acceptor" systems are studied with variable temperature STM/STS: pentacene (Pn):C60, zinc phthalocyanine (ZnPc): C60 and ZnPc: perfluorinated zinc phthalocyanine (F16ZnPc). These three model systems provide a systematic exploration of the impact of molecular shape and molecular band offset on morphology-electronic relations in thin film heterostructures. For Pn:C60, I show how domain size and architecture are controlled by composition and film processing conditions. Sequential deposition of pentacene, followed by C60, yields films that range from nanophase-separated, to co-crystalline phases, to a templated structure. These distinct structures are selectively produced from distinct pentacene phases which are controlled via pentacene coverage. For the ZnPc:C60 system, the shape of ZnPc and the lattice mismatch between ZnPc and C60 are quite different from the Pn:C60 films. Nonetheless, ZnPc:C60 films also yield chemical morphologies that can be similarly controlled from phase separated, to co-crystalline phases, to templated structures. In both of these binary films, I exploit relative differences in the component cohesive energies to control phase selection. In bilayer films of both systems, a common structural element of stress-induced defects is also observed. In ZnPc:F16ZnPc, I explore two components with similar shapes and cohesive energies while retaining molecular band offsets comparable to Pn:C60. In this shape-matched system, a checkerboard ZnPc:F16ZnPc arrangement stabilized by hydrogen bonds readily forms. This supramolecular structure introduces a new hybridization state close to the Fermi Level, yielding electronic properties distinct from the component phases. Through investigations of these three model systems, I have developed an understanding the control of chemical morphology along the donor-acceptor interface and the way this morphology influences electronic transport.Item DENSITY FUNCTIONAL CALCULATIONS OF BACKBONE 15N CHEMICAL SHIELDINGS IN PEPTIDES AND PROTEINS(2009) Cai, Ling; Fushman, David; Kosov, Daniel S; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)In this dissertation, we describe computational and theoretical study of backbone 15N chemical shieldings in peptides and proteins. Comprehensive density functional calculations have been performed on systems of different complexity, ranging from model dipeptides to real proteins and protein complexes. We begin with examining the effects of solvation, hydrogen bonding, backbone conformation, and the side chain identity on 15N chemical shielding in proteins by density functional calculations. N-methylacetamide (NMA) and N-formyl-alanyl-X (with X being one of the 19 naturally occurring amino acids excluding proline) were used as model systems for this purpose. The conducting polarizable continuum model was employed to include the effect of solvent in the calculations. We show that the augmentation of the polarizable continuum model with the explicit water molecules in the first solvation shell has a significant influence on isotropic 15N chemical shift but not as much on the chemical shift anisotropy. The difference in the isotropic chemical shift between the standard &beta-sheet and standard &alpha-helical conformations ranges from 0.8 ppm to 6.2 ppm depending on the residue type, with the mean of 2.7 ppm. This is in good agreement with the experimental chemical shifts averaged over a database of 36 proteins containing >6100 amino acid residues. The orientation of the 15N chemical shielding tensor as well as its anisotropy and asymmetry are also in the range of values experimentally observed for peptides and proteins. Having applied density functional calculation successfully to model peptides, we develop a computationally efficient methodology to include most of the important effects in the calculation of chemical shieldings of backbone 15N in a protein. We present the application to selected &alpha-helical and &beta-sheet residues of protein G. The role of long-range intra-protein electrostatic interactions by comparing models with different complexity in vacuum and in charge field is analyzed. We show that the dipole moment of the &alpha-helix can cause significant deshielding of 15N; therefore, it needs to be considered when calculating 15N chemical shielding. We emphasize the importance of including interactions with the side chains that are close in space when the charged form for ionizable side chains is adopted in the calculation. We also illustrate how the ionization state of these side chains can affect the chemical shielding tensor elements. For &alpha-helical residues, chemical shielding calculations using a 8-residue fragment model in vacuum and adopting the charged form of ionizable side chains yield a generally good agreement with experimental data. We also performed computational modeling of the chemical shift perturbations occurring upon protein-protein or protein-ligand binding. We show that the chemical shift perturbations in ubiquitin upon dimer formation can be explained qualitatively through computation. This dissertation hence demonstrates that quantum chemical calculations can be successfully used to obtain a fundamental understanding of the relationship between chemical shielding and the surrounding protein environment for the elusive case of 15N and therefore enhance the role of 15N chemical shift measurements in the analysis of protein structure and dynamics.Item DEVELOPMENT OF ION-MOBILITY AND MASS SPECTROMETRY FOR PROBING THE REACTIVITY OF NANOPARTICLES AND NANOCOMPOSITES(2009) Zhou, Lei; Zachariah, Michael; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Aerosols of diameter smaller than 100 nm, usually are referred as nanoparticles or ultrafines, have received considerable interests lately as a source of building blocks to novel materials. However, our capabilities for charactering these materials are greatly limited by lack of appropriate diagnostic tools. The objective of this work is to develop new aerosol-based techniques for the characterization of nanoparticles and nanocomposites. The scope of this dissertation can be categorized in two ways. First, to provide knowledge of just how reactive a material is, we develop particle ion-mobility spectrometry and Single Particle Mass Spectrometry methods to probe the intrinsic size-dependent reactivity of individual metal particles. And second, the development of a new Time-of-Flight mass spectrometer (TOFMS) combined with a temperature jump (T-Jump) technique to study particle-particle reaction, and probe the reactivity of nanocomposite materials under combustion-like condition.Item STRUCTURE TAILORED PROPERTIES AND FUNCTIONALITIES OF ZERO-DIMENSIONAL NANOSTRUCTURES(2009) Tang, Yun; Ouyang, Min; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The field of nanoscience and nanotechnology has achieved significant progress over last thirty years. Complex nanostructures with tunable properties for novel applications have been successfully fabricated and characterized. In this thesis, I will focus on our recent efforts on precise controlled synthesis of zero-dimensional nanostructures as well as fundamental understanding of the physical behavior of as-synthesized nanostructures. Particularly, three topics are presented: (1) Nanoscale crystallinity engineering: we have achieved nanoscale crystallinity control of noble metal nanoparticles with 100% yield by molecular engineering. We have used silver nanoparticles as example to demonstrate synthetic strategy and importance of such control in nanoscale chemical transformation, fundamental electron and phonon couplings and surface plasmon resonance based biological sensors. Such nanoscale crystallinity engineering provides a new pathway for design of complex nanostructures, tailoring nanoscale electronic and mechanical properties as well as controlling classical and quantum coupling interactions; (2) Precise control of core@shell nanostructures: we have developed a new universal strategy denoted as intermediated phase assisted phase exchange and reaction (iPAPER) to achieve layer-by-layer control of shell components in core@shell structures. Tunable plasmonic, optical and magnetic properties of core@shell structures enabled by our iPAPER strategy are further demonstrated. These characterizations are promising for understanding and manipulating nanoscale phenomena as well as assembling nanoscale devices with desirable functionality; and (3) Fundamental spin and structure manipulation of semiconductor quantum dots by hydrostatic pressure. Pressure provides a unique means of modifying materials properties. By measuring dependence of spin dynamics on pressure, we revealed that the spin states of semiconductor quantum dots are very robust. We further provided the first experimental evidence for the existence of a metastable intermediate state before the first-order phase transition of semiconductor quantum dots. Our results are crucial for the future development of quantum information processing based on spin qubits of quantum dots.Item Protein folding and amyloid formation in various environments(2008-11-21) O'Brien, Edward Patrick; Thirumalai, Devarajan; Brooks, Bernard; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Understanding and predicting the effect of various environments that differ in terms of pH and the presence of cosolutes and macromolecules on protein properties is a formidable challenge. Yet this knowledge is crucial in understanding the effect of cellular environments on a protein. By combining thermodynamic theories of solution condition effects with statistical mechanics and computer simulations we develop a molecular perspective of protein folding and amyloid formation that was previously unobtainable. The resulting Molecular Transfer Model offers, in some instances, quantitatively accurate predictions of cosolute and pH effects on various protein properties. We show that protein denatured state properties can change significantly with osmolyte concentration, and that residual structure can persist at high denaturant concentrations. We study the single molecule mechanical unfolding of proteins at various pH values and varying osmolyte and denaturant concentrations. We find that the the effect of varying solution conditions on a protein under tension can be understood and qualitatively predicted based on knowledge of that protein's behavior in the absence of force. We test the accuracy of FRET inferred denatured state properties and find that currently, only qualitative estimates of denatured state properties can be obtained with these experimental methods. We also explore the factors governing helix formation in peptides confined to carbon nanotubes. We find that the interplay of the peptide's sequence and dimensions, the nanotube's diameter, hydrophobicity and chemical heterogeneity, lead to a rich diversity of behavior in helix formation. We determine the structural and thermodynamic basis for the dock-lock mechanism of peptide deposition to a mature amyloid fibril. We find multiple basins of attraction on the free energy surface associated with structural transitions of the adding monomer. The models we introduce offer a better understanding of protein folding and amyloid formation in various environments and take us closer to understanding and predicting how the complex environment of the cell can effect protein properties.Item SINGLE MOLECULE FLUORESCENCE INVESTIGATION OF PROTEIN FOLDING(2008-09-30) liu, jianwei; Munoz, Victor; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)In addition to the well known two-state folding scenario, the energy landscape theory of protein folding predicts the possibility of downhill folding under native conditions. This intriguing prediction was extended by Victor Muñoz and coworkers to include global downhill folding. i.e. a barrierless free energy surface and unimodal conformational distributions at all degrees of unfolding stress. A small protein, BBL, has been shown to follow this behavior as evidenced from experiments and simulations. However, the identification of BBL as a global downhill folder has raised a significant amount of controversy with some groups claiming that it still folds in a two-state fashion. The objective of this thesis is to characterize the conformational distribution of BBL using single molecule Förster resonance energy transfer (SM-FRET) to obtain direct evidence for the downhill folding in BBL. We carried out SM-FRET measurements at 279 K to slow down the protein dynamics to 150 μs thus enabling the use of a 50 μs binning time (the short binning time being a first in SM measurements). By optimizing the microscope system setup and employing a novel Trolox-cysteamine fluorophore protection system, we obtained sufficient signal to construct reliable 50 μs SM-FRET histograms. The data show clear unimodal conformational distributions at varying denaturant concentrations thus demonstrating the downhill folding nature of BBL. Further SM-FRET measurements on a two-state folder, α-spectrin SH3 produced bimodal histograms indicating that our experimental setup works well and that the unimodal distributions of BBL are not due to instrumental errors. The comparison of ensemble FRET measurements on labeled proteins (both BBL and α-spectrin SH3) with CD measurements on the corresponding unlabeled proteins shows that the fluorophores do not affect the protein stability. We also simulated the expected histograms if BBL were a two-state folder using Szabo's photon statistics theory of SM-FRET. The two-state simulation results are inconsistent with the experimental histograms even under very conservative assumptions about BBL's relaxation time. Therefore, all the control experiments and simulations exclude any possible artifacts, which shows our results are quite robust. Additionally, we estimated the relaxation time of BBL from the histogram width analysis to be consistent with independent kinetic measurements.Item Statistical Mechanical Theory for and Simulations of Charged Fluids and Water(2008-07-31) Rodgers, Jocelyn Michelle; Weeks, John D; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Treatment of electrostatic interactions in simulations remains a topic of current research. These interactions are present in most biomolecular simulations, and they remain an expensive part of the simulation. Herein we explore the application of local molecular field (LMF) theory to this problem. Local molecular field theory splits the Coulomb potential $1/r$ into short-ranged and long-ranged components. The short-ranged component may be treated explicitly in simulations and the long-ranged component is contained in a mean-field-like average external electrostatic potential. In this thesis, the derivations and approximations inherent in using the previously developed LMF theory are explored, and connections to classical electrostatics are made. Further the approach is justified for molecular systems. The application of LMF theory to several systems is explored. First, a simple system of uniformly charged walls with neutralizing counterions is treated via simulations using LMF theory. We then explore systems involving molecular water at ambient conditions. A simple approximation to LMF theory using only the short-ranged component of $1/r$ is quite powerful for bulk water. A full treatment using LMF theory extends the validity of such spherical truncations to nonuniform systems. This thesis studies the successful treatment of water confined between hydrophobic walls with and without an applied electric field -- a system which is a classic example of the failings of spherical truncations in molecular simulations. Additional results exemplify the applicability of LMF simulations to more molecularly realistic simulations. Connection is also made between these simulations of confined water and a related theory of hydrophobicity due to Lum, Chandler, and Weeks (1999).Item Ferrocene-based molecular electronics and nanomanufacturing of Pd nanowires.(2007-11-27) Wang, Lixin; Sita, Lawrence; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Two test structures were tried out for molecular junction formation and subsequent I-V characteristics measurements. One is formed by insertion of certain dithiol molecules into an alkanethiol self-assembled monolayer (SAM), followed by tethering the free thiol end with gold nanoparticles. The test structure can then be measured with CP-AFM. The matrix SAM, mixed monolayer with inserted dithiol molecules, and final test structure with gold nanoparticles were prepared and characterized by ellipsometry, AFM and STM. However, the CP-AFM measurements were very irreproducible, even on an alkanethiol SAM. This problem was analyzed and believed to come from two possible causes, namely thermal drift and deformation of the metalized tips. The other test structure was from insertion of molecules into nanogaps made by electromigration technique. Two molecules were tested and drastically different properties were observed from junctions with each molecule. For Fc-OPE molecules, near perfect conductance peaks (>0.6G0) were observed in some junctions and analysis indicates that such molecular junction contains only one or two molecules inside the nanogap. The formation of conductance peaks was analyzed with Landauer formula and a simple metal-molecule-metal model. Computational calculation also predicted high conductance through such junctions and the existence of resonant peaks. The junctions with OPE molecules, however, showed poor conductance. Possible causes such as molecular structure and easiness of molecular junction formation were discussed. In the second part of this dissertation, a new method was developed to fabricate Pd nanowires on HOPG surface using a sacrificial Cu film. The morphology and composition of the nanowires were characterized by AFM, SEM and XPS. The formation of such Pd nanowires was explained with a galvanic displacement mechanism and some test experiments were carried out to prove such growth mechanism. It was also found that the size of the Pd nanowires can be directly controlled by the thickness of the Cu film that was initially deposited. However, attempts to make Au, Pt and Ag nanowires with the same method failed, and possible causes were discussed.