Structure, Thermodynamics, and Dynamical Properties of Nucleic Acids, Proteins, and Glass-Forming Liquids

Thesis advisor: Udayan MohantyThe stabilization of particular conformations of protein and nucleic acid structure is believed to play an important role in many important biological functions. In chapter one, the α -helical conformation and structural stability of single and double stapled all- hydrocarbon cross-linked p53 peptides when bound and unbound to MDM2 are investigated. Our study provides a comprehensive rationalization of the relationship between peptide stapling strategy, the secondary structural stability, and the binding affinity of p53-MDM2 complex. In chapter two, we study counterion-mediated collapse of a strongly charged model polyelectrolyte chain by Group-II divalent metal cations using coarse-grained Brownian dynamics simulations. Polyelectrolyte effects govern the association of counterions with the chain. Large ions are less effective in counterion condensation than small ions. However, upon counterion condensation, the reduction of the backbone charge is independent of size of the metal cations. Above a threshold value of Coulomb strength parameter, counterion release entropy drives the formation of counterion-induced compact states. In chapter three, the nature of surface tension in the random first order theory of supercooled liquid is analyzed within the framework of Landau-Lifshitz fluctuation theory. We show that the surface tension of a droplet satisfies the differential equation 4πr2(dσ)+ 8πrσ(r)− Br1/2 = 0 , where B/ T = 12πkBcv , T is temperature, kB is dr Boltzmann constant, and cv is heat capacity. A consequence is that the slope of the relaxation time at the glass transition temperature, i.e., the fragility index, is expressed as the square of the ratio of heat capacity and configurational entropy of the supercooled liquid. When backbone extended nucleosides are incorporated into a double helix, a unique helical structure is formed. In chapter four, we find that the predicted stability of modified backbone DNA strands in aqueous solution is in good agreement with experimental melting temperature data. The incorporation of extended backbone nucleosides into a duplex results in elongation of the end-to-end chain distance due to the distortion of the B-DNA conformation at the mutated base-pair insertion. We also find that the modified backbone helical twist is approximately 40 degrees, larger than B-DNA helical twist and closer to the twist angle predicted for D-form DNA. The folding of RNA tertiary structure has been described as an equilibrium between partially folded I (intermediate) states, and the fully folded native conformation, or N state. RNA is highly sensitive to the ionic environment due to its negative charge, and tertiary structures tend to be strongly stabilized by Mg2+. There is a need for models capable of describing the ion atmosphere surrounding RNA with quantitative accuracy. In chapter 5, we present a generalized Manning condensation model of RNA electrostatics for studying the Mg2+-induced RNA folding of the 58mer ribosomal fragment.Thesis (PhD) — Boston College, 2016.Submitted to: Boston College. Graduate School of Arts and Sciences.Discipline: Chemistry

Development of a Spectroscopic Map to Explain the Broad Raman Peak for Alkynes Solvated in Triethylamine

The terminal alkyne C≡C stretch has a large Raman scattering cross section in the “silent” region for biomolecules. Experimental work taking advantage of this property provide an impetus for the development of theoretical tools addressing the vibration. In prior work, we have developed a localized normal mode method for computing terminal alkyne vibrational frequencies using a discrete variable representation of the potential energy surface. Using this method and molecular dynamics simulations, we interpret the unusually broad Raman spectrum of alkynes solvated in triethylamine. Energy decomposition analysis is performed on alkyne-triethylamine dimers to determine that charge transfer, electrostatics, and Pauli repulsion have large effects on the frequency. Molecular dynamics simulations of triethylamine-solvated alkynes are performed and uncover that the terminal alkyne hydrogen interacts strongly with the triethylamine nitrogen. Interactions persist for 3–10 ps. Using this data, a spectroscopic map for terminal alkynes is developed and used to compute Raman spectra for alkynes in triethylamine. We find that the broad experimental spectra result from the combination of a population of alkynes associated with the solvent nitrogens and a population not associated with those nitrogens. This work sets the stage for investigations of alkynes in more complex environments like proteins and nanomaterial surfaces

An Accurate and Universal Method for the Anharmonic Vibrational Analysis of the Raman Active C≡C Stretch of Terminal Alkynes

The terminal alkyne C≡C stretch has a large Raman scattering cross section in the “silent” region for biomolecules. This has led to many Raman tag and probe studies using molecules with this moiety. Computational investigation of these systems is vital to aid in the interpretation of the results. In this work, we develop a localized normal mode discrete variable representation (DVR) method for computing terminal alkyne vibrational frequencies and transition isotropic polarizabilities which can easily and accurately be applied to any terminal alkyne molecule. The errors of localization to the terminal alkyne moiety, anharmonic normal mode isolation, and discretization of the Born-Oppenheimer potential energy surface are quantified and found to oppose each other. This results in a method with low error compared to other anharmonic vibrational methods like VPT2 and experiment. Several density functionals are tested using the method, and TPSS-D3 is found to perform surprisingly well. Additionally, diffuse functions are found to be important for the accuracy of computed frequencies. Finally, the computation of vibrational properties like transition isotropic polarizabilities and the universality of the normal mode atomic displacements across molecules are demonstrated