Development and application of conformational methodologies: eliciting enthalpic global minima and reaction pathways

2014 Fall.The information granted by assembling the global minimum and low-enthalpy population of a chemical species or ensemble can be utilized to great effect across all fields of chemistry. With this population, otherwise impossible tasks including (but not limited to) reaction pathway characterization, protein folding, protein-ligand docking, and constructing the entropy to characterize free energy surfaces becomes a reasonable undertaking. For very small systems (single molecule with 1-3 torsions) generating the low-enthalpy population is a trivial task. However as the system grows, the task exponentially increases in difficulty. This dissertation will detail the two sides of this problem, generating the low-energy population of larger and more complex species and then utilizing those populations to garner a greater understanding of their systems. The first discussion describes a new model, Surface Editing Molecular Dynamics (SEMD), which aids in accelerating conformational searching by removing minima from the potential energy surface by adding Gaussian functions. Accompanying this new method are a multitude of new tools that can be utilized to aid in molecular dynamics simulations. The first of these tools, named CHILL, performs a projection of unproductive degrees of freedom from the molecular dynamics velocity to smooth atomic motions without artificially constraining those degrees of freedom. Another tool, Conjugate Velocity Molecular Dynamics (CVMD), rigorously generates a list of productive velocities via the biorthogonalization of local modes with a vector representation of previously explored conformational minima. In addition to these tools, a new description of distance in torsional space was developed to provide a robust means of conformational uniqueness. With each of these tools working in concert, the global minimum and associated low-enthalpy population of conformations have been obtained for various benchmark species. The second section discusses the application of conformational searching and the subsequent electronic structure calculations to characterize the reaction pathway for the ruthenium tris(2,2'-bipyridine) photocatalyzed [2+2] cycloaddition of aromatically substituted bis(enones). The APFD hybrid density functional is used along with a 6-311+g* basis and a PCM solvent model. The reaction is computed to proceed through a rate-limited formation of a cyclopentyl intermediate. Lithium tetrafluoroborate is found to facilitate initial bis(enone) reduction as well as final product distribution. In addition, aromatic substituents are found to impact both initial reduction and final product distribution

Computational study of structure formation and dynamic properties of organic molecules in hybrid inorganic/organic interfaces

Hybridstrukturen aus organischen und anorganischen Halbleitern (HIOS) vereinen die besten Eigenschaften beider Materialklassen zu Konjugaten mit großem Anwendungspotential. Ihre engen Struktur-Eigenschafts-Beziehungen, eröffnen viele interessante wissenschaftliche Herausforderungen. Um z.B. ihre optoelektronischen Eigenschaften vorherzusagen, müssen die früher Stadien des Dünnschichtwachstums erforscht werden. Das erste Ziel dieser Arbeit ist es, den Einfluss der Entropie auf die Oberflächendiffusion von kurzen Polyphenyl Molekülen auf amorphem Siliziumdioxid, a-SiO2 zu untersuchen. Das zweite Ziel ist es, den Einfluss partieller Fluorierung auf para-Sexiphenyls (p-6P) zu untersuchen. Des Weiteren untersuchen wir Selbstdiffusion von p-6P auf einer Zinkoxid (ZnO) Oberfläche und Selbstorganisation bzw. Schichtwachstum auf a-SiO2. Hierfür verwenden wir klassische atomistische Molekular- und Langevin-Dynamik-Simulationen, kombiniert mit klassischer Diffusionstheorie. In Bezug auf das erste Ziel quantifizieren wir die entropischen Beiträge zu den Freie-Energie-Barrieren für die Oberflächendiffusion von Polyphenylen unterschiedlicher Länge und zeigen, dass die Entropie zum dominierenden Teil der freien Energie für längere Moleküle wird. Zweitens demonstrieren wir, dass die Erhöhung der Anzahl fluorierter Gruppen im p-6P die Diffusion in der apolaren Richtung der ZnO-Oberfläche verringert, aber die Diffusion in der polaren Richtung erhöht. Drittens untersuchen wir den Einfluss der Fluorierung auf die Nukleation und das Wachstum von p-6P auf a-SiO2 mit einem Simulationsmodell, das experimentelle Gasphasenepitaxie nachahmt. Wir reproduzieren korrekte Einheitszellen bei Raumtemperatur und zeigen, dass die Erhöhung der Anzahl fluorierter Gruppen zu einem Schicht-für-Schicht-Wachstum auf der Oberfläche führt. Diese Arbeit ebnet den Weg für zukünftige Simulationen von Dünnschichtwachstum kleiner organischer Moleküle auf anorganischen Oberflächen.Hybrid structures of organic molecules and inorganic semiconductors (HIOS) combine favorable properties of each material into conjugates with great application potential. The optoelectronic properties of hybrid materials depend on the structure of individual molecules and their alignment relative to the inorganic surface. It is an interesting scientific challenge to predict the optoelectronic properties of HIOS based on studying the early stages of thin film growth and interface formation. The aim of this thesis is to investigate the effect of entropy in surface diffusion of short polyphenyl molecules on an amorphous silicon dioxide, a-SiO2. Second objective is to study the influence of partial fluorination of the organic para-sexiphenyl molecule (p-6P) on self-diffusion on an inorganic zinc oxide (ZnO) surface and on self-assembly and growth on the a-SiO2. For this we employ all-atom molecular dynamics and Langevin dynamics simulations, combined with classical diffusion theory. In respect to the first aim, we quantify entropic contributions to the free energy barrier of surface diffusion for short oligophenyls of varying length and demonstrate that entropy becomes even the dominant part of the free energy for longer molecules. For the second aim, we demonstrate that the increase in the number of fluorinated groups inside of the p-6P decreases the diffusivity in the apolar direction of the ZnO surface but increases the diffusivity in the polar direction. Thirdly, we study the influence of fluorination on nucleation and growth on a-SiO2 with a simulation model that mimics experimental deposition from the vapor. We reproduce the structures with correct room-temperature unit-cell parameters and demonstrate that the increase in the number of fluorinated groups leads to a layer-by-layer growth on the surface. This work can stimulate ideas for future simulations of nucleation and growth of small organic molecules with high tuning potential, on inorganic surfaces

Free Energy, Enthalpy and Entropy from Implicit Solvent End-Point Simulations

Free energy is the key quantity to describe the thermodynamics of biological systems. In this perspective we consider the calculation of free energy, enthalpy and entropy from end-point molecular dynamics simulations. Since the enthalpy may be calculated as the ensemble average over equilibrated simulation snapshots the difficulties related to free energy calculation are ultimately related to the calculation of the entropy of the system and in particular of the solvent entropy. In the last two decades implicit solvent models have been used to circumvent the problem and to take into account solvent entropy implicitly in the solvation terms. More recently outstanding advancement in both implicit solvent models and in entropy calculations are making the goal of free energy estimation from end-point simulations more feasible than ever before. We review briefly the basic theory and discuss the advancements in light of practical applications. \ua9 2018 Fogolari, Corazza and Esposito

Energy required to pinch a DNA plectoneme

DNA supercoiling plays an important role on a biological point of view. One of its consequences at the supra-molecular level is the formation of DNA superhelices named plectonemes. Normally separated by a distance on the order of 10 nm, the two opposite double-strands of a DNA plectoneme must be brought closer if a protein or protein complex implicated in genetic regulation is to be bound simultaneously to both strands, as if the plectoneme was locally pinched. We propose an analytic calculation of the energetic barrier, of elastic nature, required to bring closer the two loci situated on the opposed double-strands. We examine how this energy barrier scales with the DNA supercoiling. For physically relevant values of elastic parameters and of supercoiling density, we show that the energy barrier is in the $k_{\rm B} T$ range under physiological conditions, thus demonstrating that the limiting step to loci encounter is more likely the preceding plectoneme slithering bringing the two loci side by side.Comment: Published version (new title to conform to editorial policy

Molecular Modeling of Nucleic Acid Structure: Energy and Sampling

An overview of computer simulation techniques as applied to nucleic acid systems is presented. This unit expands an accompanying overview unit (UNIT ) by discussing methods used to treat the energy and sample representative configurations. Emphasis is placed on molecular mechanics and empirical force fields.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143698/1/cpnc0708.pd

Development and analysis of Tinker-OpenMM as a GPU-based free energy perturbation engine

The utilization of computational technologies for the lead optimization process is one of the biggest challenges in the computational chemistry field. In this dissertation, I describe the addition of GPU-based absolute and relative free energy calculation methods using polarizable force field AMOEBA to Tinker-OpenMM. I then proceed to test the capabilities of this platform by studying the binding free energy and binding structures of derivatives of the MELK inhibitor IN17. Also, I present the implementation of virial-based pressure control to the Tinker-OpenMM platform that is needed for performing isobaric simulations.Cellular and Molecular Biolog

Molecular-Level Characterisation of Crystal-Solution Interfaces

The shape of solution-grown crystal particles is largely dependent on the relative growth rate of the morphologically dominant crystal faces, which is known to be affected by the solvent. Developing accurate models for predicting crystal morphologies requires a molecular-level understanding of the solid-liquid interface. Using a combination of molecular dynamics simulations and enhanced sampling methods, this work carries out a comprehensive study on the dynamics and thermodynamics of crystal-solution interfaces for the case of ibuprofen, focusing on aspects often neglected in mesoscopic models for crystal growth. An investigation on the conformational isomerism of ibuprofen shows that conformational rearrangements at the crystal-solution interface are governed by specific surface-solvent interactions and can have a non-negligible impact on the surface growth/dissolution kinetics. An unsupervised clustering algorithm is proposed to extend the study of conformational isomerism for systems with a large number of conformationally relevant degrees of freedom. By assessing thermodynamic and kinetic information on the solvent in contact with crystal surfaces, surface-solvent interactions are found to be solvent- and face-specific. Following this analysis, a computational screening procedure is proposed for identifying solvents which can significantly affect the relative growth rate of the crystal facets and hence, the growth morphology of the crystal. To gain an in-depth understanding into the role of the solvent on the ease of association/dissociation of solute molecules at the crystal surface, a study on the formation of a vacancy on the morphologically dominant crystal faces of ibuprofen is carried out. Thermodynamics of the process reveal a distinct solvent-dependency for several faces, indicating in such cases desolvation-dominated defect formation. The research subject of this dissertation contributes to developing general and computationally-affordable workflows necessary to obtain a comprehensive and quantitative understanding of molecular processes, impacting the solid-liquid interface, which will contribute towards the formulation of detailed mesoscopic growth and dissolution models

Simulations of Nucleic Acids under Stress, in Solution, and Complexed to Proteins.

Molecular dynamics (MD) simulations have become an important tool in advancing our understanding of the structure, function, and dynamics of biomolecules. It is only within the last several years that computational resources and techniques have advanced enough to allow for simulations extending into the multiple nanosecond range, systems of multiple biomolecules, and accurate free energy calculations. This dissertation reports on multiple studies focused on MD simulations of nucleic acids. In the first the effects of torque and tension on canonical B-DNA and A-RNA helices are examined and transitions to P-form, supercoiled P-form, and denatured states are observed. The free energies and forces of the transitions to P-form are then computed, which in the case of B-DNA agree with an experimentally derived torque-tension phase diagram while with A-RNA offer predictions for forces and torques required in single molecule experiments. Following this a study of the entropies of left and right handed DNA and RNA duplexes is presented aimed at understanding the effects of sequence, solvent, and ionic conditions on experimentally observed thermally induced transitions. Third, an in depth analysis of the free energies and mechanisms of DNA supercoil relaxation by human topoisomerase I is presented. It demonstrates the possibility of distinct mechanisms (with similar rates) for the relaxation of positive and negative supercoils while suggesting the presence of ``semi-open'' states. Additional calculations with the inhibitor topotecan show distinct mechanistic differences which selectively inhibit the rate of positive supercoil relaxation (in accord with experimental results). Finally a new method for enhanced sampling of rare events is developed in which a negative frictional coefficient is utilized in Langevin dynamics to introduce energy into the system along a specified reaction coordinate. It is demonstrated that this method efficiently scales to systems of many dimensions and with proper reweighting correlation functions for the physical positive friction system may be recovered from these negative friction calculations.Ph.D.BiophysicsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/61770/1/jmweresz_1.pd