The Chemical Computing Group Excellence Award for Graduate Students Winners for Denver (spring 2015)

MD-generated volume profiles as a tool for probing transition states of conformational changes

Heather Wiebe, Noham Weinberg. Simon Fraser University, Burnaby, British Columbia, Canada and Chemistry, University of the Fraser Valley, Abbotsford, British Columbia, Canada

The mechanism by which conformational changes, particularly folding and unfolding, occur in proteins and other biopolymers has been widely discussed in the literature. Molecular dynamics (MD) simulations of protein folding present a formidable challenge since these conformational changes occur on a time scale much longer than what can be afforded at the current level of computational technology. Transition state (TS) theory offers a more economic description of kinetic properties of a reaction system by relating them to the properties of the TS, or for flexible systems, the TS ensemble (TSE). The volumetric properties of TSE’s are expressed as the logarithmic pressure derivatives of the rate constants, known as activation volumes △V‡ = -RT(∂lnk/∂P)T. Experimental activation volumes are available for a number of protein systems1. According to TST, activation volumes can be identified as the difference in volume between the TSE and reactant species △V‡ = V‡ - VR. The concept of a volume profile △VMD(y), describing how the volume of a molecular system varies along its reaction coordinate y, is widely used in discussing the mechanisms of high pressure reactions. Volume profiles can be calculated theoretically using our recently developed method2 based on molecular dynamics (MD) simulations. If the position y‡ of the TSE along the reaction coordinate is unknown, it can be found by locating △V‡ on the MD-generated volume profile: △VMD(y‡) = △V‡. We illustrate this approach by its successful application to the unfolding of a model chain system.

1For example: J. Woenckhaus, et al., Biophys. J. 80, p1518 (2001).

2H. Wiebe, et al., J. Phys. Chem. C 116, p2240 (2012).

Theoretical investigations of the fumarate addition reaction: Implications for the biological stability of future fuels and opportunities for bioremediation of hydrocarbon contaminated areas

Christopher Maupin, Anthony Dean, Vivek Bharadwaj. Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado and College of Applied Science and Engineering, Colorado School of Mines, Golden, Colorado

The biodegradation of hydrocarbons by anaerobic bacterial cultures is the leading cause of bio-corrosion and is a major concern for the petroleum industry and the military. Fumarate addition (FA) reaction is the first step in the metabolism of hydrocarbon fuels and is catalyzed by glycyl radical enzymes (GREs). While the ability of these enzymes to harbor a highly reactive radical in the protein and utilize a free radical catalytic mechanism at room temperature is intriguing from an academic point of view, this also has significant practical applications. However, the free radical nature of the FA reaction has challenged experimental investigations.

Here we present the varied computational approaches used to gain insight into the FA mechanism. We predicted the structure for benzylsuccinate synthase enzyme (a GRE) and provided a basis for the FA mechanism using a comprehensive approach involving homology modeling, docking, and molecular dynamics (MD) simulations. This work identified the substrate binding pockets and conserved amino acid residues involved in stabilizing substrates. The simulations also established the experimentally observed syn addition of toluene to fumarate and reinforces the proposed substrate assisted radical transfer pathway for the reaction mechanism.

Understanding the impact of hydrocarbon structure on the energetics of the FA mechanism is the first step towards categorizing fuels on the basis of their susceptibility towards biodegradation. We have utilized high level electronic structure calculations to explore the potential energy landscape governing FA in aromatic (toluene) and aliphatic (butane) fuels in the gas-phase. The thermodynamic data from the electronic structure calculations is utilized to develop a kinetic model that provides hydrocarbon biodegradation rates for the two fuels. The model predicts that aromatics degrade faster than aliphatics and that the first abstraction step in the FA mechanism is kinetically significant, which is consistent with deuterium isotope effect studies on toluene degradation. The detailed computations also provide insights into a possible basis for the experimentally observed stereo-preferential nature of FA and demonstrates the importance of considering pre-reaction and product complexes to accurately model systems that involve intra and intermolecular non-covalent interactions.

Simulations of the self-assembly of polyelectrolyte block copolymers using dissipative particle dynamics with an implicit solvent ionic strength (ISIS) method

Nan Li, William Fuss, Yaroslava Yingling. North Carolina State University

Polyelectrolyte block copolymers, which combine structural features of polyelectrolyte, block copolymers and surfactants, may self-assemble in a variety of nanoaggregates in aqueous environment, such as micelles, vesicles, lamellar mesophases, or micellar aggregates. The morphology and size of formed aggregates are determined by the characteristically complex equilibrium of noncovalent forces (electrostatic, steric, hydrogen bonding, Van der Waals, and hydrophobic interactions). The strength of repulsive Coulomb interactions between the polyelectrolyte segments can be efficiently tuned by variations in ionic strength or/and pH in the aqueous solution. In order to explore the self-assembly process of polyelectrolyte block copolymers, we developed implicit solvent ionic strength (ISIS) model for use with the Dissipative Particle Dynamics (DPD) method to simulate the behavior of polyelectrolyte block copolymers with incorporated electrostatic interactions to achieve a good balance between reasonable physical description and computational feasibility. We applied this coarse-grained model to explore the influence of block length, block architecture, and solvent quality on the properties of the assemblies formed in aqueous solutions. Our DPD model enables us to obtain the main characteristics of the micelles formed from the self-assembly of polyelectrolyte diblock/triblock copolymers as a function of the block length and salt concentration. Based on a comprehensive set of data obtained we constructed a morphological diagram of polyelectrolyte block copolymers in aqueous solution. The coarse-grained modeling and simulation, which is demonstrated as a complimentary approach in addition to experimental and theoretical methods, can deliver insight into self-assembly processes of diblock/triblock copolymers and provide evaluation of the size of aggregates obtained along with their scaling relation representation. The simulation results suggest that this coarse-grained simulation scheme gives a route wherein one can effectively and efficiently capture the self-assembly behaviors of polyelectrolyte block copolymers, such as DNA, RNA and other natural and synthetic polycations and polyanions.

Sum frequency generation spectra of the air/water interface from first principles-based models

Gregory Medders, Francesco Paesani. University of California, San Diego

Vibrational sum frequency generation (vSFG) spectroscopy has emerged as a potentially powerful tool for probing the molecular structure and dynamics of interfaces. However, while vSFG provides an experimentally measurable probe of molecular motions at the interface, resolving the spectral features into a molecular level picture poses substantial difficulties. Previously, we developed “first principles”-based models for the potential energy surface, dipole moment surface, and polarizability surface of arbitrary water systems by fitting highly correlated electronic structure calculations of the many-body intermolecular properties. In this contribution, these models are used together with classical molecular dynamics simulations to calculate the vSFG spectrum of the air/water interface. Importantly, since the models were fitted only to correlated electronic structure calculations and, by construction, accurately describe the two-body induced electrostatic properties at the MP2/aug-cc-pVTZ level and the three-body intermolecular interactions at the CCSD(T)/aug-cc-pVTZ level, these simulations shed light on the controversial hypotheses for the molecular level origins of the complex part of the vSFG susceptibility of the air/water interface.