Scientists, in four plenary talks, will explore a variety of subjects related to the "Computers in Chemistry" theme of the 251st National Meeting & Exposition of the American Chemical Society (ACS), the world's largest scientific society. The meeting will take place March 13-17 in San Diego.
The presentations, which are among more than 12,500 scheduled to take place at the meeting, will be held on Sunday, March 13, from 3 p.m. to 6 p.m. PDT, in Room 20A-C of the San Diego Convention Center.
Overall, the presentations will illustrate the wide variety of applications for computers in science from helping develop more potent anti-HIV agents to creating brand-new proteins with the help of the general public. The titles of the plenary talks are listed below:
- George Schatz, Ph.D.: "Using self-assembly to make functional materials: Computational perspectives"
- Sharon Hammes-Schiffer, Ph.D.: "Proton-coupled electron transfer in catalysis and energy conversion"
- David Baker, Ph.D.: "Post-evolutionary biology: Design of novel protein structures, functions and assemblies"
- William Jorgensen, Ph.D.: "30 years of free energy perturbation theory: From free energies of hydration to drug discovery"
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Schatz:
Title
Using self-assembly to make functional materials: Computational perspectives
Abstract
Self-assembly of amphiphilic molecules provides a way to make nanoscale (and larger) supramolecular structures including micelles, ribbons, sheets and aggregates that are important in biomedical applications. Soft materials composed of crystalline superlattices of nanoparticles can be fabricated using DNA, RNA and similar molecules to act as linkers of the nanoparticles. This talk describes computational methods that can be used to model the assembly of these materials and to determine the chemical and optical properties of the assembled structures. Emphasis will be placed on the use of theory to guide and interpret experiment, and to optimize structure and function.
Hammes-Schiffer:
Title
Proton-coupled electron transfer in catalysis and energy conversion
Abstract
Proton-coupled electron transfer (PCET) reactions play a vital role in a wide range of chemical and biological processes. Recent advances in the theory of PCET will be presented. The quantum mechanical effects of the active electrons and transferring proton, as well as the motions of the proton donor-acceptor mode and solvent or protein environment, are included in a general theoretical formulation. This formulation enables the calculation of rate constants and kinetic isotope effects for comparison to experiment. Applications to PCET reactions in solution, enzymes, and electrochemical systems will be presented. Studies of the enzyme soybean lipoxygenase provide a physical explanation for the experimental observation of unusually high kinetic isotope effects for C-H bond activation at room temperature. Investigations of molecular electrocatalysts for hydrogen production identify the thermodynamically and kinetically favorable mechanisms and guide the theoretical design of more effective molecular electrocatalysts. In addition, recent developments of theoretical approaches for simulating the ultrafast dynamics of photoinduced PCET will be discussed. These calculations provide insights into the roles of proton vibrational relaxation and nonequilibrium solvent dynamics in photoinduced PCET processes.
Baker:
Title
Post-evolutionary biology: Design of novel protein structures, functions and assemblies
Abstract
Proteins mediate the critical processes of life and beautifully solve the challenges faced during the evolution of modern organisms. Our goal is to design a new generation of proteins that address current day problems not faced during evolution. In contrast to traditional protein engineering efforts, which have focused on modifying naturally occurring proteins, we design new proteins from scratch based on Anfinsen's principle that proteins fold to their global free energy minimum. We compute amino acid sequences predicted to fold into proteins with new structures and functions, produce synthetic genes encoding these sequences, and characterize them experimentally. I will describe the design of ultra-stable idealized proteins, flu neutralizing proteins, high affinity ligand binding proteins, and self-assembling protein nanomaterials. I will also describe the contributions of the general public to these efforts through the distributed computing project Rosetta@Home and the online protein folding and design game Foldit. Finally, I will briefly describe significant progress in ab initio protein structure prediction.
Jorgensen:
Title
30 years of free energy perturbation theory: From free energies of hydration to drug discovery
Abstract
FEP calculations have had a revolutionary effect on computational chemistry. In conjunction with molecular dynamics and Monte Carlo simulations, they have enabled the calculation of free energy changes for wide-ranging phenomena including fundamental solution thermodynamics, conformational equilibria, reactions in solution, and protein-ligand binding. An overview of our FEP efforts beginning with the ethane to methanol calculation in 1985 and leading to our recent discoveries of extraordinarily potent anti-HIV agents and inhibitors of human macrophage migration inhibitory factor (MIF) will be presented.