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| Darrin York, University of Minnesota |
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Professor York is an associate professor in the Department of Chemistry at the University of Minnesota since 1999, following postdoctoral work at Duke University and Harvard. Research has focused on the development of multi-scale quantum models to study chemical reactions that take place in complex biological environments. Professor York has pioneered breakthroughs in the development of linear-scaling methods for treatment of electrostatics, solvation and electronic structure that have allowed molecular simulations and quantum chemical calculations to be extended to very large systems. The application focus is on the molecular mechanisms of RNA catalysis - a challenging area that requires design of new-generation quantum and molecular simulation models. Professor York's group has published over 20 papers in peer-reviewed journals in the last year alone, including 10 papers that have appeared in 2004. Additional information can be found at the York Group web site http://riesling.chem.umn.edu/
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Application of a Database of Quantum Calculations for RNA Catalysis (QCRNA) in the Design of New Multi-scale Quantum Models for Phosphoryl Transfer Reactions
Darrin M. York, University of Minnesota, Department of Chemistry, 207 Pleasant St. SE, Minneapolis, MN 55455-0431, USA
Computer simulation methods provide a tool of enormous potential impact in problems of biocatalysis. Reliable molecular simulations of RNA-catalyzed reactions need to take into account accurate quantum models, complex macromolecular, ionic and solvent environments, and extensive conformational sampling. Consequently, in order to make accurate predictions about the mechanism and rates of phosphoryl transfer reactions, this requires theoretical methods that are robust and reliable over a broad range of time and length scales. The present work describes a multi-faceted theoretical approach toward the development of methods that allow simulation of catalytic RNA systems to be performed with increased reliability and predictive capability. A database of quantum calculations for RNA catalysis has been developed and is applied in the design of new, highly accurate semiempirical quantum models that can be used in linear-scaling electronic structure calculations and hybrid quantum mechanical/molecular mechanical simulations of biological phosphoryl transfer reactions. A knowledge of structure and mechanism derived from these calculations provides insight into drug design and discovery. The methods are applied to non-enzymatic and enzymatic phosphoryl transfer reactions in solution with new linear-scaling methods for treatment of electrostatic interactions.
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Simulations of phosphoryl transfer reactions using new hybrid quantum mechanical/molecular mechanical methods (Web Conference Presentation)
Darrin York, University of Minnesota
Modern computational chemistry is faced with exciting new challenges in the new millennium. A rapidly advancing research area is at the interface of traditional disciplines in chemistry and biology, and involves the integration of experimental and theoretical methods that, together, are able to paint a detailed picture of processes that span individual molecule, nano-scale and even meso-scale domains. Consequently, it is a major goal of computational chemistry to develop "multi-scale" quantum models that are able to simultaneously span a broad range of spatial and temporal domains.
In this talk, several advancements in the development of accurate quantum models for molecular simulations of biological reactions and the characterization of macromolecular reactivity are presented. Techniques that will be discussed include: new quantum models for hybrid quantum mechanical/molecular mechanical activated dynamics simulations, and linear-scaling electronic structure and solvation methods for macromolecules. Applications will focus on the study of phosphoryl transfer reactions in solution and catalyzed by ribozymes.
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