Douglas J. TobiasAssociate Professor, Chemistry |
|
|
|
Research Interests |
Computational Chemistry, Biophysical Chemistry, Atmospheric Chemistry | |
| URL | www.chem.uci.edu/people/faculty/dtobias/ | |
|
Academic Distinctions |
National Institutes of Health Postdoctoral,1991-1993, National Institutes of Health Predoctoral Trainee, 1987-1990. Appointments: 1991-95, Department of Chemistry, University of Pennsylvania. 1995-97, NIST Center for Neutron Research, National Institute of Standards and Technology. |
|
| Appointments |
1991-95, Department of Chemistry, University of Pennsylvania. 1995-97, NIST Center for Neutron Research, National Institute of Standards and Technology. |
|
|
Research Abstract |
Our research involves using atomic-scale computer simulation techniques based on classical and quantum mechanics to study the structure and dynamics of biological molecules and biomimetic materials, and aqueous interfaces with air that are important in atmospheric chemical processes. A substantial portion of our work is devoted to the development, implementation, and optimization of novel simulation methodology and analysis tools. Current areas of research in our lab include: Interactions of Peptides and Proteins with Lipids and Protein Folding in Membranes Membrane proteins comprise roughly 25% of the genome and 90% of pharmaceutical targets, but only a few structures of membrane proteins are known. In order to be able to predict their functions, we need to know how membrane proteins interact with membranes. In collaboration with Professor Stephen White in the UCI College of Medicine, we are modeling peptides and proteins in lipid bilayers, and developing methods for using simulations to refine low-resolution structures of membrane proteins determined by X-ray and neutron diffraction. We are also developing coarse grained models for studying generic aspects of the thermodynamics and kinetics of protein folding in membranes. Structure and Function of Pulmonary Surfactant Proteins Pulmonary surfactant (PS) is a mixture of lipids and proteins that resides at the alveolar air/water interface and keeps the surface tension low during breathing, thereby providing stability to the expanding and contracting alveoli. We are simulating native and mutant PS proteins in lipid monolayers to predict their structures and to elucidate the role of particular residues in their function. The resulting insight will be applied to the development of synthetic replacement surfactant components to treat respiratory diseases associated with the lack of PS proteins, e.g. respiratory distress syndrome in premature infants. Dynamics of Native and Denatured Proteins We are using molecular dynamics simulations to study several fundamental aspects of protein dynamics related to protein function and folding: the transition from an inactive, glassy state at low temperature to the active, liquid-like state at higher temperatures; the role of solvent in affacting the glass transition; the storage and dissipation of vibrational energy in photoexcited heme proteins; the dynamics of proteins and water molecules in denatured states. This work is being carried out in collaboration with Dr. Mounir Tarek and experimental scientists at the NIST Center for Neutron Research. Structure and Reactivity at the Interfaces of Sea Salt and Organic Aerosols The role of aqueous aerosols (small water droplets suspended in air) in atmospheric chemical processes are currently a subject of great interest to atmospheric chemists. The interfaces of aerosol particles are the sites of unique chemistry that does not take place in gas phase or bulk solution environments. We are using molecular dynamics simulations to provide an atomic scale view of the structure and dynamics at the interfaces of concentrated ionic solutions (e.g. sea salt aerosols) and water droplets coated with organic molecules (e.g. organic aerosols), and their interactions with reactive gases present in the atmosphere (e.g. OH radical and ozone). In addition to providing fundamental insight in to the physicochemical properties of these interfaces, our simulations are leading to the proposal of new mechanisms for reactions that could be important in the chemistry of the atmosphere. This work is being performed in collaboration with Professor Barbara Finlayson-Pitts in the Chemistry Department at UCI, and Dr. Pavel Jungwirth at the Czech Academy of Sciences. Fundamental Aspects of Ion-Water Hydrogen Bonds Ion-water hydrogen bonds play an important role in determining the reactivity and thermodynamic and transport properties of aqueous solutions. Recent advances in spectroscopic techniques have led to a renaissance of interest in the quantitative details of the structure, energetics, and dynamics of hydrogen bonds between water and ions. We are using ab initio molecular dynamics simulations, in which the forces between the atoms are computed from the electronic structure using density functional theory, to study the solvation of ions in clusters of water molecules and bulk solutions. Our calculations are providing new information regarding the role of electronic polarization and quantum nuclear motion in ion-water hydrogen bonds. |
|
| Publications | "Polarizability of the Nitrate Anion and Its Solvation at the Air/Water Interface," P. Salvador, J. E. Curtis, D. J. Tobias and P. Jungwirth, Phys. Chem.-Chem. Phys. 5 3752-3757 (2003). | |
| "Polarizability and Aqueous Solvation of the Sulfate Dianion," P. Jungwirth, J. E. Curtis and D. J. Tobias, Chem. Phys. Lett. 367,704-710 (2003). | ||
| "Molecular Dynamics Simulations of a Pulmonary Surfactant Protein B Peptide in a Lipid Monolayer," J. A. Freites, Y. Choi and D. J. Tobias, Biophys. J. 84, 2169-2180 (2003). | ||
| "Single-Particle and Collective Dynamics of Protein Hydration Water: A Molecular Dynamics Study," M. Tarek and D. J. Tobias, Phys. Rev. Lett. 89, 275501 (2002). | ||
| "Environmental Dependence of the Dynamics of Protein Hydration Water," M. Tarek and D. J. Tobias, J. Am. Chem. Soc. 121, 9740-9741 (1999). | ||
| "Amplitudes and Frequencies of Protein Dynamics: an Analysis of Discrepancies Between Neutron Scattering and Molecular Dynamics Simulations," M. Tarek, G. J. Martyna, and D. J. Tobias, J. Am. Chem. Soc. 102, 10450-10451 (2000). | ||
| "Experiments and Molecular/Kinetics Simulations of Ion-Enhanced Interfacial Chemistry on Aqueous NaCl Aerosols," E. Knipping, M. J. Lakin, P. Jungwirth, D. J. Tobias, R. B. Gerber, D. Dabdub, and B. J. Finlayson-Pitts, Science 288, 301-306 (2000). | ||
|
"Real-Time Monitoring of the Kinetics and Gas Phase Products of the Reaction of Ozone with 1-oleoyl-2-palmitoyl-sn-glycero-3-phosphocholine at the Air/Water Interface," Y. Wadia, D. J. Tobias, R. Stafford, B. J. Finlayson-Pitts, Langmuir 16, 9321-9330 (2000). |
||
| "Surface Solvation of Halogen Ions in Water Clusters: an Ab Initio Molecular Dynamics Study of the Cl,-(H2O)6 Complex," D. J. Tobias, P. Jungwirth, and M. Parrinello, J. Chem. Phys., 114, 7036-7044 (2001). | ||
|
"Electronic Polarization and the Hydration of the Dimethylphosphate Ion," I. Kuo and D. J. Tobias, J. Phys. Chem. B, 105, 5827-5832 (2001). |
||
| "Role of Protein-Water Hydrogen Bond Dynamics in the Protein Dynamical Transition," M. Tarek and D. J. Tobias, Phys. Rev. Lett. 88, art. no. 138101 (2002). | ||
| "Ions at the Air/Water Interface," P. Jungwirth and D. J. Tobias, J. Phys. Chem. B 106, 6361-6373 (2002). | ||
| "The Molecular Structure of Salt Solutions: A New View of the Interface with Implications for Heterogeneous Atmospheric Chemistry," P. Jungwirth and D. J. Tobias, J. Phys. Chem. B 105, 10468-10472 (2001). | ||
| "Short Wavelength Collective Dynamics in Phospholipid Bilayers: a Molecular Dynamics Study," M. Tarek, D. J. Tobias, S.-H. Chen, and M. L. Klein, Phys. Rev. Lett. 87, art. no. 238101 (2001). | ||
| Link to this profile | http://www.faculty.uci.edu/profile.cfm?faculty_id=4581 | |
| Last updated | 10/16/2003 | |
