Greater Boston Area Theoretical Chemistry Lecture Series

2014-2015 Speaker Schedule

Electronic Dynamics in Complex Environments: From Electron Transfer to Singlet Fission

09/10/14 4:00pm

MIT Building 4, Room 163

Troy Van Voorhis

MIT




Troy Van Voorhis

Some of the most basic chemical reactions are those that involve primarily the motion of electrons with little rearrangement of the nuclei. Prominent examples include electron transport and excitonic energy transfer as well as more exotic phenomena such as singlet fission. These reactions are the centerpiece of artificial photosynthetic complexes, organic PVs and essentially all of redox chemistry. In treating the dynamics of these reactions, it becomes clear that knowledge of the molecular conformation alone is not sufficient to define a reaction coordinate (since the nuclei may not more appreciably during the course of the reaction). In this talk, we will discuss how the "reactant" and "product" states for these types reactions can be clearly defined using the electron density as the fundamental variable. We will illustrate the utility of this approach using two examples: electron transfer in solution the simulation of singlet fission in organic photovoltaics.

Systematic Approach to Density Functional Theory

10/15/14 4:00pm

MIT Building 4, Room 163

Kieron Burke

University of California, Irvine




Kieron Burke

Density functional calculations of electronic structure appeared in about 30,000 papers last year. Claims to its first principles nature are being undermined by the hundreds of different approximations available to users. (see J. Chem. Phys. 136, 150901 (2012).) I will explain what DFT is and why it has become so popular. Then I will show how, in fact, density functional approximations are simply semiclassical approximations to the many-electron problem, and that expansion in powers of hbar leads to the systematic construction of density functional approximations. This has produced acGGA, the most accurate generalized gradient approximation ever for atomic correlation energies (see arXiv:1409.4834).

Electronic structure theory: Beyond the black box

10/29/14 4:00pm

MIT Building 4, Room 163

Toru Shiozaki

Northwestern University




Toru Shiozaki

One of the biggest challenges in quantum chemistry is to accurately simulate the electronic structure of molecules and materials in which electron correlation is beyond the perturbative regime. I will first explain conventional theories, such as multi-configuration methods and density matrix renormalization group (DMRG), with an emphasis on the structure and interpretation of their wave functions. Then I will describe a method recently developed by us, called active space decomposition (ASD), which uses molecular geometries to compress the wave functions. This method not only allows us to simulate multi-configuration wave functions of unprecedented size, but also provides natural links to a few-state model Hamiltonians for excitonic/electronic processes. Finally I will present ASD with multiple active sites using the DMRG algorithm and its application to "chemically" one-dimensional systems.

TBD

02/11/15 4:00pm - CANCELLED

MIT Building 4, Room 163

Pablo DeBenedetti

Princeton University




Pablo DeBenedetti

The Protein Folding Problem

02/25/15 4:00pm

MIT Building 4, Room 163

Peter Wolynes

Rice University




Peter Wolynes

Protein folding can be understood as a biased search on a funelled but rugged energy landscape. The funneled nature of the protein energy landscape is a consequence of natural selection. I will discuss how this rather simple picture quantitatively predicts folding mechanism from native structure and sequence. I will also discuss recent advances using energy landscape ideas to create algorithms capable of predicting protein tertiary structure from sequence, protein binding sites and the nature of structurally specific protein misfolding relevant to disease. Finally I will compare the physical folding energy landscape with the apparent fitness landscape of evolution as inferred from large genomic data sets.

Membrane potential and small charge movement in membrane protein systems

03/04/15 3:00pm

MIT Building 66, Room 144

Benoit Roux

University of Chicago




Benoit Roux

A theoretical framework is elaborated to account for the effect of a transmembrane potential in explicit solvent computer simulations of membrane proteins [1]. The framework relies on a modified Poisson-Boltzmann equation previously developed from statistical mechanical considerations [2]. It is shown that a simulation with a constant external electric field applied in the direction normal to the membrane is equivalent to the influence of surrounding infinite baths maintained to a voltage difference via ion-exchanging electrodes connected to an electromotive force. It is also shown that the linearly-weighted displacement charge within the simulation system tracks the net flow of charge through the external circuit comprising the electromotive force and the electrodes. Using a statistical mechanical reduction of the degrees of freedom of the external system, three distinct theoretical routes are formulated and examined for the purpose of characterizing the free energy of a protein embedded in a membrane that is submitted to a voltage difference: the W-route constructed from the variations in the voltage-dependent potential of mean force along a reaction path connecting two conformations of the protein, the Q-route based on the average displacement charge as a function of the conformation of the protein, and the G-route based on the relative charging free energy of specific residues, with and without applied membrane potentials. The theory is applied to examine atomic models of the Kv1.2 potassium channel in the active and resting state [2]. Methodologies to treat asymmetric membrane conditions have also been developed [3]. Calculations of the fractional transmembrane potential, acting upon key charged residues of the voltage sensing domain of the Kv1.2 potassium channel, reveals that the applied field varies rapidly over a narrow region of 10 to 15 Angstroms, corresponding to the outer leaflet of the bilayer [4]. The focused field allows the transfer of a large gating charge without translocation of S4 across the membrane. The theory is also applied to examine the binding of sodium and potassium ions to the Na,K ATPase membrane pump.

1. B. Roux. Influence of the membrane potential on the free energy of an intrinsic protein. Biophysical Journal. 1997;73(6):2980-9.

2. B. Roux. The membrane potential and its representation by a constant electric field in computer simulations. Biophys J. 2008;95(9):4205-16.

3. F. Khalili-Araghi, B. Ziervogel, J.C. Gumbart, B. Roux. Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations. J Gen Physiol. 2013;142(4):465-75.

4. F. Khalili-Araghi, V. Jogini, V. Yarov-Yarovoy, E. Tajkhorshid, B. Roux, K. Schulten. Calculation of the gating charge for the Kv1.2 voltage-activated potassium channel. Biophys J. 2010;98(10):2189-98.

TBD

03/11/15 4:00pm

MIT Building 4, Room 163

Anastasia Alexandrova

UCLA




Anastasia Alexandrova

TBD

03/18/15 4:00pm

MIT Building 4, Room 163

Alan Aspuru-Guzik

Harvard




Alan Aspuru-Guzik

TBD

03/25/15 4:00pm

MIT Building 4, Room 163

Bill Miller

University of California, Berkeley




Bill Miller

TBD

04/15/15 4:00pm

MIT Building 4, Room 163

Jeremy Smith

UT/ORNL




Jeremy Smith

TBD

05/06/15 4:00pm

MIT Building 4, Room 163

Shaul Mukamel

University of California, Irvine




Shaul Mukamel



TBD

TBD

05/13/15 4:00pm

MIT Building 4, Room 163

Lorenz Cederbaum

Universitat Heidelberg




Lorenz Cederbaum



TBD

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