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 (snow)

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

Slides - first hour

Slides - second hour

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.

Design of artificial enzymes: catalysis ahead of nature

03/11/15 4:00pm

MIT Building 4, Room 163

Anastassia Alexandrova

UCLA




Anastasia Alexandrova

Enzymes are superb catalysts, green, economical, and exceptionally selective. It is desired to mimic enzymatic strategies in catalysis of reactions that interest humankind. This talk will focus on using theory to design new enzymes that can be tested experimentally (the approach can be considered complementary to directed evolution). There has been quite and advancement in being able to design non-metal enzymes, which will be reviewed. However, less progress is seen in the design of metalloenzymes, whereas metalloenzymes are arguably the most interesting biological catalysts, performing dramatic chemical transformations in a very few steps, by virtue of the electronic structure of the metal(s). Also, metalloenzymes give us a chance to outdo nature in catalysis through the use of nonphysiological metals or clusters. The reason for slow progress in this field has been that computational approached that would allow for reasonable predictions must treat the metal center(s) quantum mechanically throughout the design process, and the backbone of the protein needs to move efficiently, and the methodology of this sort was not available until recently. We developed a set of tools for metalloenzyme design. These tools, first designs, and other considerations related to metalloenzyme design will be discussed.

A decade of quantum computing for quantum chemistry

03/18/15 4:00pm

MIT Building 4, Room 163

Alan Aspuru-Guzik

Harvard University




Alan Aspuru-Guzik

The last time I spoke about quantum computing and chemistry to a theoretical chemistry audience in the Boston area was at this very same seminar back in 2006 or 2007. In this seminar, I will give an update on what has happened in the last 10 years since the original full configuration interaction quantum chemistry proposal (Aspuru-Guzik, et al., Science, 2005). I will give a 2-hour talk(with more details as usual) of why large-enough quantum computers will be relevant, perhaps game-changing for chemistry. I will discuss several ways of solving the electronic structure problem in quantum computers, and also their relevant experimental realizations, either proposed or actually carried out in small quantum devices. An important point relevant to these, is their scaling and potential for realization in the near future assuming quantum computers continue to develop rapidly. I will discuss this interesting aspect. I will also briefly discuss applications in optimization problems (e.g. folding proteins) and quantum dynamics. If time permits, I will discuss the use of our recent Boson Sampling experimental setup to simulate molecular vibrionic spectra.

Symmetrical Quasi-Classical Model for Classical Molecular Dynamics Simulations of Electronically Non-Adiabatic Processes

03/25/15 4:00pm

MIT Building 4, Room 163

Bill Miller

University of California, Berkeley




Bill Miller

A recently described symmetrical windowing methodology [J. Phys. Chem. A 117, 7190 (2013)] for quasi-classical trajectory simulations is applied here to the Meyer-Miller [J. Chem. Phys. 70, 3214 (1979)] model for the electronic degrees of freedom in electronically non-adiabatic dynamics. Results generated using this classical approach are observed to be in very good agreement with accurate quantum mechanical results for a variety of test applications, including cases where coherence effects are significant and also the challenging asymmetric spin-boson system.

Real-time dynamics of strongly correlated quantum systems with the time-dependent density matrix renormalization group

04/07/15 4:00pm

Harvard, Pfizer Lecture Hall

Adrian Feguin

Northeastern University




Adrian Feiguin

The study of models of strongly correlated electrons is a difficult problem since methods based on perturbation theory generally fail. The lack of controlled and well-behaved approximations has led physicist and chemists to study these systems using numerical techniques. In 1992, Steven White invented the Density Matrix Renormalization Group method. With roots that can be traced to Wilson's Renormalization Group, this technique has proven to be remarkably effective computational tool to calculate static, ground state properties of low-dimensional strongly correlated systems. During the past ten years, the DMRG has experienced an unprecedented evolution. Through a convergence with quantum information ideas, we now have a much better understanding of its range of applicability, and the consequences of quantum entanglement on the effectiveness of the method. In a subsequent development we adapted it to solve the time-dependent Schroedinger's Equation. I will present both algorithms, discuss different applications, and show results for spin and electronic transport in nano-structures, decoherence in open quantum systems, and spectral properties of low dimensional electronic systems. I will finally show how the method can be extended to imaginary time to study thermodynamics and finite-temperature properties.

Concepts of Protein Dynamics in Drug Design

04/15/15 4:00pm

MIT Building 4, Room 163

Jeremy Smith

UT/ORNL




Jeremy Smith

The design of drugs using protein structures is undergoing a renaissance. Now, internal motions of proteins have begun to be incorporated into structure-based drug development. We examine the variety of motions in proteins, demonstrate entropy-driven vibrational softening on the binding of a cancer drug to its target and show that inter-domain motion can be described by the principle of De Gennes Narrowing. Curiously, over the typical biological lifespan of a protein internal motions remain out of equilibrium, obeying a self-similar (fractal) time dependence over thirteen decades in time. Metastability analysis can be used to produce a thermodynamically rigorous representation of the conformational transitions involved. Finally, we show how the incorporation of protein dynamics into virtual high-throughput screening has permitted the successful generation of lead compounds to combat hypophosphatemia, antibiotic resistance and thrombosis.

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

Past Schedules

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