Greater Boston Area Theoretical Chemistry Lecture Series

2016-2017 Speaker Schedule

The biophysics of lipid membranes: elasticity meets geometry and biology

11/02/16 4:15pm

MIT Building 4, Room 163

Markus Deserno

Carnegie Mellon University




Markus Deserno

All living cells have a barrier that separates them from their environment: a thin self-assembled structure called a “lipid bilayer membrane”. Eukaryotic cells also have numerous membraneous structures inside themselves to further compartmentalize distinct organelles, such as the cell nucleus or the endoplasmic reticulum. It turns out that biomembranes play important roles in innumerable cellular processes, and that one key to their functional diversity lies in the remarkable elastic properties which they exhibit: lipid bilayers are molecularly thin two dimensional fluids which resists bending, stretching, and lipid tilting in such a way as to communicate forces and information through elasticity and geometry. In my talk I will discuss some of the fascinating aspects of lipid membrane biophysics, and I will explain in more detail several novel approaches we have developed in my group to probe both the various phenomena and the elastic properties of these amazing structures.

Digging Deep into Reactions with New First Principles Techniques

11/09/16 4:15pm

MIT Building 4, Room 163

Paul Zimmerman

University of Michigan




Paul Zimmerman

Effective sampling of reaction pathways is a longstanding challenge in molecular simulation. Difficulties in this area often result from chemical interactions between the environment and the reactive groups, resulting in a high dimensionality of the reaction pathway. In addition to this well-known issue of sampling environmental degrees of freedom, a second challenge is just as basic: realistic hypotheses of the reaction mechanism are needed, but not always available for systems of emerging interest. In this talk, I will introduce graph-based approaches that can thoroughly evaluate reaction coordinates in order to computationally locate the most kinetically feasible reaction pathways. Complementary advances in the Growing String Method for optimizing reaction paths at low effort will also be discussed. These tools are widely applicable to stoichiometric and catalytic systems that include simple environments and complex, solution-phase reactions. Examples will be provided for reactive systems where solvent was found to play an important role in the reaction. These will include catalysis involving transmetalation reactions for electronic polymer growth, and C-H activation reactions.

Excited States and Energy Conversion in Organic Crystals and at Interfaces via First-Principles Methods

11/16/16 4:15pm

Note the location change:

Harvard University, Mallinckrodt Building, Pfizer Lecture Hall

Jeffrey Neaton

University of California, Berkeley




Jeffrey Neaton

Organic crystals and hybrid interfaces are highly tunable, diverse classes of cheap-to-process materials with promise for next-generation optoelectronics. Further development of new materials requires new intuition that links atomic- and molecular-scale morphology to underlying excited-state properties and phenomena. I will review ab initio methods for calculating excited-state and transport properties of crystalline solids and interfaces, and show several applications, where we have used these methods to explain or drive new experiments. Specifically, I will cover the use of first-principles density functional theory with tuned hybrid functionals, and many-body perturbation theory within the GW approximation and the Bethe-Salpeter equation approach, for computing and understanding spectroscopic properties of acene crystals, including new insights into measured multiexciton phenomena such as singlet fission; as time permits, I will additionally share preliminary results on low-dimensional materials, such as 2d chalcogenides, and halide perovskites. I will also discuss multiple approaches to calculating level alignment at metal-molecule interfaces, where we have recently generalized optimally-tuned range-separated hybrid functionals to treat the electronic structure with accuracy comparable to many-body perturbation theory, and describe implications for single-molecule junction transport measurements.

Insights into the structure and dynamics of biomolecules in cellular environments from computer simulations

11/30/16 4:15pm

MIT Building 4, Room 163

Michael Feig

Michigan State University




Michael Feig

Biological macromolecules such as proteins and nucleic acids have become well-understood at the single molecule level but it is much less clear how the structure-dynamics-function paradigms established largely under dilute and homogeneous conditions hold up under realistic biological conditions where crowding, heterogeneity, and the presence of a diverse set of metabolites are important factors. Using computational approaches we are exploring model systems of dense crowded systems ranging from simple spherical crowder models to concentrated protein solutions and a comprehensive model of a bacterial cytoplasm with all of the key components present in full atomistic detail. Simulations of these systems show altered dynamic properties, suggest the possibility of protein native state destabilization due to protein-protein and protein-metabolite interactions, altered solvent and metabolite behavior, and non-specific interactions between functionally related enzymes as a result of crowding. Some of the work described involves very large scale computer simulations that were enabled by methodological advances that will also be briefly discussed.

Exploration and learning of free energy landscapes of molecular crystals and oligopeptides

02/01/17 4:15pm

MIT Building 4, Room 237

Mark Tuckerman

New York University




Mark Tuckerman

Theory, computation, and high-performance computers are playing an increasingly important role in helping us understand, design, and characterize a wide range of functional materials, chemical processes, and biomolecular/biomimetic structures. The synergy of computation and experiment is fueling a powerful approach to address some of the most challenging scientific problems. In this talk, I will describe the efforts we are making in my group to develop new computational methodologies that address specific challenges in free energy exploration and generation. In particular, I will describe our recent development of enhanced free energy based methodologies for predicting structure and polymorphism in molecular crystals and for determining conformational equilibria of oligopeptides. The strategies we are pursuing include heterogeneous multiscale modeling techniques, which allow “landmark” locations (minima and saddles) on a high-dimensional free energy surface to be mapped out, and temperature-accelerated methods, which allow relative free energies of the landmarks to be generated efficiently and reliably. I will then discuss new schemes for using machine learning techniques to represent and perform computations using multidimensional free energy surfaces and navigate chemical compound space in an effort to discover new compounds.

Some advances in density functional theory for calculating and analyzing chemical interactions

03/01/17 4:15pm

MIT Building 4, Room 237

Martin Head-Gordon

University of California, Berkeley




Martin Head-Gordon

Density functional theory (DFT) is the most widely used electronic structure theory. Crucial to its future is the problem of designing functionals with improved predictive power. I shall describe a new approach to functional design, “survival of the most transferable”, and show how the resulting functionals offer unprecedented accuracy for DFT calculations of intermolecular interactions. As a counterpoint to this vital numerical development, I will discuss the challenge of obtaining physical insight into DFT calculations of intermolecular and intra-molecular interactions. We are aiming to meet this challenge with new energy decomposition analysis (EDA) methods that variationally separate interactions associated with frozen fragment electronic structure, from any spin-coupling, from induced electrostatics, and forward and backwards charge transfer.

Proton-Coupled Electron Transfer: Theory and Applications

03/08/17 4:15pm

MIT Building 4, Room 237

Sharon Hammes-Schiffer

University of Illinois at Urbana-Champaign




Sharon Hammes-Schiffer

Proton-coupled electron transfer (PCET) reactions play a vital role in a wide range of chemical and biological processes. This talk will present a general theory for PCET reactions. The quantum mechanical effects of the active electrons and transferring proton(s), as well as the motions of the proton donor-acceptor mode and solvent or protein environment, are included in this theory. This formulation enables the calculation of rate constants and kinetic isotope effects for comparison to experiment. This theory has also been extended to electrochemical processes. 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 nonequilibrium dynamics of photoinduced PCET processes will be presented. Quantum mechanical/molecular mechanical nonadiabatic dynamics simulations enable the investigation of the relaxation pathways following photoexcitation. These calculations provide insights into the roles of proton vibrational relaxation and nonequilibrium solvent dynamics in photoinduced PCET processes in solution and photoreceptor proteins.

Semiclassical initial value representations: Basics and applications to quantum dissipation

03/15/17 4:15pm

MIT Building 4, Room 237

Frank Grossmann

Technische Universität Dresden




Frank Grossmann

The semiclassical initial value formalism to solve the time-dependent Schroedinger equation will be reviewed. Special focus will be laid on the Herman Kluk method [1] and Heller's thawed Gaussians [2]. A combination of the two methods for multi degree of freedom systems, the semiclassical hybrid dynamics [3], will then be introduced. After a brief digression to the semiclassical description of the scattering of two identical particles [4], we present results for the quantum-classical transition of a nonlinear oscillator coupled to an Ohmic heat bath [5] as well as for the thermalization of the expectation values of such an oscillator [6]. We contrast two different approaches to open system dynamics: the explicit treatment of the bath degrees of freedom and the reduced density matrix method, respectively. [1] M. Herman and E. Kluk, Chem. Phys. 91, 27 (1984) [2] E. J. Heller, J. Chem. Phys. 62, 1544 (1975) [3] F. Grossmann, J. Chem. Phys. 125, 014111 (2006) [4] F. Grossmann, M. Buchholz, E. Pollak and M. Nest, Phys. Rev. A 89, 032104 (2014) [5] C.-M. Goletz and F. Grossmann, J. Chem. Phys. 130, 244107 (2009) [6] W. Koch, F. Grossmann, J. T. Stockburger and J. Ankerhold, Phys. Rev. Lett.100, 230402 (2008)

Accelerating atomistic simulations of proteins by Bayesian inference with unreliable information; Cell biology is sometimes cell physics

03/22/17 4:15pm

MIT Building 4, Room 237

Ken Dill

Stony Brook University




Ken Dill

Molecular simulations give insights and quantitation to protein folding, drug discovery and the binding of ligands, and biological mechanistic actions in the cell. But, even with current sampling methods, such as Replica Exchange, physical simulations are much too slow, and don't scale well to larger proteins or larger actions. We have developed MELD, which melds together vague external knowledge to accelerate physics-based molecular simulations. I will describe proofs of principle in folding proteins in the blind prediction event called CASP, and in computing binding affinities of peptide ligands to proteins.

Some behaviors of cells are not due to single proteins or pathways, but are due to the physical properties of proteomes as a whole. For example, the growth rates of bacteria as a function of temperature or salt can be explained the folding stability and diffusion rates of the proteins in the proteome. Using simple physical models, we explore physical aspects of cell mechanisms and evolution, also including cellular energy balance and proteostasis, the machinery that folds and disaggregates proteins.

Nanoscale Disorder Drives the Dynamics of Excitons in Molecular Semiconductors; What Can Interfacial Water Molecules Tell Us About Solute Structure?

03/29/17 4:15pm

MIT Building 4, Room 237

Adam Willard

Massachusetts Institute of Technology




Adam Willard

Many organic electronic materials are composed of soft condensed matter that is both electronically active and disordered on the nanoscale. The electronic properties of these materials can depend sensitively on the details of molecular morphology, reflecting a complex coupling between excited electrons and the disordered nuclear environment. To better understand this coupling and how nanoscale disorder affects the electronic dynamics in these materials we utilize numerical simulation. In this talk I describe our approach to unraveling the effects of nanoscale disorder on the dynamics of excitons, which utilizes atomistic simulation, coarse-grained models, and quantum dynamics.

The molecular structure of bulk liquid water reflects a molecular tendency to engage in tetrahedrally coordinated hydrogen bonding. At a solute interface water’s preferred three-dimensional hydrogen bonding network must conform to a locally anisotropy interfacial environment. Interfacial water molecules adopt configurations that balance water-solute and water-water interactions. The arrangements of interfacial water molecules, therefore encode information about the effective solute-water interactions. This solute-specific information is difficult to extract, however, because interfacial structure also reflects water’s collective response to an anisotropic hydrogen bonding environment. Here I present a methodology for characterizing the molecular-level structure of liquid water interface from simulation data. This method can be used to explore water’s static and/or dynamic response to a wide range of chemically and topologically heterogeneous solutes such as proteins.

Challenges for Density Functional Theory and Progress with Local Scaling Corrections and Pairing Fluctuations

04/12/17 4:15pm

MIT Building 4, Room 237

Weitao Yang

Duke University




Weitao Yang

Density functional theory of electronic structure is widely and successfully used in simulations throughout engineering and sciences. However, there are major failures for many predicted properties. These errors are in the approximate functionals and can be characterized and understood through the perspective of fractional charges and fractional spins. The fractional perspectives offer a possible pathway forward. For an effective and universal alleviation of the delocalization error, we develop a local scaling correction scheme by imposing the Perdew-Parr-Levy- Balduz linearity condition to local regions of a system. Our novel scheme is applicable to various mainstream density functional approximations. It substantially reduces the delocalization error, as exemplified by the significantly improved description of dissociating molecules, transition-state species, and charge-transfer systems. The usefulness of our novel scheme affirms that the explicit treatment of fractional electron distributions is essentially important for reducing the intrinsic delocalization error associated with approximate density functionals. Progress with many-body theory approach will be also be presented. We have formulated the ground-state exchange-correlation energy in terms of pairing matrix linear fluctuations, opening new a channel for density functional approximations. This method has many highly desirable properties. It has minimal delocalization error with a nearly linear energy behavior for systems with fractional charges, describes van der Waals interactions similarly and thermodynamic properties significantly better than the conventional RPA, and eliminates static correlation error for single bond systems. It is the first known functional with closed-form dependence on orbitals, which captures the energy derivative discontinuity in strongly correlated systems. We also adopted pp-RPA to approximate the pairing matrix fluctuation and then determine excitation energies by the differences of two-electron addition/removal energies. This approach captures all types of interesting excitations: single and double excitations are described accurately, Rydberg excitations are in good agreement with experimental data and CT excitations display correct 1/R dependence. Applications to the singlet-triplet energy gaps of diradicals and poly-acenes and conical intersections will be featured.

Quantum Field Theory in Chemistry

04/19/17 4:15pm

MIT Building 4, Room 237

So Hirata

University of Illinois at Urbana-Champaign




So Hirata

In the first part of this lecture, we review widely used quantum-field-theoretical techniques (second quantization, normal-ordered second quantization and Wick’s theorem, and Feynman-Goldstone diagrams) in nonrelativistic molecular quantum mechanics. In the second part, we illustrate their power in formulating new electronic and vibrational structure methods (finite-temperature many-body perturbation and coupled-cluster methods; vibrational many-body Green’s function and coupled-cluster methods) and algorithms (Monte Carlo many-body perturbation and Green’s function methods) or in understanding their properties (the linked- and irreducible-diagram theorems of many-body Green’s functions and self-energies; existence of thermodynamic limit and size-consistency theorems; incompatibility of size-consistency and variationality).

QM/QM embedding scheme for strongly correlated problems

04/26/17 4:15pm

MIT Building 4, Room 237

Dominika Zgid

University of Michigan




Dominika Zgid

We present a detailed discussion of self-energy embedding theory (SEET) which is a QM/QM embedding scheme expressed in a Green's function language allowing us to describe a chosen subsystem very accurately while keeping the description of the environment at a lower cost. We apply SEET to molecular examples where commonly our chosen subsystem is made out of a set of strongly correlated orbitals while the weakly correlated orbitals constitute an environment. Such a separation is very general and can be applied to both molecules and solids. On a set of carefully chosen molecular examples, we demonstrate that SEET, which is a controlled, systematically improvable Green's function method can be as accurate as established wave function quantum chemistry methods. Finally, we discuss possible generalization of SEET to periodic problems.

Synchronization (and anti-synchronization) of noisy arrays of coupled oscillators: the simplest models

05/03/17 4:15pm

MIT Building 4, Room 237

Katja Lindenberg

University of California, San Diego




Katja Lindenberg

Synchronization is observed in many systems in nature, from microscopic to macroscopic, in biological systems, mechanical systems, ecology, epidemiology; the list is endless. In these systems, a collection of coupled units, if coupled sufficiently strongly, can undergo a transition to synchronized behavior. Noise in these systems can arise from a number of sources, for instance inherent fluctuations in each unit, fluctuations due to finite numbers of units, or external fluctuating forces. Theoretical analysis of these phenomena is often notoriously difficult, and numerical simulations notoriously resource intensive. My scientific life has covered many topics in addition to synchronization, but most of it has shared two features: (1) Rather than the analysis of any one “real” system, I search for the simplest models that exhibit some interesting common behavior seen in many “real” systems, and (2) Effects of noise. Among other topics, I have spent many years studying anomalous diffusion, diffusion in disordered media, reaction-diffusion and reaction-transport phenomena, thermodynamics of small systems, thermodynamics away from equilibrium, and energy propagation in granular media. Here I will focus on synchronization. I will present a few of the simplest models that we have studied to gain insight into synchronization (and anti-synchronization) of coupled two-state (“on-off”) and three-state (“functional-neutral-dysfunctional”) units.

TBA

05/10/17 4:15pm

MIT Building 4, Room 237

Ivet Bahar

University of Pittsburgh




Ivet Bahar

Past Schedules