Greater Boston Area Theoretical Chemistry Lecture Series
2012-2013 Speaker Schedule
Chemical Reaction Rates from Ring Polymer Molecular Dynamics
09/24/12 4:00pm
Harvard Chemistry Department, Pfizer Lecture Hall
David Manolopoulos
After presenting an introduction to imaginary time path integrals, I will review the ring polymer molecular dynamics (RPMD) theory of chemical reaction rates and compare this theory with the exact quantum mechanical and classical limit theories. I will then present some example applications of RPMD to chemical reactions in the gas phase and in solution. Since RPMD is a classical rate theory in an extended phase space, it is routinely applicable to genuinely complex chemical reactions in their full dimensionality. Moreover it becomes exact in the high temperature limit, and it gives a rate coefficient within a factor of 2 of the exact quantum mechanical result at temperatures in the deep tunneling regime (where the classical rate is too small by several orders of magnitude). RPMD is almost certainly the best exacting technique for calculating the rates of chemical reactions in complex environments (in liquids, in enzymes, and on surfaces).
Part I : Chemical Reaction Dynamics in Complex Environments
Part II: Free Energies and Structure along Reaction Paths
09/26/12 4:00pm
MIT Building 4, Room 163
Rigoberto Hernandez
In the first hour, we will discuss the fundamentals of reaction rate theory in the gas andliquid phases. Transition state theory has proven to be a powerful tool for describing the leading order terms in reaction rates. At the cutting edge, we and many others are working to increase its accuracy particularly in cases involving much higher dimensionality either in the reacting system, the surrounding solvent or both. Meanwhile, the environments themselves may change over time leading to changes in the response —as represented by colored friction kernels in a generalized Langevin equation— or even wholesale changes —as represented by nonstationarity. Such increasingly complex environments are commonplace in present-day materials and the theory is expanding to include them.
In the second hour, we will discuss our recent work characterizing the potential of mean force along a chosen path of a molecular motion. In particular, we have developed adaptive steered molecular dynamics (ASMD) in order to efficiently obtain the potential of mean force along a long-distance path. This relies on the convergence of Jarzynski's equality, which becomes increasingly computationally expensive as the contributing nonequilibrium paths spread father from the initial point. In ASMD, we break up the path into a series of segments, with each having a smaller distance along which to spread. Equally important, we use the information found in the nonequilibrium distribution at the end of each segment to select the initial structures for the subsequent segment. We have found that ASMD converges to the same and correct potential of mean force in the stretching of decaalanine in vacuum using substantially fewer computer cycles and at pulling speeds faster than that required to obtain it reversibly. Decaalanine has also been stretched in an aqueous solvent. The intramolecular hydrogen-bonding in this latter case appears to be entirely different than that seen in the vacuum case, suggesting the importance of including explicit water models at least in the vicinity of the internal hydrogen bonds of the protein.
Crystallization of Water: From the Bulk to the Nanoscale
10/10/12 4:00pm
MIT Building 4, Room 163
Valeria Molinero
The dynamics of genomic sequence evolution in microbial populations
11/07/12 4:00pm
MIT Building 4, Room 163
Michael Desai
I will discuss theoretical and experimental approaches to the evolutionary dynamics and population genetics of natural selection in large populations. In these populations, many mutations are often present simultaneously, and because recombination is limited, selection cannot act on them all independently. Rather, it can only affect whole combinations of mutations linked together on the same chromosome. Methods common in theoretical population genetics have been of limited utility in analyzing this coupling between the fates of different mutations. In the past few years it has become increasingly clear that this is a crucial gap in our understanding, as sequence data has begun to show that selection appears to act pervasively on many linked sites in a wide range of populations, including viruses, microbes, Drosophila, and humans. I will describe approaches that combine analytical tools drawn from statistical physics and dynamical systems with traditional methods in theoretical population genetics to address this problem, and describe how experiments in budding yeast can help us directly observe these evolutionary dynamics.
Molecular superfluids
11/14/12 4:00pm
MIT Building 4, Room 163
Pierre-Nicholas Roy
When cooled to very low temperatures, many-body quantum systems exhibit peculiar collective behaviours. One of them is superfluidity which is characterized by transport without dissipation or viscosity. This phenomenon has been known to take place in bulk liquid helium for several decades and has been a at the centre of low temperature physics research. Can these phenomena be observed at the nanoscale? Can molecular systems behave as superfluids? How would we probe them?
In the first part of my lecture, I will present the recent history of the field of nanoscale superfluidity in clusters and droplets with special attention to experimental observations and theoretical tools used to interpret those measurements. A hallmark of superfluid response in such systems is the nearly free rotation of a molecular probe. I will also introduce a powerful computer simulation approach, based on Feynman path integrals, used to predict superfluid properties.
In the second portion of the lecture, I will present recent simulation results from our group that show that indeed, a molecule such as parahydrogen can behave like a superfluid in doped nanoscale clusters [ Phys. Rev. Lett. 105, 133401 (2010); Phys. Rev. Lett. 108, 253402 (2012)]. Such a confirmation was possible through joint experimental and theoretical efforts. I will conclude with an outlook on the current challenges of the field and potential new directions.
02/27/13 4:00pm
MIT Building 4, Room 163
Gustavo Scuseria
I will present our recent results on the calculation of symmetry-projected wave functions [1,2] for electronic structure theory. For Hartree-Fock and spin projection, this is a 50-year old problem in quantum chemistry, going all the way back to Lowdin and his "extended HF" theory. For Hartree-Fock-Bogoliubov and number projection, our approach offers new perspectives on Antisymmetrized Geminal Power (AGP) wavefunctions that were the focus of much attention in the 1980s. In our work, all molecular symmetries (electron number, spin S2 and Sz , point group, and complex conjugation) are deliberately broken and restored in a self-consistent variation-after-projection approach. The resulting method yields a comprehensive black-box treatment of static correlation with one-electron (mean-field) computational cost. The ensuing wave function is of high quality multireference character competitive with exact diagonalization. Recent application of the methodology to copper oxide cores shows great promise [3]. The method can also be applied to calculate excited states and spectral functions [4]. I will also discuss recent applications to polycyclic aromatic hydrocarbons, oligoacenes, and singlet-triplet splittings. The curse of the thermodynamic limit and the quest for a low-cost treatment of residual correlations will also be addressed.
[1] Projected quasiparticle theory for molecular electronic structure, G. E. Scuseria, C. A. Jimenez-Hoyos, T. M. Henderson, J. K. Ellis, and K. Samanta, J. Chem. Phys. 135, 124108 (2011).
[2] Projected Hartree-Fock theory, C. A. Jimenez-Hoyos, T. M. Henderson, and G. E. Scuseria, J. Chem. Phys. 136, 164109 (2012).
[3] Exploring copper oxide cores using Projected Hartree-Fock theory, K. Samanta, C. A. Jimnez-Hoyos, and G. E. Scuseria, J. Chem. Theory Comput. 8, 4944-4949 (2012).
[4] Symmetry-projected variational approach for ground and excited states of the two-dimensional Hubbard model, R. Rodriguez-Guzman, K. W. Schmid, C. A. Jimenez-Hoyos, and G. E. Scuseria, Phys. Rev. B 85, 245130 (2012).
03/06/13 4:00pm
MIT Building 4, Room 163
Jeff Grossman
Studies of PCET in Natural and Artificial Photosynthesis
04/10/13 4:00pm
MIT Building 4, Room 163
Victor Batista
Proton coupled electron transfer (PCET) plays a fundamental role in the mechanism of water-splitting at the oxygen-evolving complex (OEC) of photosystem II (PSII). We address the underlying reaction mechanism by structural studies of catalytic intermediates. Many physical techniques have provided important insights into the OEC structure and function, including X-ray diffraction (XRD) and extended X-ray absorption fine structure (EXAFS)spectroscopy as well as mass spectrometry (MS), electron paramagnetic resonance (EPR) spectroscopy, and Fourier transform infrared spectroscopy applied in conjunction with mutagenesis studies. However, experimental studies have yet to yield consensus as to the exact configuration of the catalytic metal cluster and its ligation scheme. Computational modeling studies, including density functional (DFT) theory combined with quantum mechanics/molecular mechanics (QM/MM) hybrid methods for explicitly including the influence of the surrounding protein, have proposed chemically satisfactory models of the fully ligated OEC within PSII that are maximally consistent with experimental results. The inorganic core of these models is similar to the crystallographic model upon which they were based, but comprises important modifications due to structural refinement, hydration, and proteinaceous ligation which improve agreement with a wide range of experimental data. The computational models are useful for rationalizing spectroscopic and crystallographic results and for building a complete structure-based mechanism of water-splitting assisted by PCET as described by the intermediate oxidation states of oxomanganese complexes. This talk summarizes recent advances on studies of the OEC of PSII and biomimetic oxomanganese complexes for artificial photosynthesis.
Statistical Genetics and Dynamics of Natural Selection
04/24/13 4:00pm
MIT Building 4, Room 163
Boris Shraiman
This talk will review recent progress in understanding the dynamics of natural selection under the conditions of high genetic diversity, focusing on the effects of interactions and seeking "emergent simplicity" of the limit when fitness differentials are due to a large number of mutations each having a only a small effect.
Protein Structure, Stability, and Folding in the Cell - in silico Biophysical Approaches
05/15/13 4:00pm
MIT Building 4, Room 163
Margeret Cheung
How the crowded environment inside a cell affects the structural conformation and function of a protein with aspherical shape is a vital question because the geometry of proteins and protein-protein complexes are far from globules in vivo. Here we address this question by combining computational and experimental studies of a spherical protein (i.e. apoflavodoxin), a football-shaped protein (i.e., Borrelia burgdorferi VIsE) and a pac-man shaped protein (i.e. phosphoglycerate kinase) under crowded, cell-like conditions. The results show that macromolecular crowding affects protein folding dynamics as well as an overall protein shape associated with changes in secondary structures. Our work demonstrates the malleability of 'native' protein and implies that crowding-induced shape changes is important for protein function and malfunction in vivo.
Past Schedules