Greater Boston Area Theoretical Chemistry Lecture Series
2011-2012 Speaker Schedule
Dynamics and Mechanism of a Most Proficient Enzyme from QM/MM Simulations: Orotidine Monophosphate Decarboxylase.
10/19/11 4:00pm
MIT Building 4, Room 231
Jiali Gao
Orotidine 5'-monophosphate decarboxylase (OMPDC) catalyzes the exchange of CO2 for a proton at the C6 position to form uridine 5'-monophosphate (UMP),
with a rate acceleration of 21 orders of magnitude. The remarkable catalytic proficiency was analyzed using combined QM/MM simulations. In this talk,
I will briefly describe computational methods developed for studying enzymatic reactions and proton-coupled electron transfer reactions, with an emphasis
on multistate density functional theory. The computational results indicate that there is a direct coupling between the intrinsic dynamics of the protein,
characterized by a hinge domain motion, with the reaction coordinate motion of the chemistry process. Both computation and experiments show that there is an
upper limit that the transition state can be stabilized in the OMPDC catalyzed reaction, whereas the remaining effects are elucidated from structural and
dynamics investigations.
Controlling Electronic Properties of Molecules by Distortion: Fixing Pathways
01/11/12 1:00pm
MIT Building 4, Room 237
Mark Ratner
Both pathways and fluxes for electronic motion through molecules have become standard in contemporary chemical literature. With the capabilities that
scanning probe microscopy and creative synthesis offer to control molecular geometries and shapes, we can imagine that molecular current transport could
be controlled by fixing the molecular geometry, even at a highly non-equilibrium position. In this talk, I will discuss some computations concerning exactly
this kind of molecular distortion, and the resulting transport features.
We begin by defining a local current metric, and its graphical implementation. Then we examine transport in a series of molecules ranging from rotaxanes through
new custom designed pi stack molecules, whose currents will change substantially upon distortion.
Using the nonequilibrium aspects that can be provided by molecular pulling permits investigation of transport behavior in very different and very wonderful
geometries. How this relates to more usual structures will be briefly discussed.
Electronic Structure of Open-Shell and Electronically Excited Species: Theory, Methodology, and Applications
1/18/12 4:00pm
MIT Building 56, Room 154
Anna Krylov
Quantum mechanics provides fundamental laws governing properties of matter on the atomic scale. H, the Hamiltonian, defines the system (number of nuclei and electrons
and their interactions with each other and external potentials), and the wave function, has all the answers. By solving the Schrodinger equation, one can determine
equilibrium structures of molecules and materials, compute all sorts of spectra, as well as thermochemical quantities that determine reaction rates
and yields. Thus, as eloquently pointed out by Dirac in 1929, the laws determining all of chemistry (and a large part of physics) are completely known. Yet, the practical
application of these laws is limited by the computationally demanding nature of the underlying equations. Developing approximate practical methods for applying quantum
mechanics to describe matter is what defines the field of Quantum Chemistry. Advances in computer technology along with the the progress in developing efficient approximate
methods and computer codes for solving the Schrodinger equation has made quantum chemistry tools indispensable in modern research.
In the first part of the lecture I will review a hierarchy of systematic approximations to the molecular electronic Schrodinger equation and compare configuration interaction (CI)
and coupled-cluster approaches. I will then present a variational view of CC formalism and introduce equation-of-motion (EOM) theory. Different EOM-CC models that allow one to
describe various multi-configurational wave functions within strictly single-reference formalism will be discussed.
The second part of the lecture will illustrate the theory by examples from our recent studies of the green fluorescent protein and its chromophore. In particular, the interplay
between electronically excited and ionized states will be discussed.
The third part of the lecture will discuss the extension of EOM-CC to electronic states that are meta-stable with respect to electron detachment/ionization via complex-scaling formalism.
Suggested reading:
1. A.I. Krylov, Equation-of-motion coupled-cluster methods for open-shell and electronically excited species: The hitchhikers guide to Fock space, Ann. Rev. Phys. Chem. 59, 433 (2008).
2. K.B. Bravaya, B.L. Grigorenko, A.V. Nemukhin, A.I. Krylov, Quantum chemistry behind bioimaging: Insights from ab initio studies of fluorescent proteins and their chromophores, Acc. Chem. Res.,
in press (2012). Can be downloaded from the ACS website as an ASAP paper.
3. W.P. Reinhardt, Complex coordinates in the theory of atomic and molecular structure and dynamics, Ann. Rev. Phys. Chem. 33, 232 (1982).
Quantum energy flow and localization during photochemical reactions in proteins
1/26/12 4:00pm
MIT Building 56, Room 154
David Leitner
Many photochemical reactions in proteins occur in vibrationally unrelaxed states, as evident from the coherent, low-frequency oscillations observed
during a variety of such reactions. Examples include low frequency oscillations observed in the primary step in vision, light-harvesting complexes,
and excited state proton transfer in green fluorescent protein. The observation of coherent vibrations during reaction is surprising since, as chemists,
we are accustomed to equilibration prior to reaction, which we exploit to predict reaction rates. Structures that are highly improbable when energy is
thermally distributed may be accessed, structures that could facilitate reaction. In this talk, I will discuss some of the ways in which vibrational
relaxation controls the kinetics of simple chemical reactions, and how quantum effects, in particular localization of vibrational states, control vibrational
relaxation in molecules and can give rise to long-lived, low-frequency oscillations during photochemical reactions of large molecules.
The first part of the talk will provide background on connections between kinetics of conformational isomerization and vibrational relaxation in molecules.
We shall review simple quantum mechanical models for vibrational energy flow in large molecules that yield criteria for localization of vibrational states,
which is analogous to Anderson localization in disordered solid state systems. The effects of localization in vibrational state space, which persist when
accounting for coupling to the environment, can severely limit vibrational energy relaxation in large molecules and influence reaction kinetics.
In the second part of the talk we turn to specific examples. I will discuss calculation of lifetimes of vibrational modes of proteins, then address the
relatively long lifetimes of low-frequency chromophore modes, including the chromophore of green fluorescent protein and retinal, the chromophore of
rhodopsin, as examples. Finally, we look beyond effects of vibrational energy relaxation on conformational transitions between two structures and
examine how conformational dynamics on an energy landscape is influenced by vibrational energy flow.
3/07/12 4:00pm
MIT Building 4, Room 231
Jack Simons
Understanding the molecule-plasmon coupling
3/21/12 4:00pm
MIT Building 4, Room 231
Lasse Jensen
Controlling the optical behavior of molecules near the vicinity of noble metal nanoparticles continues to be an active research area in nanoscience.
A molecular level understanding of the optical properties of such metal-molecule complexes is important for many applications such as energy harvesting,
nanoscale optical circuits, and ultra-sensitive chemical and biological sensors. In this talk we will discuss our recent theoretical studies aimed at
understanding the coupling between molecules and plasmons. We will show how electrodynamics simulations can be used to describe the optical properties
of mixed exciton-plasmon states arising when strongly absorbing dyes interacts with plasmons. Electronic structure methods will be used to explore the
chemical coupling in surface-enhanced Raman scattering (SERS), and resonance effects in SERS and surface-enhanced hyper-Raman scattering.
The diverse physical consequences of interfacial fluctuations: From Hofmeister effects to the self-assembly of passivated nanocrystals
4/04/12 4:00pm
MIT Building 4, Room 231
Phill Geissler
At molecular scales, liquid interfaces feature strong and inhomogeneous fluctuations: in density, in surface topography, and, in the case of polar liquids,
electric field. Interplay among them can lead to surprising and rich behavior quite distinct from corresponding well-understood phenomena in bulk solution.
For example, many computer simulations and experiments suggest that certain small ions can strongly adsorb to the air-water interface, contrary to expectations
from successful theories of bulk solvation. I will present detailed evidence that capillary waves and inhomogeneous density fluctuations play a significant role
in driving this behavior. As a second example, I will discuss the effective interactions among inorganic nanorods in solution. Here, ordering of passivating ligands
on the rods' surface, together with induced layering of solvent density at the liquid-rod interface, mediates a strong and unexpected attraction between rods that
could not be anticipated from traditional continuum theories.
Quantum Coherence and Incoherence in Molecular Dynamics and Control
4/18/12 4:00pm
MIT Building 4, Room 231
Paul Brumer
An essential feature of quantum mechanics is interference resulting from
multiple pathways to the same final state. Loss of this coherence
(i.e. decoherence) can lead to classical-like behavior. I will review the
nature of this interference, the origins of decoherence, and the role of perturbations,
such as lasers, in creating quantum coherence in molecules. Examples of
the role of coherence in controlling molecular processes (such as
internal conversion and chemical reactions) will be described. The
role (?) of quantum coherence in natural biological processes will be
discussed, both in models of retinal isomerization and light harvesting
systems. Time permitting I will introduce a general scheme for assessing
when a given external perturbation creates quantum interference in a
molecular system upon which it acts.
Continuum Models for Biomembrane Dynamics
4/25/12 3:30pm
MIT Building 3, Room 442
Frank Brown
Simulation of biomembranes and lipid bilayers over length and time scales relevant to cellular biology is not currently feasible with Molecular Dynamics
or similarly detailed methods. Barring an unforeseen revolution in the computer industry, this situation will not soon change. Two aspects of mesoscopic
membrane dynamics will be discussed: in-plane flow/diffusion in inhomogeneous membrane systems and out-of-plane membrane undulations. Both problems are
treated within the context of stochastic continuum models, which allow thermodynamically and hydrodynamically consistent access to length and time scales
up to and beyond the micron and second regimes, using simple numerical methods. Applications to phase separation kinetics and domain boundary fluctuations
in ternary “model membrane” systems, membrane shape fluctuations above a solid supporting matrix and diffusion of curved membrane proteins will be discussed.
Toward Arrays of Coupled Dipolar Molecular Rotors
5/09/12 4:00pm
MIT Building 4, Room 231
Josef Michl
The presentation describes the synthesis and study of
non-interacting surface-mounted molecular rotors and efforts directed toward
a fabrication of ordered arrays of such rotors. The goal is to achieve rotor
dipole-dipole interactions strong enough and rotational barriers small
enough for the ground state to be ferroelectric.
A Survey of Electronic Structure and Quantum Embedding Theories
5/16/12 4:00pm
MIT Building 4, Room 231
Garnet Chan
In this first talk, I will classify and discuss electronic structure
methods from a top-down perspective in terms of both the quantum
variable formulation (wavefunctions, density matrices, Green's
functions and densities), as well as from the viewpoint of
phenomenology (types of chemistry, correlations, and phases). If there
time and interest, I may also give a survey of low-entanglement
approaches and tensor networks.
In this second talk, I will focus on the question: how can we describe
the correlated electronic structure of an infinite i.e. condensed
phase system? I will show how quantum embedding theories provide a way
forward, and discuss in particular the density matrix embedding theory
we have recently proposed (arXiv:1204.5783). I will also spend time
introducing lattice Hamiltonians and some of the interesting
phenomenology.
The Physical Properties of Cells Are Encoded In Their Proteomes
5/23/12 4:00pm
MIT Building 4, Room 231
Ken Dill
Protein molecules make up most of the biomass of a cell. So,
cell physics is a strong reflection of protein physics. We look at three
examples. First, we seek an explanation in protein physics for why cells
are so sensitive to temperature. Second, we seek an explanation for why
cells are so densely packed with proteins. Third, we seek an explanation
for the time scales of prokaryotes: why do cells replicate in minutes rather
than seconds or years, for example?
In the first part of this talk, I will give a little background on the
physics of protein folding. Also, because a big part of protein physics is
the physics of solvation in water, I will also discuss new theory and
simulations to understand water as a solvent, for nonpolar, polar and ionic
solutes.
Past Schedules