August 30

Site-Directed Spin Labeling Studies of the GM2 Activator Protein: A comparison of X-ray Structure and EPR Data
Luis Galiano, Department of Chemistry, University of Florida (galiano@qtp.ufl.edu)

The GM2 activator protein (GM2AP) is an essential component in the degradation pathway of neuronal gangliosides in lysosomal compartments of the central nervous system. GM2AP is a required co-factor for the hydrolytic conversion of GM2 to GM3 by the water soluble enzyme (beta)-N-acetylhexoaminidase A (HexA). Here, site-directed spin labeling (SDSL) with EPR spectroscopy were undertaken to probe protein conformation and dynamics at selected sites and to determine the membrane bound conformation of GM2AP on lipid vesicles. We also compare mobilities determined from simulated lineshapes to the crystal structure models. Our results also show evidence for a ligand specific aggregation/oligomerization.

Conformational Sampling and Folding in polyalanine peptides
Seonah Kim, Department of Chemistry, University of Florida (kim@qtp.ufl.edu)

Density Matrix Treatment of the Non-Markovian Dissipative Dynamics of Adsorbates on Metal Surfaces
Andrew Leathers, Department of Chemistry, University of Florida (leathers@qtp.ufl.edu)

A general density matrix treatment is presented for the vibrational relaxation of the frustrated translational mode of a molecule adsorbed on a metal surface. The system is modeled as a harmonic oscillator coupled to a bath of harmonic oscillators. The integrodifferential equations for time evolution of the density matrix including a (non-Markovian) delayed dissipation are solved using a generalized Runge-Kutta scheme. The equations are also solved in the instantaneous dissipation and the Markov limits. Numerical results are presented for Na/Cu, CO/Cu, and CO/Pt systems. The population of an initially excited state is given over time for varying temperatures. It shows that memory effects are needed in a proper description. We also investigate the effect on

populations of different coupling strengths between adsorbate species and the substrate metal surface, which show that weaker couplings lead to increased oscillations and longer relaxation times. The time evolution of quantum coherence is also described.

Frozen Natural Orbital Coupled-Cluster: Energies and Gradients
Andrew G. Taube, Department of Chemistry, University of Florida (taube@qtp.ufl.edu)

To overcome the undesirable scaling of coupled cluster theory with increasing basis sets, a new method of basis set truncation is developed, implemented and evaluated.  Truncating the exact natural orbitals (eigenfunctions of the one-particle reduced density matrix) best approximates the expectation value of a bounded operator.  Because the determination of the exact natural orbitals requires the solution of the Full Configuration Interaction problem, approximate natural orbitals are constructed.   The virtual-virtual block of the MBPT(2) density matrix is diagnolized yielding the so-called "Frozen Natural Orbitals."  The least occupied of these orbitals are removed, and the Hartree-Fock solution is constructed in the truncated space.  A coupled cluster calculation is then performed based on this reference function.

The formulation and implementation of the frozen natural orbital coupled-cluster method for both energies and gradients for RHF, UHF, and ROHF reference functions is reported.  Results for a series of small diatomic and triatomic test molecules were performed, verifying the quality of this truncation.  Truncation of 60% of the virtual space recovered greater than 90% of the correlation energy of the full basis set for CCSD and CCSD(T) calculations.  The dependence of the truncated results on geometry and different starting basis sets was also determined.  Geometry optimizations using the frozen natural orbitals have also been performed, utilizing the full relaxation of the FNOs.  Test systems show that the FNO approximation for gradients is successful at reproducing equilibrium geometries and potential energy curves.  Calculations of systems of chemical interest, such as RDX, at the CCSD(T) level are reported as well; calculations that would have been computationally unapproachable without basis set truncation.

Blends of a Polystyrene-block-Poly(ethylene oxide) Copolymer and its Corresponding Homopolymers at the Air-Water Interface
Sophie Bernard, Department of Chemistry, University of Florida (bernards@ufl.edu)

The two-dimensional structure of a polystyrene-block-poly(ethylene oxide) (PS-b-PEO) diblock copolymer at the air-water interface, was studied using Langmuir-Blodgett methods and atomic force microscopy (AFM). Measurements were also made for blends of the PS-b-PEO copolymer with both a PS and a PEO homopolymer. When increasing the amount of PS homopolymer, the isotherms did not show any change in the high surface area region. However, a linear dependence of the condensed area was observed. An increase in the PEO ratio proved to affect the biphasic region of the isotherms but no change was detected for the condensed area. Each of these blends was subsequently studied by AFM. The data indicated a significant effect of the homopolymers on the monolayer structure. In fact depending on the homopolymer added, a change in the chaining behavior of the copolymer was observed. Also, when introducing more PEO, a phase separation between the layer of PEO and clusters of two-dimensional micelles was detected.

Energy Transfer in Extended Systems
Jeff Krause, Department of Chemistry, University of Florida (krause@qtp.ufl.edu)

We present a theoretical analysis of the dynamics of energy transfer in dendrimers. In one example, energy transfer occurs between donor groups on the periphery of the molecule and an acceptor group in the core. Detailed structural studies show that comparatively rare events, in which the peripheral groups wrap to the core, dominate the energy transfer rates. Coarse-grained models, in which the rates are expressed in terms of an average rate constant, fail to capture the relevant dynamics.  In a second example, energy transfer occurs via a series of independent steps down an energy gradient. We find that the venerable Forster model, which describes the Coulombic interaction in terms of point dipoles, is inadequate to determine the transfer rates. Extensions of the methods to study single-molecule spectroscopy of polypeptides and DNA are discussed.  In particular, we find that a well-known "molecular ruler" must be recalibrated.

September 27

Sandra Rosenthall, Department of Chemistry, Vanderbilt University
(sjr@femto.cas.vanderbilt.edu)

Energy landscapes from pi-stacking to bond-breaking
C. David Sherrill, Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology (sherrill@chemistry.gatech.edu)
http://www.chemistry.gatech.edu/faculty/sherrill/

Weak interactions, such as the noncovalent interactions governing drug binding and the structures of organic crystals, are very challenging to understand.  Experimentally, these interactions are often seen in complex environments, where it can be difficult to pick out only the interaction of interest.  Theoretically, they feature shallow potential energy surfaces and require very accurate quantum-mechanical modeling for reliable results. Definitive theoretical investigations of pi-pi, alkyl-pi, and sulfur-pi interactions which elucidate the strength, geometrical preferences, and fundamental nature of these prototype biomolecular interactions will be presented.  In particular, it is shown that the current paradigm for understanding pi-pi interactions, which emphasizes electrostatic interactions, fails qualitatively. Better models developed on the basis of high-quality quantum mechanical benchmarks will aid in rational design of drugs and supramolecular architectures. Complementary challenges for intermediate bonding regimes (e.g., lithium clusters) and strong bonding (reactions breaking covalent bonds) will also be briefly discussed.

The Xe chemical shift in channels, cages, and other nanopores
Cynthia Jameson, Department of Chemistry, University of Illinois at Chicago (cjjames@uic.edu)

The Xe intermolecular chemical shift is exquisitely sensitive to the nature of the environment of the Xe atom. This sensitivity permits the Xe nucleus to report on a wide variety of attributes of the physical system in which the Xe atom finds itself. An understanding of the intermolecular Xe chemical shift at a fundamental level enhances our ability to elicit the desired detailed information about the physical system (a liquid, a cage in solution or in a solid, a nanochannel in a molecular crystal, a protein in solution, a chemisorbed over-layer on a single crystal surface, an amorphous polymer, etc.).

We will present some examples of our recent efforts toward this understanding. When the Xe shielding response as a function of configuration and the distribution of configurations, as determined by the potential energy of intermolecular interactions, are taken together in an appropriate averaging process in an assumed model of the real physical system, the predicted results may be tested against experimental observations. Structural as well as dynamic information may be obtained.

Tim Keiderling, Department of Chemistry, University of Illinois at Chicago (tak@uic.edu)

Molecular negative ions are of great technological importance. However, studies of their formation and structure have represented a formidable challenge to both theory and experiment. A proper description of a molecular negative ion must take into account all of the available electronic and ro-vibrational interactions. Nevertheless, in some cases it is possible to consider only the long-range electron molecule interactions in order to obtain a meaningful description of the anion. For example, many polar molecules can bind an excess electron into a very diffuse negative ion state due primarily to the dipole moment of the molecule. A plot of the electron affinities for over fifty dipole-bound anions suggests a minimum dipole moment of ~ 2.5 Debye to bind an excess electron. This agrees with general theoretical estimates of the “minimum” dipole moment required to bind an electron to a polar molecule. There is recent interest in quadrupole-bound anions. For example, we have shown that the succinonitrile molecule can support both a dipole-bound anion in its gauche form (EA ~ 108 meV) and a quadrupole-bound anion in its trans form (EA ~ 20 meV)[ PRL, 92, 83003]. The concept of electron-molecule multipole expansion is especially useful in the description of multiply-charged negative ions. The combined monopole (Coulomb repulsion) and polarizability attraction of an electron with a molecular negative ion gives rise to a “Coulomb barrier” for the addition or removal of the extra electron. This simple picture qualitatively explains many of the prominent features of multiply charged anions. Multiply-charged negative ions have been widely studied within the past fifteen years. We have recently focused upon the mechanisms for their formation, e.g., electron attachment and charge exchange. This talk will discuss some of these results with particular emphasis on the important role of theory in the field of multi-pole bound anions.

Raphael Bruschweiler, Department of Chemistry and Biochemistry, Florida State University (bruschweiler@magnet.fsu.edu)

Alex Angerhofer, Department of Chemistry, University of Florida (alex@chem.ufl.edu)