Solvation Dynamics of a Single Water Molecule Probed by Infrared Spectra—Theory Meets Experiment

The dynamics and energetics of water at interfaces or in biological systems plays a fundamental role in all solvation and biological phenomena in aqueous solution. In particular, the migration of water molecules is the first step that controls the overall process in the time domain. Experimentally, the dynamics of individual water molecules is nearly impossible to follow in solution, because signals from molecules in heterogeneous environments overlap. Although molecular dynamics simulations do not have this restriction, there is a lack of experimental data to validate the calculated dynamics. Here, we demonstrate a new strategy, in which the calculated dynamics are verified by measured time‐resolved infrared spectra. The coexistence of fast and slow migrations of water molecules around a CONH peptide linkage is revealed for a model system representative of a hydrate peptide.     

Understanding Reaction Dynamics in Coordination Chemistry—Application of High Pressure Techniques

In order to understand the dynamics of chemical reactions in general, detailed information on electronic, structural and kinetic properties is required. The key questions on how chemical reactions actually occur can in many cases only be answered in terms of information obtained from kinetic studies. In conventional kinetic studies of chemical reactions in solution, the variables usually selected include concentration, acidity, solvent, and temperature. In recent years, pressure has become an additional selected variable in such studies. It enables the measurement of the volume of activation and the construction of reaction volume profiles and thus assists in the elucidation of the underlying mechanism; it also completes the comprehension of reaction kinetics by adding another kinetic parameter that the suggested reaction mechanism must account for. Furthermore, the volume of activation is the only transition state property that can be correlated with the corresponding ground state property in an experimentally simple manner. In this paper, the insights so gained in our understanding of the dynamics of reactions involving coordination complexes will be presented. Such reactions are of fundamental interest to chemists since they often form the basis of catalytic, biological, environmental and energy related processes. Any additional information that will add to the understanding of the reaction dynamics is therefore of exceptional importance.     

RedMD—Reduced molecular dynamics package

We developed a software package (RedMD) to perform molecular dynamics simulations and normal mode analysis of reduced models of proteins, nucleic acids, and their complexes. With RedMD one can perform molecular dynamics simulations in a microcanonical ensemble, with Berendsen and Langevin thermostats, and with Brownian dynamics. We provide force field and topology generators which are based on the one‐bead per residue/nucleotide elastic network model and its extensions. The user can change the force field parameters with the command line options that are passed to generators. Also, the generators can be modified, for example, to add new potential energy functions. Normal mode analysis tool is available for elastic or anisotropic network models. The program is written in C and C++ languages and the structure/topology of a molecule is based on an XML format. OpenMP technology for shared‐memory architectures was used for code parallelization. The code is distributed under GNU public licence and available at http://bionano.icm.edu.pl/software/ . © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

PEPCAT—A new tool for conformational analysis of peptides

We report a new technique for the efficient analysis and visualization of peptide and protein conformations and conformational relationships, which we have implemented in a computer program called PEPCAT. PEPCAT (an abbreviation for Peptide Conformational Analysis Tool) provides a simple, graphical, and flexible framework that allows the user to define a specific structural feature or juxtaposition of amino acids and to follow the fate of the motif during a molecular dynamics simulation. Here we describe the PEPCAT analysis of the effects of environmental and chemical modifications on conformational preferences of a regulator of hemopoiesis, namely the pentapeptide pyro‐EEDCK, and of a conformational transition in the immunosuppressant drug cyclosporin A. PEPCAT, however, can be applied to the conformational analysis of peptides and proteins in general. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 446–461, 2000     

Topotecan dynamics,tautomerism and reactivity—1H/13C NMR and ESI MS study

Topotecan (TPT) is in clinical use as an antitumor agent, hycamtin^?. Because of this, it requires both biologically and chemically useful information to be available. TPT acts by binding to the covalent complex formed by nicked DNA and topoisomerase I. This has a poisonous effect since inserted into the single‐strand nick and TPT inhibits its religation. We used NMR to trace TPT dynamics, tautomerism and solvolysis products in various solvents and conditions. Chemical stability was assessed in methanol and DMSO as compared to water, and the regioselectivity of the N‐ and O‐methylation was studied using various alkylating agents. The reaction products of quaternization of the nitrogen atom and methylation of the oxygen atom were characterized by means of ESI MS, ¹H/¹³C‐HMBC and ‐HSQCAD NMR. We have focused on the NMR characterization of TPT with an anticipation that its aggregation, tumbling properties and the intramolecular dipolar interactions will be a common feature for other compounds described in this article. These features can also be useful in tracing the interactions of this class of topoisomerase I (TopoI) poisons with DNA. Moreover, the results explained shed light on the recently disclosed problem of lack of stability of TPT in the heart tissue homogenate samples using the analytical assays developed for this class of compounds carried out in the presence of methanol. Copyright © 2010 John Wiley & Sons, Ltd.     

Solvent‐driven symmetry of self‐assembled nanocrystal superlattices—A computational study

The preference of experimentally realistic sized 4‐nm facetted nanocrystals (NCs), emulating Pb chalcogenide quantum dots, to spontaneously choose a crystal habit for NC superlattices (Face Centered Cubic (FCC) vs. Body Centered Cubic (BCC)) is investigated using molecular simulation approaches. Molecular dynamics simulations, using united atom force fields, are conducted to simulate systems comprised of cube‐octahedral‐shaped NCs covered by alkyl ligands, in the absence and presence of experimentally used solvents, toluene and hexane. System sizes in the 400,000–500,000‐atom scale followed for nanoseconds are required for this computationally intensive study. The key questions addressed here concern the thermodynamic stability of the superlattice and its preference of symmetry, as we vary the ligand length of the chains, from 9 to 24 ? CH₂ groups, and the choice of solvent. We find that hexane and toluene are “good” solvents for the NCs, which penetrate the ligand corona all the way to the NC surfaces. We determine the free energy difference between FCC and BCC NC superlattice symmetries to determine the system's preference for either geometry, as the ratio of the length of the ligand to the diameter of the NC is varied. We explain these preferences in terms of different mechanisms in play, whose relative strength determines the overall choice of geometry. © 2012 Wiley Periodicals, Inc.