Probe mapping is a common approach for identifying potential binding sites in structure-based drug design; however, it typically relies on energy minimizations of probes in the gas phase and a static protein structure. The mixed-solvent molecular dynamics (MixMD) approach was recently developed to account for full protein flexibility and solvation effects in hot-spot mapping. Our first study us...

The laser excited, jet-cooled Ã2E′′ − X̃2E′ electronic spectrum of the silver trimer yields detailed information about its Ãand X̃-state vibronic structure. Following extensive parameter fitting, the absorption and emission spectra are simulated and the bands are assigned. The JahnTeller analysis includes both linear and quadratic coupling terms, considered simultaneously with spin-orbit coupling...

We perform systematical studies on transverse-mass spectra of π 0 , η, ω, φ, K + and K − mesons for C + C, Ni + Ni, Au + Au collisions at SIS energies within the HSD transport approach. We find that the m T-spectra sensitively reflect the in-medium properties of the mesons. The 'bare mass' scenario leads to a general scaling behaviour for the meson m T-spectra when including a mass shift due to...

Previous results from deep-sea pore fluid data demonstrate that the glacial deep ocean was filled with salty, cold water from the South. This salinity stratification of the ocean allows for the possible accumulation of geothermal heat in the deep-sea and could result in a water column with cold fresh water on top of warm salty water and with a corresponding increase in potential energy. For an ...

The dynamics of bimolecular chemical reactions can be examined in liquid solutions using infrared absorption spectroscopy with picosecond time resolution. On such short time scales, the transient absorption spectra reveal vibrational mode and quantum-state-specific energy disposal, followed by vibrational relaxation as the energy is dissipated to the surrounding solvent. Comparison with energy ...

Protein solubility and conformational stability are a result of a balance of interactions both within a protein and between protein and solvent. The electrostatic solvation free energy of oligoglycines, models for the peptide backbone, becomes more favorable with an increasing length, yet longer peptides collapse due to the formation of favorable intrapeptide interactions between CO dipoles, in...

Solvation is of fundamental importance to biomolecular systems. Implicit solvent models, particularly those based on the Poisson-Boltzmann equation for electrostatic analysis, are established approaches for solvation analysis. However, ad hoc solvent-solute interfaces are commonly used in the implicit solvent theory. Recently, we have introduced differential geometry based solvation models whic...

The solvation energy and entropy at infinite dilution consist of a solute-solvent term and a solvent reorganization term representing the contributions of changes in solvent structure upon solute insertion. In the standard, homogeneous treatment of solutions, changes in solvent structure are expressed through derivatives of the homogeneous pair correlation function, which are very difficult to ...

We explore solvent dynamics effects in interfacial bond breaking electron transfer in terms of a multimode approach and make an attempt to interpret challenging recent experimental results (the nonmonotonous behavior of the rate constant of electroreduction of S2O8(2-) from mixed water-EG solutions when increasing the EG fraction; see Zagrebin, P.A. et al. J. Phys. Chem. B 2010, 114, 311). The ...

Solvation is an elementary process in nature and is of paramount importance to more sophisticated chemical, biological and biomolecular processes. The understanding of solvation is an essential prerequisite for the quantitative description and analysis of biomolecular systems. This work presents a Lagrangian formulation of our differential geometry based solvation models. The Lagrangian represe...