Quantum-Chemical Electron Densities of Proteins and of Selected Protein Sites from Subsystem Density Functional Theory

The ability to calculate accurate electron densities of full proteins or of selected sites in proteins is a prerequisite for a fully quantum-mechanical calculation of protein-protein and protein-ligand interaction energies. Quantum-chemical subsystem methods capable of treating proteins and other biomolecular systems provide a route to calculate the electron densities of proteins efficiently and further make it possible to focus on specific parts. Here, we evaluate and extend the 3-partition frozen-density embedding (3-FDE) scheme [Jacob, C. R.; Visscher, L. J. Chem. Phys.2008, 128, 155102] for this purpose. In particular, we have extended this scheme to allow for the treatment of disulfide bridges and charged amino acid residues and have introduced the possibility to employ more general partitioning schemes. These extensions are tested both for the prediction of full protein electron densities and for focusing on the electron densities of a selected protein site. Our results demonstrate that 3-FDE is a promising tool for the fully quantum-chemical treatment of proteins. © 2013 American Chemical Society

A Comparison Between QM/MM And QM/QM Based Fitting of Condensed-Phase Atomic Polarizabilities

Recently we reported a combined QM/MM approach to estimate condensed-phase values of atomic polarizabilities for use in (bio)molecular simulation. The setup relies on a MM treatment of the solvent when determining atomic polarizabilities to describe the response of a QM described solute to its external electric field. In this work, we study the effect of using alternative descriptions of the solvent molecules when evaluating atomic polarizabilities of a methanol solute. In a first step, we show that solute polarizabilities are not significantly affected upon substantially increasing the MM dipole moments towards values that are typically reported in literature for water solvent molecules. Subsequently, solute polarization is evaluated in the presence of a QM described solvent (using the frozen-density embedding method). In the latter case, lower oxygen polarizabilities were obtained than when using MM point charges to describe the solvent, due to introduction of Pauli-repulsion effects. This journal is © the Partner Organisations 2014

PyADF - A scripting framework for multiscale quantum chemistry

Applications of quantum chemistry have evolved from single or a few calculations to more complicated workflows, in which a series of interrelated computational tasks is performed. In particular multiscale simulations, which combine different levels of accuracy, typically require a large number of individual calculations that depend on each other. Consequently, there is a need to automate such workflows. For this purpose we have developed PYADF, a scripting framework for quantum chemistry. PYADF handles all steps necessary in a typical workflow in quantum chemistry and is easily extensible due to its object-oriented implementation in the Python programming language. We give an overview of the capabilities of PYADF and illustrate its usefulness in quantum-chemical multiscale simulations with a number of examples taken from recent applications. © 2011 Wiley Periodicals, Inc

Abgangschancen aus der Arbeitslosigkeit: e. Kombination von Bestands- u. Bewegungsdaten

Summary in EnglishAvailable from Bibliothek des Instituts fuer Weltwirtschaft, ZBW, Duesternbrook Weg 120, D-24105 Kiel C 140876 / FIZ - Fachinformationszzentrum Karlsruhe / TIB - Technische InformationsbibliothekSIGLEDEGerman

Investigation of the resonance Raman spectra and excitation profiles of a monometallic ruthenium(II) [Ru(bpy)2(HAT)]2+ complex by time-dependent density functional theory.

The resonance Raman (RR) properties of the [Ru(bpy)(2)(HAT)](2+) (where bpy = 2,2'-bipyridine and HAT = 1,4,5,8,9,12-hexaazatriphenylene) complex have been investigated by means of time-dependent density functional theory calculations employing the hybrid B3LYP-35 XC functional and by including the effects of the solvent within the polarizable continuum model approach. Analysis of the electronic excited-state energies has demonstrated that mainly four different metal-to-ligand charge-transfer excitations contribute to the first absorption band in vacuo and water. The simulation of the absorption spectra by including the vibronic structure of the states has shown a general agreement with the experimental spectrum recorded in water. Furthermore, significant variations of the excited-state energies and compositions have been found when the effects of the solvent are included. Calculation of the short-time-approximation RR spectra has provided the vibrational signature of each contributing state and has shown that considering only one excited state is not sufficient to accurately simulate the RR spectra for excitation frequencies in resonance with the first absorption band. A comparison of the RR spectra calculated using the vibronic theory for different excitation wavelengths with the measured spectra at 514 and 458 nm has demonstrated that inclusion of the solvent effects in the simulation scheme leads to substantial improvements of the RR intensity patterns, which allow assignment of the vibrational bands. In particular, the calculations are able to reproduce the variations of the HAT and bpy RR intensities as illustrated by their RR excitation profiles, highlighting the strong dependence of the RR intensities with respect to the excitation frequency.Journal Articleinfo:eu-repo/semantics/publishe

Effective Time-Independent Calculations of Vibrational Resonance Raman Spectra of Isolated and Solvated Molecules Including Duschinsky and Herzberg-Teller Effects

We present a method of modeling vibrational resonance Raman scattering (RRS) spectra of isolated and solvated systems with the inclusion of FranckCondon (FC) and HerzbergTeller (HT) effects and a full account for possible differences between the harmonic potential energy surfaces of the initial and resonant electronic states. It describes fundamentals, overtones, and combination bands and computes the RRS spectrum as a two-dimensional function of the incident and scattered frequencies. The theoretical foundations of the method are described and the differences with other currently available methodologies are outlined. Applications to the phenoxyl radical in the gas phase and indolinedimethine malononitrile (IDMN) in acetonitrile and cyclohexane solution are reported, as well as comparisons with available experimental data