Performance Analysis, PVM and MPI Implementation of a DSCF Hartree Fock Program

A new Direct SCF-Hartree Fock program (DSCF) has been improved by the method of DIIS. (17), (18) General performance measurement tools, as provided on the SGIPower Challenge/R10000 (194 MHz) running IRIX 6.2, which are the shell-commands perfex -a a.out and ssrun -(pcsampl, ideal, usertime) a.out, have been used for profiling the code. The main cpu-time-consuming subroutine was detected and parallel versions for PVM 3.3 as well as MPI have been deduced. An additional module for the purpose of achieving load-balancewas introduced and obtained speed-up parameters are presented and compared

Langevin behavior of the dielectric decrement in ionic liquid water mixtures

We present large scale polarizable simulations of mixtures of the ionic liquids 1-ethyl-3-methylimidazolium trifluoromethanesulfonate and 1-ethyl-3-methylimidazolium dicyanamide with water, where the dielectric spectra, the ion hydration and the conductivity were evaluated. The dielectric decrement, the depression of the dielectric constant of water upon addition of ions, is found to follow a universal functional of Langevin type. Only three physical properties need to be known to describe the complete range of possible concentrations, namely the dielectric constant of pure water, of pure ionic liquid and the linear slope of the dielectric decrement at low ionic liquid concentrations. Both the generalized dielectric constant, as well as the water contribution to the dielectric permittivity follow the functional dependence. We furthermore find that a scaling of van der Waals parameters upon addition of polarizable forces to the force field is necessary to correctly describe the frequency dependent dielectric conductivity and its contribution to the dielectric spectrum, as well as the static electric conductivity, which is also treated in the framework of a pseudolattice theoryThis work was funded by the Austrian Science Fund FWF in the context of Project No. P23494 and by the Cost Action CM 1206: “Exchange on ionic liquids”. Funding from Spanish Ministry of Economy and Competitiveness (Projects MAT2014-57943-C3-1-P and MAT2017-89239-C2-1-P) is gratefully acknowledged. Moreover, this work was funded by the Xunta de Galicia (AGRUP2015/11 and GRC ED431C 2016/001). E. H. is recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Computational Biological ChemistryS

[6] Rapid Assessment of Protein Structural Stability and Fold Validation via NMR

Abstract In structural proteomics, it is necessary to efficiently screen in a highthroughput manner for the presence of stable structures in proteins that can be subjected to subsequent structure determination by X-ray or NMR spectroscopy. Here we illustrate that the 1 H chemical distribution in a protein as detected by 1 H NMR spectroscopy can be used to probe protein structural stability (e.g., the presence of stable protein structures) of proteins in solution. Based on experimental data obtained on well-structured proteins and proteins that exist in a molten globule state or a partially folded -helical state, a well-defined threshold exists that can be used as a quantitative benchmark for protein structural stability (e.g., foldedness) in solution. Additionally, in this chapter we describe a largely automated strategy for rapid fold validation and structure-based backbone signal assignment. Our methodology is based on a limited number of NMR experiments (e.g., HNCA and 3D NOESY-HSQC) and performs a Monte Carlo-type optimization. The novel feature of the method is the opportunity to screen for structural fragments (e.g., template scanning). The performance of this new validation tool is demonstrated with applications to a diverse set of proteins

Hydrated Ionic Liquids with and without Solute: The Influence of Water Content and Protein Solutes

In this computational study, the network of 1-ethyl-3-methylimidazolium trifluoromethanesulfonate/water mixtures is analyzed in the presence (and absence) of the protein ubiquitin and a zinc finger motif. Thereby, common radial distribution functions are decomposed into contributions from different Voronoi shells, and the mutual orientation of cations, anions, and water in the bulk phase as a function of the water mole fraction is discussed. Single particle translation and the reorientation of the dipolar axis seem to follow hydrodynamic relations. Using the body-fixed frame as an alternative reference system, translation and rotation can be decomposed into contributions along and about the axes of a well-defined orthogonal trihedron, thus elucidating the principal motions of the cations and anions as a function of the water mole fraction. The structural dipolar orientation may be correlated with single particle dynamics and can be characterized by the static collective Kirkwood order parameter

Revival of the Intermolecular Nuclear Overhauser Effect for Mapping Local Protein Hydration Dynamics

The highly heterogeneous hydration dynamics of protein–water interfaces is considered important for protein stability and dynamics, protein folding, enzymatic activity, and even drug design. The nuclear Overhauser effect (NOE) between protein and water protons is the only experimental observable which, in principle, can provide a map of locally resolved hydration dynamics. However, its utility was questioned in various theoretical studies that emphasized the contributions of long-range NOE interactions. We show by a detailed analysis based on molecular dynamics simulations that, contrary to recent claims, the protein–water NOE is an excellent observable to map local hydration dynamics at the protein surface

The Intermolecular NOE Depends on Isotope Selection: Short Range vs Long Range Behavior

The nuclear Overhauser effect (NOE) is a powerful tool in molecular structure elucidation, combining the subtle chemical shift of NMR and three-dimensional information independent of chemical connectivity. Its usage for intermolecular studies, however, is fundamentally limited by an unspecific longranged interaction behavior. This joint experimental and computational work shows that proper selection of interacting isotopes can overcome these limitations: Isotopes with strongly differing gyromagnetic ratios give rise to short-ranged intermolecular NOEs. In this light, existing NOE experiments need to be reevaluated and future ones can be designed accordingly. Thus, a new chapter on intermolecular structure elucidation is opened