XPS of oxygen atoms on Ag(111) and Ag(110) surfaces: Accurate study with SAC/SAC‐CI combined with dipped adcluster model

O1s core‐electron binding energies (CEBE) of the atomic oxygens on different Ag surfaces were investigated by the symmetry adapted cluster‐configuration interaction (SAC‐CI) method combined with the dipped adcluster model, in which the electron exchange between bulk metal and adsorbate is taken into account properly. Electrophilic and nucleophilic oxygens (O_elec and O_nuc) that might be important for olefin epoxidation in a low‐oxygen coverage condition were focused here. We consider the O1s CEBE as a key property to distinguish the surface oxygen states, and series of calculation was carried out by the Hartree–Fock, Density functional theory, and SAC/SAC‐CI methods. The experimental information and our SAC/SAC‐CI results indicate that O_elec is the atomic oxygen adsorbed on the fcc site of Ag(111) and that O_nuc is the one on the reconstructed added‐row site of Ag(110) and that one‐ and two‐electron transfers occur, respectively, to the O_elec and O_nuc adclusters from the silver surface. © 2013 Wiley Periodicals, Inc.     

CHARMM36 all‐atom additive protein force field: Validation based on comparison to NMR data

Protein structure and dynamics can be characterized on the atomistic level with both nuclear magnetic resonance (NMR) experiments and molecular dynamics (MD) simulations. Here, we quantify the ability of the recently presented CHARMM36 (C36) force field (FF) to reproduce various NMR observables using MD simulations. The studied NMR properties include backbone scalar couplings across hydrogen bonds, residual dipolar couplings (RDCs) and relaxation order parameter, as well as scalar couplings, RDCs, and order parameters for side‐chain amino‐ and methyl‐containing groups. It is shown that the C36 FF leads to better correlation with experimental data compared to the CHARMM22/CMAP FF and suggest using C36 in protein simulations. Although both CHARMM FFs contains the same nonbond parameters, our results show how the changes in the internal parameters associated with the peptide backbone via CMAP and the χ₁ and χ₂ dihedral parameters leads to improved treatment of the analyzed nonbond interactions. This highlights the importance of proper treatment of the internal covalent components in modeling nonbond interactions with molecular mechanics FFs. © 2013 Wiley Periodicals, Inc.     

Computational gibberellin‐binding channel discovery unraveling the unexpected perception mechanism of hormone signal by gibberellin receptor

Gibberellins (GAs) are phytohormones essential for many developmental processes in plants. In this work, fundamental mechanism of hormone perception by receptor GID1 has been studied by performing computational simulations, revealing a new GA‐binding channel of GID1 and a novel hormone perception mechanism involving only one conformational state of GID1. The novel hormone perception mechanism demonstrated here is remarkably different from the previously proposed/speculated mechanism [Murase et al., Nature 2008 , 456, 459] involving two conformational states (“OPEN” and “CLOSED”) of GID1. According to the new perception mechanism, GA acts as a “conformational stabilizer,” rather than the previously speculated “allosteric inducer,” to induce the recognition of protein DELLA by GID1. The novel mechanistic insights obtained in this study provide a new starting point for further studies on the detailed molecular mechanisms of GID1 interacting with DELLA and various hormones and for mechanism‐based rational design of novel, potent growth regulators that target crops and ornamental plants. © 2013 Wiley Periodicals, Inc.     

New basis sets for the evaluation of interaction‐induced electric properties in hydrogen‐bonded complexes

Interaction‐induced static electric properties, that is, dipole moment, polarizability, and first hyperpolarizability, of the CO? (HF)_n and N₂? (HF)_n, n = 1–9 hydrogen‐bonded complexes are evaluated within the finite field approach using the Hartree–Fock, density functional theory, Møller–Plesset second‐order perturbation theory, and coupled cluster methods, and the LPol‐n (n = ds, dl, fs, fl) basis sets. To compare the performance of the different methods with respect to the increase of the complex size, we consider as model systems linear chains of the complexes. We analyze the results in terms of the many‐body and cooperative effects. © 2012 Wiley Periodicals, Inc.     

Water PMF for predicting the properties of water molecules in protein binding site

Water is an important component in living systems and deserves better understanding in chemistry and biology. However, due to the difficulty of investigating the water functions in protein structures, it is usually ignored in computational modeling, especially in the field of computer‐aided drug design. Here, using the potential of mean forces (PMFs) approach, we constructed a water PMF (wPMF) based on 3946 non‐redundant high resolution crystal structures. The extracted wPMF potential was first used to investigate the structure pattern of water and analyze the residue hydrophilicity. Then, the relationship between wPMF score and the B factor value of crystal waters was studied. It was found that wPMF agrees well with some previously reported experimental observations. In addition, the wPMF score was also tested in parallel with 3D‐RISM to measure the ability of retrieving experimentally observed waters, and showed comparable performance but with much less computational cost. In the end, we proposed a grid‐based clustering scheme together with a distance weighted wPMF score to further extend wPMF to predict the potential hydration sites of protein structure. From the test, this approach can predict the hydration site at the accuracy about 80% when the calculated score lower than ?4.0. It also allows the assessment of whether or not a given water molecule should be targeted for displacement in ligand design. Overall, the wPMF presented here provides an optional solution to many water related computational modeling problems, some of which can be highly valuable as part of a rational drug design strategy. © 2012 Wiley Periodicals, Inc.     

PHI: A powerful new program for the analysis of anisotropic monomeric and exchange‐coupled polynuclear d‐ and f‐block complexes

A new program, PHI, with the ability to calculate the magnetic properties of large spin systems and complex orbitally degenerate systems, such as clusters of d‐block and f‐block ions, is presented. The program can intuitively fit experimental data from multiple sources, such as magnetic and spectroscopic data, simultaneously. PHI is extensively parallelized and can operate under the symmetric multiprocessing, single process multiple data, or GPU paradigms using a threaded, MPI or GPU model, respectively. For a given problem PHI is been shown to be almost 12 times faster than the well‐known program MAGPACK, limited only by available hardware. © 2013 Wiley Periodicals, Inc.     

FEW: A workflow tool for free energy calculations of ligand binding

In the later stages of drug design projects, accurately predicting relative binding affinities of chemically similar compounds to a biomolecular target is of utmost importance for making decisions based on the ranking of such compounds. So far, the extensive application of binding free energy approaches has been hampered by the complex and time‐consuming setup of such calculations. We introduce the free energy workflow (FEW) tool that facilitates setup and execution of binding free energy calculations with the AMBER suite for multiple ligands. FEW allows performing free energy calculations according to the implicit solvent molecular mechanics (MM‐PB(GB)SA), the linear interaction energy, and the thermodynamic integration approaches. We describe the tool's architecture and functionality and demonstrate in a show case study on Factor Xa inhibitors that the time needed for the preparation and analysis of free energy calculations is considerably reduced with FEW compared to a fully manual procedure. © 2013 Wiley Periodicals, Inc.     

Equilibrium and Dynamic Surface Tension of Carboxymethylchitosan and Alkyl Trimethylammonium Bromide Mixtures

A water-soluble derivative of chitosan, carboxymethylchitosan (CMCH), was mixed with alkyltrimethylammoniumbromides (C_mTAB) and was studied on the adsorption at air/water interface using equilibrium and dynamic surface tension method. The effects of surfactant and polymer concentrations, surfactant chain length, as well as pH of solution were investigated. Addition of the surfactants remarkably promotes the polymer adsorption. Increasing any one of surfactant concentration, surfactant chain length, and pH will facilitate the adsorption of the mixture whereas little effects of polymer concentration were observed. The results are explained in terms of the interaction between CMCH and C_mTAB under different conditions.     

Study on the Interaction Between Bovine Serum Albumin and Potassium Perfluoro Octane Sulfonate

The interactions between potassium perfluorooctanesulfonate (PFOS) and bovine serum albumin (BSA) were studied by fluorescence spectroscopy. The association constants between PFOS and BSA were obtained by fluorescence enhancing and fluorescence quenching respectively. Furthermore, fluorescence quenching was studied at different temperatures, and the binding constant was also determined by the method of fluorescence quenching. According to the thermodynamic parameters, the main binding force could be judged. The experimental results revealed that BSA and PFOS had strong interactions. The mechanism of quenching belonged to dynamic quenching and the main sort of binding force was hydrophobic force. IR-spectra proved the interaction changed the conformation of BSA.     

Analysis of the Interactions of Polyvinylpyrrolidone with Conventional Anionic and Dimeric Anionic Surfactant

Classical physical method has been applied in the present study of interaction between water soluble polymer with anionic dimeric and conventional anionic surfactants. Micellization activity of carboxylate-based anionic dimeric (CAD) as well as sodium dodecyl sulfate (SDS) surfactants in the presence of nonionic polymer, that is, polyvinylpyrrolidone (PVP), has been studied through conductometric and surface tensiometric measurements. From these methods the critical aggregation concentrations (CACs), critical micelle concentrations (CMCs), and the effective degree of counterion binding (β) were determined. For the evaluation of behavior of CAD toward the PVP various thermodynamic properties viz. standard Gibbs energy of micellization, standard enthalpy, and entropy of micellization of CAD/PVP mixed system have also been estimated and discussed. The results exhibit that anionic dimeric surfactant interacts strongly with PVP as compared to conventional surfactant.