Hydrogen Bond Network (hydrogen + bond_network)

Distribution by Scientific Domains


Selected Abstracts


Ab initio QM/MM dynamics of H3O+ in water

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2006
Pathumwadee Intharathep
Abstract A molecular dynamics (MD) simulation based on a combined ab initio quantum mechanics/molecular mechanics (QM/MM) method has been performed to investigate the solvation structure and dynamics of H3O+ in water. The QM region is a sphere around the central H3O+ ion, and contains about 6,8 water molecules. It is treated at the Hartree-Fock (HF) level, while the rest of the system is described by means of classical pair potentials. The Eigen complex (H9O) is found to be the most prevalent species in the aqueous solution, partly due to the selection scheme of the center of the QM region. The QM/MM results show that the Eigen complex frequently converts back and forth into the Zundel (H5O) structure. Besides the three nearest-neighbor water molecules directly hydrogen-bonded to H3O+, other neighbor waters, such as a fourth water molecule which interacts preferentially with the oxygen atom of the hydronium ion, are found occasionally near the ion. Analyses of the water exchange processes and the mean residence times of water molecules in the ion's hydration shell indicate that such next-nearest neighbor water molecules participate in the rearrangement of the hydrogen bond network during fluctuative formation of the Zundel ion and, thus, contribute to the Grotthuss transport of the proton. 2006 Wiley Periodicals, Inc. J Comput Chem, 2006 [source]


Structures of the Chromophore Binding Sites in BLUF Domains as Studied by Molecular Dynamics and Quantum Chemical Calculations,

PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2008
Kazuya Obanayama
BLUF (blue-light sensing using FAD) domains constitute a new family of flavin-based blue light photoreceptors. The photocycle of BLUF is unique in the sense that a few hydrogen bond rearrangements are accompanied by only slight structural changes in the bound chromophore. The hydrogen bond rearrangements upon illumination have been inferred from spectral changes in the chromophore: ,10 nm redshift of the absorption maximum and ,16 cm,1 downshift of the C4=O stretching frequency. However, the exact features of the hydrogen bond network around the active site are still the subject of some controversy. In particular, the orientation of a conserved Gln (Gln63 in AppA) is presently one of the most questioned topics in the field. Here we perform molecular dynamics simulations for the wild-type AppA, AppA1-124C20S, BlrB and T110078 and furthermore quantum chemical calculations to investigate their spectroscopic properties in the dark and signaling states. On the basis of these results, we reveal the dynamic aspect of hydrogen bonding networks at the active site and propose theoretically reasonable models for the dark and signaling states of the BLUF domains. [source]


Affinity enhancement of an in vivo matured therapeutic antibody using structure-based computational design

PROTEIN SCIENCE, Issue 5 2006
Louis A. Clark
Abstract Improving the affinity of a high-affinity protein,protein interaction is a challenging problem that has practical applications in the development of therapeutic biomolecules. We used a combination of structure-based computational methods to optimize the binding affinity of an antibody fragment to the I-domain of the integrin VLA1. Despite the already high affinity of the antibody (Kd ,7 nM) and the moderate resolution (2.8 ) of the starting crystal structure, the affinity was increased by an order of magnitude primarily through a decrease in the dissociation rate. We determined the crystal structure of a high-affinity quadruple mutant complex at 2.2 . The structure shows that the design makes the predicted contacts. Structural evidence and mutagenesis experiments that probe a hydrogen bond network illustrate the importance of satisfying hydrogen bonding requirements while seeking higher-affinity mutations. The large and diverse set of interface mutations allowed refinement of the mutant binding affinity prediction protocol and improvement of the single-mutant success rate. Our results indicate that structure-based computational design can be successfully applied to further improve the binding of high-affinity antibodies. [source]


Hydration of polysaccharide hyaluronan observed by IR spectrometry.

BIOPOLYMERS, Issue 1 2003

Abstract This article is the first one in a series dedicated to the study of hyaluronan as observed by IR spectrometry. The goal is to determine its hydration mechanism and the structural changes this mechanism implies. Hyaluronan is a natural polysaccharide that is widely used in biomedical applications and cosmetics. Its macroscopic properties are significantly dependent on its degree of hydration. In this article we record the IR spectrum of a several micron thick dried film and deduce that four or five residual H2O molecules remain around each disaccharide repeat unit in the dried film. We then compare the spectra of sodium hyaluronan and its acid form to assign vibrational bands linked to the carboxylate group. We proceed with a qualitative analysis of the spectral changes induced by changes of temperature and hygroscopicity, two independent parameters that act by modifying the hydrogen bond network of the sample. This enables us to assign most of the vibrational bands of the hydrophilic groups and to distinguish the bands that are due to these hydrophilic groups when they are or are not hydrogen bonded. It constitutes a prerequisite for the quantitative analysis of hydration spectra that will be described in the following articles of this series. 2002 Wiley Periodicals, Inc. Biopolymers (Biospectroscopy) 72: 10,20, 2003 [source]


Understanding Promiscuous Amidase Activity of an Esterase from Bacillus subtilis

CHEMBIOCHEM, Issue 1 2008
Robert Kourist
Water works. Bacillus subtilis esterase BS2 is a promiscuous esterase that shows amidase activity. This amidase activity was shown to depend on a hydrogen-bond network with the substrate amide hydrogen (indicated by arrow). When this stabilising hydrogen bond network was removed by a point mutation, the amide activity was significantly lowered in comparison with the esterase activity. [source]


Thermodynamic and structural aspects of sulfonamide crystals and solutions

JOURNAL OF PHARMACEUTICAL SCIENCES, Issue 12 2009
German L. Perlovich
Abstract The crystal structures of three sulfonamides with the general structure 4-NH2 -C6H4 -SO2NH-C6H4/3 -R (R,=,4-Et; 4-OMe; 5-Cl-2-Me) have been determined by X-ray diffraction. On the basis of our previous data and the results obtained a comparative analysis of crystal properties was performed: molecular conformational states, packing architecture, and hydrogen bond networks using graph set notations. The thermodynamic aspects of the sulfonamide sublimation process have been studied by investigating the temperature dependence of vapor pressure using the transpiration method. A regression equation was derived describing the correlation between sublimation entropy terms and crystal density data calculated from X-ray diffraction results. Also correlations between sublimation Gibbs energies and melting points, on the one hand, and between sublimation enthalpies and fusion enthalpies at 298 K, on the other hand, were found. These dependencies give the opportunity to predict sublimation thermodynamic parameters by simple thermo-physical experiments (fusion characteristics). Solubility processes of the compounds in water, n -hexane, and n -octanol (as phases modeling various drug delivery pathways and different types of membranes) were investigated and corresponding thermodynamic functions were calculated as well. Thermodynamic characteristics of sulfonamide solvation were evaluated. For compounds with similar structures processes of transfer from one solvent to another one were studied by a diagram method combined with analysis of enthalpic and entropic terms. Distinguishing between enthalpy and entropy, as is possible through the present approach, leads to the insight that the contribution of these terms is different for different molecules (entropy- or enthalpy-determined). Thus, in contrast to interpretation of only the Gibbs energy of transfer, being extensively used for pharmaceuticals in the form of the partition coefficient (log,P), the analysis of thermodynamic functions of the transfer process provides additional mechanistic information. This may be important for further evaluation of the physiological distribution of drug molecules and may provide a better understanding of biopharmaceutical properties of drugs. 2009 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 98:4738,4755, 2009 [source]


Structure of Hexakis (imidazole) nickel (II) Nitrate Water Solvate: [Ni(Im)6](NO3)2 -4H2O

CHINESE JOURNAL OF CHEMISTRY, Issue 10 2002
Fang-Fang Jian
Abstract Crystal structure of the title compound, [Ni(Im)6] (NO3)24H2O (Im = imidazole), was determined by X-ray crystallographic analysis. The crystal structure consists of discrete Ni(Im)26+ cation, NO,3 anion and four uncoordinated water molecules. It crystallizes in the hexagonal system, space group P63, with lattice parameters a = b = 0.9003(2) nm, c = 2.1034(4) nm, and Z = 2. The Ni(II) ion is centro- symmetric octahedron geometry with the NiN6 core. Six imidazole molecules are coordinated to each nickel (II) atom through its tertiary nitrogen atom. The short and long bond distances of Ni-N are 0.2059(6) and 0.2204(7) nm, respectively. In the solid state, [Ni(Im)6]2+, H2O moieties and nitrate anions form the three dimensional hydrogen bonds network which stabitizes the crystal structure. [source]


Synthesis, pharmacology, crystal properties, and quantitative solvation studies from a drug transport perspective for three new 1,2,4-thiadiazoles

JOURNAL OF PHARMACEUTICAL SCIENCES, Issue 9 2010
German L. Perlovich
Abstract A novel 1,2,4-thiadiazoles were synthesized. Crystal structures of these compounds were solved by X-ray diffraction experiments and comparative analysis of molecular conformational states, packing architecture, and hydrogen bonds networks were carried out. Thermodynamic aspects of sublimation processes of studied compounds were determined using temperature dependencies of vapor pressure. Thermophysical characteristics of the molecular crystals were obtained and compared with the sublimation and structural parameters. Solubility and solvation processes of 1,2,4-thiadiazoles in buffer, n -hexane and n -octanol were studied within the wide range of temperature intervals and thermodynamic functions were calculated. Specific and nonspecific interactions of molecules resolved in crystals and solvents were estimated and compared. Distribution processes of compounds in buffer/n -octanol and buffer/n -hexane systems (describing different types of membranes) were investigated. Analysis of transfer processes of studied molecules from the buffer to n -octanol/n -hexane phases was carried out by the diagram method with evaluation of the enthalpic and entropic terms. This approach allows us to design drug molecules with optimal passive transport properties. Calcium-blocking properties of the substances were evaluated. 2010 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 99:3754,3768, 2010 [source]