Search

There is conflicting evidence as to whether cavities in proteins that are nonpolar and large enough to accommodate solvent are empty or are occupied by disordered water molecules. Here, we use multiple-wavelength x-ray data collected from crystals of the selenomethionine-substituted L99A/M 102L mutant of T4 lysozyme to obtain a high-resolution electron density map free of bias that is unavoidably associated with conventional model-based structure determination and refinement. The mutant, L99A/M102L, has four cavities, two being polar in character and the other two nonpolar. Cavity 1 (polar, volume 45.2 [[Angstrom].sup.3]) was expected to contain two well ordered water molecules, and this is confirmed in the experimental electron density map. Likewise, cavity 2 (polar, 16.9 [[Angstrom].sup.3]) is confirmed to contain a single water molecule. Cavity 3 (nonpolar, 21.4 [[Angstrom].sup.3]) was seen to be empty in conventional x-ray refinement, and this is confirmed in the experimental map. Unexpectedly, however, cavity 4 (nonpolar, volume 133.5 [[Angstrom].sup.3]) was seen to contain diffuse electron density equivalent to [approximately equal to] 1.5 water molecules. Although cavity 4 is largely nonpolar, it does have some polar character, and this apparently contributes to the presence of solvent. The cavity is large enough to accommodate four to five water molecules, and it appears that a hydrogen-bonded chain of three or more solvent molecules could occupy the cavity at a given time. The results are consistent with theoretical predictions that cavities in proteins that are strictly nonpolar will not contain solvent until the volume is large enough to permit mutually satisfying water-water hydrogen bonds. bound water | hydrogen bonding | protein cavity

The photochemical dynamics of the pyrrole-pyridine hydrogen-bonded complex has been investigated with computational methods. In this system, a highly polar charge-transfer state of [sup.1][pi][[pi].sup.*] character drives the proton transfer from pyrrole to pyridine, leading to a conical intersection of [S.sub.1] and [S.sub.0] energy surfaces. A two-sheeted potential-energy surface including 39 in-plane nuclear degrees of freedom has been constructed on the basis of ab initio multiconfiguration electronic-structure data. The non-Born-Oppenheimer nuclear dynamics has been treated with time-dependent quantum wave-packet methods, including the two or three most relevant nuclear degrees of freedom. The effect of the numerous weakly coupled vibrational modes has been taken into account with reduced-density-matrix methods (multilevel Redfield theory). The results provide insight into the mechanisms of excited-state deactivation of hydrogen-bonded aromatic systems via the electron-driven proton-transfer process. This process is believed to be of relevance for the ultrafast excited-state deactivation of DNA base pairs and may contribute to the photostability of the molecular encoding of the genetic information. conical intersection | excited-state hydrogen transfer | nonadiabatic transition

Samples of beachrock from Lakes Butler and Fellmongery, near Robe, South Australia, were examined by neutron and X-ray powder diffraction. Considerable variation in phase composition was observed, although all samples possessed monohydrocalcite, calcite, aragonite, and magnesian-calcite. The Rietveld refinement of the structure of monohydrocalcite showed significant changes in the orientation of water molecules and a major change in the orientation of a carbonate group with respect to the currently accepted structure. The current refinement shows that the hydrogen-bonding structure consists of three distinct networks, with each of the three carbonate groups being bonded to a single water molecule via one linear and one bifurcated hydrogen bond. Keywords: Monohydrocalcite, carbonate minerals, magnesian-calcite, powder diffraction

The short-time orientational relaxation of water is studied by ultrafast infrared pump-probe spectroscopy of the hydroxyl stretching mode (OD of dilute HOD in [H.sub.2]O). The anisotropy decay displays a sharp drop at very short times caused by inertial orientational motion, followed by a much slower decay that fully randomizes the orientation. Investigation of temperatures from 1[degrees]C to 65[degrees]C shows that the amplitude of the inertial component (extent of inertial angular displacement) depends strongly on the stretching frequency of the OD oscillator at higher temperatures, although the slow component is frequency-independent. The inertial component becomes frequency-independent at low temperatures. At high temperatures there is a correlation between the amplitude of the inertial decay and the strength of the O-D--O hydrogen bond, but at low temperatures the correlation disappears, showing that a single hydrogen bond (OD--O) is no longer a significant determinant of the inertial angular motion. It is suggested that the loss of correlation at lower temperatures is caused by the increased importance of collective effects of the extended hydrogen bonding network. By using a new harmonic cone model, the experimentally measured amplitudes of the inertial decays yield estimates of the characteristic frequencies of the intermolecular angular potential for various strengths of hydrogen bonds. The frequencies are in the range of [approximately equal to] 400 [cm.sup.-1]. A comparison with recent molecular dynamics simulations employing the simple point charge-extended water model at room temperature shows that the simulations qualitatively reflect the correlation between the inertial decay and the OD stretching frequency. ultrafast IR experiments | dynamics | motion | MD simulations | harmonic model

A mixed quantum/classical investigation of the dynamical magnetostructural properties, that is, 'magnetodynamics,' of oxidized Anabaena PCC7119 ferredoxin is carried out at room temperature in two distinct conformational states. This protein hosts a [2Fe-2S] cluster in which two iron centers are antiferromagnetically coupled to an overall low-spin electronic ground state that has a genuine multireference character. To study the magnetodynamics of this prosthetic group, an approximate spin projection method is formulated in the framework of density functional theory that allows for multideterminant ab initio molecular dynamics simulations to be carried out efficiently. By using this scheme, the influence of both thermal fluctuations and conformational motion on the structure of the [2Fe-2S] cluster and on the dynamics of the antiferromagnetic coupling constant, J(t), has been investigated. In addition to demonstrating how sensitively the shape of the [2Fe-2S] core itself is affected by hydrogen bonding, the analyses reveal a complex dynamical coupling of J to both local vibrations and large-amplitude motion. It is shown that this interplay can be understood in terms of specific vibrational modes and distinct hydrogen-bonding patterns between the iron-sulfur cluster and the protein backbone, respectively. This implies going beyond the Goodenough-Kanamori rules for angular magnetostructural correlations of oxidized iron-sulfur prosthetic groups. exchange coupling | extended broken-symmetry | hydrogen bonding | iron-sulfur protein | multideterminant hybrid molecular dynamics

The crystal structure of diaspore, AlO(OH), has been investigated by in situ single-crystal synchrotron X-ray diffraction at ~50 GPa using the diamond-anvil cell technique. Diaspore is found to retain its structure up to 51.5 GPa at room temperature, which is more than 30 GPa above the transition pressure to [delta]-AlO(OH) found in quenched high-temperature experiments and derived from density functional theory calculations. The compression is anisotropic and largest for the a axis. This can be explained by the fact that the structural response to pressure is mainly due to the shortening of the hydrogen bond, which is oriented nearly parallel to the a axis. The hydrogen bond becomes significantly more symmetric with pressure up to 50 GPa. Keywords: Diaspore, high pressure, crystal structure, synchrotron radiation, single crystal

We present improvements on our previous approaches for calculating vibrational spectroscopy observables for the OH stretch region of dilute HOD in liquid [D.sub.2]O. These revised approaches are implemented to calculate IR and isotropic Raman spectra, using the SPC/E simulation model, and the results are in good agreement with experiment. We also calculate observables associated with three-pulse IR echoes: the peak shift and 2D-IR spectrum. The agreement with experiment for the former is improved over our previous calculations, but discrepancies between theory and experiment still exist. Using our proposed definition for hydrogen bonding in liquid water, we decompose the distribution of frequencies in the OH stretch region in terms of subensembles of HOD molecules with different local hydrogen-bonding environments. Such a decomposition allows us to make the connection with experiments and calculations on water clusters and more generally to understand the extent of the relationship between transition frequency and local structure in the liquid. vibrational spectroscopy | water

Using [sup.29]Si, [sup.1]H, and [sup.2]H magic-angle spinning (MAS) and [sup.29]Si{[sup.1]H} heteronuclear correlation (HetCor) nuclear magnetic resonance (NMR) spectroscopy the tetrahedral sheets of the 10 [Angstrom] phase are shown to contain [Q.sup.2]-type Si bonded to silanol groups that donate hydrogen bonds to interlayer [H.sub.2]O. [sup.29]Si NMR spectra of 10 [Angstrom] phase samples synthesized from oxide and from crystalline talc starting materials contain a peak near -87 ppm for [Q.sup.2] Si, in addition to the main peak at -98 ppm for the talc-like [Q.sup.3] of the tetrahedral sheet. The [sup.1]H MAS NMR spectra of the 10 [Angstrom] phase contain two distinct peaks, at chemical shifts of +7.8 and +3.2 ppm, in addition to a narrow peak near +0.9 ppm from the talc-like hydroxyl groups. [sup.29]Si{[sup.1]H} HetCor data indicate that the +7.8 ppm [sup.1]H resonance corresponds to silanol groups and that at +3.2 ppm arises from interlayer [H.sub.2]O. Comparison of the observed data with correlations of [sup.1]H NMR chemical shift and [sup.2]H quadrupolar coupling indicates that the silanol groups donate moderate hydrogen bonds to interlayer [H.sub.2]O, d(O ... O) [approximately equal to] 2.8 [Angstrom], whereas most interlayer [H.sub.2]O donate only very weak or no hydrogen bonds at ambient conditions. Our results suggest that formation of the 10 [Angstrom], phase involves formation of vacancies, which allow favorable hydrogen bond interaction between interlayer [H.sub.2]O and the normally hydrophobic talc-like 2:1 layers. Keywords: NMR, l0 [Angstrom] phase, talc, silanol, hydrogen bond

A theoretical perspective of the different aspects of ultrafast vibrational energy transfer in water and other related systems, which are concerned with the association of the change of population of OH vibrational states is presented. The hydrogen bond plays a very important role in chemical solution processes like proton-transfer reactions and in biochemical processes and systems.

Salen-group 13 ligands are derived by combining a diamine with 2 equivalents of salicyclaldehyde and are ideal for the equatorial coordination of transition metals and catalysis. The use of group 13 compounds is generally in combination with Salen-supported trnsition metal compounds.

The R-T transfer rate falls due to mutation at the 42-alpha site, revealing the important role played by the hydrogen bond found between Tyr-42-alpha and Asp-99-beta in the R-T transfer state and in the equilibrium T state. The transition state between the R and T stages displays an incomplete hydrogen bond as seen in Hb A. Presence of the subunit interface affects the length of the T-like geometry seen in the transition state. The transition state becomes constant due to the intrasubunit hydrogen bond seen between Tyr-145-beta and Val-98-beta.

The binding of EcoRI endonuclease to a set of purine-base analogue sites was computed and each of these sites was found to be responsible for the deletion of one functional group which forms a hydrogen bond with the endonuclease in the GAATTC complex. Five out of six of these deletions lose binding free energy upto 1.7 kcal/mol. Two of these deletions occur without disturbing an interstrand Watson-Crick hydrogen bond, thus, leading to the structural adaptation in the complex.

Anion photoelectron spectroscopy is a very sensitive probe for detecting weak intermolecular interactions between gold anion and a noble-gas atom or other nonreactive molecule. The interaction between [Au.sup.-] and [H.sub.2]O is much stronger and the interaction between [Au.sup.-] and [O.sub.2] is weaker than between [Au.sup.-] and a noble-gas atom.

An analysis of hydrogen bonding strengths in proteins using unnatural amino acids show that the intramolecular hydrogen bonds in folded proteins make a net favorable contribution of 1-2 kcal per mol to protein stability relative to the corresponding hydrogen bonds to the solvent in the denatured state. Hydrogen bonds play an important role in finding the secondary and tertiary structure of proteins. The values of hydrogen bond stabilization are determined from mutational studies in which one member of a hydrogen bonded pair is deleted.

Nonphotochemical hole burning spectroscopical study of 4,4-difluoro-5-(4-phenyl-1,3-butadienyl)-4-bora-3a,4a-diaza-s-indacene-3- propionic acid succinimidyl ester (BODIPY), to analyze the chromophore-oligonucleotide conformational structure finds that the intra molecular hydrogen bond perturbs the chromophore-oligonucleotide conformation. Intramolecular hydrogen bond was formed by the oligonucleotide with BODIPY.