An ab initio molecular dynamics simulation of liquid water has been performed using density functional theory in the Kohn–Sham formulation and a plane wave basis set to determine the electronic structure and the forces at each time step. For an accurate description of the hydrogen bonding in the liquid, it was necessary to extend the exchange functional with a term that depends on the gradient of the electron density. A further important technical detail is that supersoft pseudopotentials were used to treat the valence orbitals of the oxygen atoms in a plane wave expansion. The structural and dynamical properties of the liquid were found to be in good agreement with experiment. The ab initio molecular dynamics also yields information on the electronic structure. The electronic feature of special interest is the lowest unoccupied molecular orbital (LUMO) of the liquid which is the state occupied by a thermalized excess electron in the conductive state. The main result of calculating the liquid LUMO is that it is a delocalized state distributed over interstitial space between the molecules with a significant admixture of the σ* orbitals of the individual water molecules.

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‘‘Ab initio’’ liquid water

The implementation of a cell operating with the technique of Attenuated Total Reflection (ATR) enabled us to obtain good quality IR spectra of water for the whole region above 750 cm−1 (which is the limit of the effect of the cutoff wave number of the crystal) and up to 5000 cm−1. ATR spectra have been recorded as a function of temperature ranging from −5 °C to 80 °C and of H/D molar concentration c(0<c<1). They have been transformed into spectra in e‘, using the Bertie–Eysel iteration procedure. In this paper evolutions of these spectra in e‘ upon variations of these two parameters c and T are investigated and analyzed. It is shown that any experimental spectrum in e‘ of a mixture of normal and heavy water is a superposition of three spectra due to pure H2O, pure D2O, and a spectrum that is only slightly dependent upon isotopic concentration c and is consequently mainly due to HDO. Analysis of this slight dependence upon c allows precise conclusions concerning vibrational interactions for both bending bands δ and stretching bands νs to be reached. Evolution of spectra with temperature unambiguously shows that all spectra at temperature T may be decomposed into a low temperature spectrum and a high temperature spectrum. The coefficient defining this decomposition [Eqs. (11) and (14)] displays a quadratic variation with T. It is the same for H2O, D2O, and HDO within the precision of the experiment. A low temperature spectrum corresponding to a (slightly distorted) H‐bond network with no other defects, as well as a high temperature spectrum due to ‘‘defects’’ cannot, however, be determined without any further assumption. Limits for values of the concentration of defects α(T) may nevertheless be established.

Infrared spectra of water. I. Effect of temperature and of H/D isotopic dilution

This review article focuses on the most recent advances in X-ray and neutron scattering studies of water structure, from ambient temperature to the deeply supercooled and amorphous states, and of water diffusive and collective dynamics, in disparate thermodynamic conditions and environments. In particular, the ability to measure X-ray and neutron diffraction of water with unprecedented high accuracy in an extended range of momentum transfers has allowed the derivation of detailed O-O pair correlation functions. A panorama of the diffusive dynamics of water in a wide range of temperatures (from 400 K down to supercooled water) and pressures (from ambient up to multiple gigapascals) is presented. The recent results obtained by quasi-elastic neutron scattering under high pressure are compared with the existing data from nuclear magnetic resonance, dielectric and infrared measurements, and modeling. A detailed description of the vibrational dynamics of water as measured by inelastic neutron scattering is presented. The dependence of the water vibrational density of states on temperature and pressure, and in the presence of biological molecules, is discussed. Results about the collective dynamics of water and its dispersion curves as measured by coherent inelastic neutron scattering and inelastic X-ray scattering in different thermodynamic conditions are reported.

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X-ray and Neutron Scattering of Water

http://link.springer.com/content/pdf/10.1007/978-94-009-2219-8_17.pdf

Monte Carlo and Molecular Dynamics Simulations

Most of the sequenced bacterial genomes contain a gene encoding a protein known as Hfq that resembles the eukaryotic RNA-binding proteins of the LSm family. It was originally identified in Escherichia coli as a host factor required for replication of the Qβ RNA phage. In this review, we present a comprehensive summary of 40 years of investigation to learn that Hfq is an influential, though not essential, global regulator of gene expression in bacteria and that this feature is undoubtedly linked to Hfq’s RNA-binding properties. This protein intervenes in different RNA transactions, notably the promotion of antisense interactions between messenger RNAs and small regulatory RNAs. Yet, several aspects of its molecular mechanism remain not understood. In addition, mechanistic studies have been exclusively carried out in enterobacterial models, highlighting the need to expand the research on Hfq function to other taxons. Upon reviewing the genetic, structural, biochemical, and biological aspects of this extraor...

The bacterial protein Hfq: much more than a mere RNA-binding factor

Inelastic-neutron-scattering spectroscopy is utilized to probe single-particle excitations as a function of temperature in light and heavy water over an energy range of 50 to 600 meV, covering the librational, bending, and stretch vibrational regions of molecular motion. A computer molecular-dynamics simulation of liquid water based on a simple point-charge model is also carried out to compute the Q-dependent proton density of states ${G}_{s}$(Q,E) for direct comparison with the equivalent quantity deduced from experimental measurements on an absolute scale. The calculated classical density of states is lower than the measured one by a factor of 2, indicating the importance of quantum-mechanical corrections at high-energy transfers. The classical simulation fails to predict a combination band at 525 meV which we attribute to a quantum-mechanical process of simultaneous excitation of the stretch vibrational mode and breaking of the adjacent H-O...H hydrogen bond. The temperature dependence of this band is predicted correctly by a quantum-mechanical calculation using a one-dimensional hydrogen-bond model.

Neutron-scattering measurements of wave-vector-dependent hydrogen density of states in liquid water.

Hfq is a bacterial protein involved in RNA metabolism. Besides this, Hfq's role in DNA restructuring has also been suggested. Since this mechanism remains unclear, we examined the DNA conformation upon Hfq binding by combining vibrational spectroscopy and neutron scattering. Our analysis reveals that Hfq, which preferentially interacts with deoxyadenosine rich sequences, induces partial opening of dA-dT sequences accompanied by sugar repuckering of the dA strand and hence results in a heteronomous A/B duplex. Sugar repuckering is probably correlated with a global dehydration of the complex. By taking into account Hfq's preferential binding to A-tracts, which are commonly found in promoters, potential biological implications of Hfq binding to DNA are discussed.

Jose Teixeira

Papers

Neutron-scattering measurements of wave-vector-dependent hydrogen density of states in liquid water.

Conformational transition of DNA bound to Hfq probed by infrared spectroscopy