F. J. Bermejo

Low‐temperature 1H‐NMR evidence of the folding of isolated ribonuclease S‐peptide

The temperature (−7°C to 45°C, pH 5.4) and pH (0°C) dependence of 1H chemical shifts of ribonuclease S‐peptide (5 mM, 1 M NaCl) has been measured at 360 MHz. The observed variations evidence the formation of a partial helical structure, involving the fragment Thr‐3—Met‐13. Two salt‐bridges stabilize the helix: those formed by Glu‐9−…His‐12+ and Glu‐2−…Arg‐10+. The structural features deduced from the 1H‐NMR at low temperature for the isolated S‐peptide are compatible with the structure shown by the same molecule in the ribonuclease S crystal.

Nature of the bound states of molecular hydrogen in carbon nanohorns

The effects of confining molecular hydrogen within carbon nanohorns are studied via high-resolution quasielastic and inelastic neutron spectroscopies. Both sets of data are remarkably different from those obtained in bulk samples in the liquid and crystalline states. At temperatures where bulk hydrogen is liquid, the spectra of the confined sample show an elastic component indicating a significant proportion of immobile molecules as well as distinctly narrower quasielastic line widths and a strong distortion of the line shape of the para-->ortho rotational transition. The results show that hydrogen interacts far more strongly with such carbonous structures than it does to carbon nanotubes, suggesting that nanohorns and related nanostructures may offer significantly better prospects as lightweight media for hydrogen storage applications.

On the fundamental role of the Glu 2- ... Arg 10+ salt bridge in the folding of isolated ribonuclease A S-peptide.

The fundamental role of the Glu 2- ... Arg 10+ salt bridge in the folding of isolated S-peptide (1-19 N-terminal fragment of Ribonuclease A) is demonstrated from the comparison of the helix contents, at 0 degrees C, of S-peptide and related peptides. Helix contents have been determined from the analysis of proton chemical shift vs. temperature curves. The observed data can be accounted for by assuming that two side-chain interactions contribute to stabilize the 3-13 helix of S-peptide, the salt bridges Glu 2- ... Arg 10+ and Glu 9-... His 12+, the former being more effective. The salt bridge Glu 9- ... Arg 10+ turns to a weaker interaction, a hydrogen bond Glu 2 (C delta = 0) ... Arg 10+, on protonation or esterification of the Glu 2 carboxylate.

Collective excitations in liquid methanol: A comparison of molecular, lattice‐dynamics, and neutron‐scattering results

The collective dynamics of liquid methanol‐d4 is studied by means of molecular‐dynamics simulation. The model potential is validated by means of lattice energy calculations and shows a very good agreement with the experimentally obtained crystal structure. Center‐of‐mass density and momentum fluctuations are investigated in the (Q,ω) region which is also accessible to inelastic neutron‐scattering (INS) techniques. A simple viscoelastic model previously used for the analysis of INS data is tested against the dynamic structure factor computed from the simulation. A direct comparison with the INS results themselves is also made and qualitative agreement is found. Also, a tentative assignment of the peaks appearing in the current–current correlations is made on the basis of lattice‐dynamics calculations for the polycrystalline low‐temperature α phase.

A study of the NH NMR signals of Gly-Gly-X-Ala tetrapeptides in H2O at low temperature.

Abstract The effect of temperature, pH and addition of denaturing agents on the amide and side chain NH δ values of a series of random coil linear tetrapeptides (Gly-Gly-X-Ala with X=Glu, Asp, His, Trp, Arg, Gly, Pro, Asn, Gln) has been measured in dilute aqueous solutions at two temperatures (24 and 0°C). Amide shift temperature coefficients were within the −5.8 to −9.1 ppb/K range. Amide δ changes following urea addition were ⩽ 0.03 ppm, with the exception of the Ala terminal residue of all peptides, and the His residue as well. Signs of a non-random structure near the COO − terminus were found for the Gly-Gly-His-Ala tetrapeptide.

Monte Carlo simulations of liquid n-butane

We have carried out Monte Carlo (MC) simulations for a model of liquid n-butane in three thermodynamic states. In each case, both the flexible model in the limit when bond-length and bond-angle forces become infinite and the constrained model were studied. The different trajectories followed by each model lead to different ensemble averages for the intramolecular properties, such as the conformational distribution and intramolecular energy. The changes observed in the external configurational properties, such as the intermolecular energy and pressure are less than the statistical error. In all the cases we have found a weak shift of the trans conformational population with respect to the ideal-gas distribution (i.e. less than 3%). In addition, we have explored the possibilities of a purely repulsive model as a reference system for this liquid. As in the case of simple atomic liquids, the standard hard-core theoretical approaches are good starting points for obtaining the contribution of the external degre...

How well do we know the structure of simple molecular liquids? CCl4 revisited

New experimental results for the full intermolecular pair correlation function for liquid carbon tetrachloride have been obtained from analysis of structure factors measured using reactor and pulsed neutron sources. A brief comparison between the results derived from both techniques is presented. The liquid structure is discussed within the framework of the site-site Ornstein-Zernike equation with the hypernetted chain (HNC) and Percus-Yevick (PY) like closures. The Coulomb potentials are handled using Ngs method. The predictions show that the octupolar interactions have a small effect on the radial distribution functions.

Ethanol force fields: A molecular dynamics study of polarization effects on different phases

We have studied two simple approaches to consider thermodynamic state dependent electrostatic interactions for molecular modeling of different phases of ethanol: the addition of an isotropic point polarizability located in the oxygen, and a self-consistent calculation of the effective dipole moment at each thermodynamic state. We have performed molecular dynamics simulations in order to investigate the thermodynamic properties, structure and dynamics of the liquid phase at three experimental densities, as well as in the monoclinic crystal and at critical conditions. In order to rationalize the effects of changing the dipole moment of the molecules, simulations with a nonpolarizable model for ethanol were also performed. The results show that a nonpolarizable model with an effective dipole moment is able to reproduce most of the static and dynamic properties of the condensed phases of ethanol, while the need to take into account the real dipole moment of the isolated molecule by using a polarizable model i...

Diffusional dynamics of hydrogen-bonded liquids: methanol

Medium-resolution ( Delta E approximately=0.1 meV) quasielastic neutron scattering spectra have been measured for partially (CD3OH) and fully deuterated methanol, (CD3OD) in the temperature range between 200 and 300 K. The spectra are analysed in terms of a simplified model which takes into account both coherent and incoherent contributions, and includes translational and rotational motions of the molecular frame as well as the rapid reorientation of the CD3 group. Such a procedure enabled the separation of the translational and rotational contributions to the measured intensity. The apparent lack of saturation of the translational linewidths versus the momentum transfer is finally discussed in terms of a phenomenological stochastic model.

Statistical mechanics of small chain molecular liquids. I. Conformational properties of modeled n‐butane

The density functional formalism can also be profitably applied to the statistical mechanics of molecular fluids with internal degrees of freedom. The change of the intrinsic chemical potential for different conformers of nonpolar molecules is given by a zeroth order perturbation approach. This approach is applied to study the isomerization of n‐butane in liquids, which models the neat liquid and CCl4 solutions. We find that a nonpolar solvent medium produces a shift in the conformational equilibria of model liquid n‐butane from that found in the gas phase. The theoretical predictions show a good agreement with recent Monte Carlo and molecular dynamics simulations results. Discrepancies with Jorgensen et al.’s data are explained in terms of the attractive intermolecular forces used in their MC codes.