Intermolecular correlations are necessary to explain diffuse scattering from protein crystals

Conformational changes drive protein function, including catalysis, allostery, and signaling. X-ray diffuse scattering from protein crystals has frequently been cited as a probe of these correlated motions, with significant potential to advance our understanding of biological dynamics. However, recent work challenged this prevailing view, suggesting instead that diffuse scattering primarily originates from rigid body motions and could therefore be applied to improve structure determination. To investigate the nature of the disorder giving rise to diffuse scattering, and thus the potential applications of this signal, a diverse repertoire of disorder models was assessed for its ability to reproduce the diffuse signal reconstructed from three protein crystals. This comparison revealed that multiple models of intramolecular conformational dynamics, including ensemble models inferred from the Bragg data, could not explain the signal. Models of rigid body or short-range liquid-like motions, in which dynamics are confined to the biological unit, showed modest agreement with the diffuse maps, but were unable to reproduce experimental features indicative of long-range correlations. Extending a model of liquid-like motions to include disorder across neighboring proteins in the crystal significantly improved agreement with all three systems and highlighted the contribution of intermolecular correlations to the observed signal. These findings anticipate a need to account for intermolecular disorder in order to advance the interpretation of diffuse scattering to either extract biological motions or aid structural inference.Comment: 12 pages, 5 figures (not including Supplementary Information

Molecular dynamics simulations of aqueous urea solutions: Study of dimer stability and solution structure, and calculation of the total nitrogen radial distribution function GN(r

Molecular dynamics simulations have been performed in order to study the structure of two molal urea solutions in D2O. Several initial dimer configurations were considered for an adequate sampling of phase space. Eventually all of them appeared to be unstable, when system size and periodic boundary conditions are chosen properly, even after a very careful equilibration. The total nitrogen scattering function GN(r), calculated from these simulations, is in good agreement with neutron scattering experiments when both intra- and intermolecular correlations are considered and the experimental truncation ripples are introduced by a Fourier transform of GN(r) back and forth. The simple pair potential model that we used gives results in good agreement with experiments and with a much more involved potential model, recently described in the literature [J. Chem. Phys. 95, 8419 (1991)]

Structure of liquid and glassy methanol confined in cylindrical pores

We present a neutron scattering analysis of the density and the static structure factor of confined methanol at various temperatures. Confinement is performed in the cylindrical pores of MCM-41 silicates with pore diameters D=24 angstrom and D=35 angstrom. A change of the thermal expansivity of confined methanol at low temperature is the signature of a glass transition, which occurs at higher temperature for the smallest pore. This is an evidence of a surface induced slowing down of the dynamics of the fluid. The structure factor presents a systematic evolution with the pore diameter, which has been analyzed in terms of excluded volume effects and fluid-matrix cross-correlation. Conversely to the case of Van der Waals fluids, it shows that stronger fluid-matrix correlations must be invoked most probably in relation with the H-bonding character of both methanol and silicate surface.Comment: version March 12 200

Low-Temperature Quantum Relaxation in a System of Magnetic Nanomolecules

We argue that to explain recent resonant tunneling experiments on crystals of Mn$_{12}$ and Fe$_8$, particularly in the low-T limit, one must invoke dynamic nuclear spin and dipolar interactions. We show the low-$T$, short-time relaxation will then have a $\sqrt{t/\tau}$ form, where $\tau$ depends on the nuclear $T_2$, on the tunneling matrix element $\Delta_{10}$ between the two lowest levels, and on the initial distribution of internal fields in the sample, which depends very strongly on sample shape. The results are directly applicable to the $Fe_8$ system. We also give some results for the long-time relaxation.Comment: 4 pages, 3 PostScript figures, LaTe

Generating multi-chain configurations of an inhomogeneous melt from the knowledge of single-chain properties

Mean-field techniques provide a rather accurate description of single-chain conformations in spatially inhomogeneous polymer systems containing interfaces or surfaces. Intermolecular correlations, however, are not described by the mean-field approach and information about the distribution of distance between different molecules is lost. Based on the knowledge of the exact equilibrium single-chain properties in contact with solid substrates, we generate multi-chain configurations that serve as nearly equilibrated starting configurations for molecular dynamics simulations by utilizing the packing algorithm of Auhl and co-workers [J. Chem. Phys. 119, 12718 (2003)] for spatially inhomogeneous systems, i.e., a thin polymer film confined between two solid substrates. The single-chain conformations are packed into the thin film conserving the single-chain properties and simultaneously minimizing local fluctuations of the density. The extent to which enforcing the near-incompressibility of a dense polymer liquid during the packing process is able to re-establish intermolecular correlations is investigated by monitoring intermolecular correlation functions and the structure function of density fluctuations as a function of the distance from the confining solid substrates.Comment: 10 pages, 8 figure

Second-Harmonic Scattering as a Probe of Structural Correlations in Liquids

Second-harmonic scattering experiments of water and other bulk molecular liquids have long been assumed to be insensitive to interactions between the molecules. The measured intensity is generally thought to arise from incoherent scattering due to individual molecules. We introduce a method to compute the second-harmonic scattering pattern of molecular liquids directly from atomistic computer simulations, which takes into account the coherent terms. We apply this approach to large-scale molecular dynamics simulations of liquid water, where we show that nanosecond second-harmonic scattering experiments contain a coherent contribution arising from radial and angular correlations on a length scale of < 1 nm, much shorter than had been recently hypothesized (Shelton, D. P. J. Chem. Phys. 2014, 141). By combining structural correlations from simulations with experimental data (Shelton, D. P. J. Chem. Phys. 2014, 141), we can also extract an effective molecular hyperpolarizability in the liquid phase. This work demonstrates that second-harmonic scattering experiments and atomistic simulations can be used in synergy to investigate the structure of complex liquids, solutions, and biomembranes, including the intrinsic intermolecular correlations

Answer to the comment of Chudnovsky: On the square-root time relaxation in molecular nanomagnets

Answer to the comment of E. Chudnovsky concerning the following papers: (1) N.V. Prokof'ev, P.C.E. Stamp, Phys. Rev. Lett.80, 5794 (1998). (2) W. Wernsdorfer, T. Ohm, C. Sangregorio, R. Sessoli, D. Mailly, C. Paulsen, Phys. Rev. Lett. 82, 3903 (1999).Comment: 1 page