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The present study explores the hydrogen-bond network in an equimolar mixture of acetic acid and water (AA-W). The investigation was conducted using a combination of neutron scattering and Density Functional Theory (DFT). New neutron scattering data at large scattering wave vectors were analyzed to determine the total structure factor SM(q) and the molecular form factor F1(q) of the system. DFT calculations using the 6-311++G(d, p) basis set were performed to optimize the monomers and various AA-W H-bonded clusters, including one acetic acid (AA) molecule connected to one, two, and three water molecules. Consequently, three dimers, three trimers, and one tetramer have been considered in order to describe the local order in the mixture. In addition, this study focused on the H-bond interactions in the most probable clusters in the solution, using the natural bond orbital and the atoms in molecules analyses. Our analysis particularly shows that stronger H-bond interactions occur in the ring structures.
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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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Water is an essential participant in the stability, structure, dynamics, and function of proteins and other biomolecules. Thermodynamically, changes in the aqueous environment affect the stability of biomolecules. Structurally, water participates chemically in the catalytic function of proteins and nucleic acids and physically in the collapse of the protein chain during folding through hydrophobic collapse and mediates binding through the hydrogen bond in complex formation. Water is a partner that slaves the dynamics of proteins, and water interaction with proteins affect their dynamics. Here we provide a review of the experimental and computational advances over the past decade in understanding the role of water in the dynamics, structure, and function of proteins. We focus on the combination of X-ray and neutron crystallography, NMR, terahertz spectroscopy, mass spectroscopy, thermodynamics, and computer simulations to reveal how water assist proteins in their function. The recent advances in computer simulations and the enhanced sensitivity of experimental tools promise major advances in the understanding of protein dynamics, and water surely will be a protagonist.
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Proteínas/química , Agua/química , Enlace de Hidrógeno , Presión Hidrostática , Canales Iónicos/química , Estructura Molecular , Muramidasa/química , Transición de Fase , Desnaturalización Proteica , Temperatura , Espectroscopía de Terahertz/métodosRESUMEN
In the present work, we have investigated the intermolecular associations of formamide with water in an equimolar formamide-water solution (FA-Water) by means of neutron scattering in combination with density functional theory calculations. The neutron scattering data were analyzed to deduce the structure factor SM(q) and the intermolecular pair correlation function gL(r). By considering different hydrogen bonded FA-Water associations, it has been shown that some of them describe well the local order in the solution. Natural bond orbital and atoms in molecules analyses have been performed to give more insight into the properties of hydrogen bonds involved in the more probable models.
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Formamidas/química , Teoría Cuántica , Agua/química , Enlace de Hidrógeno , NeutronesRESUMEN
We have measured the dynamics of water confined in a porous magnesium carbonate material, Upsalite®, using the high-resolution neutron backscattering spectrometer SPHERES. We found quasielastic scattering that does not flatten out up to 360 K, which means that the dynamics of water are much slower than in other matrix materials. Specifically, a single Lorentzian line could be fitted to the quasielastic part of the acquired spectra between 220 and 360 K. This, accompanied by an elastic line from dynamically frozen water present at all experimental temperatures, even above the melting point, signaled a significant amount of bound or slow water.
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Apo-calmodulin, a small soluble mainly α protein, is a calcium-dependent protein activator. Calcium binding affects the calmodulin conformation but also its stability. Calcium free form unfolds between 40 and 80°C, whereas the calcium-saturated form is stable up to temperatures as high as 100°C, forbidding comparison of the thermal unfolding pathways of the two forms. Thus, this paper focuses especially on the conformation of pressure-induced unfolding states of both forms of calmodulin, by combining small-angle neutron scattering (SANS) with biophysical techniques such as tyrosines and ANS fluorescence. In contrast to heat denaturation (Gibrat et al., BBA, 2012), the pressure denaturation of calmodulin is reversible up to pressures of 3000bar (300MPa). A pressure-induced compact intermediate state has been found for the two calmodulin forms, but their unfolding pathways are different. A domain compaction and an increase of the ANS fluorescence of holo form have been evidenced. On the contrary, a domain dilatation and an ANS fluorescence decrease have been found for the apo form. The pressure induced an increase of the interdomain distance for both calmodulin forms, suggesting that the central linker of calmodulin is flexible in solution.
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Apoproteínas/química , Calcio/química , Calmodulina/química , Desplegamiento Proteico , Naftalenosulfonatos de Anilina , Dicroismo Circular , Colorantes Fluorescentes , Humanos , Modelos Moleculares , Difracción de Neutrones , Presión , Conformación Proteica , Desnaturalización Proteica , Pliegue de Proteína , Proteínas Recombinantes/química , Dispersión del Ángulo Pequeño , Espectrometría de Fluorescencia , Temperatura , TermodinámicaRESUMEN
In complementarity with X-ray scattering and as extension of our previous publication, neutron scattering measurements are combined to DFT calculation to investigate the structural features of N-methylformamide-water mixtures (NMF-water) for three water molar fractions x w = 0.5 , 0.66 and x w = 0.75 . The recorded data at atmospheric pressure and room temperature are analyzed to yield the structure factor, the molecular form factor and the pair correlation function. Neutron investigations corroborate the X-ray ones and clearly show that liquid order in solutions is well accounted for by a tetramer. In this cluster, an NMF molecule is connected to three water molecules by one N-D···O and two O-D···O hydrogen bonds.
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Óxido de Deuterio/química , Formamidas/química , Enlace de Hidrógeno , Difracción de Neutrones , Difracción de Rayos XRESUMEN
Structural and dynamic properties of ß-lactoglobulin (ß-LG) were revealed as a function of alcohol concentration in ethanol- and trifluoroethanol(TFE)-water mixtures with circular dichroism (CD), small-angle neutron scattering (SANS) and quasi-elastic neutron scattering (QENS). The CD spectra showed that an increase in TFE concentration promotes the formation of the ß-sheet structure of ß-LG. The SANS-intensities were fitted using form factors for two attached spheres for the native and native-like states of the protein. At higher alcohol concentrations, where aggregation takes place, a form factor modelling diffusion limited colloidal aggregation (DLCA) was employed. The QENS-data were analyzed in terms of internal motions for all alcohol concentrations. While low concentrations of TFE (10% (v/v)) lead to an increase of the mean square amplitudes of vibrations and a retention of a native-like structure - but not to an increase of the characteristic radius of proton diffusion processes a. Addition of 20% (v/v) of TFE induces aggregation, going along with a further increase of . Further increase of TFE concentration to 30% (v/v) changes the nanoscale structure of the oligomeric nucleate, but induces no further significant changes in . The present study underlines the necessity of methods sensitive to the dynamics of a system to obtain a complete picture of a molecular process.
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Etanol/química , Lactoglobulinas/química , Trifluoroetanol/química , Animales , Bovinos , Dicroismo Circular , Cinética , Difracción de Neutrones , Pliegue de Proteína , Isoformas de Proteínas/química , Estructura Secundaria de Proteína , Dispersión del Ángulo Pequeño , Soluciones , Agua , Difracción de Rayos XRESUMEN
Apo-calmodulin, a small, mainly α, soluble protein is a calcium-dependent protein activator. It is made of two N- and C-terminal domains having a sequence homology of 70%, an identical folding but different stabilities, and is thus an interesting system for unfolding studies. The use of small angle neutron scattering (SANS) and other biophysical techniques has permitted to reveal conformational difference between native and thermal denatured states of apo-calmodulin. The results show that secondary and tertiary structures of apo-calmodulin evolve in a synchronous way, indicating the absence in the unfolding pathway of molten-globule state sufficiently stable to affect transition curves. From SANS experiments, at 85 °C, apo-calmodulin adopts a polymer chain conformation with some residual local structures. After cooling down, apo-calmodulin recovers a compact state, with a secondary structure close to the native one but with a higher radius of gyration and a different tyrosine environment. In fact on a timescale of few minutes, heat denaturation of apo-calmodulin is partially reversible, but on a time scale of hours (for SANS experiments), the long exposure to heat may lead to a non-reversibility due to some chemical perturbation of the protein. In fact, from Mass Spectrometry measurements, we got evidence of dehydration and deamidation of heated apo-calmodulin.
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Calmodulina/química , Biofisica , Dicroismo Circular , Difracción de Neutrones , Conformación Proteica , Dispersión del Ángulo Pequeño , Espectrometría de Fluorescencia , Espectrofotometría Ultravioleta , TermodinámicaRESUMEN
We performed complementary inelastic neutron scattering (INS) experiments and molecular dynamics (MD) simulations to study the influence of pressure on the low-frequency vibrational modes of lysozyme in aqueous solution in the 1 atm-6 kbar range. Increasing pressure induces a high-frequency shift of the low-frequency part (<10 meV = 80 cm(-1)) of the vibrational density of states (VDOS), g(ω), of both lysozyme and water that reveals a stiffening of the interactions ascribed to the reduction of the protein and water volumes. Accordingly, high pressures increase the curvature of the free energy profiles of the protein quasiharmonic vibrational modes. Furthermore, the nonlinear influence of pressure on the g(ω) of lysozyme indicates a change of protein dynamics that reflects the nonlinear pressure dependence of the protein compressibility. An analogous dynamical change is observed for water and stems from the distortion of its tetrahedral structure under pressure. Moreover, our study reveals that the structural, dynamical, and vibrational properties of the hydration water of lysozyme are less sensitive to pressure than those of bulk water, thereby evidencing the strong influence of the protein surface on hydration water.
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Simulación de Dinámica Molecular , Muramidasa/química , Difracción de Neutrones/métodos , Agua/química , Animales , Pollos , Neutrones , Presión , Análisis de Componente Principal , Dispersión de Radiación , Termodinámica , VibraciónRESUMEN
High-speed photographic studies and neutron diffraction measurements have been made of water under tension in a Berthelot tube. Liquid water was cooled below the normal ice-nucleation temperature and was in a doubly-metastable state prior to a collapse of the liquid state. This transition was accompanied by an exothermic heat release corresponding with the rapid production of a solid phase nucleated by cavitation. Photographic techniques have been used to observe the phase transition over short time scales in which a solidification front is observed to propagate through the sample. Significantly, other images at a shorter time interval reveal the prior formation of cavitation bubbles at the beginning of the process. The ice-nucleation process is explained in terms of a mechanism involving hydrodynamically-induced changes in tension in supercooled water in the near vicinity of an expanding cavitation bubble. Previous explanations have attributed the nucleation of the solid phase to the production of high positive pressures. Corresponding results are presented which show the initial neutron diffraction pattern after ice-nucleation. The observed pattern does not exhibit the usual crystalline pattern of hexagonal ice [I(h)] that is formed under ambient conditions, but indicates the presence of other ice forms. The composite features can be attributed to a mixture of amorphous ice, ice-I(h)/I(c) and the high-pressure form, ice-III, and the diffraction pattern continues to evolve over a time period of about an hour.
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A study has been made as a function of temperature of the phase transformation of water and ice in two samples of mesoporous silica gel with pore diameters of approximately 50 A. One sample was modified by coating with a layer of trimethylchlorosilane, giving a predominantly hydrophobic internal surface, whereas the unmodified sample has a hydrophilic interface. The pore structure was characterised by nitrogen gas adsorption and NMR cryoporometry and the melting/freezing behaviour of water and ice in the pores was studied by DSC and neutron diffraction for cooling and heating cycles, covering a range of 200 to 300 K. Measurements were made for several filling-factors in the range 0.2 to 0.9. The results show a systematic difference in the form of ice created in each of the samples. The non-modified sample gives similar results to previous studies with hydrophilic silicas, exhibiting a defective form of cubic ice superimposed on a more disordered pattern that changes with temperature and has been characterised as 'plastic' ice [Liu et al., 2006, Webber et al., 2007]. The modified sample has similar general features but displays important variability in the ice transformation features, particularly for the case of the low filling-factor (f = 0.2). The results exhibit a complex temperature-dependent variation of the crystalline and disordered components that are substantially altered for the different filling-factors.
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Molecular dynamics simulations have been performed for liquid formamide using two different types of potential model (OPLS, Cordeiro). The structural results obtained from simulation were compared to experimental (x-ray and neutron diffraction measurements) outcomes. A generally good agreement for both models examined has been found, but in the hydrogen bonded region (2.9 A) the Cordeiro model shows a slightly better fit. Besides the evaluation of partial radial distribution functions, orientational correlation functions and energy distribution functions, describing the hydrogen bonded structure, have been calculated based on the statistical analysis of configurations, resulting into a new insight in the clustering properties and topology of hydrogen bonded network. It has been shown that in liquid formamide exists a continuous hydrogen bonded network and from the analysis of the distribution of small rings revealed the ring size distribution in liquid formamide. Our study resulted that the ring size distribution of the hydrogen bonded liquid formamide shows a broad distribution with a maximum around 11. It has been found that the topology in formamide is significantly different than in water.
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Formamidas/química , Enlace de Hidrógeno , Modelos Químicos , Simulación de Dinámica Molecular , Estructura MolecularRESUMEN
The structure of a series of aqueous sodium nitrate solutions (1.9-7.6 M) was studied using a combination of experimental and theoretical methods. The results obtained from diffraction (X-ray, neutron) and molecular dynamics simulation have been compared and the capabilities and limitations of the methods in describing solution structure are discussed. For the solutions studied, diffraction methods were found to perform very well in description of hydration spheres of the sodium ion but do not yield detailed structural information on the anion's hydration structure. Molecular dynamics simulations proved to be a suitable tool in the detailed interpretation of the hydration sphere of ions, ion pair formation, and bulk structure of solutions.
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Nitratos/química , Agua/química , Simulación por Computador , Modelos Moleculares , Difracción de Neutrones , Oxígeno/química , Soluciones/química , Difracción de Rayos XRESUMEN
Apo-calmodulin, a small, mainly alpha, soluble protein is a calcium-dependent protein activator. This article presents a study of internal dynamics of native and thermal unfolded apo-calmodulin, using quasi-elastic neutron scattering. This technique can probe protein internal dynamics in the picosecond timescale and in the nanometer length-scale. It appears that a dynamical transition is associated with thermal denaturation of apo-calmodulin. This dynamical transition goes together with a decrease of the confinement of hydrogen atoms, a decrease of immobile protons proportion and an increase of dynamical heterogeneity. The comparison of native and unfolded states dynamics suggests that the dynamics of protein atoms is more influenced by their distance to the backbone than by their solvent exposure.
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Calmodulina/metabolismo , Temperatura de Transición , Calmodulina/química , Elasticidad , Humanos , Movimiento , Difracción de Neutrones , Desnaturalización Proteica , Pliegue de ProteínaRESUMEN
Thermodynamic, structural, and dynamic properties of heavy water (D(2)O) confined in mesoporous silica glass MCM-41 C10, C12, and C14 were investigated by differential scanning calorimetry, neutron diffraction, and neutron spin echo (NSE) measurements, respectively. The DSC data showed that no crystallization of D(2)O confined in C10 occurs in a temperature range between 298 and 180 K, and that crystalline ice is formed at 204 and 221 K for C12 and C14, respectively. For C10, the neutron radial distribution functions of confined D(2)O suggested a structural change in the supercooled state between 223 and 173 K. For C10 sample, it has been found that the tetrahedral-like water structure is partially enhanced in the central part of pores at 173 K. For all the samples, the intermediate scattering functions from the NSE measurements are fitted by the Kohlrausch-Williams-Watts stretched exponential function which implies that confined supercooled D(2)O exhibits a wide distribution of relaxation times. For C10, C12, and C14 samples, between 298 and 240 K, the relaxation times of supercooled D(2)O follow remarkably well the Vogel-Fulcher-Tamman equation; for C10 sample, below 240 K, the relaxation times of nonfreezing D(2)O show an Arrhenius type behavior. From the present experimental results on calorimetric, structural, and dynamic properties, it has been concluded that supercooled D(2)O confined in MCM-41 C10 experiences a transition from high-density to low-density hydrogen-bonded structure at around 229 K.
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The data presented in this article are related to the research article entitled "Probing the dynamics of complexed local anesthetics via neutron scattering spectroscopy and DFT calculations (http://dx.doi.org/10.1016/j.ijpharm.2017.03.051)" (Martins et al., 2017) [1]. This work shows the molecular and structural behavior of the local anesthetics (LAs) bupivacaine (BVC, C18H28N2O) and ropivacaine (RVC, C17H26N2O) before and after complexation with the water-soluble oligosaccharide 2-hydroxypropyl-ß-cyclodextrin (HP-ß-CD).
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Since potential changes in the dynamics and mobility of drugs upon complexation for delivery may affect their ultimate efficacy, we have investigated the dynamics of two local anesthetic molecules, bupivacaine (BVC, C18H28N2O) and ropivacaine (RVC, C17H26N2O), in both their crystalline forms and complexed with water-soluble oligosaccharide 2-hydroxypropyl-ß-cyclodextrin (HP-ß-CD). The study was carried out by neutron scattering spectroscopy, along with thermal analysis, and density functional theory computation. Mean square displacements suggest that RVC may be less flexible in crystalline form than BVC, but both molecules exhibit very similar dynamics when confined in HP-ß-CD. The use of vibrational analysis by density functional theory (DFT) made possible the identification of molecular modes that are most affected in both molecules by insertion into HP-ß-CD, namely those of the piperidine rings and methyl groups. Nonetheless, the somewhat greater structure in the vibrational spectrum at room temperature of complexed RVC than that of BVC, suggests that the effects of complexation are more severe for the latter. This unique approach to the molecular level study of encapsulated drugs should lead to deeper understanding of their mobility and the respective release dynamics.
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Amidas/análisis , Anestésicos Locales/análisis , Bupivacaína/análisis , 2-Hidroxipropil-beta-Ciclodextrina/química , Difracción de Neutrones , Ropivacaína , Análisis Espectral , beta-CiclodextrinasRESUMEN
A structural investigation of fully deuterated liquid N-methylacetmide (NMAd7) is performed at 308 K and atmospheric pressure by using neutron diffraction together with density-functional theory (DFT). The analysis of experimental data yields the total structure factor SM(Q), the molecular form factor F1(Q), and the distinct pair correlation function gL(r). The DFT calculations are performed to study the relative stability of the two possible isomers (trans and cis) and to examine some possible clusters recently published that may describe the intermolecular arrangement in the liquid state. Neutron measurements can be interpreted in terms of trans linear trimer (T1) and cis cyclic trimer (T2) where the total number of hydrogen bonds is respectively equal to two and three. The theoretical structure factors obtained on the basis of intermolecular arrangements agree fairly well with the experimental one beyond Q = 2 A-1. All through the study, a comparison is made with complementary X-ray results.
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Acetamidas/química , Deuterio/química , Modelos Químicos , Algoritmos , Enlace de Hidrógeno , Difracción de Neutrones , Teoría CuánticaRESUMEN
The microstructures of pure water and aqueous NaCl solutions over a wide range of salt concentrations (0-4 m) under ambient conditions are characterized by X-ray scattering and molecular dynamics (MD) simulations. MD simulations are performed with the rigid SPC water model as a solvent, while the ions are treated as charged Lennard-Jones particles. Simulated data show that the first peaks in the O...O and O...H pair correlation functions clearly decrease in height with increasing salt concentration. Simultaneously, the location of the second O...O peak, the signature of the so-called tetrahedral structure of water, gradually disappears. Consequently, the degree of hydrogen bonding in liquid water decreases when compared to pure fluid. MD results also show that the hydration number around the cation decreases as the salt concentration increases, which is most likely because some water molecules in the first hydration shell are occasionally substituted by chlorine. In addition, the fraction of contact ion pairs increases and that of solvent-separated ion pairs decreases. Experimental data are analyzed to deduce the structure factors and the pair correlation functions of each system. X-ray results clearly show a perturbation of the association structure of the solvent and highlight the appearance of new interactions between ions and water. A model of intermolecular arrangement via MD results is then proposed to describe the local order in each system, as deduced from X-ray scattering data.