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PubMed Journals Articles About "Conformation Induced Dynamical Heterogeneity Water Solvation Shell Zwitterionic" RSS

02:07 EST 15th November 2019 | BioPortfolio

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Showing "Conformation Induced Dynamical Heterogeneity Water Solvation Shell Zwitterionic" PubMed Articles 1–25 of 26,000+

Conformation Induced Dynamical Heterogeneity of Water in the Solvation Shell of Zwitterionic γ-Aminobutyric Acid.

The structure and dynamics of water molecules around the carboxylate and amino groups of gamma-aminobutyric acid (GABA), a primary neurotransmitter in mammals, are investigated by means of ab initio molecular dynamics simulation. Zwitterionic GABA has two major conformations in water, namely the open or the closed conformations. The angle-averaged one dimensional structures of water in the solvation shells around the carboxylate and amino groups are found to be quite similar for the closed and open conforma...


Dynamics and Spectral Response of Water Molecules around Tetramethylammonium Cation.

Till now, there lies ambiguity about the structural heterogeneity inside solute solvation shell and dynamical response of the surrounding solvent molecules. To address the dynamics and spectral response of solvent molecules, we performed first principles molecular dynamics simulations for the comprehensive study of water's hydroxyl stretch frequency evolution due to environmental variations (also called 'spectral diffusion') in the vicinity of a hydrophobe, tetramethylammonium (TMA) cation. N-Ow radial dist...

Spatially-Decomposed Free Energy of Solvation Based on the Endpoint Density-Functional Method.

A spatially resolved version of the density-functional method for solvation thermodynamics is presented by extending the free-energy functional previously established in the one-dimensional, energy representation and formulating a new expression in a mixed four-dimensional representation (three dimensions for position and one dimension for energy). The space was further divided into a set of discrete regions with respect to the relative position of a solvent molecule from the solute, and the spatially decom...


Understanding Water Structure in an Ion-Pair Solvation Shell in the Vicinity of a Water/Membrane Interface.

The anomalous properties of interfacial water at the surface of a lipid membrane and their implications on nearby chemical processes are well recognized. However, we have found that ion pairing thermodynamics may not be significantly affected by interfacial water in a classical, non-polarizable force field. To trace the root cause of such a counter-intuitive finding, we performed atomistic molecular dynamics simulations to explore the impact of polarizable interactions and characterize the hydration structu...

Effect of Cation Size on Solvation and Association with Superoxide Anion in Aprotic Solvents.

Influence of cation size on solvation strength, diffusion and kinetics of the association reaction with anions O2- in aprotic solvents, such as acetonitrile and dimethyl sulfoxide, has been investigated using molecular dynamics simulation. The work is motivated by the need to understand the molecular nature of the solvent-induced changes in capacity of Li-air batteries. We have shown that the dependence of the solvation shell stability on the cation size has a maximum at a particular ion radius that corresp...

How do ribozymes accommodate additional water molecules upon hydrostatic compression deep into the kilobar pressure regime?

Solvation by water plays an important role in the functional dynamics of biomacromolecules such as proteins or nucleic acids. This suggests that changes in solvation might drastically affect their functionality. Among other solvation stressors such as temperature, cosolvents or crowding agents, applying pressure in the multi-kilobar regime is known to modulate the hydration pattern of solutes, from simple to complex. In this study, we simulated a hairpin ribozyme, being catalytic RNA, using extensive replic...

The Role of Displacing Confined Solvent in the Conformational Equilibrium of β-Cyclodextrin.

This study investigates the role of hydration and its relationship to the conformational equilibrium of the host molecule β-cyclodextrin. Molecular dynamics simulations indicate that the unbound β-cyclodextrin exhibits two state behavior in explicit solvent due to the opening and closing of its cavity. In implicit solvent, these transitions are not observed and there is one dominant conformation of β-cyclodextrin with an open cavity. Based on these observations, we investigate the hypothesis that the exp...

Origin of Slow Solvation Dynamics in DNA: DAPI in Minor Groove of Dickerson-Drew DNA.

The measurement and understanding of collective solvation dynamics in DNA have vital biological implications as protein and ligand binding to DNA can be directly controlled by complex electrostatic interactions of anionic-DNA and surrounding dipolar-water, and ions. Time-resolved fluorescence Stokes shift (TRFSS) experiments revealed anomalously slow solvation dynamics in DNA much beyond 100 ps that follow either power-law or slow multi-exponential decay over several nanoseconds. The origin of such disperse...

Striking Isotopologue Dependent Photodissociation Dynamics of Water Molecules: The Signature of an Accidental Resonance.

Investigations of the photofragmentation patterns of both light and heavy water at the state-to-state level are a pre-requisite for any thorough understanding of chemical processing and isotope heterogeneity in the interstellar medium (ISM). Here we reveal dynamical features of the dissociation of water molecules following excitation to the (010) state using a tunable vacuum ultraviolet source in combination with the high resolution H(D)-atom Rydberg tagging time-of-flight technique. The action spectra for ...

Proton Thermodynamics in a Protic Ionic Liquid, Ethylammonium Nitrate.

In order to investigate the proton solvation state in protic ionic liquids, ten acid dissociation enthalpies and entropies of eight compounds were determined in ethylammonium nitrate (EAN). Regardless of the nature of the compound, both enthalpy and entropy values were observed 24 kJ/mol and 65 J/(mol K), respectively, greater than those in water. These values were reasonably explained by the differences in the proton solvation structure in EAN and water. Namely, protons in EAN exist as HNO3, which intrinsi...

Heterogeneous Occupancy and Vibrational Dynamics of Spatially Patterned Water Molecules.

We performed first principles molecular dynamics simulations of relatively dilute aqueous solutions of sulfate and thiosulfate dianions to analyze the structure, dynamics and vibrational spectral properties of water molecules around the solute, especially the spatially patterned solvent molecules in the first solvation layer and the extended layers. This study also involves the investigation of dynamics of dangling OH groups in these layers and their role in patterning the water molecules around the dianion...

Unraveling the Origin of the Apparent Charge of Zwitterionic Lipid Layers.

The structure of water molecules in contact with zwitterionic lipid molecules is of great biological relevance since biological membranes are largely composed of such lipids. The interaction of the interfacial water molecules with the amphiphilic lipid molecules drives the formation of membranes and greatly influences various processes at the membrane surface as the field that arises from the aligned interfacial water molecules masks the charges of the lipid headgroups from the approaching metabolites. To i...

Structural and dynamical basis of G protein inhibition by YM-254890 and FR900359: an inhibitor in action.

Specific inhibition of G proteins holds a great pharmacological promise to, e.g. target oncogenic Gq/11 proteins and can be achieved by the two natural products FR900359 (FR) and YM-254890 (YM). Unfortunately, recent rational-design-based approaches to address G proteins other than Gq/11/14 subtypes were not successful mainly due to the conformational complexity of these new modalities-like compounds. Here, we report the water-derived NMR structure of YM, which strongly differs from the conformation of Gq-b...

The solvation effect on the rattling behaviour of the hydrated excess proton in water.

The solvation effect on the kinetic rattling behaviour of the hydrated excess proton H+(aq) in water is theoretically modeled by using density functional theory (DFT) and the quantum chemical cluster model (CM). To test the solvation effects on the proton morphology and rattling kinetics, different solvation models for the proton are constructed based on the gas phase (GP) Zundel cation, which include the gas phase-polarizable continuum model (GP-PCM), the gas phase-supermolecule model (GP-SM), and the gas ...

Anomalous Dynamics of Concentrated Silica-PNIPAm Nanogels.

We present the structure and dynamics of highly concentrated core-shell nanoparticles composed of a silica core and a poly(N-isoproylacrylamide) (PNIPAm) shell suspended in water. With X-ray photon correlation spectroscopy we are able to follow dynamical changes over the volume phase transition of PNIPAm at LCST = 32°C. On raising the temperature beyond LCST, the structural relaxation times continue to decrease. The effect is accompanied by a transition from stretched to compressed exponential shape of the...

Snowball formation for Cs solvation in molecular hydrogen and deuterium.

Interactions of atomic cations with molecular hydrogen are of interest for a wide range of applications in hydrogen technologies. These interactions are fairly strong despite being non-covalent, hence one can ask whether hydrogen molecules would form dense, solid-like, solvation shells around the ion (snowballs) or rather a more weakly bound compound. In this work, the interactions between Cs+ and H2 are studied both experimentally and computationally. Isotopic substitution of H2 by D2 is also investigated....

Spherical Sandwich Au@Pd@UIO-67/Pt@UIO-n (n = 66, 67, 69) Core-Shell Catalysts: Zr-Based Metal-Organic Frameworks for Effectively Regulating the Reverse Water-Gas Shift Reaction.

In this study, spherical sandwich Au@Pd@UIO-67/Pt@UIO-n (n = 66, 67, 69) core-shell catalysts were assembled. Au nanoparticles (NPs) were used as the core for the epitaxial growth of Pd shells, and Au@Pd core-shell NPs were successfully encapsulated in the center of monodispersed Au@Pd@UIO-67 nanospheres. Pt NPs were fully fixed onto the nanosphere surfaces to obtain Au@Pd@UIO-67/Pt composites; further coating with UIO-n led to Au@Pd@UIO-67/Pt@UIO-n, in which Pt NPs are sandwiches between the Au@Pd@UIO-67 c...

Preparation and characterization of zwitterionic functionalized starch nanoparticles.

Zwitterionic polymers have attracted great attention due to their unique structure, which can be used for various applications, such as the improvement of nanoparticle stability, ion exchange, sewage treatment, and biomedicine. Here, zwitterionic functionalized starch nanoparticles (SNPs) were successfully prepared in two steps by carboxymethylation and quaternization. The structure of the modified SNPs was confirmed using Fourier transform infrared spectroscopy, nuclear magnetic resonance spectroscopy, and...

Synthesis of far-red- and near-infrared-emitting Cu-doped InP/ZnS (core/shell) quantum dots with controlled doping steps and their surface functionalization for bioconjugation.

In this study, we designed and synthesized far-red- and near-infrared-emitting Cu-doped InP-based quantum dots (QDs), and we also demonstrated their highly specific and sensitive biological imaging ability. Cu-doped InP/ZnS (core/shell) QDs were prepared using the hot colloidal synthesis method in the organic phase. The ZnS shell passivates the surface and improves the photoluminescence (PL) intensity. However, the InP : Cu/ZnS (core : dopants/shell) QDs, which were obtained after the Cu dopant was ...

Principal Component Analysis of a Conotoxin Delineates the Link among Peptide Sequence, Dynamics and Disulfide Bond Isoforms.

Replica exchange molecular dynamics (REMD) and subsequent principal component analysis (PCA) of the dynamical modes of α-conotoxins, GI and its two mutants, in water and an aqueous biocompatible ionic liquid, 1-ethyl-3-methyl-imidazolium acetate (50% v/v) provide perceptions into how the mutations affect the global correlated motions in the peptide backbone, eventually ending up influencing the combination of disulfide links in such multiple cysteine containing venom toxins. Region-wise breakup of the cont...

A Comprehensive Picture of Water Dynamics in Nafion Membranes at Different Levels of Hydration.

1H NMR spectroscopy is employed to study the long-range (diffusion) and short-range (relaxation) motions of water in the hydrophilic channels of Nafion at different stages of hydration, λwater. From Bloembergen, Purcell and Pound (BPP) analysis of the temperature-dependent 1H spin-lattice relaxation rates, the coexistence of two motional modes for λwater < 9 was observed, which can be attributed to the non-freezing behavior of water molecules. At higher hydration levels, a clear transition between two dif...

Multi-State Reactive Molecular Dynamics Simulations of Proton Diffusion in Water Clusters and in Bulk.

The molecular mechanics with proton transfer (MMPT) force field is combined with multi state adiabatic reactive molecular dynamics (MS-ARMD) to describe proton transport in the condensed phase. Parametrization for small protonated water clusters based on electronic structure calculations at the MP2/6-311+G(2d,2p) level of theory and refinement by comparing with infrared spectra for protonated water tetramer yields a force field which faithfully describes minimum energy structures of small protonated water c...

Experimental and Theoretical Studies on the Aqueous Solvation and Reactivity of SmCl and Comparison with SmBr and SmI.

Water addition to Sm(II) has been shown to increase reactivity for both SmI and SmBr. Previous work in our groups has demonstrated that this increase in reactivity can be attributed to coordination induced bond weakening enabling substrate reduction through proton-coupled electron transfer. The present work examines the interaction of water with samarium dichloride (SmCl) and illustrates the importance of the Sm-X interaction and bond distance upon water addition critical for the reactivity of the reagent s...

Probing Surface Hydration and Molecular Structure of Zwitterionic and Polyacrylamide Hydrogels.

A hydrogel is a hydrophilic cross-linked polymer network which can contain a large amount of water. Hydrogels with distinguished interfacial physical toughness were analyzed for their potential application as antifouling coating materials, utilizing sum frequency generation (SFG) spectroscopy as the interfacial analytical technique. The surface structures of one sulfobetaine (SBMA) zwitterionic hydrogel (ZWHG) and two polysaccharide hydrogels (PHGs) were probed in air; their interfacial structures with sili...

Perturbation of Hydrogen Bonding Networks Over Supported Lipid Bilayers by Poly (allylamine hydrochloride).

Water is vital to many biochemical processes and is necessary for driving many fundamental interactions of cell membranes with their external environments, yet it is difficult to probe the membrane/water interface directly and without the use of external labels. Here, we employ vibrational sum frequency generation (SFG) spectroscopy to understand the role of interfacial water molecules above bilayers formed from zwitterionic (phosphatidylcholine, PC) and anionic (phosphatidylglycerol, PG, and phosphatidylse...


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