Showing papers in "The Journal of Physical Chemistry in 2012"

Origin of Long-Lived Coherences in Light-Harvesting Complexes

Abstract: A vibronic exciton model is applied to explain the long-lived oscillatory features in the two-dimensional (2D) electronic spectra of the Fenna–Matthews–Olson (FMO) complex. Using experimentally determined parameters and uncorrelated site energy fluctuations, the model predicts oscillations with dephasing times of 1.3 ps at 77 K, which is in a good agreement with the experimental results. These long-lived oscillations originate from the coherent superposition of vibronic exciton states with dominant contributions from vibrational excitations on the same pigment. The oscillations obtain a large amplitude due to excitonic intensity borrowing, which gives transitions with strong vibronic character a significant intensity despite the small Huang–Rhys factor. Purely electronic coherences are found to decay on a 200 fs time scale.

Glyme–Lithium Salt Equimolar Molten Mixtures: Concentrated Solutions or Solvate Ionic Liquids?

Abstract: To demonstrate a new family of ionic liquids (ILs), i.e., “solvate” ionic liquids, the properties (thermal, transport, and electrochemical properties, Lewis basicity, and ionicity) of equimolar molten mixtures of glymes (triglyme (G3) and tetraglyme (G4)) and nine different lithium salts (LiX) were investigated. By exploring the anion-dependent properties and comparing them with the reported data on common aprotic ILs, two different classes of liquid regimes, i.e., ordinary concentrated solutions and “solvate” ILs, were found in the glyme–Li salt equimolar mixtures ([Li(glyme)]X) depending on the anionic structures. The class a given [Li(glyme)]X belonged to was governed by competitive interactions between the glymes and Li cations and between the counteranions (X) and Li cations. [Li(glyme)]X with weakly Lewis basic anions can form long-lived [Li(glyme)]⁺ complex cations. Thus, they behaved as typical ionic liquids. The lithium “solvate” ILs based on [Li(glyme)]X have many desirable properties for lithium-conducting electrolytes, including high ionicity, a high lithium transference number, high Li cation concentration, and high oxidative stability, in addition to the common properties of ionic liquids. The concept of “solvate” ionic liquids can be utilized in an unlimited number of combinations of other metal salts and ligands, and will thus open a new field of research on ionic liquids.

Molecular dynamics simulations of water structure and diffusion in silica nanopores

Abstract: We present molecular dynamics (MD) simulations of water-filled silica nanopores such as those that occur in ordered oxide ceramics (MCM-41, SBA-15), controlled pore glasses (such as Vycor glass), mesoporous silica, bioglasses, and hydrous silica gel coatings of weathered minerals and glasses. Our simulations overlap the range of pore diameters (1–4 nm) where confinement causes the disappearance of bulk-liquid-like water. In ≥2 nm diameter pores, the silica surface carries three statistical monolayers of density-layered water, interfacial water structure is independent of confinement or surface curvature, and bulk-liquid-like water exists at the center of the pore (this last finding contradicts assumptions used in most previous neutron diffraction studies and in several MD simulation studies of silica nanopores). In 1 nm diameter pores, bulk-liquid-like water does not exist and the structural properties of interfacial water are influenced by confinement. Predicted water diffusion coefficients in 1–4 nm dia...

Role of Nanoparticle Surface Charge on the Nucleation of the Electroactive β-Poly(vinylidene fluoride) Nanocomposites for Sensor and Actuator Applications

Abstract: The electroactive β-phase of poly(vinylidene fluoride) (PVDF) can be nucleated by introducing CoFe2O4 nanoparticles within the polymer matrix, leading to electroactive materials with large potential for sensor and actuator applications. The effects of the CoFe2O4 nanoparticle electrostatic charge on the phase crystallization of PVDF polymer is reported. For this purpose, CoFe2O4 nanoparticles were coated with anionic (SDS), nonanionic (Triton X-100), and cationic (CTAB) surfactants, and the obtained coated nanoparticles were used as fillers. It is found that the piezoelectric β-form of the polymer increases when CoFe2O4 nanoparticles with higher negative electrostatic charge are added. This behavior is attributed to the interaction between the negatively charged magnetic particles and the polymer CH2 groups, having a positive charge density. Further the relationship between the β-phase content and the piezoelectric response has been demonstrated. The magnetostriction of the ferrite nanoparticles and the p...

Solubility of CO2, H2S, and Their Mixture in the Ionic Liquid 1-Octyl-3-methylimidazolium Bis(trifluoromethyl)sulfonylimide B

Abstract: Gaseous solubilities of carbon dioxide (1), hydrogen sulfide (2), and their binary mixture (x₂ ≈ 0.2, 0.5, 0.8) have been measured in the ionic liquid 1-octyl-3-methylimidazolium bis(trifluoromethyl)sulfonylimide ([C₈mim][Tf₂N]) at temperatures ranging from (303.15 to 353.15) K and at pressures under 2 MPa. The observed PTx solubility data were used to obtain Henry's law constants and correlated by three models: (1) the simple Krichevsky–Kasarnovsky (KK) equation, (2) a model comprised of the extended Henry's law and the Pitzer's virial expansion for the excess Gibbs free energy, and (3) the generic Redlich–Kwong (RK) cubic equation of state proposed for gas–ionic liquid systems. The correlations from the three models show quite good consistency with the experimental data for IL/CO₂ and IL/H₂S binary mixtures within experimental uncertainties. For IL/CO₂/H₂S ternary mixtures, the RK model shows the best correlation with the experimental data. The comparison showed that the solubility of H₂S is about two times as great as that of CO₂ in the ionic liquid studied in this work. It was further found, by comparison of the experimental data of this study with those of previous reports, that the solubility of H₂S in [Cₙmim][Tf₂N] ILs increases as the number of carbon atoms in the alkyl substituent of methylimidazolium cation, n, increases. In addition, quantum chemical calculations at DFT/B3LYP level of theory using 6-311+G(d) and 6-311++G(2d,2p) basis sets were performed on the isolated systems studied in this work to provide explanations from a molecular point of view for the observed experimental trends.

Sitting at the Edge: How Biomolecules use Hydrophobicity to Tune Their Interactions and Function

Abstract: Water near extended hydrophobic surfaces is like that at a liquid–vapor interface, where fluctuations in water density are substantially enhanced compared to those in bulk water. Here we use molecular simulations with specialized sampling techniques to show that water density fluctuations are similarly enhanced, even near hydrophobic surfaces of complex biomolecules, situating them at the edge of a dewetting transition. Consequently, water near these surfaces is sensitive to subtle changes in surface conformation, topology, and chemistry, any of which can tip the balance toward or away from the wet state and thus significantly alter biomolecular interactions and function. Our work also resolves the long-standing puzzle of why some biological surfaces dewet and other seemingly similar surfaces do not.

Discrete Molecular Dynamics: An Efficient And Versatile Simulation Method For Fine Protein Characterization

Abstract: Until now it has been impractical to observe protein folding in silico for proteins larger than 50 residues. Limitations of both force field accuracy and computational efficiency make the folding problem very challenging. Here we employ discrete molecular dynamics (DMD) simulations with an all-atom force field to fold fast-folding proteins. We extend the DMD force field by introducing long-range electrostatic interactions to model salt-bridges and a sequence-dependent semiempirical potential accounting for natural tendencies of certain amino acid sequences to form specific secondary structures. We enhance the computational performance by parallelizing the DMD algorithm. Using a small number of commodity computers, we achieve sampling quality and folding accuracy comparable to the explicit-solvent simulations performed on high-end hardware. We demonstrate that DMD can be used to observe equilibrium folding of villin headpiece and WW domain, study two-state folding kinetics, and sample near-native states in ab initio folding of proteins of ∼100 residues.

A Simple AIMD Approach to Derive Atomic Charges for Condensed Phase Simulation of Ionic Liquids B

Abstract: The atomic charges for two ionic liquids (ILs), 1-n-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) and 1-ethyl-3-methylimidazolium hexafluorophosphate ([EMIM][PF6]), were derived from periodic crystal phase calculations with density functional theory (DFT) and plane wave basis sets (denoted as “AIMD-c charge”). For both ILs, the total charge was found to be ±0.8 e for the cation and anion, respectively, due to the charge transfer between ions and polarization caused by the environment. These atomic charges were used in a force field developed within the general Amber force field framework. Using this force field, static, dynamic, and thermodynamic properties were computed for the two ILs using molecular dynamics simulation. The results were compared against results obtained using the same Amber force field but four different sets of partial charges, denoted as full charge, scaled charge, AIMD-l charge, and AIMD-b charge, respectively. The full charge was derived from quantum chemistry calculation of isolated ions in a vacuum and resulted in a total charge of unity on each ion. The scaled charge was obtained by uniformly scaling the full charge by 0.8. AIMD-l and AIMD-b charges were derived from liquid phase ab initio molecular dynamics simulations. The scaled charges have the same total charge on the ions as the AIMD-c charge but different distributions. It was found that simulation results not only depend on the total charge of each ion, but they are also sensitive to the charge distribution within an ion, especially for dynamic and thermodynamic properties. Overall, for the two ILs under study, the AIMD-c charge was found to predict experimental results better than the other four sets of charges, indicating that fitting charges from crystal phase DFT calculations, instead of extensive sampling of the liquid phase configurations, is a simple and reliable way to derive atomic charges for condensed phase ionic liquid simulations.

Spectroscopic Exploration of Mode of Binding of ctDNA with 3-Hydroxyflavone: A Contrast to the Mode of Binding with Flavonoids Having Additional Hydroxyl Groups B

Abstract: Binding interaction of 3-hydroxyflavone (3HF), a bioactive flavonoid, with calf-thymus DNA (ctDNA) has been explored exploiting various experimental techniques. The dual fluorescence of 3HF resulting from the excited state intramolecular proton transfer (ESIPT) is modified remarkably upon binding with the biomacromolecule. The determined binding constant, fluorescence quenching experiment, circular dichroism (CD) study, comparative binding study with the known intercalative binder ethidium bromide and thermometric experiment relating to the helix melting of ctDNA confirm the groove binding of 3HF with the DNA. This is in contrast to two other members of the flavonoid group, namely, fisetin and quercetin, where the bindings are established to be intercalative. The structural difference of 3HF from the other two probes with respect to the absence/presence of the additional hydroxyl groups is ascribed to be responsible for the difference in the mode of binding.

Structures of the Amyloid β-Peptides Aβ1–40 and Aβ1–42 as Influenced by pH and a d-Peptide B

Abstract: In this simulation study, we present a comparison of the secondary structure of the two major alloforms of the Alzheimer’s peptide (Aβ₁–₄₀ and Aβ₁–₄₂) on the basis of molecular dynamics (MD) simulations on thea microsecond time scale using the two GROMOS96 force fields ffG43a2 and ffG53a6. We observe peptide and force-field related differences in the sampled conformations of Aβ₁–₄₀ and Aβ₁–₄₂, which we characterize in terms of NMR chemical shifts calculated from the MD trajectories and validate against the corresponding experimental NMR results. From this analysis, we can conclude that ffG53a6 is better able to model the structural propensities of Aβ₁–₄₀ and Aβ₁–₄₂ than ffG43a2. Furthermore, we provide a description of the influences of pH and binding of D3, a 12-residue d-enantiomeric peptide with demonstrated antiamyloid effects, on the structure of Aβ₁–₄₂. We demonstrate that, under slightly acidic conditions, protonation of the three histidine residues in Aβ₁–₄₂ promotes the formation of β-sheets via a reduction in electrostatic repulsion between the two terminal regions. Our studies further reveal that the binding between D3 and Aβ₁–₄₂ is driven by electrostatic interactions between negatively charged Aβ₁–₄₂ residues and the five positively charged arginine residues of D3. The binding of D3 was found to induce large conformational changes in the amyloid peptide, with a reduction in β-sheet units being the most significant effect recorded, possibly explaining the observed amyloid-inhibiting properties of the d-peptide.

Thermodynamic Modeling of Ionic Liquid Systems: Development and Detailed Overview of Novel Methodology Based on the PC-SAFT B

Abstract: We present the results of an extensive study on a novel approach of modeling ionic liquids (ILs) and their mixtures with molecular compounds, incorporating perturbed-chain statistical associating fluid theory (PC-SAFT). PC-SAFT was used to calculate the thermodynamic properties of different homologous series of ILs based on the bis(trifluormethylsulfonyl)imide anion ([NTf₂]). First, pure fluid parameters were obtained for each IL by means of fitting the model predictions to experimental liquid densities over a broad range of temperature and pressure. The reliability and physical significance of the parameters as well as the employed molecular scheme were tested by calculation of density, vapor pressure, and other properties of pure ILs (e.g., critical properties, normal boiling point). Additionally, the surface tension of pure ILs was calculated by coupling the PC-SAFT equation of state with density gradient theory (DGT). All correlated/predicted results were compared with literature experimental or simulation data. Afterward, we attempted to model various thermodynamic properties of some binary systems composed of IL and organic solvent or water. The properties under study were the binary vapor–liquid, liquid–liquid, and solid–liquid equilibria and the excess enthalpies of mixing. To calculate cross-interaction energies we used the standard combining rules of Lorentz–Berthelot, Kleiner–Sadowski, and Wolbach–Sandler. It was shown that incorporation of temperature-dependent binary corrections was required to obtain much more accurate results than in the case of conventional predictions. Binary corrections were adjusted to infinite dilution activity coefficients of a particular solute in a given IL determined experimentally or predicted by means of the modified UNIFAC (Dortmund) group contribution method. We concluded that the latter method allows accurate and reliable calculations of bulk-phase properties in a totally predictive manner.

Local Structure Evolution and its Connection to Thermodynamic and Transport Properties of 1-Butyl-3-methylimidazolium Tetrafluoroborate and Water Mixtures by Molecular Dynamics Simulations B

Abstract: Our recently developed improved united atom force field shows a good quality to reproduce both the static and transport properties of neat ionic liquids (ILs). Combined with the TIP4P-Ew water model, the force field is used to simulate the mixture of 1-butyl-3-methylimidazolium tetrafluoroborate ([C₄mim][BF₄]) and water without further optimization to adjust any cross parameters. Liquid densities of the mixture are well predicted over the entire concentration range at temperatures from 298.15 to 353.15 K. Simulations also reproduce the positive values of excess volumes and excess enthalpies, as well as their increase with temperature. The simulated viscosities are in good agreement with experimental values, especially in the water-rich region. We found three distinct regions by analyzing the concentration dependent self-diffusion coefficients via Stokes–Einstein (SE) relation, indicating the mixture experiences significant microheterogeneity with the adding of water. This observation is well connected to the structure features obtained in simulations, such as radial distribution functions (RDFs), spatial distribution functions (SDFs) and water clustering analysis. At the water mole fraction (x₂) less than 0.2, most of the water molecules are isolated in the polar cation–anion network in ionic liquids. With the increase of x₂ from 0.2 to 0.8, large water cluster forms and eventually percolates the whole system. When x₂ > 0.8, ionic liquids show a moderate degree of aggregation (with maximum around 0.9 to 0.95) before the cations and anions are fully dissolved in water.

Hydration and Mobility of Trehalose in Aqueous Solution B

Abstract: The disaccharide trehalose stabilizes proteins against unfolding, but the underlying mechanism is not well understood. Because trehalose is preferentially excluded from the protein surface, it is of interest to examine how trehalose modifies the structure and dynamics of the solvent. From the spin relaxation rates of deuterated trehalose and ¹⁷O-enriched water, we obtain the rotational dynamics of trehalose and water in solutions over wide ranges of concentration (0.025–1.5 M) and temperature (236–293 K). The results reveal direct solute–solute interactions at all concentrations, consistent with transient trehalose clusters. Similar to other organic solutes, the trehalose perturbation of water rotation (and hydrogen-bond exchange) is modest: a factor 1.6 (at 298 K) on average for the 47 water molecules in the first hydration layer. The deviation of the solute tumbling time from the Stokes–Einstein–Debye relation is partly caused by a dynamic solvent effect that is often modeled by incorporating “bound water” in the hydrodynamic volume. By comparing the measured temperature dependences of trehalose and water dynamics, we demonstrate that a more realistic local viscosity model accounts for this second-order dynamic coupling.

Validation of a Novel Molecular Dynamics Simulation Approach for Lipophilic Drug Incorporation into Polymer Micelles B

Abstract: Polymer micelles can be used to facilitate the aqueous solubilization of lipophilic, poorly water-soluble compounds and drugs. Even if the evaluation of the efficiency of drug incorporation into such micelles can be tested experimentally, a theoretical approach based on molecular simulation can constitute a useful tool that reduces time and cost. Here we present a promising method, based on molecular dynamics simulation, for the calculation of the Flory–Huggins interaction parameters as a measure of the potential for drug incorporation into polymer micelles. The data from modeling are validated on four drug compounds with different physical-chemical properties by means of a comparison with the data obtained from experiments.

Site-Specific Hydration Dynamics of Globular Proteins and the Role of Constrained Water in Solvent Exchange with Amphiphilic Cosolvents

Abstract: The thermodynamic driving forces for protein folding, association, and function are often determined by protein–water interactions. With a novel covalently bound labeling approach, we have used sensitive vibrational probes, site-selectively conjugated to two lysozyme variantsin conjunction with ultrafast two-dimensional infrared (2D-IR) spectroscopyto investigate directly the protein–water interface. By probing alternatively a topologically flat, rigid domain and a flexible domain, we find direct experimental evidence for spatially heterogeneous hydration dynamics. The hydration environment around globular proteins can vary from exhibiting bulk-like hydration dynamics to dynamically constrained water, which results from stifled hydrogen bond switching dynamics near extended hydrophobic surfaces. Furthermore, we leverage preferential solvation exchange to demonstrate that the liberation of dynamically constrained water is a sufficient driving force for protein–surface association reactions. These results provide an intuitive picture of the dynamic aspects of hydrophobic hydration of proteins, illustrating an essential function of water in biological processes.

Vibrational Properties of Metal Nanoparticles: Atomistic Simulation and Comparison with Time-Resolved Investigation C

Abstract: Knowledge of the vibrational spectrum of metal clusters and nanoparticles is of fundamental interest since it is a signature of their morphology, and it can be used to determine their mechanical, thermodynamical, and other physical properties It is expected that such a vibrational spectrum depends on the material, size, and shape of clusters and nanoparticles In this work, we report the vibrational spectra and density of states of Au, Pt, and Ag nanoparticles in the size range of 05–4 nm (13–2057 atoms), with icosahedral, Marks decahedral, and FCC morphologies The vibrational spectra were calculated through atomistic simulations (molecular dynamics and a normal-mode analysis) using the many-body Gupta potential A discussion on the dependence of the vibrational spectrum on the material, size, and shape of the nanoparticle is presented Linear relations with the nanoparticle diameter were obtained for the periods of two characteristic oscillations: the quasi-breathing and the lowest frequency (acoustic gap) modes These linear behaviors are consistent with the calculation of the periods corresponding to the breathing and acoustic gap modes of an isotropic, homogeneous metallic nanosphere, performed with continuous elastic theory using bulk properties Additionally, experimental results on the period corresponding to isotropic volume oscillations of Au nanoparticles measured by time-resolved pump–probe spectroscopy are presented, indicating a linear variation with the mean diameter in the size range of 2–4 nm These, and similar results previously obtained for Pt nanoparticles with size between 13 and 3 nm, are in good agreement with the calculated quasi-breathing mode periods of the metal nanoparticles, independently of their morphologies On the other hand, the calculated period of the mode with the highest (cutoff) frequency displays weak size and shape dependencies up to ∼4 nm, for all nanoparticles under study In contrast with the behavior of other physicochemical properties, the clear consistency between experiments with atomistic and continuous media approaches resulting from this work indicates the existence of simple relations with size and weak dependence with the material and shape, for vibrational properties of metal nanoparticles

Influence of Alkyl Chain Length and Temperature on Thermophysical Properties of Ammonium-Based Ionic Liquids with Molecular Solvent B

Abstract: Mixing of ionic liquids (ILs) with molecular solvent can expand the range of structural properties and the scope of molecular interactions between the molecules of the solvents. Exploiting of these phenomena essentially require a basic fundamental understanding of mixing behavior of ILs with molecular solvents. In this context, a series of protic ILs possessing tetra-alkyl ammonium cation [R₄N]⁺ with commonly used anion hydroxide [OH]⁻ were synthesized and characterized by temperature dependent thermophysical properties. The ILs [R₄N]⁺[OH]⁻ are varying only in the length of alkyl chain (R is methyl, ethyl, propyl, or butyl) of tetra-alkyl ammonium on the cationic part. The ILs used for the present study included tetramethyl ammonium hydroxide [(CH₃)₄N]⁺[OH]⁻ (TMAH), tetraethyl ammonium hydroxide [(C₂H₅)₄N]⁺[OH]⁻ (TEAH), tetrapropyl ammonium hydroxide [(C₃H₇)₄N]⁺[OH]⁻ (TPAH) and tetrabutyl ammonium hydroxide [(C₄H₉)₄N]⁺[OH]⁻ (TBAH). The alkyl chain length effect has been analyzed by precise measurements such as densities (ρ), ultrasonic sound velocity (u), and viscosity (η) of these ILs with polar solvent, N-methyl-2-pyrrolidone (NMP), over the full composition range as a function of temperature. The excess molar volume (Vᴱ), the deviation in isentropic compressibility (Δκₛ) and deviation in viscosity (Δη) were predicted using these properties as a function of the concentration of ILs. Redlich–Kister polynomial was used to correlate the results. A qualitative analysis of the results is discussed in terms of the ion-dipole, ion-pair interactions, and hydrogen bonding between ILs and NMP molecules. Later, the hydrogen bonding features between ILs and NMP were also analyzed using a molecular modeling program with the help of HyperChem 7.

Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration B

Abstract: We have carried out an extended reference set of explicit solvent molecular dynamics simulations (63 simulations with 8.4 μs of simulation data) of canonical A-RNA duplexes. Most of the simulations were done using the latest variant of the Cornell et al. AMBER RNA force field bsc0χOL₃, while several other RNA force fields have been tested. The calculations show that the A-RNA helix compactness, described mainly by geometrical parameters inclination, base pair roll, and helical rise, is sequence-dependent. In the calculated set of structures, the inclination varies from 10° to 24°. On the basis of simulations with modified bases (inosine and 2,6-diaminopurine), we suggest that the sequence-dependence of purely canonical A-RNA double helix is caused by the steric shape of the base pairs, i.e., the van der Waals interactions. The electrostatic part of stacking does not appear to affect the A-RNA shape. Especially visible is the role of the minor groove amino group of purines. This resembles the so-called Dickerson–Calladine mechanical rules suggested three decades ago for the DNA double helices. We did not identify any long-living backbone substate in A-RNA double helices that would resemble, for example, the B-DNA BI/BII dynamics. The variability of the A-RNA compactness is due to mutual movements of the consecutive base pairs coupled with modest change of the glycosidic χ torsion. The simulations further show that the A-RNA compactness is modestly affected by the water model used, while the effect of ionic conditions, investigated in the range from net-neutral condition to ∼0.8 M monovalent ion excess salt, is smaller.

Impact of Self-Aggregation on the Formation of Ionic-Liquid-Based Aqueous Biphasic Systems B

Abstract: This work reports on the systematic investigation of the influence of the cation alkyl side-chain length of 1-alkyl-3-methylimidazolium chloride ionic liquids ([CₙC₁im]Cl, with n = 1–14), as well as the substitution of the most acidic hydrogen in the imidazolium core by a methyl group, in the formation of aqueous biphasic systems. Ternary phase diagrams, tie-lines, tie-line slopes, tie-line lengths, and critical points for the several systems (ionic liquid + water + K₃PO₄) were determined and reported at 298 K and atmospheric pressure. It is shown that the increase of the cation alkyl chain length enhances the formation of aqueous biphasic systems if alkyl chain lengths until the hexyl are considered. The results for longer alkyl side chains show, nevertheless, that the phenomenon is more complex than previously admitted and that the capacity of the ionic liquid to self-aggregate also governs its ability to phase separate. The effect of the alkyl side-chain length on the phase-forming ability of the studied systems was quantitatively evaluated based on their salting-out coefficients derived from a Setschenow-type behavior. The aptitude of each ionic liquid for liquid–liquid demixing as a function of the cation alkyl side-chain length clearly follows three different patterns. The results obtained for the trisubstituted cation indicate that the hydrogen-bonding interactions between the ionic liquid cation and water are not a relevant issue in the formation of aqueous two-phase systems. In general, for the [CₙC₁im]Cl series, a multifaceted ratio between entropic contributions and the ability of each ionic liquid to self-aggregate in aqueous media control the phase behavior.

Unusual Arginine Formations in Protein Function and Assembly: Rings, Strings, and Stacks

Abstract: Protein–protein interfaces are often stabilized by a small number of dominant contacts, exemplified by the overrepresentation of arginine residues at oligomerization interfaces. Positively charged arginines are most commonly involved in ion pairs of opposite charge; however, previous work of Scheraga and co-workers described the stable, close range interaction between guanidinium pairs in a solvated environment. To extend this work, we searched over 70 thousand protein structures and complexes for unusual formations of arginine residues supported by the electron density. Symmetry transformations were used to generate full assemblies. Clusters of four to eight arginine residues with Cζ–Cζ distances <5 A, organized as rings with four to eight members, stacks of two arginines, and strings of stacked arginines, are commonly located at the interfaces of oligomeric proteins. The positive charge is properly balanced by negatively charged counterions in about 90% of the cases. We also observed planar stacking of guanidinium groups, bridged by hydrogen bonds and interactions with water molecules. The guanidinium groups are commonly involved in five hydrogen bonds with water molecules and acceptor groups from surrounding amino acids. Water molecules have a bridging effect on the arginine pairs, but in some cases, small molecular weight chemicals in the crystallization buffer may be misinterpreted as water molecules. In summary, despite electrostatic repulsion, arginines do form various clusters that are exposed to interact with and potentially be controlled or switched by charged metabolites, membrane lipids, nucleic acids, or side chains of other proteins. Control of the stability of arginine clusters may play an important role in protein–protein oligomerization, molecular recognition, and ligand binding.

Development of Polarizable Models for Molecular Mechanical Calculations. 3. Polarizable Water Models Conforming to Thole Polarization Screening Schemes

Abstract: As an integrated step toward a coherent polarizable force field for biomolecular modeling, we analyzed four polarizable water models to evaluate their consistencies with the Thole polarization screening schemes utilized in our latest Amber polarizable force field. Specifically, we studied the performance of both the Thole linear and exponential schemes in these water models to assess their abilities to reproduce experimental water properties. The analysis shows that the tested water models reproduce most of the room-temperature properties of liquid water reasonably well but fall short of reproducing the dynamic properties and temperature-dependent properties. This study demonstrates the necessity to further fine-tune water polarizable potentials for more robust polarizable force fields for biomolecular simulations.

Modification of a Styryl Dye Binding Mode with Calf Thymus DNA in Vesicular Medium: From Minor Groove to Intercalative B

Abstract: This paper reports an interesting transformation of binding mode of 2-(4-(dimethylamino)styryl)-1-methylpyridinium iodide (DASPMI) with calf thymus DNA from minor groove binding in buffer solution to intercalative binding when the dye is encapsulated inside a vesicle formed by the interaction of 1,8-naphthalimide (a charge transfer dye) with the supramolecular association of sodium dodecyl sulfate and block-copolymer polyethylene-b-polyethylene glycol. The pre-encapsulated dye in the vesicular interior binds intercalatively to ct-DNA, as evinced by the high value of equilibrium binding constant of DASPMI–DNA complex, changes in CD-spectra of DNA and isosbestic point, along with downshift and hypochromicity of absorption band. Increase in anisotropy decay by 1.5 times with a single component strongly confirms restricted motion of the probe inside ct-DNA confirming intercalative binding. The compaction of ct-DNA caused by the interaction of the vesicle allows DASPMI to bind ct-DNA in the intercalative mode. However, the groove binding mode in ct-DNA–DASPMI remains unaffected by the retro-addition of the vesicles to the already bound dye to ct-DNA.

Growth Mechanisms of Fluorescent Silver Clusters Regulated by Polymorphic DNA Templates: A DFT Study B

Abstract: The aggregation behaviors of silver atoms modulated by polymorphic DNA templates involving i-motif, G-quadruplex, and the Watson–Crick duplex, were investigated by using the density functional theory (DFT) calculations, combining with the experimental characterizations of CD, UV, fluorescence measurements and TEM, in order to understand the reason in the molecular level that polymorphic DNA templates affect the fluorescence emitting species of Ag nanomaterials. First, the affinity sites of silver ions on different DNA templates were analyzed by using DFT calculations, and the conformational variations of DNA templates caused by silver ions and atoms were disclosed. Second, the aggregation behaviors of silver atoms constrained by the polymorphic DNA templates were studied by DFT modeling, and distinct fluorescence property of nanosilvers templated by polymorphic DNA were evaluated using the time-dependent DFT calculations. It is illustrated that with the DNA template adopting i-motif or the duplex the silver atoms tend to aggregate inside the encapsulated spaces of nucleobases, and the formed silver nanoclusters are positively charged with high fluorescent spectral features; whereas with the template of the G-quadruplex the silver atoms are preferential to aggregate outside of the G-tetrad, which results in the formation of larger silver crystals without fluorescence property. The results obtained here are useful to explore the nucleation and growth mechanism of silver nanomaterials regulated by the structure-specific DNA templates, which is important to rational design of desirable fluorescent emitters for sensing in the field from biology to nanoscience.

Hofmeister Phenomena in Nonaqueous Media: The Solubility of Electrolytes in Ethylene Carbonate B

Abstract: The solubility of some potassium salts (KF, KCl, KBr, KI, KNO₃, KClO₄, KSCN, and KSeCN) in ethylene carbonate (EC) was determined at different temperatures with an inductively coupled plasma atomic emission spectrometer. From the solubility measurements, the thermodynamic parameters ΔG, ΔH, and ΔS, of solution and of solvation, were calculated. Measurements were carried out via XRD, ATR, and FTIR to determine the effect of each salt on the properties of the solvent. The open question of whether specific ion (Hofmeister) effects are restricted to hydration peculiar to water is resolved. As for water, the effects are due to solute (ion, dipolar) induced solvent structure not accounted for by electrostatic forces. Cooperative quantum mechanical forces are necessary to understand the phenomena.

Structural Characteristics of Novel Ca–Mg Orthosilicate and Suborthosilicate Glasses: Results from 29Si and 17O NMR Spectroscopy B

Abstract: The structural characteristics of novel alkaline-earth suborthosilicate glasses along the compositional join (1 – x)(Ca₀.₅Mg₀.₅O) – xSiO₂ with 0.28 ≤ x ≤ 0.33 are investigated using high resolution ²⁹Si and ¹⁷O nuclear magnetic resonance spectroscopy. The structures of these glasses consist of isolated Q⁰ and Q¹ anionic species and Mg²⁺ and Ca²⁺ countercations that are held together by Coulombic interactions. The concentration of the Q¹ species rapidly decreases with decreasing SiO₂ content and becomes undetectable in the glass with x = 28 mol %. The compositional variation of the physical properties of these glasses such as glass transition temperature and density can be attributed to the Q-speciation in the structure. The NBOs are associated with a random distribution of the alkaline-earth cations in their nearest neighbor coordination shell. The resulting random packing of dissimilar Ca-NBO and Mg-NBO coordination polyhedra may give rise to structural and topological frustration responsible for the unusual glass-forming ability of these suborthosilicate liquids with extremely low SiO₂ contents. Finally, the composition and the formation of Q¹ species necessitate the formation of free O²– ions in the structure of these glasses that are only bonded to Mg²⁺ and Ca²⁺ cations. The ¹⁷O NMR results presented in this study allow for direct observation of such oxygen species.

High-Resolution Structural Insights into Bone: A Solid-State NMR Relaxation Study Utilizing Paramagnetic Doping

Abstract: The hierarchical heterogeneous architecture of bone imposes significant challenges to structural and dynamic studies conducted by traditional biophysical techniques. High-resolution solid-state nuclear magnetic resonance (SSNMR) spectroscopy is capable of providing detailed atomic-level structural insights into such traditionally challenging materials. However, the relatively long data-collection time necessary to achieve a reliable signal-to-noise ratio (S/N) remains a major limitation for the widespread application of SSNMR on bone and related biomaterials. In this study, we attempt to overcome this limitation by employing the paramagnetic relaxation properties of copper(II) ions to shorten the ¹H intrinsic spin–lattice (T₁) relaxation times measured in natural-abundance ¹³C cross-polarization (CP) magic-angle-spinning (MAS) NMR experiments on bone tissues for the purpose of accelerating the data acquisition time in SSNMR. To this end, high-resolution solid-state ¹³C CPMAS experiments were conducted on type I collagen (bovine tendon), bovine cortical bone, and demineralized bovine cortical bone, each in powdered form, to measure the ¹H T₁ values in the absence and in the presence of 30 mM Cu(II)(NH₄)₂EDTA. Our results show that the ¹H T₁ values were successfully reduced by a factor of 2.2, 2.9, and 3.2 for bovine cortical bone, type I collagen, and demineralized bone, respectively, without reducing the spectral resolution and thus enabling faster data acquisition. In addition, paramagnetic quenching of particular ¹³C NMR resonances on exposure to Cu²⁺ ions in the absence of mineral was also observed, potentially suggesting the relative proximity of three main amino acids in the protein backbone (glycine, proline, and alanine) to the bone mineral surface.

Conductance, a Contrivance To Explore Ion Association and Solvation Behavior of an Ionic Liquid (Tetrabutylphosphonium Tetrafluoroborate) in Acetonitrile, Tetrahydrofuran, 1,3-Dioxolane, and Their Binaries

Abstract: Precise measurements on electrical conductance (Λ) of solutions of an ionic liquid (IL) tetrabutylphosphonium tetrafluoroborate in acetonitrile (ACN), tetrahydrofuran (THF), and 1,3-dioxolane (1,3-DO) and their binary mixtures have been reported at 298.15 K. The conductance data have been analyzed by the Fuoss conductance equation (1978) in terms of the limiting molar conductance (Λₒ), the association constant (KA), and the association diameter (R) for ion-pair formation. The Walden product is obtained and discussed. However, the deviation of the conductometric curves (Λ versus √c) from linearity for the electrolyte in THF and 1,3-DO and their binary mixtures indicated triple-ion formation and therefore the corresponding conductance data have been analyzed by the Fuoss–Kraus theory of triple ions. The limiting ionic conductances (λₒ±) have been estimated from the appropriate division of the limiting molar conductivity value of tetrabutylammonium tetraphenylborate [Bu₄NBPh₄] as the “reference electrolyte” method along with a numerical evaluation of ion-pair and triple-ion formation constants (KP ≈ KA and KT). The results have been discussed in terms of solvent properties and configurational theory. Ionic association in the limiting molar conductances as well as the single-ion conductivity values have been determined for the electrolyte in the solvent media.

Combined Application of High-Field Diffusion NMR and Molecular Dynamics Simulations To Study Dynamics in a Mixture of Carbon Dioxide and an Imidazolium-Based Ionic Liquid B

Abstract: Self-diffusion and related short-time dynamic and structural properties were investigated for mixtures of carbon dioxide and the ionic liquid 1-n-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide [bmim]⁺[Tf2N]⁻ for a broad range of carbon dioxide molar fractions and at different temperatures. The studies were performed by a novel multinuclear pulsed field gradient (PFG) NMR technique, which combines the advantages of a high magnetic field (17.6 T) and a high magnetic field gradient (up to 30 T/m), in combination with molecular dynamics simulations. In general, a satisfactory agreement was observed between the experimental and simulation diffusion data. Under all conditions examined, the self-diffusion coefficients of carbon dioxide were found to be approximately an order of magnitude larger than the corresponding self-diffusion coefficients of the ions. It was observed that an increase in temperature and in the amount of carbon dioxide in the ionic liquid led to an increase in the ion self-diffusivities without changing the relationship between the self-diffusion coefficients of the cations and anions. An observation of a slightly higher diffusivity of the cations in comparison to that of the anions is attributed to the preferential mobility of the cations in the direction of the ring plane. The diffusion activation energies of the ions were found to decrease gradually with an increase of the carbon dioxide content in the ionic liquid. The activation energy of the carbon dioxide diffusion in all cases was found to be smaller than those of the ions.

Multilayers at Interfaces of an Oppositely Charged Polyelectrolyte/Surfactant System Resulting from the Transport of Bulk Aggregates under Gravity B

Abstract: We show conclusively that multilayers at interfaces of an oppositely charged polyelectrolyte/surfactant system can result from the transport under gravity of bulk aggregates with internal molecular structure. This process was demonstrated by measurements of poly(diallyldimethylammonium chloride)/sodium dodecyl sulfate solutions at the air/liquid and solid/liquid interfaces using neutron reflectometry. In the latter case a novel approach involving the comparison of reflection up versus down measurements provided key evidence. Interfacial multilayers indicated by a strong Bragg peak and clear off-specular scattering are exhibited under three conditions: (1) only for samples in the phase separation region, (2) only for fresh samples where a suspension of bulk aggregates remains in solution, and (3) only when the creaming or sedimentation process occurs in the direction of the interface under examination. This bulk transport mechanism is an alternative route of formation of interfacial multilayers to surface induced self-assembly. The two processes evidently give rise to interfaces with very different structural and rheological properties. Such directionality effects in the formation of nanostructured liquid interfaces may have implications for a broad range of soft matter and biophysical systems containing macromolecules such as synthetic polymers, proteins, or DNA.

Hydrophobic Segregation, Phase Transitions and the Anomalous Thermodynamics of Water/Methanol Mixtures B

Abstract: When water and methanol are mixed, the entropy of mixing decreases, whereas mixing simple liquids normally leads to an increase in entropy. One speculation on the origin of the anomaly involves formation of water icebergs next to the hydrophobic methanol group, while more recent theories point to nanoscale clustering of methanol molecules. To elucidate the origin of this effect, we carried out extensive molecular dynamics calculations on water/methanol mixtures ranging from 0 to 100% and applied the 2PT method to extract the entropy and free energy changes of each component as a function of concentration. We find that water molecules lose at most 1/35 of their liquid entropy in mixtures. Methanol molecules, on the other hand, lose 3 times as much entropy as the water molecules, and their rotational entropy contains the signature of the entropic loss. We find that methanol has a discontinuous specific heat profile in these mixtures with a maximum at 40% methanol. These results do not support the iceberg model of immobilized waters and instead suggests a molecular mechanism of hydrophobic segregation at low methanol concentration where ordering of the methanol molecules bury the hydrophobic group away from the water phase. For higher methanol concentrations, there is insufficient water to accomplish this effect, and the system freely mixes and transitions to one better described as water dissolved into methanol.