Intermolecular Distance Distribution Research Articles

Simple Model for the Benzene Hexafluorobenzene Interaction.

While the experimental intermolecular distance distribution functions of pure benzene and pure hexafluorobenzene are well described by transferable all-atom force fields, the interaction between the two molecules (in a 1:1 mixture) is not well simulated. We demonstrate that the parameters of the transferable force fields are adequate to describe the intermolecular distance distribution if the charges are replaced by a set of charges that are not located at the atoms. The simplest model that well describes the experimental distance distribution, between benzene and hexafluorobenzene, is that of a single ellipsoid for each molecule, representing the van der Waals interactions, and a set of three point charges (on the axis perpendicular to the arene plane) which give the same quadrupole moment as do the all atom charges from the transferable force fields.

Destabilization of Human Serum Albumin by Ionic Liquids Studied Using Enhanced Molecular Dynamics Simulations.

Ionic liquid (IL) containing solvents can change the structure, dynamics, function, and stability of proteins. In order to investigate the mechanisms by which ILs induce structural changes in a large multidomain protein, we study the interactions of human serum albumin (HSA) with two different ILs, 1-butyl-3-methylimidazolium tetrafluoroborate and choline dihydrogen phosphate. Root mean square deviation and fluctuation calculations indicate that high concentrations of ILs in mixtures with water lead to protein structures that remain close to their crystallographic structures on time scales of hundreds of nanoseconds. To overcome potential time scale limitations due to the high viscosity of the solvent, we employed enhanced sampling techniques to estimate the free energy of an experimentally determined important transition within the protein structure. Metadynamics simulations show that the free energy landscape of the unfolding of loop 1 of domain I is different in the presence of ILs than it is in water, consistent with previously published experimental evidence. We then apply essential dynamics coarse graining to systematically predict differences in the dynamics of proteins solvated in IL-water mixtures versus pure water systems. We also demonstrate that the presence of ionic liquids changes the distribution of intermolecular distances among several ligands, indicating that the protein structure swells in the presence of certain ILs, consistent with experimental evidence.

EPR with Rigidly Bound Spin Labels used to Probe the Interaction of Calmodulin with the Ryanodine Receptor

We have used site-directed spin labeling and EPR spectroscopy to probe the structural dynamics of calmodulin bound to a ryanodine receptor target peptide. Calmodulin binds to a conserved 30-amino acid sequence on the sarcoplasmic reticulum calcium release channel (ryanodine receptor, RyR) and directly modulate its activity in muscle contraction. In order to characterize the structural details of this crucial interaction, a bifunctional spin label was used to rigidly label di-cysteine mutant calmodulin at positions 34 and 38. Solid-phase peptide synthesis was used to create a peptide corresponding to the calmodulin binding site on the ryanodine receptor channel (RyRp, residues 3614-3643 in RyR1) with a TOAC spin label rigidly coupled to the backbone. The intermolecular distance distribution between the two spin probes was determined by EPR, using both continuous wave dipolar broadening and dipolar electron-electron resonance (DEER). The center of the distance distribution was in good agreement with the crystal structure of the complex (18 A), but the width of the distribution was ∼ 1 nm, comparable to that observed previously within calmodulin itself. Thus calmodulin retains significant inter-lobe domain motion, even after RyRp binding. These results are consistent with a model in which calmodulin binds RyRp, bringing its two terminal lobes close together but preventing them from physical contact with each other, allowing flexibility in each of the lobe.

Ferrocene in the metal–organic framework MOF-5 studied by homo- and heteronuclear correlation NMR and MD simulation

Advanced solid-state 2D NMR spectroscopy and molecular dynamics computation are employed to investigate the interaction between adsorbed ferrocene molecules and the MOF-5 lattice. Relayed 13C–1H heteronuclear correlation (HETCOR) 2D NMR spectra clearly indicate short-distance contacts between the ferrocene guests and the benzene-1,4-dicarboxylic-acid linkers, mediated via intermolecular 1 H spin diffusion. By use of 2D 1H–1H correlation spectroscopy the distances between 1H nuclei in the guests and the linkers are estimated to be shorter than 0.5nm. MD computer simulations support the interpretation of the 2D solid state NMR studies. Moreover, they suggest a wide distribution of intermolecular distances in this host–guest system with the shortest intermolecular hydrogen–hydrogen distances of 0.15nm.

Equilibrium structure of dense gases

The computer aided analysis of precise thermophysical data for pure real gases and denser fluids is developed here to provide a vision of their equilibrium molecular structure [1, 2]. The structure of fluids means the structural features of disordered systems. It differs from the regular structures of molecules or solids [3] and reflects the structural features of the temporarily existing local molecular complexes, such as clusters and pores of different dimensions. Pure fluids are actively used in modern chemical technologies as initial and intermediate substances and final products. For further improvement of technological processes with pure fluids it is important to know better their molecular interaction mechanisms and parameters. The purity of gases and denser fluids by itself presents a great scientific value: it opens possibility to discover the details of the molecular interactions and the cluster structure by the computer aided processing of precise thermophysical data for pure substances. The distribution of intermolecular distances in fluids is not uniform. The diminishing of the fluid density from its maximal value does not mean the uniform expansion of all intermolecular distances. Some of distances stay the same as in a dense liquid, but others become noticeably enlarged. In real gases some part of molecules forms the short distance complexes, named clusters. The clusters in real gases now attract a large attention of researches [48]. The Water vapor clusters are responsible for clouds formation in upper layers of atmosphere [9]. The factors complicating determination of the molecular interaction mechanisms [1]: Densely spaced and disarranged by thermal movement bound states in clusters; The plurality of the cluster isomer configurations, growing with a number of particles in a cluster; The difference between the thermodynamically averaged energetic level of the bound state and the minimal potential energy of a cluster; Long relaxation times for tightly bound cluster isomers preventing from a fast reaching the equilibrium and thus distorting the experimental data at low temperatures. There are various approaches to molecular interaction mechanisms. The earlier models of fluids described in [10, 11], such as the famous van der Waals equation of state or the corresponding states law, have been based on the experimental data taken with not very high precision. They provided only a general picture of fluids sacrificing very important details of their molecular interactions. Now, the individual characteristics of molecular interactions in substances are being actively studied asing in the precise experimental data [12]. The constantly growing precision of thermophysical data opens new ways to penetrate deeper into details of the fluids’ structure. But this task is not very easy. It may be referred to the class of reverse mathematical problems, the results of which widely diverge at slight changes of initial data. Therefore, we should use the methods of data processing capable to limit the level of this divergence by both the regularization of the initial data and selecting the appropriate set of the molecular interaction parameters. This set should be adjusted to real features of the molecular interactions in gases instead of the purely mathematical parameterization of experimental data. An alternative approach to the molecular interactions in fluids is based on the simulations of the many particle systems behavior with different model potentials [4-9, 13]. The problem of this approach lies in rather arbitrary assumptions about the model potentials describing interactions between molecules in fluids. I.G. Kaplan [13] used more than 50 model potentials in his investigations. He came to very important conclusions for the dispersion forces temperature dependence. The optimal way to the physically correct picture of fluids may be in the mutually correlated utilization of both approaches: from the experimental data and from the model potentials. These approaches should converge in the molecular interaction parameters to be found. That may serve as the criterion of the most appropriate model potential selection. This work deals with the main thermodynamics principles extension to real gases and denser fluids and develops the methods of the molecular interaction parameters extraction from the experimental data. It is aimed at the cluster fractions’ characteristics near the saturation Dsat and even critical Dcr densities of pure gases basing on precise data from [15].

Validating a Strategy for Molecular Dynamics Simulations of Cyclodextrin Inclusion Complexes through Single-Crystal X-ray and NMR Experimental Data: A Case Study

A theoretical and experimental study about the formation and structure of the inclusion complex (-)-menthyl-O-beta-D-glucopyranoside 1 with beta-cyclodextrin (beta-CD) 2 is presented as paradigmatic case study to test the results of molecular dynamics (MD) simulations. The customary methodological approach-the use of experimental geometrical parameters as restraints for MD runs-is logically reversed and the calculated structures are a posteriori compared with those obtained from NMR spectroscopy in D(2)O solution and single crystal X-ray diffraction so as to validate the simulation procedure. The guest molecule 1 allows for a broad repertoire of intermolecular interactions (dipolar, hydrophobic, hydrogen bonds) concurring to stabilize the host-guest complex, thus providing the general applicability of the simulation procedure to cyclodextrin physical chemistry. Many starting geometries of the host-guest association were chosen, not assuming any a priori inclusion. The simulation protocol, involving energy minimization and MD runs in explicit water, yielded four possible inclusion geometries, ruling out higher-energy outer adducts. By analysis of the average energy at room temperature, the most stable geometry in solution was eventually obtained, while the kinetics of formation showed that it is also kinetically favored. The reliability of such geometry was thoroughly checked against the NOE distances via the pair distribution functions, that is, the statistical distribution of intermolecular distances among selected diagnostic atoms calculated from the MD trajectories at room temperature. An analogous procedure was adopted both with implicit solvent and in vacuo. The most stable geometry matched that found with explicit solvent but major differences were observed in the relative stability of the metastable complexes as a consequence of the lack of hydration on the polar moiety of the guest. Finally, a control set of geometrical parameters of the thermodynamically favored complex matched the corresponding one obtained from the X-ray structure, while local conformational differences were indicative of packing effects.

Hydration of Aprotic Donor Solvents Studied by Means of FTIR Spectroscopy

The paper attempts to explain the mutual influence of nonpolar and electron-donor groups on solute hydration, the problem of big importance for biological aqueous systems. Aprotic organic solvents have been used as model solutes, differing in electron-donating power. Hydration of acetonitrile, acetone, 2-butanone, and triethylamine has been studied by HDO and (partially) H2O spectra. The quantitative version of difference spectra method has been applied to determine solute-affected water spectra. Analysis of the data suggests that solvent-water interaction via the donor center of the solute is averaged between water-water interactions around the solute. Such behavior can be simply explained by the model of solute rotating in a cavity of water structure, which is formed by clathratelike hydrogen-bonded water network. On the basis of the band shape of solute-affected HDO spectra and the corresponding distribution of intermolecular distances, the criterion for hydrophobic type hydration has been proposed. From that point of view, all the studied solutes could be treated as hydrophobic ones. The limiting band position and the corresponding intermolecular distance of affected water, gained with increasing electron-donating power of solutes, has been inferred from the data obtained. These observations are important for interpretation of vibrational spectra of water as well as for volumetric measurements of solutions. The simple model of hydration, proposed to better justify the results, connects the values obtained from the methods providing microscopic and macroscopic characteristics of the system studied.

Activity analysis of trans-[RuCl 2(NH 3) 4] + incorporated into Nafion membrane for water oxidation catalyst

Activity of trans-tetraamminedichlororuthenium(III) complex as water oxidation catalyst was studied both in a homogeneous aqueous solution (AS) and in a heterogeneous Nafion membrane (HM) using Ce(IV) oxidant. This trans-[RuCl 2(NH 3) 4] + was more active than any other mononuclear ammine ruthenium complex studied before. In the AS, the rate of evolved dioxygen is second order with respect to the complex concentration, indicating that the complexes oxidize water molecules bimolecularly in low concentration regions. In high concentration regions, the activity of water oxidation decreased with the increase of the concentration, and at the same time dinitrogen (N 2) evolved by a bimolecular decomposition process. In the HM, the activity of the complex was remarkably high, and it was maintained for a long time at low concentrations (<0.02 mol dm −3). At middle concentrations for the HM (0.02–0.05 mol dm −3), the activity of the complex decreased with increasing concentration because of bimolecular decomposition. However, in high concentration regions the complex recovered the activity most probably due to polymerization of the complex. The activity in the HM was analyzed in terms of the cooperative catalysis, the bimolecular decomposition and the polymerization of the complex based on intermolecular distance distribution.

Analysis of Water Oxidation Catalysis by Dinuclear Ruthenium Complex [(NH3)5Ru-O-Ru(NH3)5]4+ Incorporated in a Nafion® Membrane

Abstract Catalytic activity of a dinuclear ammine ruthenium complex, [(NH3)5Ru-O-Ru(NH3)5]4+, for water oxidation to evolve O2 was investigated both in homogeneous aqueous solution and in heterogeneous Nafion® membrane systems using CeIV oxidant. It was suggested that the complex works as a four-electron water oxidation catalyst and that the water oxidation by the complex is in competition with a bimolecular decomposition between the complexes. The first-order rate constant (kO2 (s-1)) for O2 evolution and second-order rate constant (kdeact (M-1 s-1)) for bimolecular decomposition were obtained by a kinetic analysis. It was found that kdeact decreased by one order of magnitude by incorporating the complex in the membrane; this was ascribed to the suppression of the bimolecular decomposition. The critical decomposition distance (rd (nm)) between the catalysts was analyzed to be 1.06 nm based on an intermolecular distance distribution.

Effect of immobilization and activity analysis of water oxidation catalysts adsorbed into clay

The catalytic activity of a trinuclear Ru complex; ([(NH 3) 5Ru-O-Ru(NH 3) 4-O-Ru(NH 3) 5] 6+) (Ru-red) for water oxidation was investigated both in a homogeneous aqueous solution system (AS) and a heterogeneous montmorillonite adsorbed system (clay). It was shown that water oxidation by the catalyst in the clay to evolve O 2 is a competitive reaction with bimolecular decomposition of the catalyst. The bimolecular decomposition was remarkably suppressed in the clay as compared with the aqueous solution, and the catalytic activity was maintained under higher concentration conditions. This was ascribed to the immobilization and isolation of the complex in the clay. The catalytic activity was analyzed by a model equation based on intermolecular distance distribution of the complex. The catalytic activity ( k O 2 ) and the critical decomposition distance ( r d) were obtained as 1.7×10 −2 s −1 and 2.39 nm, respectively.

Cooperative catalysis and critical decomposition distances in water oxidation by tris(ethylenediamine)ruthenium (III) complex confined in a Nafion membrane

The activity of tris(ethylenediamine)ruthenium (III) complex, [Ru(en) 3] 3+, as a water oxidation catalyst was studied in a homogeneous aqueous solution and a heterogeneous Nafion (Nf) membrane. In the aqueous solution, the apparent catalytic activity ( k app (s −1)) decreased monotonously with the concentration due to a bimolecular decomposition of the complex. The bimolecular decomposition of the complex was remarkably suppressed by incorporating it into a Nf membrane. An optimum complex concentration for k app in the Nf membrane was exhibited, which was explained both by a cooperative catalysis and a bimolecular decomposition of the complex. The k app in the Nf membrane was analyzed in terms of an intrinsic catalytic activity ( k O 2 (s −1)) of the complex, a cooperative catalysis distance ( r co (nm)) and a critical decomposition distance ( r d (nm)) between them based on intermolecular distance distribution to obtain the k O 2 =8.5×10 −5 s −1, r co=1.44 nm and r d=1.07 nm. The results in the [Ru(en) 3] 3+ system were compared with those obtained in the [Ru(NH 3) 6] 3+ system.

Analysis of cooperative catalysis by a molecular water oxidation catalyst adsorbed onto an inorganic particle matrix

Electrocatalytic water oxidation was carried out using a basal-plane pyrolytic graphite (BPG) electrode coated with electrodeposited Platinum black (Pt-black) adsorbing [Ru(NH 3) 5Cl] 2+. The amount of O 2 evolved ( V O 2 , mol h −1) remarkably increased by adsorbing the complex onto Pt-black. The plots of V O 2 vs. the complex amount on the Pt-black gave a sigmoidal curve, which was explained by both the cooperative catalysis by two molecules of the complex and their bimolecular decomposition. The electrocatalytic activity of the complex was analyzed in terms of its intrinsic activity, k (h −1), cooperative catalysis distance, r co (nm) and critical decomposition distance, r d (nm) for both the void space adsorption model (VAM) and surface adsorption model (SAM) based on intermolecular distance distribution. k=940 h −1, r co=1.21 nm and r d=0.97 nm for VAM and 950 h −1 r co=0.82 nm and r d=0.78 nm for SAM were obtained, respectively. Remarkable high intrinsic activities are ascribed to the efficient charge transfer from the electrode to the complex attached to the Pt-black.

Activity Analysis of [(NH3)5RuORu(NH3)5]5+, Confined in a Coated-Polymer Membrane for Electrochemical Water Oxidation

The activity of the electrochemical water oxidation catalyst, [(NH3)5RuORu(NH3)5]Cl5, incorporated in an electrode-coated Nafion membrane was studied. The turnover number (TN) of the catalyst increased with the increase, of its concentration in the membrane in low concentration regions because of facilitated charge transfer between the catalysts, while that decreased with the concentration in high concentration regions because of bimolecular decomposition of the catalyst. An activity model for the electrochemical catalyst in a membrane was applied based on intermolecular distance distribution, and the activity was analyzed in terms of a charge transfer distance (r0/nm) and a critical decomposition distance (rd/nm); their values were obtained as 1.14 nm and 1.09 nm, respectively. The, activity was compared with other complexes. It was elucidated that the activity of the catalysts increased with the number of the metal ion present in one molecule.

Activity analysis of mononuclear ruthenium ammine complex dispersed in a polymer membrane as an electrochemical water oxidation catalyst

The activity of an electrochemical water oxidation catalyst based on pentaamminechlororuthenium(III) ([Ru(NH 3) 5Cl] 2+) complex incorporated in an electrode-coated Nafion membrane was investigated. The complex worked as an active electrochemical catalyst, and an optimum concentration for the turnover number (TN) of the catalyst in the O 2 evolution was exhibited. The TN increased with the concentration at low concentrations, which was ascribed either to charge transfer between the catalysts or to cooperative catalysis by the complex. The TN decrease at high concentrations was ascribed to bimolecular decomposition of the catalyst. The catalyst activity (TN) was analyzed in terms of a charge transfer distance between the catalysts ( r 0/nm), a cooperative catalysis distance by the complex ( r co/nm), and a critical decomposition distance of the catalyst ( r d/nm) based on intermolecular distance distribution. It was suggested that the activity was controlled mainly by r co and r d, and the values r co=1.26 nm and r d=0.82 nm were obtained.

Activity analysis of electrocatalytic water oxidation by trinuclear ruthenium complex on an Au particle matrix

Electrocatalytic water oxidation was carried out using a basal-plane pyrolytic graphite (BPG) electrode coated with electrodeposited Au particles adsorbing Ru-red ([(NH 3) 5Ru-O-Ru(NH 3) 4-O-Ru(NH 3) 5] 6+). The amount of O 2 evolved, V O 2 (mol h −1), increased remarkably by adsorbing the complex onto Au particles. The plots of V O 2 versus the complex amount on Au particles gave an almost straight line at its low surface coverage, but deviated downward with an increase in its amount, which is ascribed to the bimolecular decomposition. The intrinsic turnover number (TN) of the complex is larger than that of the Au particle by three orders of magnitude. The catalytic activity of the complex was analyzed in terms of its intrinsic TN, k (h −1) and critical decomposition distance, r d (nm) based on intermolecular distance distribution to obtain k=21.4 h −1 and r d=1.11 nm.

Charge transfer distance between trinuclear ruthenium complexes incorporated in a polymer membrane studied by potential-step chronoamperospectrometry

Charge transfer in a Nafion membrane incorporating a trinuclear ruthenium complex, Ru-red ([(NH 3) 5Ru(μ-O)Ru(NH 3) 4(μ-O)Ru(NH 3) 5] 6+), was studied using potential-step chronoamperospectrometry (PSCAS). Reversible oxidation of Ru-red (Ru III–Ru IV–Ru III) to Ru-brown (Ru IV–Ru III–Ru IV) was observed under a potential-step from 0 to 0.5 V vs. SCE in the PSCAS measurement. The charge transport rate by the oxidation of Ru-red to Ru-brown in the membrane depended on the complex concentration and was analyzed by both the physical displacement of the complexes and charge hopping between them. It was found that the charge transport takes place in the membrane by both the physical displacement and charge hopping. The charge transfer distance was analyzed based on a intermolecular distance distribution between the redox centers, and the real charge hopping distance was estimated to be 1.1 nm.

Charge transport analysis of [(bpy)2(H2O)Ru–O–Ru(H2O)(bpy)2]4+ incorporated in a Nafion membrane as studied by potential-step chronocoulospectrometry

Charge transport in a Nafion membrane incorporating a μ-oxobis[aqabis(2,2′-bipyridine)ruthenium(III)] complex, [(bpy)2(H2O)Ru–O–Ru(H2O)(bpy)2]4+ [abbreviated to RuIII(OH2)–O–RuIII(OH2)], was studied by using a potential-step chronocoulospectrometry (PSCCS). The oxidation of RuIII(OH2)–O–RuIII(OH2) to RuIII(OH2)–O–RuIV(OH) was observed on a potential-step from 0 V vs. SCE to 1.0 V in the PSCCS measurement. The charge transport rate, vCT, is remarkably depended on the complex concentration. The analysis showed that the charge propagation takes place by charge hopping, whose rate constant is dependent on the complex concentration. Charge hopping distance between the complexes in the membrane was analyzed to be 1.09 nm based on an intermolecular distance distribution between them.

Enhancing Effects of Amino Acid Residue Model Compounds on Catalytic Activity of an Artificial Oxygen Evolving Center

Electrocatalytic water oxidation was studied for an artificial oxygen evolving center (OEC) model using Nafion (Nf) membrane-coated electrode incorporating Ru-red ([(NH3)5Ru−O−Ru(NH3)4−O−Ru(NH3)5]6+) and an amino acid residue model compound. On the cyclic voltammogram (CV) of Ru-red in the presence of a Tyr residue model, p-cresol (p-Cre) or a His residue model, 4-methylimidazole (MIm), the anodic current in an oxidative scan is much higher than that without the model compounds. The amount of O2 evolved in the potentiostatic electrolysis increased remarkably in the presence of p-Cre or MIm. The enhancing effect of the model compounds on the catalytic activity was analyzed in terms of the intrinsic activity, charge-transfer distance between the complexes, and their critical decomposition distance based on the intermolecular distance distribution. The charge-transfer distance was remarkably prolonged from 1.28 to 2.25 nm by the presence of p-Cre and to 1.60 nm by MIm, which strongly suggests that p-Cre and MIm work as mediators for charge transfer in an artificial OEC model.

Ab initio simulation of ‘liquid’ water on a Pd surface

We report on the application of the Car–Parrinello molecular dynamics method (CPMD) to the interaction of water ensembles with Pd(100) model surfaces. Periodic Pd50O8 and Pd18O2 slabs covered with nine and 18 water molecules, respectively, were employed to analyze the balance of adsorbate–adsorbate and adsorbate–surface interactions as a function of water ensemble size, in the limiting cases of a clean surface and high surface coverage with atomic oxygen. Our simulations suggest that ‘liquid’ water molecules are distributed, for the most part, randomly on Pd(100) at 300 K, with a characteristic intermolecular distance distribution in distinct regions of the water/metal interface. The structure of low-mobility local water clusters which stay close to the surface resembles that of earlier proposals based on thin film experiments. In addition, our results corroborate the experimental finding that a high surface coverage with oxygen reduces the water–Pd interaction compared to that on the clean solid.

Cooperative Catalysis and Critical Decomposition Distances between Molecular Water Oxidation Catalysts Incorporated in a Polymer Membrane

Activity of a pentaamminechlororuthenium(III) ([Ru(NH3)5Cl]2+) complex as a water oxidation catalyst was investigated in a homogeneous aqueous solution (AS) as well as in a heterogeneous Nafion membrane (HM). In the AS, the apparent catalytic activity (kapp/s-1) decreased monotonically with the concentration. In competition with water oxidation catalysis, dinitrogen (N2) evolution by oxidation of its ammine ligands was also observed, whose rate is second order with respect to its concentration, showing that a bimolecular decomposition of the complexes takes place at high concentrations. The bimolecular decomposition was suppressed remarkably by incorporating the complex into a HM. In the HM, kapp increased with the catalyst concentration at low concentrations below 1.5 × 10-2 M, indicating that four-electron water oxidation is cooperatively catalyzed by two complex molecules. The kapp was strikingly higher for HM than for AS in the whole concentration range, which was ascribed to both a favorable interaction for the cooperative catalysis and the suppression of the bimolecular decomposition by immobilization of the complex. The effect of intermolecular distance distribution of the complex in the membrane on kapp was analyzed in terms of cooperative catalysis distance (rco/nm) and critical decomposition distance (rd/nm) to give rco = 1.21 nm and rd = 0.84 nm. The rco value obtained might suggest cooperative catalysis through hydrogen bonds between water and ammine ligands.