Molecular Simulations

We reformulate a previous rotational coherent state (CS) to obtain temporally stable (TS) CSs for the spherical rotor (SR) and linear rotor (LR): TSSR and TSLR CSs, respectively. Being TS, the new CSs remain within their own classes during dynamics by evolving exclusively through their CS parameters. The new TS CSs are now appropriate to reconstruct quantum rotational properties from classical-mechanics simulations of chemical reactions. Following literature precedents, we enforce temporal stability by incorporating action-angle-related phase factors into the parameters of the original CS. In addition, to elucidate CS quantum reconstruction procedures, we derive one more rotational CS from a quantum electron nuclear dynamics description of a diatomic rotor (DR). The DR CS and the TSLR CS are not identical but display similar structures and properties. We rigorously demonstrate and examine the key properties of the three CSs: continuity, resolution of unity, temporal stability, actio...

Force field methods can be used in molecular dynamics simulations to compute and infer macro-level properties of chemical or material systems. However, these force fields can often predict erroneous values due to not being accurate at the quantum level. The ideal would be able to simulate the system from first principles (quantum-level) and scale up to get the material properties. However, this is computationally infeasible. In this paper, we develop a Programmable Potentials methodology that utilizes high-fidelity QM/MM data sets to inform a molecular dynamics (MD) potential. This methodology uses encoding functions containing small neural networks that automatically learn the quantum-level interaction logic of the system from the data and uses these encoding functions to modify standard MD potentials, like LennardJones, which capture the correct long range behavior, but do poorly in the near range. We test the method on the adsorption of hydrocarbons in a zeolite framework. We sho...

The contamination of wastewater with antibiotics has emerged as a critical global challenge, with profound implications for environmental integrity and human well-being. Adsorption techniques have been meticulously investigated and developed to mitigate and alleviate their effects. In this study, we have investigated the adsorption behaviour of Erythromycin (ERY), Gentamicin (GEN), Levofloxacin (LEVO), and Metronidazole (MET) antibiotics as pharmaceutical contaminants (PHCs) on amide-functionalized (RC (=O)NH2)/MIL-53 (Al) (AMD/ML53A), using molecular simulations and density functional theory (DFT) calculations. Based on our DFT calculations, it becomes apparent that the adsorption tendencies of antibiotics are predominantly governed by the presence of AMD functional groups on the adsorbent surface. Specifically, hydrogen bonding (HB) and van der Waals (vdW) interactions between antibiotics and AMD groups serve as the primary mechanisms facilitating adsorption. Furthermore, we have observed that the adsorption behaviors of these antibiotics are influenced by their respective functional groups, molecular shapes, and sizes. Our molecular simulations delved into how the AMD/ML53A surfaces interact with antibiotics as PHCs. Moreover, various chemical quantum descriptors based on Frontier Molecular Orbitals (FMO) were explored to elucidate the extent of AMD/ML53A adsorption and to assess potential alterations in their electronic properties throughout the adsorption process. Monte Carlo simulation showed that ERY molecules adsorb stronger to the adsorbent in acidic and basic conditions than other contaminants, with high energies: -404.47 kcal/mol in acidic and −6375.26 kcal/mol in basic environments. Molecular dynamics (MD) simulations revealed parallel orientation for the ERY molecule’s adsorption on AMD/ML53A with 80% rejection rate. In conclusion, our study highlighted the importance of modeling in developing practical solutions for removing antibiotics as PHCs from wastewater. The insights gained from our calculations can facilitate the design of more effective adsorption materials, ultimately leading to a more hygienic and sustainable ecosystem.

In this paper, we present a compression framework, for molecular dynamics (MD) simulation data, which yields significant performance by combining the strength of principal component analysis (PCA) and discrete cosine transform (DCT). Though it is a lossy compression technique, the effect on analytics performed on decompressed data is very minimal. Compression ratio up to 13 is achieved with acceptable errors in results of analytical functions.

The reaction of the V‐shaped linker molecule 5‐hydroxyisophthalic acid (H2L0), with Al or Ga nitrate under almost identical reaction conditions leads to the nitration of the linker and subsequent formation of metal–organic frameworks (MOFs) with CAU‐10 or MIL‐53 type structure of composition [Al(OH)(L)], denoted as Al‐CAU‐10‐L0, 2, 4, 6 or [Ga(OH)(L)], denoted as Ga‐MIL‐53‐L2. The Al‐MOF contains the original linker L0 as well as three different nitration products (L2, L4 and L4/6), whereas the Ga‐MOF mainly incorporates the linker L2. The compositions were deduced by 1H NMR spectroscopy and confirmed by Rietveld refinement. In situ and ex situ studies were carried out to follow the nitration and crystallization, as well as the composition of the MOFs. The crystal structures were refined against powder X‐ray diffraction (PXRD) data. As anticipated, the use of the V‐shaped linker results in the formation of the CAU‐10 type structure in the Al‐MOF. Unexpectedly, the Ga‐MOF crystallize...

We present first MD simulation results of C 60 adsorption inside a single-walled carbon nanohorn. The assumed carbon nanohorn model and the values of the force field parameters lead to relatively good agreement between simulation and experiment. We show that the confinement of water and ethanol inside a carbon nanohorn strongly changes the properties of confined liquids leading to a decrease in the number of hydrogen bonds, and diffusion coefficients in comparison to bulk. The appearance of C 60 inside the nanohorn leads to further decrease in diffusion coefficients of confined solvents.

Molecular dynamics simulations of the rat m3-muscarinic seven-helix-bundle receptor models were performed on the free, agonist-bound and antagonist-bound forms. A comparative structural/dynamics analysis was performed in order to explain the perturbations induced by the functionally different ligands when binding to their target receptor. Theoretical quantitative structure-activity relationship models were developed; a good correlation was obtained between the interaction energies of the minimized average ligand-receptor complexes and the pharmacological affinities of the considered ligands. The consistency obtained between the structural rearrangement of the transmembrane seven-helix-bundle models considered and the experimental pharmacological efficacies and affinities of the ligands constitutes an important validation of the 3-D models proposed and allows the inference of the mechanism of ligand-induced or mutation-induced receptor activation at the molecular level.

The aim of this study was to investigate the molecular changes associated with the transition of the human oxytocin receptor from its inactive to its active states. Mutation of the conserved arginine of the glutamate/aspartate-arginine-tyrosine motif located in the second intracellular domain gave rise to the first known constitutively active oxytocin receptor (R137A), whereas mutation of the aspartic acid located in the second transmembrane domain led to an inactive receptor (D85A). The structural features of the constitutively active and inactive receptor mutants were compared with those of the wild type in its free and agonist-bound states. The results suggest that, although differently triggered, the activation process induced by the ago-This work was supported by grants from Consiglio Nazionale delle Richerche (CNR) and Associazione Italiana Ricerca sul Cancro to B.C.

The highly-diversified composition of lipid bilayers across living cells is crucial for many biological processes. Lipid bilayers mainly consist of phosphatidylcholines (PC), phosphatidylethanolamines (PE), sphingomyelin (SM) and cholesterol, with eukaryotic membranes containing high percentage of sphingomyelin and cholesterol. In this study, we have modeled bilayers with different concentration of PC, PE and SM to understand the changes in bilayer properties with varied SM concentrations. In addition, membrane models with 33% cholesterol have been simulated to understand the influence of cholesterol. To quantitatively access the structure and dynamics of membranes, deuterium order parameters (S CD), mass density profiles, lipid relaxation times, clustering analysis, and radial distribution functions are calculated. The S CD s compare favorably with past NMR experiments and increase with an increase in SM content. The surface area calculations, showed that on addition of 50% palmitoyl-SM (PSM), surface area decreases (60.0±0.6 Å 2) from that of pure POPC (64.7 Å 2), which is further lowered in presence of cholesterol (44.4±0.2 Å 2). The lipid axial relaxation time decreases with increase in concentration of glycerophospholipids. The accuracy of these lipid membranes allows for future studies with more complex lipid mixtures containing SM to represent the diversity of lipids in natural membranes.

We present a method of parallelising flat histogram Monte Carlo simulations, which give the free energy of a molecular system as an output. In the serial version, a constant probability distribution, as a function of any system parameter, is calculated by updating an external potential which is added to the system Hamiltonian. This external potential is related to the free energy. In the parallel implementation, the simulation is distributed on to different processors. With regular intervals the modifying potential is summed over all processors and distributed back to every processor, thus spreading the information of which parts of parameter space have been explored. This implementation is shown to decrease the execution time linearly with added number of processors.. . .

We present a method of parallelising flat histogram Monte Carlo simulations, which give the free energy of a molecular system as an output. In the serial version, a constant probability distribution, as a function of any system parameter, is calculated by updating an external potential which is added to the system Hamiltonian. This external potential is related to the free energy. In the parallel implementation, the simulation is distributed on to different processors. With regular intervals the modifying potential is summed over all processors and distributed back to every processor, thus spreading the information of which parts of parameter space have been explored. This implementation is shown to decrease the execution time linearly with added number of processors.. . .

One of the most challenging areas to which molecular simulation has contributed significantly over the last decades is without a doubt the accurate and efficient prediction of fluid phase equilibria. In this work we combine two of the most powerful methods that have greatly enhanced our ability to simulate accurately fluid phase equilibria: (a) the "Gibbs ensemble" method (A.Z. Panagiotopoulos, Molecular Physics 61 (1987) 813-826) and (b) the multiple histogram method (A.M. Ferrenberg, R.H. Swendsen, Physical Review Letters 61 (1988) 2635-2638). The result of such combination is a simple and very accurate method of predicting fluid phase equilibrium close to and away from the critical point.

The Kirkwood-Buff (KB) theory provides a rigorous framework to predict thermodynamic properties of isotropic liquids from the microscopic structure [1, 2]. Several thermodynamic quantities relate to KB integrals, such as partial molar volumes. KB integrals are expressed as integrals of Radial Distribution Functions (RDF) over volume but can also be obtained from density fluctuations in the grandcanonical ensemble [3]. Various methods have been proposed to estimate KB integrals from molecular simulation. In this presentation, based on reference [4], I will review the available methods to compute KB integrals from molecular simulations of finite systems, and particular attention will be paid to finite-size effects [4, 5]. I will also review various applications of KB integrals computed from simulations. These applications demonstrate the importance of computing KB integrals for relating findings of molecular simulation to macroscopic thermodynamic properties of isotropic liquids.

Aim of this work is to assess the informativeness of protein dynamics in the detection of similarities among distant homologous proteins. To this end, an approach to perform large-scale comparisons of protein domain flexibilities is proposed. CONCOORD is confirmed as a reliable method for fast conformational sampling. The root mean square fluctuation of alpha carbon positions in the essential dynamics subspace is employed as a measure of local flexibility and a synthetic index of similarity is presented. The dynamics of a large collection of protein domains from ASTRAL/SCOP40 is analyzed and the possibility to identify relationships, at both the family and the superfamily levels, on the basis of the dynamical features is discussed. The obtained picture is in agreement with the SCOP classification, and furthermore suggests the presence of a distinguishable familiar trend in the flexibility profiles. The results support the complementarity of the dynamical and the structural information, suggesting that information from dynamics analysis can arise from functional similarities, often partially hidden by a static comparison. On the basis of this first test, flexibility annotation can be expected to help in automatically detecting functional similarities otherwise unrecoverable.

Partial atomic charge, which determines the magnitude of the Coulombic non-bonding interaction, represents a critical parameter in molecular mechanics simulations. Partial charges may also be used as a measure of physical properties of the system, ie. covalency, acidic/catalytic sites, etc. A range of methods, both empirical and ab initio, exist for calculating partial charges in a given solid, and several of them are compared here for siliceous (pure silica) zeolites. The relationships between structure and the predicted partial charge are examined. The predicted partial charges from different methods are also compared with related experimental observations, showing that a few of the methods offer some guidance towards identifying the T-sites most likely to undergo substitution or for proton localization in acidic framework forms. Finally, we show that assigning unique calculated charges to crystallographically unique framework atoms makes an appreciable difference in simulating predicting N2 and O2 adsorption with common dispersion-repulsion parameterizations.

The Kirkwood-Buff (KB) theory provides a rigorous framework to predict thermodynamic properties of isotropic liquids from the microscopic structure [1, 2]. Several thermodynamic quantities relate to KB integrals, such as partial molar volumes. KB integrals are expressed as integrals of Radial Distribution Functions (RDF) over volume but can also be obtained from density fluctuations in the grandcanonical ensemble [3]. Various methods have been proposed to estimate KB integrals from molecular simulation. In this presentation, based on reference [4], I will review the available methods to compute KB integrals from molecular simulations of finite systems, and particular attention will be paid to finite-size effects [4, 5]. I will also review various applications of KB integrals computed from simulations. These applications demonstrate the importance of computing KB integrals for relating findings of molecular simulation to macroscopic thermodynamic properties of isotropic liquids.

One of the most challenging areas to which molecular simulation has contributed significantly over the last decades is without a doubt the accurate and efficient prediction of fluid phase equilibria. In this work we combine two of the most powerful methods that have greatly enhanced our ability to simulate accurately fluid phase equilibria: (a) the "Gibbs ensemble" method (A.Z. Panagiotopoulos, Molecular Physics 61 (1987) 813-826) and (b) the multiple histogram method (A.M. Ferrenberg, R.H. Swendsen, Physical Review Letters 61 (1988) 2635-2638). The result of such combination is a simple and very accurate method of predicting fluid phase equilibrium close to and away from the critical point.

We report here two new small-size peptides acting as modulators of the β-site APP cleaving enzyme 1 (BACE1) exosite. Ac-YPYFDPL-NH2 and Ac-YPYDIPL-NH2 displayed a moderate but significant inhibitory effect on BACE1. These peptides were obtained from a molecular modeling study. By combining MD simulations with ab initio and DFT calculations, a simple and generally applicable procedure to evaluate the binding energies of small-size peptides interacting with the exosite of the BACE1 is reported here. The structural aspects obtained for the different complexes were analyzed providing a clear picture about the binding interactions of these peptides. These interactions have been investigated within the framework of the density functional theory and the quantum theory of atoms in molecules using a reduced model. Although the approach used here was traditionally applied to the study of noncovalent interactions in small molecules complexes in gas phase, we show, through in this work, that this methodology is also a very powerful tool for the study of biomolecular complexes, providing a very detailed description of the binding event of peptides modulators at the exosite of BACE1.

The effect of the replacement of CaO for MgO on the structural properties of the 45S5 Bioglass with composition 46.2SiO 2 • 24.3Na 2 O • (26.9x)CaO • 2.6P 2 O 5 • xMgO where x) 0, 5, 10, 15, 20, and 26.9 mol has been studied by means of molecular dynamics simulations. The results confirmed the complexity of the local environment of Mg ions which are coordinated by 5 nonbridging oxygens of different TO 4 tetrahedra (T) Si/P) leading to large rings in the structures. A rough correlation between the average dimension of the rings found in the structure and the computed Young's modulus is obtained. The Young's modulus decrease at low Mg-content reaching a minimum for the 46.2SiO 2 • 24.3Na 2 O • 16.9CaO • 2.6P 2 O 5 • 10MgO glass. At this composition, Mg is homogeneously distributed in the silica rich region together with Ca and Na ions but is almost totally absent from the Ca-Na-phosphate rich regions. The results suggest that the ideal glass composition for lowering the Young's modulus preserving a specific bioactivity can be found below 10% of MgO content.

Motivated by single molecule experiments on biopolymers we explore equilibrium morphologies and force-extension behavior of copolymers with hydrophobic segments using Langevin dynamics simulations. We find that the interplay between different length scales, namely, the persistence length p, and the disorder correlation length p, in addition to the fraction of hydrophobic patches f play a major role in altering the equilibrium morphologies and mechanical response. In particular, we show a plethora of equilibrium morphologies for this system, e.g. core-shell, looped (with hybridised hydrophilic-hydrophobic sections), and extended coils as a function of these parameters. A competition of bending energy and hybridisation energies between two types of beads determines the equilibrium morphology. Further, mechanical properties of such polymer architectures are crucially dependent on their native conformations, and in turn on the disorder realisation along the chain backbone. Thus, for flexible chains, a globule to extended coil transition is effected via a tensile force for all disorder realisations. However, the exact nature of the force-extension curves are different for the different disorder realisations. In contrast, we find that force-extension behavior of semi-flexible chains with different equilibrium configurations e.g. core-shell, looped, etc. reveal a cascade of force-induced conformational transitions.

Context: Water kefir is a fermented beverage that is typically made in the home by inoculating a sugar-rich solution with a microbial community (water kefir grains). Several studies on the metabolite content and hepatoprotective effects of water kefir have been published, but carbon tetrachloride (CCl4)-induced acute liver injury has not been studied. Aims: To evaluate the efficacy of water kefir in vivo against hepatoprotective CCl4-induced acute liver injury and to in silico investigate metabolites that play an important role in hepatoprotective mechanisms. Methods: The present study aimed to investigate the hepatoprotective activity of water kefir in an animal model caused by CCl4. Furthermore, using molecular docking, the metabolites found in water kefir were evaluated for their role in the NF-κB and Nrf2 signaling pathways. Results: Water kefir significantly and dose-dependently alleviated acute liver injury caused by CCl4. Water kefir administration at all doses produced results comparable to the positive control (Curcuma extract). Molecular docking simulations showed that, compared to Nrf2, the 25 metabolites were more likely to interact with the NF-κB receptor. Fumaric acid is the strong metabolite that interacts with the NF-κB receptor with a free energy of binding and an inhibition constant of-6.66 kcal/mol and 13.22 µM, respectively. Conclusions: Water kefir administration improved the condition of liver damage, characterized by a decrease in serum levels of AST, ALT, TNF-a, TGF-b, and an improvement in the liver tissue profile. In silico evaluation showed that the metabolites in water kefir were able to interact with target proteins in the NF-κB and Nrf2 pathways. It was concluded that water kefir improves the condition of the liver by reducing the level of necrosis and fibrosis.

The effect of the replacement of CaO for MgO on the structural properties of the 45S5 Bioglass with composition 46.2SiO 2 • 24.3Na 2 O • (26.9x)CaO • 2.6P 2 O 5 • xMgO where x) 0, 5, 10, 15, 20, and 26.9 mol has been studied by means of molecular dynamics simulations. The results confirmed the complexity of the local environment of Mg ions which are coordinated by 5 nonbridging oxygens of different TO 4 tetrahedra (T) Si/P) leading to large rings in the structures. A rough correlation between the average dimension of the rings found in the structure and the computed Young's modulus is obtained. The Young's modulus decrease at low Mg-content reaching a minimum for the 46.2SiO 2 • 24.3Na 2 O • 16.9CaO • 2.6P 2 O 5 • 10MgO glass. At this composition, Mg is homogeneously distributed in the silica rich region together with Ca and Na ions but is almost totally absent from the Ca-Na-phosphate rich regions. The results suggest that the ideal glass composition for lowering the Young's modulus preserving a specific bioactivity can be found below 10% of MgO content.

The highly-diversified composition of lipid bilayers across living cells is crucial for many biological processes. Lipid bilayers mainly consist of phosphatidylcholines (PC), phosphatidylethanolamines (PE), sphingomyelin (SM) and cholesterol, with eukaryotic membranes containing high percentage of sphingomyelin and cholesterol. In this study, we have modeled bilayers with different concentration of PC, PE and SM to understand the changes in bilayer properties with varied SM concentrations. In addition, membrane models with 33% cholesterol have been simulated to understand the influence of cholesterol. To quantitatively access the structure and dynamics of membranes, deuterium order parameters (S CD), mass density profiles, lipid relaxation times, clustering analysis, and radial distribution functions are calculated. The S CD s compare favorably with past NMR experiments and increase with an increase in SM content. The surface area calculations, showed that on addition of 50% palmitoyl-SM (PSM), surface area decreases (60.0±0.6 Å 2) from that of pure POPC (64.7 Å 2), which is further lowered in presence of cholesterol (44.4±0.2 Å 2). The lipid axial relaxation time decreases with increase in concentration of glycerophospholipids. The accuracy of these lipid membranes allows for future studies with more complex lipid mixtures containing SM to represent the diversity of lipids in natural membranes.

Aim of this work is to assess the informativeness of protein dynamics in the detection of similarities among distant homologous proteins. To this end, an approach to perform large-scale comparisons of protein domain flexibilities is proposed. CONCOORD is confirmed as a reliable method for fast conformational sampling. The root mean square fluctuation of alpha carbon positions in the essential dynamics subspace is employed as a measure of local flexibility and a synthetic index of similarity is presented. The dynamics of a large collection of protein domains from ASTRAL/SCOP40 is analyzed and the possibility to identify relationships, at both the family and the superfamily levels, on the basis of the dynamical features is discussed. The obtained picture is in agreement with the SCOP classification, and furthermore suggests the presence of a distinguishable familiar trend in the flexibility profiles. The results support the complementarity of the dynamical and the structural information, suggesting that information from dynamics analysis can arise from functional similarities, often partially hidden by a static comparison. On the basis of this first test, flexibility annotation can be expected to help in automatically detecting functional similarities otherwise unrecoverable.

We use molecular simulations to explore how sample dimensions and interfacial properties impact some generic aspects of the mechanical and structural behavior of nanoconfined materials. Specifically, we calculate the strain-dependent properties of minimum-energy thin-film particle configurations (i.e., inherent structures) confined between attractive, parallel substrates. We examine how the relationship between the transverse strain and the stress tensor (the equation of state of the energy landscape) depends on the properties of the film and substrate. We find that both film thickness and film-substrate attractions influence not only the mechanical properties of thin films, but also the shape and location of the "weak spots" where voids preferentially form in a film as it is strained beyond its point of maximum tensile stress. The sensitivity of weak spots to film properties suggests that nanoscale materials may be intrinsically vulnerabile to specific mechanisms of mechanical failure.

Many thanks for your comments on our manuscript: Mallard Blue binding to heparin, its SDS micelle-driven de-complexation, and interaction with human serum albumin: a combined experimental/modeling investigation. We have addressed all your specific comments, point by point and inserting the relevant sentences within the paper as evidenced in the highlighted version of the manuscript. In thanking you for their time and attention, we strongly hope this revised manuscript is now suitable for publication in the special issue of Fluid Phase Equilibria, as a part of joyful contribution to John's important B-day.

Molecular simulation techniques are used to explore and characterize the atomic scale structure, and to predict binding energies and basal spacing of polymer/clay nanocomposites based on polypropylene (PP) and maleated polypropylene (PPMA), montmorillonite (MMT), and different alkylammonium ions (quats) as surfactants. Our evidences suggest that shorter hydrocarbonic chains are more effective in producing favorable binding energies with respect to longer ones, and the substitutions of hydrogen atoms with polar groups on the quaternary ammonium salt (quat) generally results in greater interaction between quat and both polymer and clay. Under the hypothesis, that montmorillonite platelets are uniformly dispersed in a polymer matrix, the modified polypropylene yields higher interfacial strength with clay than neat polypropylene. The use of neat PP and quats with higher molecular volume offer the higher values of the basal spacing and thus, in principle, they should be more effective in the exfoliation process.

Molecular mechanics/dynamics computer simulations are used to explore the atomic scale structure and to predict binding energy values for polymer/clay nanocomposites based on random poly(butylene terephtalate-co-thiodiethylene terephtalate) copolyesters, montmorillonite and several, different organic surfactant. Our results reveal that the energy of binding between the polymeric matrix and the montmorillonite platelet shows a decreasing trend with increasing molecular volume, V, of the organic compounds used as surfactant, and that the substitution of hydrogen atoms with aSH moiety in the organic molecules results in progressively increasing interaction of the surfactant with the copolymer, as the sulfur-containing comonomer concentration is increased. Finally, under the hypothesis that the clay platelets are uniformly dispersed within the polymer matrix, the pristine clay still yields a high interfacial strength between MMT and copolymers.

The heuristic-direct quantitative structure-activity relationship approach has been applied to fifteen non-congeneric cu,-adrenergic receptor (al-AR) ligands interacting with the rat ~,A,~-AR subtype. The good linear correlations, which have been obtained between calculated binding energies and the pharmacological affinities, allow one to predict the pharmacological affinity of new ligands. Moreover, according to the alAjo-receptor model proposed, it has been possible to speculate on the amino acid residues which are mainly involved in the interaction with the ligands. This novel procedure constitutes a powerful tool for the design of new selective leads based on explicit intermolecular interactions and for suggesting site-directed mutagenesis studies, in order to give, iteractively, further support and improvement to the predictive and interpretative aspects of the model.

ZIF-8 membrane for gas separation evaluated by molecular simulations. Rigid framework sufficient for adsorption but flexible one needed for diffusivity. Simulated adsorption and diffusion consistent with available experiments. Gas exiting between permeances from estimation and measurement even at low pressure. Multiple porosity effects not to be ignored for permeability prediction.

Considering the thermodynamic grand potential for more than one adsorbate in an isothermal system, we generalize the model of adsorption-induced deformation of microporous carbons developed by Kowalczyk et al. [1]. We report a comprehensive study of the effects of adsorption-induced deformation of carbonaceous amorphous porous materials due to adsorption of carbon dioxide, methane and their mixtures. The adsorption process is simulated by using the Grand Canonical Monte Carlo (GCMC) method and the calculations are then used to analyze experimental isotherms for the pure gases and mixtures with different molar fraction in the gas phase. The pore size distribution determined from an experimental isotherm is used for predicting the adsorption-induced deformation of both pure gases and their mixtures. The volumetric strain (ε) predictions from the GCMC method are compared against relevant experiments with good agreement found in the cases of pure gases.

The Kirkwood-Buff (KB) theory provides a rigorous framework to predict thermodynamic properties of isotropic liquids from the microscopic structure [1, 2]. Several thermodynamic quantities relate to KB integrals, such as partial molar volumes. KB integrals are expressed as integrals of Radial Distribution Functions (RDF) over volume but can also be obtained from density fluctuations in the grandcanonical ensemble [3]. Various methods have been proposed to estimate KB integrals from molecular simulation. In this presentation, based on reference [4], I will review the available methods to compute KB integrals from molecular simulations of finite systems, and particular attention will be paid to finite-size effects [4, 5]. I will also review various applications of KB integrals computed from simulations. These applications demonstrate the importance of computing KB integrals for relating findings of molecular simulation to macroscopic thermodynamic properties of isotropic liquids.

D. Inbakandan, Sumit Raj , C. Kumar, R. Venkatesan & S. Ajmal Khan Centre for Ocean Research, Sathyabama University, Chennai 600 119, India Department of Bioinformatics, Sathyabama University, Chennai 600 119, India National Institute of Ocean Technology, Pallikaranai, Chennai 600 100, India Centre of Advanced Study in Marine Biology, Annamalai University, Parangipettai 608 502, India [ E.Mail: [email protected] ]

In this work we present results from fully atomistic molecular dynamics simulations of aqueous solutions of poly(amido amine) dendrimers and poly-(methacrylic) acid in the dilute regime and at low ionic strength and physiological pH conditions, in which the polymeric components are charged. We have studied stoichiometric (1:1) and non-stoichiometric (1:2) systems, comprised by dendrimers of two different generations and two different lengths of the linear polyelectrolyte. For all systems studied, a polymer-rich and a solvent-rich region is formed. The polymerrich region consists of aggregated complexes between the polymeric components bearing similarities to percolated structures met in physical hydrogels. We examine morphological characteristics of the two components as well as the degree of ionic pairing between the different ionic moieties, providing information regarding the degree of physical adsorption of the linear chains on the dendrimer's surface and that of the respective counterions on the oppositely charged monomers.

Interactions between the components of lysozyme/cytochrome c (lysozyme/ Cyt,c) and lysozyme/zein protein mixtures were determined by following the in vitro synthesis of gold (Au) nanoparticles (NPs). Both UV−visible and fluorescence studies were employed to monitor the interactions and simultaneous synthesis of protein coated NPs. Protein coated NPs were characterized by gel electrophoresis and TEM studies. Lysozyme/ Cyt,c complex coated NPs showed remarkable pH responsive behavior due to their amphiphilic nature, while lysozyme/zein complex coated NPs were not pH sensitive because of the predominantly hydrophobic nature. The results were further supported by molecular dynamics studies (MD) of protein−protein interactions and interactions of protein with the gold surface. Molecular simulations helped us to identify the amino acids that drove such interactions. Biological applications of protein coated NPs were determined from hemolytic and antimicrobial studies to demonstrate their potential in pharmaceutical and food industries. The results clearly differentiated between the greater applicability of predominantly amphiphilic lysozyme/Cyt,c complex coated NPs in comparison to predominantly hydrophobic lysozyme/zein complex coated NPs.

Acting either coordinately or independently, these two This work describes the ab initio procedure employed to build species bind and modulate the activities of downstream an activation model for the a 1b-adrenergic receptor (a 1b-AR). The effector molecules. G proteins are released from effirst version of the model was progressively modified and complifectors on the breakdown of GTP that results from the cated by means of a many-step iterative procedure characterized slow GTPase activity of the a subunit. The inactive a by the employment of experimental validations of the model in subunit can recombine with bg, reforming the heteroeach upgrading step. A combined simulated (molecular dynamtrimer, which can then reassociate with its receptor ics) and experimental mutagenesis approach was used to deterand undergo a new cycle of signal transduction (3). mine the structural and dynamic features characterizing the in-Despite the fact that recent crystallographic studies active and active states of a 1b-AR. The latest version of the of G protein a subunits and heterotrimers have begun model has been successfully challenged with respect to its abilto show how G proteins might work (3), the challenge ity to interpret and predict the functional properties of a large for the future is to discover how the intracellular donumber of mutants. The iterative approach employed to describe mains of activated receptors bind to the heterotrimer a 1b-AR activation in terms of molecular structure and dynamics and catalyze the nucleotide exchange. This remains a allows further complications of the model to allow prediction daunting task in part because the direct determination, and interpretation of an ever-increasing number of experimental by X-ray crystallography or electron microscopy, of the data. ᭧ 1998 Academic Press atomic structure of any member of the rhodopsin family of GPCRs is still lacking. The discovery that mutations in the C-terminal portion of i3 of different adrenergic receptor subtypes can Hundreds of cell surface receptors employ guanine dramatically increase their agonist-independent activnucleotide-binding proteins (G proteins) to initiate sigity (4-7) led to the hypothesis that GPCRs can exist nal transduction (1). All the members of the rhodopsin in equilibrium between two interconvertible allosteric family of G protein coupled receptors (GPCRs) share states R and R* (7). In the absence of ligand, the inacthe presence of seven hydrophobic regions that are betive state predominates, possibly because a structural lieved to form a bundle of a-helical transmembrane constraint prevents sequences of the intracellular loops domains (TMDs) connected by alternating intracellular from interacting with the G proteins. The release of and extracellular hydrophilic loops (2). The G proteins these constraints would trigger the conversion into the consist of three subunits: a, b, and g. In the inactive active state R* which couples with the G proteins. The state, G proteins form membrane-associated abg hetequilibrium between R and R* can be altered by agonist erotrimers, with GDP tightly bound to the a subunit binding or mutations, and can be responsible for the (3). On activation by extracellular signals, the recepvarious levels of basal activity of different GPCRs (8). tors catalyze the exchange of bound GDP for GTP. The Successively, spontaneously occurring activating mu-GTP-bound form of the heterotrimer is unstable and tations have been described in diverse areas of various dissociates to form active GTP-a and bg complexes. GPCRs (9). Recently, biophysical and biochemical studies on rhodopsin showed that a relative displacement of helices

She is now an Assistant Scientist of the Dulbecco Telethon Institute. Her research since 1991 has been almost entirely devoted to developing computational protocols and molecular models to unravel the chemical communication mechanisms involving G protein-coupled receptors.

Experimental values of the absorption of carbon dioxide in two ionic liquids with carboxylate anions-the 1-butyl-3-methylimidazolium levulinate [C 1 C 4 Im][LEV] and the 1-butyl-1-methylpyrrolidinium acetate [C 1 C 4 Pyrro][OAc]-are reported as a function of temperature and at pressures close to atmospheric. Mole fraction absorption of carbon dioxide in [C 1 C 4 Im][LEV] and [C 1 C 4 Pyrro][OAc] is equal to 0.93 × 10 −2 and 1.10 × 10 −2 at 303.15 K and 89.2 kPa and 353.15 K and 67.1 kPa, respectively. The effect of the presence of controlled amounts of water on the absorption of carbon dioxide was measured for [C 1 C 4 Pyrro][OAc]. The presence of a 0.35 mole fraction of water in [C 1 C 4 Pyrro][OAc] decreases the viscosity of the ionic liquid phase and dramatically increases the amount of carbon dioxide absorbed, pointing toward a chemical reaction between the gas and the liquid absorbent. Increasing the amounts of water lowers the viscosity further but also the absorption capacity of the ionic liquid. Molecular dynamics simulations were used to interpret the molecular mechanism of solvation of carbon dioxide in [C 1 C 4 Pyrro][OAc]. Results show that carbon dioxide is solvated preferentially in the non-polar domain of the solvent, and that the CO 2-anion interactions dominate over the CO 2-cation interactions. Molecular simulations could reproduce the experimental solubility of CO 2 in [C 1 C 4 Im][TFA] (known to be a physical process), but not in [C 1 C 4 Pyrro][OAc] and reinforcing the conclusion that the higher solubility of carbon dioxide in the acetate based ionic liquid can be ascribed to a chemical reaction.

Samples of Mg 4 Al 2 layered double hydroxide (LDH) intercalated with p-methylbenzoate and p-bromobenzoate anions were prepared by reconstruction of calcined LDH. The interlayer arrangement of guests was investigated by molecular modeling combined with X-ray powder diffraction and thermogravimetry. Molecular modeling was carried out in a Cerius 2 modeling environment. In both structures the guest anions adopt a nearly perpendicular arrangement of their long axis with respect to the host layers and they are anchored to the OH groups of the layers through COO − groups via electrostatic interactions. Molecular modeling revealed that both structures of the intercalates exhibit a certain disorder of guest anions in the interlayer space. In the case of LDH-p-methylbenzoate intercalate the anions tend to be situated in disordered rows, and the LDH-p-bromobenzoate intercalate exhibits a total disorientation of guest anions. A good agreement between calculated and measured Xray diffraction patterns and between experimental and calculated basal spacings was obtained. In the LDH-p-methylbenzoate intercalate d exp = 16.96 Å and d calc = 16.97 Å, and in the case of LDH-p-bromobenzoate intercalate d exp = 17.19 Å and d calc = 17.40 Å.

The Crystal Packer module in the Cerius 2 modeling environment has been used to study the structure of montmorillonite intercalated with Al(OH)3-fragment (gibbsite-like) polymers. Basal spacings in gibbsite-like polymers arranged in 2 layers in the interlayer of montmorillonite varied in the range 19.54-20.13 A, depending on the type and arrangement of AI(OH) 3 fragments. The inhomogeneous distribution of intercalating species in the interlayer and, consequently, the turbostratic stacking of layers has been found for gibbsite-like polymers as well as in the case of Keggin cations (Capkov~i et al. 1998). The dominating contribution to the total sublimation energy comes from electrostatic interactions for both intercalating species, gibbsite-like polymers and Keggin cations.

This paper discusses the evaluation of hydrodynamic variables in the presence of spontaneous fluctuations, such as in molecular simulations of fluid flows. The principal point is that hydrodynamic variables such as fluid velocity and temperature must be defined in terms of mechanical variables such as momentum and energy density). Because these relations are nonlinear and because fluctuations of mechanical variables are correlated, care must be taken to avoid introducing a bias when evaluating means, variances, and correlations of hydrodynamic variables. The unbiased estimates are formulated; some alternative, incorrect approaches are presented as cautionary warnings. The expressions are verified by numerical simulations, both at thermodynamic equilibrium and at a nonequilibrium steady state.

Les aluminosilicates poreux cristallins tels que les zeolithes cationiques de type faujasite sont largement etudies en raison de leurs proprietes d’adsorption, d’echange ionique et de catalyse, ce qui leurs valent d’etre engagees dans de nombreuses applications industrielles, qui font intervenir de plus en plus de cations multivalents (detergents/ adoucissants, craquage catalytique, decontamination,...). Ces differentes applications industrielles ont en commun les proprietes d’adsorption, resultant d’une part de la taille de leurs pores du meme ordre de grandeur que les especes introduites, et d’autre part de leur composition chimique qui conduit a des charges de charpente, a l’origine de sites de forte interaction ou de repulsion localises. Dans ces applications, les zeolithes sont hydratees. L’eau est associee aux processus mis en jeu et influence ainsi les autres proprietes du materiau. La modelisation moleculaire est un outil de choix pour predire et comprendre les proprietes mi...

When adsorbing guest molecules, the porous metal−organic framework MIL-53(Cr) may vary its cell parameters drastically while retaining its crystallinity. A first approach to the thermodynamic analysis of this "framework breathing" consists of comparing the osmotic potential in two distinct shapes only (large-pore and narrow-pore). In this paper, we propose a generic parametrized free energy model including three contributions: host free energy, guest−guest interactions, and host−guest interaction. Free energy landscapes may now be constructed scanning all shapes and any adsorbed amount of guest molecules. This allows us to determine which shapes are the most stable states for arbitrary combinations of experimental control parameters, such as the adsorbing gas chemical potential, the external pressure, and the temperature. The new model correctly reproduces the structural transitions along the CO 2 and CH 4 isotherms. Moreover, our model successfully explains the adsorption versus desorption hysteresis as a consequence of the creation, stabilization, destabilization, and disappearance of a second free energy minimum under the assumptions of a first-order phase transition and collective behavior. Our general thermodynamic description allows us to decouple the gas chemical potential μ and mechanical pressure P as two independent thermodynamic variables and predict the complete (μ, P) phase diagram for CO 2 adsorption in MIL-53(Cr). The free energy model proposed here is an important step toward a general thermodynamics description of flexible metal−organic frameworks.