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Ion association in aqueous LiCl solutions at high concentration: predicted results via molecular simulation.

We perform molecular dynamics simulations to study the ionic solvation and association behavior in concentrated aqueous LiCl solutions at ambient conditions, including consideration of expected signatures of ion pairing that might be found in neutron diffraction experiments with isotopic substitution. The ten possible pair radial distribution functions that define the microstructure of the systems are determined and used to assess the first-order difference of the neutron-weighted correlation functions for these solutions in heavy and null water. Then, both sets of correlation functions are applied to the interpretation of the ion's local environment in terms of the location of the relevant peaks and the penetration of ions into the counterion solvation shells as a signature of ion-pair formation. Finally, we illustrate how first-order difference experiments involving null and heavy water might be used to assess the magnitude of the M(v+) - X(v-) ion-pair formation for a salt M(v+)X(n) v- in an aqueous solution, provided the significant experimental challenges in these studies could be overcome.

Journal Article↗

Cracks and crazes: on calculating the macroscopic fracture energy of glassy polymers from molecular simulations.

We combine molecular dynamics simulations of deformation at the submicron scale with a simple continuum fracture mechanics model for the onset of crack propagation to calculate the macroscopic fracture energy of amorphous glassy polymers. Key ingredients in this multiscale approach are the elastic properties of polymer crazes and the stress at which craze fibrils fail through chain pullout or scission. Our results are in quantitative agreement with dimensionless ratios that describe experimental polymers and their variation with temperature, polymer length, and polymer rigidity.

Journal Article↗

The behaviour of beta-carotene in the phosphatidylcholine bilayer as revealed by a molecular simulation study.

A molecular dynamics (MD) simulation of the fully hydrated bilayer made of 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) and containing beta-carotene (beta-Car) molecules was carried out as a complementary approach to experimental techniques to investigate the orientation of beta-Car in the lipid membrane as well as its influence on the bilayer properties. The bilayer reached thermal equilibrium after 1200 ps of MD simulation and the productive run was carried out for 2800 ps. The results indicate that the carotene rings are located in the region occupied by the carbonyl groups of the POPC gamma-chain with no trace of penetration towards the centre of the bilayer. Carotene exhibits an ordering effect on both the beta- and the gamma-chain. While the fully saturated gamma-chain is affected evenly along, the order of the mono-unsaturated beta-chain is modified mainly below the double bond. In general, a high value of the order parameter and the chain tilt in the range from 11.4 degrees to 26.7 degrees were observed for the beta-Car molecules. However, for chain segment adjacent to methyl groups the value of the order parameter is low and the tilt angle is close to 75 degrees . Moreover, the probability of trans conformation being generally close to 1.0 along the beta-Car chain is reduced for these segments. Our MD simulation study suggests two pools of the preferential orientation of beta-Car: a slightly bent structure corresponding to a small chain tilt angle and a rather stretched structure that corresponds to a higher chain tilt. The results are discussed in the light of experimental findings.

Computer Simulation↗

Framework-based design of a new all-purpose molecular simulation application: the Adun simulator.

Here we present Adun, a new molecular simulator that represents a paradigm shift in the way scientific programs are developed. The traditional algorithm centric methods of scientific programming can lead to major maintainability and productivity problems when developing large complex programs. These problems have long been recognized by computer scientists; however, the ideas and techniques developed to deal with them have not achieved widespread adoption in the scientific community. Adun is the result of the application of these ideas, including pervasive polymorphism, evolutionary frameworks, and refactoring, to the molecular simulation domain. The simulator itself is underpinned by the Adun Framework, which separates the structure of the program from any underlying algorithms, thus giving a completely reusable design. The aims are twofold. The first is to provide a platform for rapid development and implementation of different simulation types and algorithms. The second is to decrease the learning barrier for new developers by providing a rigorous and well-defined structure. We present some examples on the use of Adun by performing simple free-energy simulations for the adiabatic charging of a single ion, using both free-energy perturbation and the Bennett's method. We also illustrate the power of the design by detailing the ease with which ASEP/MD, an elaborated mean field QM/MM method originally written in FORTRAN 90, was implemented into Adun.

Algorithms↗

Computation of methodology-independent ionic solvation free energies from molecular simulations. I. The electrostatic potential in molecular liquids.

The computation of ionic solvation free energies from atomistic simulations is a surprisingly difficult problem that has found no satisfactory solution for more than 15 years. The reason is that the charging free energies evaluated from such simulations are affected by very large errors. One of these is related to the choice of a specific convention for summing up the contributions of solvent charges to the electrostatic potential in the ionic cavity, namely, on the basis of point charges within entire solvent molecules (M scheme) or on the basis of individual point charges (P scheme). The use of an inappropriate convention may lead to a charge-independent offset in the calculated potential, which depends on the details of the summation scheme, on the quadrupole-moment trace of the solvent molecule, and on the approximate form used to represent electrostatic interactions in the system. However, whether the M or P scheme (if any) represents the appropriate convention is still a matter of on-going debate. The goal of the present article is to settle this long-standing controversy by carefully analyzing (both analytically and numerically) the properties of the electrostatic potential in molecular liquids (and inside cavities within them). Restricting the discussion to real liquids of "spherical" solvent molecules (represented by a classical solvent model with a single van der Waals interaction site), it is concluded that (i) for Coulombic (or straight-cutoff truncated) electrostatic interactions, the M scheme is the appropriate way of calculating the electrostatic potential; (ii) for non-Coulombic interactions deriving from a continuously differentiable function, both M and P schemes generally deliver an incorrect result (for which an analytical correction must be applied); and (iii) finite-temperature effects, including intermolecular orientation correlations and a preferential orientational structure in the neighborhood of a liquid-vacuum interface, must be taken into account. Applications of these results to the computation methodology-independent ionic solvation free energies from molecular simulations will be the scope of a forthcoming article.

Journal Article↗

Discussion on the mechanism of Lingguizhugan Decoction in treating hypertension based on network pharmacology and molecular simulation technology.

To explore the mechanism of Lingguizhugan Decoction in treating hypertension based on network pharmacology and molecular simulation. The active ingredients and potential targets were screened by the Systematic Pharmacological Analysis Platform of Traditional Chinese Medicine (TCMSP). Hypertension-related targets were obtained from OMIM and GeneCards databases. Common targets between drug and hypertension were screened in the Venny platform. A protein-protein interaction (PPI) network was constructed in the STRING database using intersection targets. Key targets in PPI network were analyzed by Cytoscape. R language program was used for Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Finally, the binding abilities of the main active ingredients to critical targets were verified by molecular simulation. Naringenin, quercetin, kaempferol, and β-sitosterol in Lingguizhugan Decoction, and potential targets such as STAT3, AKT1, TNF, IL6, JUN, PTGS2, MMP9, CASP3, TP53, and MAPK3, were screened out. KEGG Enrichment analysis revealed that the common targets of Lingguizhugan Decoction and hypertension are mainly involved in the lipid and atherosclerosis signaling pathway, AGE-RAGE signaling pathway in diabetic complications, fluid shear stress and atherosclerosis, and IL17 signaling pathway. The molecular simulation results showed that naringenin-MAPK3, quercetin-MMP9, quercetin-PTGS2, and quercetin-TP53 were the top four in the docking scores. Naringenin-MAPK3 and quercetin-MMP9 were stable, with binding free energies of -27.97 ± 1.41 kcal/mol and -21.15 ± 3.17 kcal/mol, respectively. The possible mechanism of Lingguizhugan Decoction in treating hypertension is characterized of multi-component, multi-target, and multi-pathway.Communicated by Ramaswamy H. Sarma.

Network Pharmacology↗

Cholesterol effects on the phosphatidylcholine bilayer polar region: a molecular simulation study.

A molecular dynamics (MD) simulation of a fully hydrated, liquid-crystalline dimyristoylphosphatidylcholine (DMPC)-Chol bilayer membrane containing approximately 22 mol% Chol was carried out for 4.3 ns. The bilayer reached thermal equilibrium after 2.3 ns of MD simulation. A 2.0-ns trajectory generated during 2.3-4.3 ns of MD simulation was used for analyses to determine the effects of Chol on the membrane/water interfacial region. In this region, 70% of Chol molecules are linked to DMPC molecules via short-distance interactions, where the Chol hydroxyl group (OH-Chol) is 1) charge paired to methyl groups of the DMPC choline moiety ( approximately 34%), via the hydroxyl oxygen atom (Och); 2) water bridged to carbonyl ( approximately 19%) and nonester phosphate ( approximately 14%) oxygen atoms, via both Och and the hydroxyl hydrogen atom (Hch); and 3) directly hydrogen (H) bonded to carbonyl ( approximately 11%) and nonester phosphate ( approximately 5%) oxygen atoms, via Hch ( approximately 17% of DMPC-Chol links are multiple). DMPC's gamma-chain carbonyl oxygen atom is involved in 44% of water bridges and 51% of direct H bonds formed between DMPC and Chol. On average, a Chol molecule forms 0.9 links with DMPC molecules, while a DMPC molecule forms 2.2 and 0.3 links with DMPC and Chol molecules, respectively. OH-Chol makes hydrogen bonds with 1.1 water molecules, preferentially via Hch. The average number of water molecules H bonded to the DMPC headgroup is increased by 7% in the presence of Chol. These results indicate that inclusion of Chol decreases interlipid links and increases hydration in the polar region of the membrane.

Cholesterol↗

Surface tension of quantum fluids from molecular simulations.

We present the first molecular simulations of the vapor-liquid surface tension of quantum liquids. The path integral formalism of Feynman was used to account for the quantum mechanical behavior of both the liquid and the vapor. A replica-data parallel algorithm was implemented to achieve good parallel performance of the simulation code on at least 32 processors. We have computed the surface tension and the vapor-liquid phase diagram of pure hydrogen over the temperature range 18-30 K and pure deuterium from 19 to 34 K. The simulation results for surface tension and vapor-liquid orthobaric densities are in very good agreement with experimental data. We have computed the interfacial properties of hydrogen-deuterium mixtures over the entire concentration range at 20.4 and 24 K. The calculated equilibrium compositions of the mixtures are in excellent agreement with experimental data. The computed mixture surface tension shows negative deviations from ideal solution behavior, in agreement with experimental data and predictions from Prigogine's theory. The magnitude of the deviations at 20.4 K are substantially larger from simulations and from theory than from experiments. We conclude that the experimentally measured mixture surface tension values are systematically too high. Analysis of the concentration profiles in the interfacial region shows that the nonideal behavior can be described entirely by segregation of H(2) to the interface, indicating that H(2) acts as a surfactant in H(2)-D(2) mixtures.

Journal Article↗

Molecular simulation study of effect of molecular association on vapor-liquid interfacial properties.

Vapor-liquid interfacial properties of square-well associating fluids are studied via transition-matrix Monte Carlo simulation. Results for one-site and two-site association models are presented. Coexistence properties, surface tension, cluster distribution, density profile, and orientation profile are presented. Molecular association affects the interfacial properties and cluster fractions more than it affects the bulk densities. We observe that the surface tension exhibits a maximum with respect to association strength. This behavior is in agreement with the recent study of Peery and Evans for one site system using a square-gradient approach.

Chemistry, Physical↗

A novel algorithm for non-bonded-list updating in molecular simulations.

Simulations of molecular systems typically handle interactions within non-bonded pairs. Generating and updating a list of these pairs can be the most time-consuming part of energy calculations for large systems. Thus, efficient non-bonded list processing can speed up the energy calculations significantly. While the asymptotic complexity of current algorithms (namely O(N), where N is the number of particles) is probably the lowest possible, a wide space for optimization is still left. This article offers a heuristic extension to the previously suggested grid based algorithms. We show that, when the average particle movements are slow, simulation time can be reduced considerably. The proposed algorithm has been implemented in the DistanceMatrix class of the molecular modeling package MESHI. MESHI is freely available at .

Algorithms↗

A mean field approach for molecular simulations of fluid systems.

In this paper we introduce a mean field method for simulating complex molecular systems like liquids and solutions. Using well-established theoretical principles and models, we obtained a relatively simple approach which seems to provide a reliable description of the bulk molecular behavior of liquid water. Moreover, we have applied this approach to study simple solutes in solution, like sodium and chloride ions and acetone. Comparison with standard simulations, performed with periodic boundary conditions, shows that such a mean field method can reproduce the same structural and thermodynamical properties at low computational costs and represents a valid alternative for simulating solute-solvent systems, like solutions of large biomolecules.

Journal Article↗

The conformation of amine- and amide-terminated poly(propylene imine) dendrimers as investigated by molecular simulation methods.

The parameters that influence the conformation of poly(propylene imine) dendrimers were investigated by molecular simulations using molecular mechanics and simulated annealing methods. Dendrimers with two types of peripheral units able to communicate via hydrogen bonding-amine and amide moieties-were considered in order to study the role that secondary interactions among the end groups have in the spatial organization of the dendritic branches. Radial atomic density profiles and radial atomic probability distributions were used to extract global properties, such as the degree of packing of the branches, the distribution of the monomers throughout the molecular volume, and the extent and characteristics of the surface region. Information was also obtained about the nature, location, and extent of formation of the hydrogen bonds, as well as their evolution with dendrimer generation and their assembly into networks. The analyses were supported by a detailed investigation of the first two generations, with an emphasis on the relationship between hydrogen bonding and the compactness and stability of the molecules; this allowed us to account for the generational evolution of hydrogen bonding that is experimentally observed in several poly(propylene imine) dendrimers.

Journal Article↗

Molecular simulation of a single-chain antibody against AChE to explore molecular basis of inhibitory effect of 3F3 McAb on enzyme activity.

AIM: To explore the molecular basis of the inhibitory effect of 3F3, a monoclonal antibody against acetylcholinesterase (AChE), by computer-aided molecular simulation. METHODS: The single-chain 3F3 antibody (Sc3F3) was designed by joining VH and VL via a flexible linker (Gly4Ser)3. The amino acid sequence of the recombinant Sc3F3 was then subjected to computer-aided molecular modeling, and docking with the antigen molecule AChE to mimic the immunoactive interaction in a three-dimensional fashion. RESULTS: The modeled structure of Sc3F3 manifested the common features of a classical antibody. Both VH and VL were composed of two ?-sheets and connecting loops. The docking profile of the action between Sc3F3 with AChE demonstrated the formation of a stable structure. The van der Waals force played an important role suggesting that the complex was formed mainly via hydrophobic interactions between Sc3F3 and AChE molecules. CONCLUSION: The spatial structure of the complex of Sc3F3 and AChE showed that Sc3F3 overlaid the entrance of the active center gorge of AChE blocking the access of substrate.

Acetylcholinesterase↗

Variational formula for the free energy based on incomplete sampling in a molecular simulation.

Finite sampling in free-energy perturbation (FEP) calculations by molecular simulation leads to reproducible systematic errors, with sign shown to depend (in a known way) only on which system governs sampling in the simulation. Thus the result of a FEP calculation can be used as a bound on the true free energy. This inequality is of a wholly different nature from established forms such as the Gibbs-Bogoliubov inequality or the second law, in that its origins relate to the performance of a molecular simulation. If one can identify a suitable reference system having a free energy known as a function of some defining parameter, variational schemes based on the finite-sampling inequalities can be implemented. This idea is demonstrated through calculation of the free energy of a hard-sphere solid by perturbing from harmonic references and of a hard-sphere fluid by perturbing from infinitely polydisperse references. The tightness of the bounds increases with the amount of sampling in the simulation and correlates with the entropy difference between the target and reference systems. The bounds are tightest near the point where the entropy difference is least.

Journal Article↗

Structure Analysis of Montmorillonite Intercalated with Cetylpyridinium and Cetyltrimethylammonium: Molecular Simulations and XRD Analysis.

Molecular mechanics and molecular dynamics simulations combined with X-ray powder diffraction were used in structure investigation of montmorillonite intercalated with cetylpyridinium (CP) and cethyltrimethylammonium (CTA) cations. Molecular modeling revealed the interlayer structure and differences in intercalation behavior of CP and CTA cations in montmorillonite. The experimental and calculated values of basal spacing were in good agreement for both intercalates: in the case of CP-montmorillonite d(exp)=20.59 Å, d(calc)=20.60 Å; for CTA-montmorillonite d(exp)=18.00 Å and d(calc)=18.10 Å. CTA-montmorillonite exhibits significantly higher total sublimation energy and higher host-guest interaction energy than the CP-montmorillonite. The main difference between both intercalates is in charge distribution on the host layers and guest species. The charge transfer from the guest species to the host layer is higher in CTA-montmorillonite than in CP-montmorillonite, and consequently the charge polarization between the host and guest layers is much higher in CTA-montmorillonite. This leads to much stronger host-guest electrostatic interaction in the case of CTA-montmorillonite. Copyright 2001 Academic Press.

Journal Article↗

Some issues on the calculation of interfacial properties by molecular simulation.

Some of the pitfalls that may befall molecular simulations of interfaces are discussed. They are all related to the calculation of the pressure tensor profiles, which are needed in order to compute surface tensions. We focus on three controversial points: (1) the calculation of the pressure tensor profiles for polyatomic systems, in particular, when the SHAKE algorithm is employed, (2) the addition of long-range corrections to compensate the truncation of the potential, and (3) the importance of including adequate error intervals with the results. Most of the conclusions are general, but some specifically apply to multiple site molecular-dynamics simulations.

Journal Article↗

DSMM: a Database of Simulated Molecular Motions.

We describe a Database of Simulated Molecular Motions (DSMM). This database is designed to serve as a single searchable site for locating movies and animations from simulations of biomolecules. DSMM is accessible via a webserver at: http://projects.villa-bosch.de/mcm/database/dsmm.

Computer Graphics↗

Insight into mutation-induced activation of the luteinizing hormone receptor: molecular simulations predict the functional behavior of engineered mutants at M398.

In this study, molecular simulations have been combined with site-directed mutagenesis experiments to explore M398(2.43), a LH (lutropin) receptor (LHR) site in helix 2 susceptible to spontaneous activating mutations, and to develop a computational tool for predicting the functionality (i.e. active or nonactive) of LHR mutants.Site-directed mutagenesis experiments engineered 15 different substitutions for M389(2.43), which resulted in variable levels of constitutive activity, inversely correlated with the size of the replacing amino acid. This inverse correlation is suggested to be mediated by I460(3.46), M571(6.37), and Y623(7.53), the tyrosine of the NPxxY motif. In fact, size reduction at position 398(2.43), which is concurrent with constitutive receptor activity, releases the van der Waals interactions found in the wild-type LHR between M398(2.43) and these three amino acids, resulting in structural modifications in the proximity to the E/DRY/W motif. An increment, above a threshold value, in the solvent accessibility of the cytosolic ends of helices 3 and 6 is the main structural feature shared by the active mutants of the LHR. This feature has been successfully used for predicting the functionality of the engineered mutants at M398(2.43), proving that molecular simulations can be useful for in silico screening of LHR mutants.

Amino Acid Motifs↗