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1.
J Chem Phys ; 159(4)2023 Jul 28.
Artículo en Inglés | MEDLINE | ID: mdl-37503850

RESUMEN

The prediction of solubilities of compounds by means of molecular simulation has been receiving increasing attention due to the key role played by solubility in countless applications. We have predicted the aqueous solubility of urea at 300 K from chemical potential calculations for two urea model combinations: Özpinar/TIP3P and Hölzl/(TIP4P/2005). The methodology assumes that the intramolecular contribution of the urea molecule to the chemical potentials is identical in the crystal and in solution and, hence, cancels out. In parallel to the chemical potential calculations, we also performed direct coexistence simulations of a urea crystal slab in contact with urea-water solutions with the aim to identify upper and lower bounds to the solubility value using an independent route. The chemical potential approach yielded similar solubilities for both urea models, despite the actual chemical potential values showing a significant dependence on the force field. The predicted solubilities for the two models were 0.013-0.018 (Özpinar) and 0.008-0.012 (Hölzl) mole fraction, which are an order of magnitude lower than the experimental solubility that lies in a range of 0.125-0.216 mole fraction. The direct coexistence solubility bounds were relatively wide and did not encompass the chemical potential based solubilities, although the latter were close to the lower bound values.

2.
J Chem Inf Model ; 62(22): 5622-5633, 2022 11 28.
Artículo en Inglés | MEDLINE | ID: mdl-36351167

RESUMEN

The development of accurate transferable force fields is key to realizing the full potential of atomistic modeling in the study of biological processes such as protein-ligand binding for drug discovery. State-of-the-art transferable force fields, such as those produced by the Open Force Field Initiative, use modern software engineering and automation techniques to yield accuracy improvements. However, force field torsion parameters, which must account for many stereoelectronic and steric effects, are considered to be less transferable than other force field parameters and are therefore often targets for bespoke parametrization. Here, we present the Open Force Field QCSubmit and BespokeFit software packages that, when combined, facilitate the fitting of torsion parameters to quantum mechanical reference data at scale. We demonstrate the use of QCSubmit for simplifying the process of creating and archiving large numbers of quantum chemical calculations, by generating a dataset of 671 torsion scans for druglike fragments. We use BespokeFit to derive individual torsion parameters for each of these molecules, thereby reducing the root-mean-square error in the potential energy surface from 1.1 kcal/mol, using the original transferable force field, to 0.4 kcal/mol using the bespoke version. Furthermore, we employ the bespoke force fields to compute the relative binding free energies of a congeneric series of inhibitors of the TYK2 protein, and demonstrate further improvements in accuracy, compared to the base force field (MUE reduced from 0.560.390.77 to 0.420.280.59 kcal/mol and R2 correlation improved from 0.720.350.87 to 0.930.840.97).


Asunto(s)
Proteínas , Programas Informáticos , Ligandos , Proteínas/química , Entropía , Unión Proteica
3.
J Chem Inf Model ; 62(23): 6094-6104, 2022 Dec 12.
Artículo en Inglés | MEDLINE | ID: mdl-36433835

RESUMEN

Force fields form the basis for classical molecular simulations, and their accuracy is crucial for the quality of, for instance, protein-ligand binding simulations in drug discovery. The huge diversity of small-molecule chemistry makes it a challenge to build and parameterize a suitable force field. The Open Force Field Initiative is a combined industry and academic consortium developing a state-of-the-art small-molecule force field. In this report, industry members of the consortium worked together to objectively evaluate the performance of the force fields (referred to here as OpenFF) produced by the initiative on a combined public and proprietary dataset of 19,653 relevant molecules selected from their internal research and compound collections. This evaluation was important because it was completely blind; at most partners, none of the molecules or data were used in force field development or testing prior to this work. We compare the Open Force Field "Sage" version 2.0.0 and "Parsley" version 1.3.0 with GAFF-2.11-AM1BCC, OPLS4, and SMIRNOFF99Frosst. We analyzed force-field-optimized geometries and conformer energies compared to reference quantum mechanical data. We show that OPLS4 performs best, and the latest Open Force Field release shows a clear improvement compared to its predecessors. The performance of established force fields such as GAFF-2.11 was generally worse. While OpenFF researchers were involved in building the benchmarking infrastructure used in this work, benchmarking was done entirely in-house within industrial organizations and the resulting assessment is reported here. This work assesses the force field performance using separate benchmarking steps, external datasets, and involving external research groups. This effort may also be unique in terms of the number of different industrial partners involved, with 10 different companies participating in the benchmark efforts.


Asunto(s)
Proteínas , Termodinámica , Ligandos , Proteínas/química , Fenómenos Físicos
4.
Molecules ; 27(2)2022 Jan 06.
Artículo en Inglés | MEDLINE | ID: mdl-35056668

RESUMEN

Imidazolidine and thiazolidine-based isatin derivatives (IST-01-04) were synthesized, characterized, and tested for their interactions with ds-DNA. Theoretical and experimental findings showed good compatibility and indicated compound-DNA binding by mixed mode of interactions. The evaluated binding parameters, i.e., binding constant (Kb), free energy change (ΔG), and binding site sizes (n), inferred comparatively greater and more spontaneous binding interactions of IST-02 and then IST-04 with the DNA, among all compounds tested under physiological pH and temperature (7.4, 37 °C). The cytotoxic activity of all compounds was assessed against HeLa (cervical carcinoma), MCF-7 (breast carcinoma), and HuH-7 (liver carcinoma), as well as normal HEK-293 (human embryonic kidney) cell lines. Among all compounds, IST-02 and 04 were found to be cytotoxic against HuH-7 cell lines with percentage cell toxicity of 75% and 66%, respectively, at 500 ng/µL dosage. Moreover, HEK-293 cells exhibit tolerance to the increasing drug concentration, suggesting these two compounds are less cytotoxic against normal cell lines compared to cancer cell lines. Hence, both DNA binding and cytotoxicity studies proved imidazolidine (IST-02) and thiazolidine (IST-04)-based isatin derivatives as potent anticancer drug candidates among which imidazolidine (IST-02) is comparatively the more promising.


Asunto(s)
Antineoplásicos/farmacología , ADN/metabolismo , Imidazolidinas/química , Isatina/farmacología , Neoplasias/tratamiento farmacológico , Tiazolidinas/química , Antineoplásicos/química , Proliferación Celular , Células HeLa , Humanos , Isatina/química , Células MCF-7 , Estructura Molecular , Neoplasias/patología , Relación Estructura-Actividad
5.
J Chem Phys ; 154(16): 164509, 2021 Apr 28.
Artículo en Inglés | MEDLINE | ID: mdl-33940822

RESUMEN

Free energies of crystals computed using a center of mass constraint require a finite-size correction, as shown in previous work by Polson et al. [J. Chem. Phys. 112, 5339-5342 (2000)]. Their reference system is an Einstein crystal with equal spring constants. In this paper, we extend the work of Polson et al. [J. Chem. Phys. 112, 5339-5342 (2000)] to the case of differing spring constants. The generalization is convenient for constraining the center of mass in crystals with atoms of differing masses, and it helps to optimize the free energy calculations. To test the theory, we compare the free energies of LiI and NaCl crystals from calculations with differing spring constants to those computed using equal spring constants. Using these center of mass finite size corrections, we compute the true free energies of these crystals for different system sizes to eliminate the intrinsic finite-size effects. These calculations help demonstrate the size of these finite-size corrections relative to other contributions to the absolute free energy of the crystals.

6.
J Chem Phys ; 155(20): 204801, 2021 Nov 28.
Artículo en Inglés | MEDLINE | ID: mdl-34852489

RESUMEN

Community efforts in the computational molecular sciences (CMS) are evolving toward modular, open, and interoperable interfaces that work with existing community codes to provide more functionality and composability than could be achieved with a single program. The Quantum Chemistry Common Driver and Databases (QCDB) project provides such capability through an application programming interface (API) that facilitates interoperability across multiple quantum chemistry software packages. In tandem with the Molecular Sciences Software Institute and their Quantum Chemistry Archive ecosystem, the unique functionalities of several CMS programs are integrated, including CFOUR, GAMESS, NWChem, OpenMM, Psi4, Qcore, TeraChem, and Turbomole, to provide common computational functions, i.e., energy, gradient, and Hessian computations as well as molecular properties such as atomic charges and vibrational frequency analysis. Both standard users and power users benefit from adopting these APIs as they lower the language barrier of input styles and enable a standard layout of variables and data. These designs allow end-to-end interoperable programming of complex computations and provide best practices options by default.

7.
J Chem Phys ; 152(14): 144109, 2020 Apr 14.
Artículo en Inglés | MEDLINE | ID: mdl-32295378

RESUMEN

Solid solutions, structurally ordered but compositionally disordered mixtures, can form for salts, metals, and even organic compounds. The NaCl-KCl system forms a solid solution at all compositions between 657 °C and 505 °C. Below a critical temperature of 505 °C, the system exhibits a miscibility gap with coexisting Na-rich and K-rich rocksalt phases. We calculate the phase diagram in this region using the semi-grand canonical Widom method, which averages over virtual particle transmutations. We verify our results by comparison with free energies calculated from thermodynamic integration and extrapolate the location of the critical point. Our calculations reproduce the experimental phase diagram remarkably well and illustrate how solid-solid equilibria and chemical potentials, including those at metastable conditions, can be computed for materials that form solid solutions.

8.
J Chem Phys ; 151(18): 184113, 2019 Nov 14.
Artículo en Inglés | MEDLINE | ID: mdl-31731842

RESUMEN

While the solubility of a substance is a fundamental property of widespread significance, its prediction from first principles (starting from only the knowledge of the molecular structure of the solute and solvent) remains a challenge. Recently, we proposed a robust and efficient method to predict the solubility from the density of states of a solute-solvent system using classical molecular simulation. The efficiency, and indeed the generality, of the method has now been enhanced by extending it to calculate solution chemical potentials (rather than probability distributions as done previously), from which solubility may be accessed. The method has been employed to predict the chemical potential of Form 1 of urea in both water and methanol for a range of concentrations at ambient conditions and for two charge models. The chemical potential calculations were validated by thermodynamic integration with the two sets of values being in excellent agreement. The solubility determined from the chemical potentials for urea in water ranged from 0.46 to 0.50 mol kg-1, while that for urea in methanol ranged from 0.62 to 0.85 mol kg-1, over the temperature range 298-328 K. In common with other recent studies of solubility prediction from molecular simulation, the predicted solubilities differ markedly from experimental values, reflecting limitations of current forcefields.

9.
Phys Chem Chem Phys ; 20(32): 20981-20987, 2018 Aug 15.
Artículo en Inglés | MEDLINE | ID: mdl-30070281

RESUMEN

Solubility is a fundamental property of widespread significance. Despite its importance, its efficient and accurate prediction from first principles remains a major challenge. Here we propose a novel method to predict the solubility of molecules using a density of states (DOS) approach from classical molecular simulation. The method offers a potential route to solubility prediction for large (including drug-like) molecules over a range of temperatures and pressures, all from a modest number of simulations. The method was employed to predict the solubility of sodium chloride in water at ambient conditions, yielding a value of 3.77(5) mol kg-1. This is in close agreement with other approaches based on molecular simulation, the consensus literature value being 3.71(25) mol kg-1. The predicted solubility is about half of the experimental value, the disparity being attributed to the known limitation of the Joung-Cheatham force field model employed for NaCl. The proposed method also accurately predicted the NaCl model's solubility over the temperature range 298-373 K directly from the density of states data used to predict the ambient solubility.

10.
Langmuir ; 32(48): 12732-12740, 2016 12 06.
Artículo en Inglés | MEDLINE | ID: mdl-27934534

RESUMEN

We performed molecular dynamics (MD) simulations to obtain insights into the structure and molecular interactions of colloidal structures present in fasted state intestinal fluid. Drug partitioning and interaction were studied with a mixed system of the bile salt taurocholate (TCH) and 1,2-dilinoleoyl-sn-glycero-3-phosphocholine (DLiPC). Spontaneous aggregation of TCH and DLiPC from unconstrained MD simulations at the united-atom level using the Berger/Gromos54A7 force fields demonstrated that intermolecular hydrogen bonding between TCH molecules was an important factor in determining the overall TCH and DLiPC configuration. In bilayered systems, these intermolecular hydrogen bonds resulted in embedded transmembrane TCH clusters. Free energy simulations using the umbrella sampling technique revealed that the stability of these transmembrane TCH clusters was superior when they consisted of 3 or 4 TCH per bilayer leaflet. All-atom simulations using the Slipids/GAFF force fields showed that the TCH embedded in the bilayer decreased the energy barrier to penetrate the bilayer (ΔGpen) for water, ethanol, and carbamazepine, but not for the more lipophilic felodipine and danazol. This suggests that diffusion of hydrophilic to moderately lipophilic molecules through the bilayer is facilitated by the embedded TCH molecules. However, the effect of embedded TCH on the overall lipid/water partitioning was significant for danazol, indicating that the incorporation of TCH plays a crucial role for the partitioning of lipophilic solutes into e.g. lipidic vesicles existing in fasted state intestinal fluids. To conclude, the MD simulations revealed important intermolecular interactions in lipidic bilayers, both between the bile components themselves and with the drug molecules.


Asunto(s)
Coloides/química , Intestinos/fisiología , Simulación de Dinámica Molecular , Ayuno , Humanos , Enlace de Hidrógeno , Membrana Dobles de Lípidos , Fosfatidilcolinas/química , Soluciones , Ácido Taurocólico/química , Agua
11.
Proc Natl Acad Sci U S A ; 109(4): 1041-5, 2012 Jan 24.
Artículo en Inglés | MEDLINE | ID: mdl-22232652

RESUMEN

The freezing of water to ice is fundamentally important to fields as diverse as cloud formation to cryopreservation. At ambient conditions, ice is considered to exist in two crystalline forms: stable hexagonal ice and metastable cubic ice. Using X-ray diffraction data and Monte Carlo simulations, we show that ice that crystallizes homogeneously from supercooled water is neither of these phases. The resulting ice is disordered in one dimension and therefore possesses neither cubic nor hexagonal symmetry and is instead composed of randomly stacked layers of cubic and hexagonal sequences. We refer to this ice as stacking-disordered ice I. Stacking disorder and stacking faults have been reported earlier for metastable ice I, but only for ice crystallizing in mesopores and in samples recrystallized from high-pressure ice phases rather than in water droplets. Review of the literature reveals that almost all ice that has been identified as cubic ice in previous diffraction studies and generated in a variety of ways was most likely stacking-disordered ice I with varying degrees of stacking disorder. These findings highlight the need to reevaluate the physical and thermodynamic properties of this metastable ice as a function of the nature and extent of stacking disorder using well-characterized samples.


Asunto(s)
Frío , Hielo/análisis , Modelos Moleculares , Agua/química , Simulación por Computador , Cristalización , Método de Montecarlo
12.
Angew Chem Int Ed Engl ; 54(49): 14681-4, 2015 Dec 01.
Artículo en Inglés | MEDLINE | ID: mdl-25809644

RESUMEN

Secondary nucleation, wherein crystal seeds are used to induce crystallization, is widely employed in industrial crystallizations. Despite its significance, our understanding of the process, particularly at the molecular level, remains rudimentary. An outstanding question is why do a few seeds give rise to a many-fold increase in new crystals? Using molecular simulation coupled with experiments we have uncovered the molecular processes that give rise to this autocatalytic behavior. The simulations reveal formation of molecular aggregates in solution, which on coming in contact with the surface of the seed undergo nucleation to form new crystallites. These crystallites are weakly bound to the crystal surface and can be readily sheared by fluid, making the seed surfaces available again to repeat the process. Further, the new crystallites on development can in turn serve as seeds. This mechanistic insight will enable better control in engineering crystalline products to design.

13.
Biophys Chem ; 294: 106958, 2023 03.
Artículo en Inglés | MEDLINE | ID: mdl-36682087

RESUMEN

Gentamicin is used to treat brucellosis, an infectious disease caused by the Brucella species but the drug faces several issues such as low efficacy, instability, low solubility, and toxicity. It also has a very short half-life, therefore, requiring frequent dosing. Consequently, several other antibiotics are also being used for the treatment of brucellosis as a single dose as well as in combination with other antibiotics but none of these therapies are satisfactory. Nanoparticles in particular polymer-based ones utilizing polymers that are biodegradable and biocompatible for instance PLGA are a method of choice to overcome such drug delivery issues and enable potential targeted delivery. The current study focuses on the evaluation of the structural and dynamical properties of a drug-polymer system consisting of gentamicin drug and PLGA polymer nanoparticles in the water representing a targeted drug delivery system for the treatment of brucellosis. For this purpose, all-atom molecular dynamics simulations were carried out on the drug-polymer systems in the absence and presence of the surfactant bis(2-Ethylhexyl) sulfosuccinate (AOT) to determine the structural and dynamical properties as well as the effect of the surfactant on these properties. We also investigated systems in which the polymer constituents were in the form of monomeric units toward decoupling the primary interactions of the monomer units and polymer effects. The simulation results explain the nature of the interactions between the drug and the polymer as well as transport properties in terms of drug diffusion coefficients, which characterize the molecular behavior of gentamicin-polymer nanoparticles for use in brucellosis.


Asunto(s)
Brucelosis , Nanopartículas , Humanos , Gentamicinas/química , Gentamicinas/uso terapéutico , Copolímero de Ácido Poliláctico-Ácido Poliglicólico/uso terapéutico , Ácido Poliglicólico/química , Ácido Poliglicólico/uso terapéutico , Simulación de Dinámica Molecular , Teoría Funcional de la Densidad , Ácido Láctico/química , Ácido Láctico/uso terapéutico , Antibacterianos/química , Sistemas de Liberación de Medicamentos , Brucelosis/tratamiento farmacológico , Glicolatos/uso terapéutico , Tensoactivos
14.
Pharm Res ; 29(1): 319-31, 2012 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-21845506

RESUMEN

PURPOSE: To explore the use of crystal inter-planar d-spacings and slip-plane interaction energies for predicting and characterising mechanical properties of crystalline solids. METHODS: Potential relationships were evaluated between mechanical properties and inter-planar d-spacing, inter-planar interaction energy, and dispersive surface energy as determined using inverse gas chromatography (IGC) for a set of pharmaceutical materials. Inter-planar interaction energies were determined by molecular modelling. RESULTS: General trends were observed between mechanical properties and the largest inter-planar d-spacing, inter-planar interaction energies, and IGC dispersive surface energy. A number of materials showed significant deviations from general trends. Weak correlations and outliers were rationalised. CONCLUSIONS: Results suggest that the highest d-spacing of a material could serve as a first-order indicator for ranking mechanical behaviour of pharmaceutical powders, but with some reservation. Inter-planar interaction energy normalised for surface area shows only a weak link with mechanical properties and does not appear to capture essential physics of deformation. A novel framework linking mechanical properties of crystals to the distinct quantities, slip-plane energy barrier and inter-planar interaction (detachment) energy is proposed.


Asunto(s)
Polvos/química , Estrés Mecánico , Acetaminofén/química , Albuterol/química , Anisotropía , Cromatografía de Gases , Cristalización , Ibuprofeno/química , Lactosa/química , Tamaño de la Partícula , Propiedades de Superficie , Termodinámica
15.
ACS Omega ; 7(25): 22032-22038, 2022 Jun 28.
Artículo en Inglés | MEDLINE | ID: mdl-35785332

RESUMEN

Recent studies show that curcumin, a naturally fluorescent dye, can be used for the noninvasive optical imaging of retinal amyloid-ß (Aß) plaques. We investigated the molecular basis for curcumin's specificity for hierarchical Aß structures using molecular dynamics simulations, with a focus on how curcumin is able to detect and discriminate different amyloid morphologies. Curcumin inhibits and breaks up ß-sheet formation in Aß monomers. With disordered Aß structures, curcumin forms a coarse-grained composite structure. With an ordered fibril, curcumin's interaction is highly specific, and the curcumin molecules are deposited in the fibril groove. Curcumin tends to self-aggregate, which is finely balanced with its affinity for Aß. This tendency concentrates curcumin molecules at Aß deposition sites, potentially increasing the fluorescence signal. This is probably why curcumin is such an effective amyloid imaging agent.

16.
PeerJ ; 10: e12984, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35368337

RESUMEN

Several natural mutants of the human G6PD enzyme exist and have been reported. Because the enzymatic activities of many mutants are different from that of the wildtype, the genetic polymorphism of G6PD plays an important role in the synthesis of nucleic acids via ribulose-5-phosphate and formation of reduced NADP in response to oxidative stress. G6PD mutations leading to its deficiency result in the neonatal jaundice and acute hemolytic anemia in human. Herein, we demonstrate the molecular dynamics simulations of the wildtype G6PD and its three mutants to monitor the effect of mutations on dynamics and stability of the protein. These mutants are Chatham (A335T), Nashville (R393H), Alhambra (V394L), among which R393H and V394L lie closer to binding site of structural NADP+. MD analysis including RMSD, RMSF and protein secondary structure revealed that decrease in the stability of mutants is key factor for loss of their activity. The results demonstrated that mutations in the G6PD sequence resulted in altered structural stability and hence functional changes in enzymes. Also, the binding site, of structural NADP+, which is far away from the catalytic site plays an important role in protein stability and folding. Mutation at this site causes changes in structural stability and hence functional deviations in enzyme structure reflecting the importance of structural NADP+ binding site. The calculation of binding free energy by post processing end state method of Molecular Mechanics Poisson Boltzmann SurfaceArea (MM-PBSA) has inferred that ligand binding in wildtype is favorable as compared to mutants which represent destabilised protein structure due to mutation that in turn may hinder the normal physiological function. Exploring individual components of free energy revealed that the van der Waals energy component representing non-polar/hydrophobic energy contribution act as a dominant factor in case of ligand binding. Our study also provides an insight in identifying the key inhibitory site in G6PD and its mutants which can be exploited to use them as a target for developing new inhibitors in rational drug design.


Asunto(s)
Glucosafosfato Deshidrogenasa , Simulación de Dinámica Molecular , Recién Nacido , Humanos , Glucosafosfato Deshidrogenasa/química , NADP/química , Ligandos , Mutación/genética
17.
ACS Omega ; 7(17): 15132-15144, 2022 May 03.
Artículo en Inglés | MEDLINE | ID: mdl-35572757

RESUMEN

Glycosaminoglycans (GAGs), in particular, heparan sulfate and heparin, are found colocalized with Aß amyloid. They have been shown to enhance fibril formation, suggesting a possible pathological connection. We have investigated heparin's assembly of the KLVFFA peptide fragment using molecular dynamics simulation, to gain a molecular-level mechanistic understanding of how GAGs enhance fibril formation. The simulations reveal an exquisite process wherein heparin accelerates peptide assembly by first "gathering" the peptide molecules and then assembling them. Heparin does not act as a mere template but is tightly coupled to the peptides, yielding a composite protofilament structure. The strong intermolecular interactions suggest composite formation to be a general feature of heparin's interaction with peptides. Heparin's chain flexibility is found to be essential to its fibril promotion activity, and the need for optimal heparin chain length and concentration has been rationalized. These insights yield design rules (flexibility; chain-length) and protocol guidance (heparin:peptide molar ratio) for developing effective heparin mimetics and other functional GAGs.

18.
Chemistry ; 17(40): 11186-92, 2011 Sep 26.
Artículo en Inglés | MEDLINE | ID: mdl-21922553

RESUMEN

We make the link between the size-dependent phase stability of a nanocrystal and the phase-transition behavior of emerging crystallites during the earliest stages of crystallization, by using the former as a proxy for the latter. We outline an extension of the classical nucleation theory to describe crystal nucleation and subsequent transformations of competing polymorphic phases that characterize Ostwald's rule of stages. The theoretical framework reveals that the relative stability of the competing phases is a function of cluster size, which in turn varies with time, and therefore explains the complex transformation behavior observed for some systems. We investigated the stability of a nanocrystal of dl-norleucine by means of molecular simulation as a proxy for post-nucleation phase-transformation behavior in emerging crystallites. The simulations reveal that, for nanocrystals, the surface energy of the transition state of a transformation can dominate the barrier to phase change, thus causing metastable phases to be stabilized, not because they are thermodynamically stable, but rather due to kinetic hindering. Therefore, in the context of the earliest stages of crystal growth, not only does phase stability vary as a function of cluster size, and hence time, but thermodynamically feasible transformations are also prone to kinetic hindering.


Asunto(s)
Cristalización , Nanopartículas/química , Cinética , Modelos Moleculares , Tamaño de la Partícula , Transición de Fase , Apoderado , Termodinámica
19.
Angew Chem Int Ed Engl ; 50(9): 1996-2013, 2011 Feb 25.
Artículo en Inglés | MEDLINE | ID: mdl-21271625

RESUMEN

Exploring nucleation processes by molecular simulation provides a mechanistic understanding at the atomic level and also enables kinetic and thermodynamic quantities to be estimated. However, whilst the potential for modeling crystal nucleation and growth processes is immense, there are specific technical challenges to modeling. In general, rare events, such as nucleation cannot be simulated using a direct "brute force" molecular dynamics approach. The limited time and length scales that are accessible by conventional molecular dynamics simulations have inspired a number of advances to tackle problems that were considered outside the scope of molecular simulation. While general insights and features could be explored from efficient generic models, new methods paved the way to realistic crystal nucleation scenarios. The association of single ions in solvent environments, the mechanisms of motif formation, ripening reactions, and the self-organization of nanocrystals can now be investigated at the molecular level. The analysis of interactions with growth-controlling additives gives a new understanding of functionalized nanocrystals and the precipitation of composite materials.


Asunto(s)
Simulación de Dinámica Molecular , Cristalización , Cinética , Método de Montecarlo , Nanocompuestos/química , Termodinámica
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