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1.
ACS Omega ; 9(14): 16084-16088, 2024 Apr 09.
Artigo em Inglês | MEDLINE | ID: mdl-38617615

RESUMO

For micelles, "shape" is prominent in rheological computations of fluid flow, but this "shape" is often expressed too informally to be useful for rigorous analyses. We formalize topological "shape equivalence" of micelles, both globally and locally, to enable visualization of computational fluid dynamics. Although topological methods in visualization provide significant insights into fluid flows, this opportunity has been limited by the known difficulties in creating representative geometry. We present an agile geometric algorithm to represent the micellar shape for input into fluid flow visualizations. We show that worm-like and cylindrical micelles have formally equivalent shapes, but that visualization accentuates unexplored differences. This global-local paradigm is extensible beyond micelles.

2.
J Chem Inf Model ; 62(23): 6094-6104, 2022 Dec 12.
Artigo em Inglês | MEDLINE | ID: mdl-36433835

RESUMO

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.


Assuntos
Proteínas , Termodinâmica , Ligantes , Proteínas/química , Fenômenos Físicos
3.
J Chem Theory Comput ; 16(11): 7135-7147, 2020 Nov 10.
Artigo em Inglês | MEDLINE | ID: mdl-33081471

RESUMO

Chemical heterogeneity of solid surfaces disrupts the adsorption of surfactants from the bulk liquid. While its presence can hinder the performance of some formulations, bespoke chemical patterning could potentially facilitate controlled adsorption for nanolithography applications. Although some computational studies have investigated the impact of regularly patterned surfaces on surfactant adsorption, in reality, many interesting surfaces are expected to be stochastically disordered and this is an area unexplored via simulations. In this paper, we describe a new algorithm for the generation of randomly disordered chemically heterogeneous surfaces and use it to explore the adsorption behavior of four model nonionic surfactants. Using novel analysis methods, we interrogate both the global surface coverage (adsorption isotherm) and behavior in localized regions. We observe that trends in adsorption characteristics as surfactant size, head/tail ratio, and surface topology are varied and connect these to underlying physical mechanisms. We believe that our methods and approach will prove useful to researchers seeking to tailor surface patterns to calibrate nonionic surfactant adsorption.

4.
J Phys Chem B ; 124(43): 9701-9721, 2020 10 29.
Artigo em Inglês | MEDLINE | ID: mdl-32986421

RESUMO

Using a comprehensive set of recently published experimental results for training and validation, we have developed computational models appropriate for simulations of aqueous solutions of poly(ethylene oxide) alkyl ethers, an important class of micelle-forming nonionic surfactants, usually denoted CnEm. These models are suitable for use in simulations that employ a moderate amount of coarse graining and especially for dissipative particle dynamics (DPD), which we adopt in this work. The experimental data used for training and validation were reported earlier and produced in our laboratory using dynamic light scattering (DLS) measurements performed on 12 members of the CnEm compound family yielding micelle size distribution functions and mass-weighted mean aggregation numbers at each of several surfactant concentrations. The range of compounds and quality of the experimental results were designed to support the development of computational models. An essential feature of this work is that all simulation results were analyzed in a way that is consistent with the experimental data. Proper account is taken of the fact that a broad distribution of micelle sizes exists, so mass-weighted averages (rather than number-weighted averages) over this distribution are required for the proper comparison of simulation and experimental results. The resulting DPD force field reproduces several important trends seen in the experimental critical micelle concentrations and mass-averaged mean aggregation numbers with respect to surfactant characteristics and concentration. We feel it can be used to investigate a number of open questions regarding micelle sizes and shapes and their dependence on surfactant concentration for this important class of nonionic surfactants.

5.
J Chem Theory Comput ; 16(7): 4588-4598, 2020 Jul 14.
Artigo em Inglês | MEDLINE | ID: mdl-32543855

RESUMO

Many surfactant-based formulations are utilized in industry as they produce desirable viscoelastic properties at low concentrations. These properties are due to the presence of worm-like micelles (WLMs), and as a result, understanding the processes that lead to WLM formation is of significant interest. Various experimental techniques have been applied with some success to this problem but can encounter issues probing key microscopic characteristics or the specific regimes of interest. The complementary use of computer simulations could provide an alternate route to accessing their structural and dynamic behavior. However, few computational methods exist for measuring key characteristics of WLMs formed in particle simulations. Further, their mathematical formulations are challenged by WLMs with sharp curvature profiles or density fluctuations along the backbone. Here, we present a new topological algorithm for identifying and characterizing WLMs in particle simulations, which has desirable mathematical properties that address shortcomings in previous techniques. We apply the algorithm to the case of sodium dodecyl sulfate micelles to demonstrate how it can be used to construct a comprehensive topological characterization of the observed structures.

6.
J Phys Chem B ; 123(7): 1696-1707, 2019 02 21.
Artigo em Inglês | MEDLINE | ID: mdl-30657322

RESUMO

We wished to compile a data set of results from the experimental literature to support the development and validation of accurate computational models (force fields) for an important class of micelle-forming nonionic surfactant compounds, the poly(ethylene oxide) alkyl ethers, usually denoted C nE m. However, careful examination of the experimental literature exposed a striking degree of variation in values reported for critical micelle concentrations (cmc) and mean aggregation numbers ( Nagg). This variation was so large that it masked important trends known to exist within this family of molecules, thereby rendering most of the literature data to be of limited utility for force field development. In this work, we describe some reasons for the wide variability in the experimental literature, and we present a set of cmc and aggregation number data for 12 C nE m compounds that we feel is appropriate to use for the construction of and validation of computational models. The cmc values we selected are from the existing experimental literature and represent a carefully chosen and consistent subset that conveys important trends seen by many of the experimental studies. However, for a corresponding and consistent set of weight-averaged aggregation numbers, we needed to perform new dynamic light scattering (DLS) experiments. The results of these experiments were carefully analyzed to obtain not just mean aggregation numbers but also the underlying micelle size distribution functions. Several trends observed in the cmc and Nagg observables are highlighted and serve as challenges for developers of force field and simulation methodology. The analysis of the DLS experiments accounts for the fact that a broad distribution of micelle sizes exists for many of these compounds and that one must be careful to use the appropriate weighted averages (e.g., mass-weighted vs number-weighted averages) in comparing results from different types of experiments and in comparing results from experiments with those from simulations.

7.
Molecules ; 23(12)2018 Nov 29.
Artigo em Inglês | MEDLINE | ID: mdl-30501058

RESUMO

In this work, we propose an improved QM/MM-based strategy to determine condensed-phase polarizabilities and we use this approach to optimize a new and simple polarizable four-site water model for classical molecular simulation. For the determination of the model value for the polarizability from QM/MM, we show that our proposed consensus-fitting strategy significantly reduces the uncertainty in calculated polarizabilities in cases where the size of the local external electric field is small. By fitting electrostatic, polarization and dispersion properties of our water model based on quantum and/or combined QM/MM calculations, only a single model parameter (describing exchange repulsion) is left for empirical calibration. The resulting model performs well in describing relevant pure-liquid thermodynamic and transport properties, which illustrates the merit of our approach to minimize the number of free variables in our model.


Assuntos
Modelos Químicos , Simulação de Dinâmica Molecular , Teoria Quântica , Água/química , Eletricidade Estática
8.
J Phys Chem B ; 122(21): 5356-5367, 2018 05 31.
Artigo em Inglês | MEDLINE | ID: mdl-29385796

RESUMO

We present an all-atom molecular dynamics study of the effect of a range of organic solvents (dichloromethane, diethyl ether, toluene, methanol, dimethyl sulfoxide, and tetrahydrofuran) on the conformations of a nanogel star polymeric nanoparticle with solvophobic and solvophilic structural elements. These nanoparticles are of particular interest for drug delivery applications. As drug loading generally takes place in an organic solvent, this work serves to provide insight into the factors controlling the early steps of that process. Our work suggests that nanoparticle conformational structure is highly sensitive to the choice of solvent, providing avenues for further study as well as predictions for both computational and experimental explorations of the drug-loading process. Our findings suggest that when used in the drug-loading process, dichloromethane, tetrahydrofuran, and toluene allow for a more extensive and increased drug-loading into the interior of nanogel star polymers of the composition studied here. In contrast, methanol is more likely to support shallow or surface loading and, consequently, faster drug release rates. Finally, diethyl ether should not work in a formulation process since none of the regions of the nanogel star polymer appear to be sufficiently solvated by it.


Assuntos
Portadores de Fármacos/química , Preparações Farmacêuticas/química , Polietilenoglicóis/química , Polietilenoimina/química , Polímeros/química , Solventes/química , Liberação Controlada de Fármacos , Nanogéis , Nanopartículas/química , Preparações Farmacêuticas/metabolismo
9.
J Phys Chem B ; 121(16): 4023-4039, 2017 04 27.
Artigo em Inglês | MEDLINE | ID: mdl-28306259

RESUMO

The increasing availability of high-quality experimental data and first-principles calculations creates opportunities for developing more accurate empirical force fields for simulation of proteins. We developed the AMBER-FB15 protein force field by building a high-quality quantum chemical data set consisting of comprehensive potential energy scans and employing the ForceBalance software package for parameter optimization. The optimized potential surface allows for more significant thermodynamic fluctuations away from local minima. In validation studies where simulation results are compared to experimental measurements, AMBER-FB15 in combination with the updated TIP3P-FB water model predicts equilibrium properties with equivalent accuracy, and temperature dependent properties with significantly improved accuracy, in comparison with published models. We also discuss the effect of changing the protein force field and water model on the simulation results.


Assuntos
Proteínas/química , Bases de Dados de Proteínas , Simulação de Dinâmica Molecular , Desnaturação Proteica , Teoria Quântica , Software , Termodinâmica , Água/química
10.
J Phys Chem B ; 121(13): 2902-2918, 2017 04 06.
Artigo em Inglês | MEDLINE | ID: mdl-28290691

RESUMO

We present a molecular dynamics study of the effect of core chemistry on star polymer structural and kinetic properties. This work serves to validate the choice of a model adamantane core used in previous simulations to represent larger star polymeric systems in an aqueous environment, as well as to explore how the choice of size and core chemistry using a dendrimer or nanogel core may affect these polymeric nanoparticle systems, particularly with respect to thermosensitivity and solvation properties that are relevant for applications in drug loading and delivery.


Assuntos
Simulação de Dinâmica Molecular , Polímeros/química , Interações Hidrofóbicas e Hidrofílicas , Cinética , Estrutura Molecular , Nanopartículas/química , Temperatura
11.
Macromolecules ; 50(24): 9702-9712, 2017 Dec 26.
Artigo em Inglês | MEDLINE | ID: mdl-32636533

RESUMO

Star polymers with a cross-linked nanogel core are promising carriers of cargo for therapeutic applications due to the synthetic control of amphiphilicity of arms and stability at infinite dilution. Three nanogel-core star polymers were investigated to understand how the arm-block chemical structure controls loading efficiency of a model drug, ibuprofen, and its spatial distribution. The spatial distribution profiles of hydrophobic core, hydrophilic corona, and encapsulated drug were determined by small-angle neutron scattering (SANS). SANS provides the nanometer-scale sensitivity to determine how the arm-block chemistry enhances the sequestering of ibuprofen. Validated molecular dynamics simulations capture the trends in drug profile and polymer segment distribution with further details on drug orientation distribution. This work provides a basis to study structure-function relationships in macromolecular-based carriers of cargo and represents a path toward validated and predictive simulation.

12.
J Phys Chem B ; 120(30): 7546-68, 2016 08 04.
Artigo em Inglês | MEDLINE | ID: mdl-27385087

RESUMO

To develop a detailed picture of the microscopic structure of gelcore star polymers and to elucidate parameters of the synthetic process that might be exploited to control this structure, simulations of their synthesis were performed that were based on a particular synthetic approach. A range of results was observed from gelation at high reactant concentrations to the formation of various sizes and compositions of star polymers. Contrary to the prevailing experimental viewpoint, the simulations always suggest the production of a broad distribution of star polymer sizes. However, the GPC traces computed from simulation results are in good qualitative agreement with experiment. Topologically, the gelcore star polymers produced by simulation are not compact but, rather, sparse blobs loosely connected by filaments of linker when modeled in a good solvent. This is reflected in scaling relationships that relate polymer size (e.g., radius of gyration) and degree of polymerization. The arm-core composition is observed to be stoichiometric, strongly reflecting relative reactant concentrations during the synthesis. Reactions within star polymers that result in greater intramolecular cross-linking compete with those between star polymers that result in the production of larger star polymers from the joining of smaller ones. The balance in this competition can be controlled through the overall reactant concentration to limit and control resulting star polymer size. Therefore, the mean size, as well as the mean number of arms, can be controlled during synthesis by careful tuning of the overall ratio of the arm and linker reactant concentrations and the total reactant concentration.

13.
J Phys Chem B ; 120(26): 6337-51, 2016 07 07.
Artigo em Inglês | MEDLINE | ID: mdl-27096611

RESUMO

In this paper, we present protocols for simulating micelles using dissipative particle dynamics (and in principle molecular dynamics) that we expect to be appropriate for computing micelle properties for a wide range of surfactant molecules. The protocols address challenges in equilibrating and sampling, specifically when kinetics can be very different with changes in surfactant concentration, and with minor changes in molecular size and structure, even using the same force field parameters. We demonstrate that detection of equilibrium can be automated and is robust, for the molecules in this study and others we have considered. In order to quantify the degree of sampling obtained during simulations, metrics to assess the degree of molecular exchange among micellar material are presented, and the use of correlation times are prescribed to assess sampling and for statistical uncertainty estimates on the relevant simulation observables. We show that the computational challenges facing the measurement of the critical micelle concentration (CMC) are somewhat different for high and low CMC materials. While a specific choice is not recommended here, we demonstrate that various methods give values that are consistent in terms of trends, even if not numerically equivalent.

14.
J Phys Chem B ; 119(3): 944-57, 2015 Jan 22.
Artigo em Inglês | MEDLINE | ID: mdl-25254622

RESUMO

We present a molecular simulation study of star polymers consisting of 16 diblock copolymer arms bound to a small adamantane core by varying both arm length and the outer hydrophilic block when attached to the same hydrophobic block of poly-δ-valerolactone. Here we consider two biocompatible star polymers in which the hydrophilic block is composed of polyethylene glycol (PEG) or polymethyloxazoline (POXA) in addition to a polycarbonate-based polymer with a pendant hydrophilic group (PC1). We find that the different hydrophilic blocks of the star polymers show qualitatively different trends in their interactions with aqueous solvent, orientational time correlation functions, and orientational correlation between pairs of monomers of their polymeric arms in solution, in which we find that the PEG polymers are more thermosensitive compared with the POXA and PC1 star polymers over the physiological temperature range we have investigated.


Assuntos
Interações Hidrofóbicas e Hidrofílicas , Fenômenos Físicos , Polímeros/química , Portadores de Fármacos/química , Modelos Moleculares , Conformação Molecular , Temperatura
15.
J Chem Theory Comput ; 10(10): 4515-4534, 2014 Oct 14.
Artigo em Inglês | MEDLINE | ID: mdl-25328495

RESUMO

We present the ff14ipq force field, implementing the previously published IPolQ charge set for simulations of complete proteins. Minor modifications to the charge derivation scheme and van der Waals interactions between polar atoms are introduced. Torsion parameters are developed through a generational learning approach, based on gas-phase MP2/cc-pVTZ single-point energies computed of structures optimized by the force field itself rather than the quantum benchmark. In this manner, we sacrifice information about the true quantum minima in order to ensure that the force field maintains optimal agreement with the MP2/cc-pVTZ benchmark for the ensembles it will actually produce in simulations. A means of making the gas-phase torsion parameters compatible with solution-phase IPolQ charges is presented. The ff14ipq model is an alternative to ff99SB and other Amber force fields for protein simulations in programs that accommodate pair-specific Lennard-Jones combining rules. The force field gives strong performance on α-helical and ß-sheet oligopeptides as well as globular proteins over microsecond time scale simulations, although it has not yet been tested in conjunction with lipid and nucleic acid models. We show how our choices in parameter development influence the resulting force field and how other choices that may have appeared reasonable would actually have led to poorer results. The tools we developed may also aid in the development of future fixed-charge and even polarizable biomolecular force fields.

16.
J Phys Chem B ; 118(24): 6360-3, 2014 Jun 19.
Artigo em Inglês | MEDLINE | ID: mdl-24945855
17.
J Phys Chem B ; 117(8): 2328-38, 2013 Feb 28.
Artigo em Inglês | MEDLINE | ID: mdl-23379664

RESUMO

We have developed the IPolQ method for fitting nonpolarizable point charges to implicitly represent the energy of polarization for systems in pure water. The method involves iterative cycles of molecular dynamics simulations to estimate the water charge density around the solute of interest, followed by quantum mechanical calculations at the MP2/cc-pV(T+d)Z level to determine updated solute charges. Lennard-Jones parameters are updated starting from the Amber FF99SB nonbonded parameter set to accommodate the new charge model, guided by the comparisons to experimental hydration free energies (HFEs) of neutral amino acid side chain analogs and assumptions about the computed HFEs for charged side chains. These Lennard-Jones parameter adjustments for side-chain analogs are assumed to be transferable to amino acids generally, and new charges for all standard amino acids are then derived in the presence of water modeled by TIP4P-Ew. Overall, the new charges depict substantially more polarized amino acids, particularly in the backbone moieties, than previous Amber charge sets. Efforts to complete a new force field with appropriate torsion parameters for this charge model are underway. The IPolQ method is general and applicable to arbitrary solutes.


Assuntos
Aminoácidos/química , Água/química , Simulação de Dinâmica Molecular , Teoria Quântica , Termodinâmica
18.
Chem Commun (Camb) ; 48(49): 6163-5, 2012 Jun 21.
Artigo em Inglês | MEDLINE | ID: mdl-22590707

RESUMO

Organocatalytic ring opening polymerization (OROP) is used to effect the rapid, scalable, room temperature formation of size-controlled, highly uniform, polyvalent, nanogel star polymer nanoparticles of biodegradable composition.


Assuntos
Compostos Bicíclicos Heterocíclicos com Pontes/química , Polietilenoglicóis/metabolismo , Polietilenoimina/metabolismo , Polímeros/metabolismo , Catálise , Modelos Moleculares , Estrutura Molecular , Nanogéis , Polietilenoglicóis/química , Polietilenoimina/química , Polimerização , Polímeros/química
19.
J Comput Aided Mol Des ; 26(5): 551-62, 2012 May.
Artigo em Inglês | MEDLINE | ID: mdl-22198475

RESUMO

Hydration free energy calculations have become important tests of force fields. Alchemical free energy calculations based on molecular dynamics simulations provide a rigorous way to calculate these free energies for a particular force field, given sufficient sampling. Here, we report results of alchemical hydration free energy calculations for the set of small molecules comprising the 2011 Statistical Assessment of Modeling of Proteins and Ligands challenge. Our calculations are largely based on the Generalized Amber Force Field with several different charge models, and we achieved RMS errors in the 1.4-2.2 kcal/mol range depending on charge model, marginally higher than what we typically observed in previous studies (Mobley et al. in J Phys Chem B 111(9):2242-2254, 2007, J Chem Theory Comput 5(2):350-358, 2009, J Phys Chem B 115:1329-1332, 2011; Nicholls et al. in J Med Chem 51:769-779, 2008; Klimovich and Mobley in J Comput Aided Mol Design 24(4):307-316, 2010). The test set consists of ethane, biphenyl, and a dibenzyl dioxin, as well as a series of chlorinated derivatives of each. We found that, for this set, using high-quality partial charges from MP2/cc-PVTZ SCRF RESP fits provided marginally improved agreement with experiment over using AM1-BCC partial charges as we have more typically done, in keeping with our recent findings (Mobley et al. in J Phys Chem B 115:1329-1332, 2011). Switching to OPLS Lennard-Jones parameters with AM1-BCC charges also improves agreement with experiment. We also find a number of chemical trends within each molecular series which we can explain, but there are also some surprises, including some that are captured by the calculations and some that are not.


Assuntos
Modelos Químicos , Simulação de Dinâmica Molecular , Proteínas/química , Termodinâmica , Entropia , Ligantes , Teoria Quântica , Água/química
20.
J Chem Theory Comput ; 8(10): 3733-49, 2012 Oct 09.
Artigo em Inglês | MEDLINE | ID: mdl-26593017

RESUMO

We have performed all atom explicit solvent molecular dynamics simulations of three different star polymeric systems in water, each star molecule consisting of 16 diblock copolymer arms bound to a small adamantane core. The arms of each system consist of an inner "hydrophobic" block (either polylactide, polyvalerolactone, or polyethylene) and an outer hydrophilic block (polyethylene oxide, PEO). These models exhibit unusual structure very close to the core (clearly an artifact of our model) but which we believe becomes "normal" or bulk-like at relatively short distances from this core. We report on a number of temperature-dependent thermodynamic (structural/energetic) properties as well as kinetic properties. Our observations suggest that under physiological conditions, the hydrophobic regions of these systems may be solid and glassy, with only rare and shallow penetration by water, and that a sharp boundary exists between the hydrophobic cores and either the PEO or water. The PEO in these models is seen to be fully water-solvated at low temperatures but tends to phase separate from water as the temperature is increased, reminiscent of a lower critical solution temperature exhibited by PEO-water mixtures. Water penetration concentration and depth is composition and temperature dependent with greater water penetration for the most ester-rich star polymer.

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