ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins

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 β-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

ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins

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 β-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

Influence of Solvent on the Drug-Loading Process of Amphiphilic Nanogel Star Polymers

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

Role of Hydrophilicity and Length of Diblock Arms for Determining Star Polymer Physical Properties

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

Spatial Distribution of Hydrophobic Drugs in Model Nanogel-Core Star Polymers

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

Effect of Hydrophobic Core Topology and Composition on the Structure and Kinetics of Star Polymers: A Molecular Dynamics Study

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

Simulation and Experiments To Identify Factors Allowing Synthetic Control of Structural Features of Polymeric Nanoparticles

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

Toward a Standard Protocol for Micelle Simulation

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

Structural transition of nanogel star polymers with pH by controlling PEGMA interactions with acid or base copolymers

<p>We use small angle X-ray scattering (SAXS) to characterise a class of star diblock polymers with a nanogel core on which the outer block arms are comprised of random copolymers of temperature sensitive PEGMA with pH sensitive basic (PDMAEMA) and acidic (PMAA) monomers. The acquired SAXS data show that many of the nanogel star polymers undergo a sharp structural transition over a narrow range of pH, but with unexpectedly large shifts in the apparent pKa with respect to that of the acidic or basic monomer unit, the linear polymer form or even an alternate star polymer with a tightly cross-linked core chemistry. We have demonstrated a distinct and quantifiable structural response for the nanogel star copolymers by altering the core or by pairing the monomers PDMAEMA–PEGMA and PMAA–PEGMA to achieve structural transitions that have typically been observed in stars through changes in arm length and number.</p> <p></p

Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15

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