interactive-molecular-model-assembly-with-3d-printing

Interactive Molecular Model Assembly with 3D Printing

With the growth in accessibility of 3D printing, there has been a growing application of and interest in additive manufacturing processes in chemical ...

Oklahoma State University

Previous work describes a computational solvation model called semi-explicit assembly (SEA). The SEA water model computes the free energies of solvation of nonpolar and polar solutes in water with good efficiency and accuracy. However, SEA gives systematic errors in the solvation free energies of ions and charged solutes. Here, we describe field-SEA, an improved treatment that gives accurate solvation free energies of charged solutes, including monatomic and polyatomic ions and model dipeptides, as well as nonpolar and polar molecules. Field-SEA is computationally inexpensive for a given solute because explicit-solvent model simulations are relegated to a precomputation step and because it represents solvating waters in terms of a solute's free-energy field. In essence, field-SEA approximates the physics of explicit-model simulations within a computationally efficient framework. A key finding is that an atom's solvation shell inherits characteristics of a neighboring atom, especially strongly charged neighbors. Field-SEA may be useful where there is a need for solvation free-energy computations that are faster than explicit-solvent simulations and more accurate than traditional implicit-solvent simulations for a wide range of solutes. 

Field-SEA: a model for computing the solvation free energies of nonpolar, polar, and charged solutes in water.

We perform extensive molecular dynamics (MD) simulations between pairs of ions of various diameters (2-5.5 Å in increments of 0.5 Å) and charge (+1 or -1) interacting in explicit water (TIP3P) under ambient conditions. We extract their potentials of mean force (PMFs). We develop an interpolation scheme, called i-PMF, that is capable of capturing the full set of PMFs for arbitrary combinations of ion sizes ranging from 2 to 5.5 Å. The advantage of the interpolation process is computational cost. Whereas it can take 100 h to simulate each PMF by MD, we can compute an equivalently accurate i-PMF in seconds. This process may be useful for rapid and accurate calculation of the strengths of salt bridges and the effects of bridging waters in biomolecular simulations. We also find that our data is consistent with Collins' "law of matching affinities" of ion solubilities: small-small or large-large ion pairs are poorly soluble in water, whereas small-large are highly soluble. 

Using interpolation for fast and accurate calculation of ion-ion interactions.

We present a simple optimization strategy for incorporating experimental dielectric response information on neat liquids in classical molecular models of alcohol. Using this strategy, we determine simple and transferable hydroxyl modulation rules that, when applied to an existing molecular parameter set, result in a newly dielectric corrected (DC) parameter set. We applied these rules to the general Amber force field (GAFF) to form an initial set of GAFF-DC parameters, and we found this to lead to significant improvement in the calculated dielectric constant and hydration free energy values for a wide variety of small molecule alcohol models. Tests of the GAFF-DC parameters in the SAMPL4 blind prediction event for hydration show these changes improve agreement with experiment. Surprisingly, these simple modifications also outperform detailed quantum mechanical electric field calculations using a self-consistent reaction field environment coupling term. This work provides a potential benchmark for future developments in methods for representing condensed-phase environments in electronic structure calculations. 

A fixed-charge model for alcohol polarization in the condensed phase, and its role in small molecule hydration.

We present a new approach to the calculation of solvent-accessible surface areas of molecules with potential application to surface area based methods for determination of solvation free energies. As in traditional analytical and statistical approaches, this new algorithm, called TRIFORCE, reports both component areas and derivatives as a function of the atomic coordinates and radii. Unique to TRIFORCE are the rapid and scalable approaches for the determination of sphere intersection points and numerical estimation of the surface areas, derivatives, and other properties that can be associated with the surface area facets. The algorithm performs a special tessellation and semianalytical integration that uses a precomputed look-up table. This provides a simple way to balance numerical accuracy and memory usage. TRIFORCE calculates derivatives in the same manner, enabling application in force-dependent activities such as molecular geometry minimization. TRIFORCE is available free of charge for academic purposes as both a C++ library, which can be directly interfaced to existing molecular simulation packages, and a web-accessible application.

TRIFORCE: Tessellated Semianalytical Solvent Exposed Surface Areas and Derivatives.

We are interested in the free energies of transferring nonpolar solutes into aqueous NaCl solutions with salt concentrations upwards of 2 M, the Hofmeister regime. We use the semi-explicit assembly (SEA) computational model to represent these electrolyte solutions. We find good agreement with experiments (Setschenow coefficients) on 43 nonpolar and polar solutes and with TIP3P explicit-solvent simulations. Besides being much faster than explicit solvent calculations, SEA is more accurate than the PB models we tested, successfully capturing even subtle salt effects in both the polar and nonpolar components of solvation. We find that the salt effects are mainly due to changes in the cost of forming nonpolar cavities in aqueous NaCl solutions, and not mainly due to solute-ion electrostatic interactions. 

Small molecule solvation changes due to the presence of salt are governed by the cost of solvent cavity formation and dispersion.

Alchemical transformation of solutes using classical fixed-charge force fields is a popular strategy for assessing the free energy of transfer in different environments. Accurate estimations of transfer between phases with significantly different polarities can be difficult because of the static nature of the force fields. Here, we report on an application of such calculations in the SAMPL5 experiment that also involves an effort in balancing solute and solvent interactions via their expected static dielectric constants. This strategy performs well with respect to predictive accuracy and correlation with unknown experimental values. We follow this by performing a series of retrospective investigations which highlight the potential importance of proper balancing in these systems, and we use a null hypothesis analysis to explore potential biases in the comparisons with experiment. The collective findings indicate that considerations of force field compatibility through dielectric behavior is a potential strategy for future improvements in transfer processes between disparate environments.

Predicting water-to-cyclohexane partitioning of the SAMPL5 molecules using dielectric balancing of force fields.

We describe here some tests we made in the SAMPL5 communal event of 'Semi-Explicit Assembly' (SEA), a recent method for computing solvation free energies. We combined the prospective tests of SAMPL5 with followup retrospective calculations, to improve two technical aspects of the field variant of SEA. First, SEA uses an approximate analytical surface around the solute on which a water potential is computed. We have improved and simplified the mathematical model of that surface. Second, some of the solutes in SAMPL5 were large enough to need a way to treat solvating waters interacting with 'buried atoms', i.e. interior atoms of the solute. We improved SEA with a buried-atom correction. We also compare SEA to Thermodynamic Integration molecular dynamics simulations, so that we can sort out force field errors.

Adapting the semi-explicit assembly solvation model for estimating water-cyclohexane partitioning with the SAMPL5 molecules.

How are water's material properties encoded within the structure of the water molecule? This is pertinent to understanding Earth's living systems, its materials, its geochemistry and geophysics, and a broad spectrum of its industrial chemistry. Water has distinctive liquid and solid properties: It is highly cohesive. It has volumetric anomalies-water's solid (ice) floats on its liquid; pressure can melt the solid rather than freezing the liquid; heating can shrink the liquid. It has more solid phases than other materials. Its supercooled liquid has divergent thermodynamic response functions. Its glassy state is neither fragile nor strong. Its component ions-hydroxide and protons-diffuse much faster than other ions. Aqueous solvation of ions or oils entails large entropies and heat capacities. We review how these properties are encoded within water's molecular structure and energies, as understood from theories, simulations, and experiments. Like simpler liquids, water molecules are nearly spherical and interact with each other through van der Waals forces. Unlike simpler liquids, water's orientation-dependent hydrogen bonding leads to open tetrahedral cage-like structuring that contributes to its remarkable volumetric and thermal properties.

How Water's Properties Are Encoded in Its Molecular Structure and Energies.

We present an atomistic level computational investigation of the dynamics of a signaling protein, monocyte chemoattractant protein-1 (MCP-1), that explores how simulation geometry and solution ionic strength affect the calculated diffusion coefficient. Using a simple extension of noncubic finite size diffusion correction expressions, it is possible to calculate experimentally comparable diffusion coefficients that are fully consistent with those determined from cubic box simulations. Additionally, increasing the concentration of salt in the solvent environment leads to changes in protein dynamics that are not explainable through changes in solvent viscosity alone. This work in accurate computational determination of protein diffusion coefficients led us to investigate molecular-weight-based predictors for biomolecular diffusion. By introducing protein volume- and protein surface-area-based extensions of traditional statistical relations connecting particle molecular weight to diffusion, we find that protein solvent-excluded surface area rather than volume works as a better geometric property for estimating biomolecule Stokes radii. This work highlights the considerations necessary for accurate computational determination of biomolecule diffusivity and presents insight into molecular weight relations for diffusion that could lead to new routes for estimating protein diffusion beyond the traditional approaches.

Article	Year
Field-SEA: a model for computing the solvation free energies of nonpolar, polar, and charged solutes in water. The journal of physical chemistry. B\| PubMed ID: 24299013	2014
Using interpolation for fast and accurate calculation of ion-ion interactions. The journal of physical chemistry. B\| PubMed ID: 24625086	2014
A fixed-charge model for alcohol polarization in the condensed phase, and its role in small molecule hydration. The journal of physical chemistry. B\| PubMed ID: 24702668	2014
TRIFORCE: Tessellated Semianalytical Solvent Exposed Surface Areas and Derivatives. Journal of chemical theory and computation\| PubMed ID: 25221446	2014
Small molecule solvation changes due to the presence of salt are governed by the cost of solvent cavity formation and dispersion. The Journal of chemical physics\| PubMed ID: 25494789	2014
Predicting water-to-cyclohexane partitioning of the SAMPL5 molecules using dielectric balancing of force fields. Journal of computer-aided molecular design\| PubMed ID: 27573982	2016
Adapting the semi-explicit assembly solvation model for estimating water-cyclohexane partitioning with the SAMPL5 molecules. Journal of computer-aided molecular design\| PubMed ID: 27632227	2016
How Water's Properties Are Encoded in Its Molecular Structure and Energies. Chemical reviews\| PubMed ID: 28949513	2017
Computational Signaling Protein Dynamics and Geometric Mass Relations in Biomolecular Diffusion. The journal of physical chemistry. B\| PubMed ID: 29510047	2018

Christopher J. Fennell

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