Coray M. Colina

Polymatic : a generalized simulated polymerization algorithm for amorphous polymers

This work presents a generalized structure generation methodology for amorphous polymers by a simulated polymerization technique and 21-step molecular dynamics equilibration, which is particularly effective for high-Tg polymers. The essential framework and parameters of the techniques and algorithms are described in detail, and example input scripts are provided for use with the freely available Polymatic simulated polymerization code and LAMMPS molecular dynamics package. The capabilities of the methods are examined through application to six linear, glassy polymers ranging in functionality, polarity, and rigidity. Validation of the methodology is provided by comparison of the simulations and experiments for a variety of structural, adsorption, and thermal properties, all of which showed excellent agreement with available experimental data.

Tissue factor around dermal vessels has bound factor VII in the absence of injury

Summary.  Background: ‘Idling’ or ongoing low‐level activity of the tissue factor (TF) pathway is a postulated mechanism by which the coagulation process can become active without a lag period at sites of injury. Objective: To determine whether TF around cutaneous vessels has bound factor VIIa in the absence of injury, and thus could participate in the idling process. Methods: Immunostaining of mouse skin with antibodies against a 15‐residue peptide from the sequence of mouse TF, and against the whole extracellular portion of TF. Results: The whole TF antibody recognized TF in squamous epithelium and around vessels in the dermis. By contrast, the monospecific antibody only recognized TF in the squamous epithelium, but not around vessels. We also found that biotinylated, active site‐inhibited FVIIa (FVIIai) bound to tissue sections in the same areas in which TF was recognized by the monospecific antibody (squamous epithelium), but did not bind around vessels. Molecular modeling revealed that FVIIa and FX binding to TF masked a significant part of the surface of the target peptide. Conclusions: In the aggregate, these data are most consistent with the interpretation that TF in perivascular sites has bound FVIIa, even in the absence of any injury. The presence of endogenously bound FVIIa prevents the subsequent binding of the monospecific antibody or exogenous FVIIai to perivascular TF.

Molecular Dynamics Simulations of Viral RNA Polymerases Link Conserved and Correlated Motions of Functional Elements to Fidelity

Abstract The viral RNA-dependent RNA polymerase (RdRp) is essential for multiplication of all RNA viruses. The sequence diversity of an RNA virus population contributes to its ability to infect the host. This diversity emanates from errors made by the RdRp during RNA synthesis. The physical basis for RdRp fidelity is unclear but is linked to conformational changes occurring during the nucleotide-addition cycle. To understand RdRp dynamics that might influence RdRp function, we have analyzed all-atom molecular dynamics simulations on the nanosecond timescale of four RdRps from the picornavirus family that exhibit 30–74% sequence identity. Principal component analysis showed that the major motions observed during the simulations derived from conserved structural motifs and regions of known function. The dynamics of residues participating in the same biochemical property, for example, RNA binding, nucleotide binding or catalysis, were correlated even when spatially distant on the RdRp structure. The conserved and correlated dynamics of functional structural elements suggest coevolution of dynamics with structure and function of the RdRp. Crystal structures of all picornavirus RdRps exhibit a template–nascent RNA duplex channel too small to fully accommodate duplex RNA. Simulations revealed opening and closing motions of the RNA and nucleoside triphosphate channels, which might be relevant to nucleoside triphosphate entry, inorganic pyrophosphate exit and translocation. A role for nanosecond timescale dynamics in RdRp fidelity is supported by the altered dynamics of the high-fidelity G64S derivative of PV RdRp relative to wild-type enzyme.

Molecular Dynamic Simulations and Vibrational Analysis of an Ionic Liquid Analogue

Deep eutectic solvents, considered ionic liquid (IL) analogues, show promise for many material science and engineering applications over typical ILs because they are readily available and relatively inexpensive. Atomistic molecular dynamics simulations have been performed over a range of temperatures on one eutectic mixture, 1:2 choline chloride/urea, using different force field modifications. Good agreement was achieved between simulated density, volume expansion coefficient, heat capacity, and diffusion coefficients and experimental values in order to validate the best performing force field. Atom-atom and center-of-mass radial distribution functions are discussed in order to understand the atomistic interactions involved in this eutectic mixture. Experimental infrared (IR) spectra are also reported for choline chloride-urea mixtures, and band assignments are discussed. The distribution of hydrogen-bond interactions from molecular simulations is correlated to curve-resolved bands from the IR spectra. This work suggests that there is a strong interaction between the NH2 of urea and the chlorine anion where the system wants to maximize the number of hydrogen bonds to the anion. Additionally, the disappearance of free carbonyl groups upon increasing concentrations of urea suggests that at low urea concentrations, urea will preferentially interact with the anion through the NH2 groups. As this concentration increases, the complex remains but with additional interactions that remove the free carbonyl band from the spectra. The results from both molecular simulations and experimental IR spectroscopy support the idea that key interactions between the moieties in the eutectic mixture interrupt the main interactions within the parent substances and are responsible for the decrease in freezing point.

Characterizing the Structure of Organic Molecules of Intrinsic Microporosity by Molecular Simulations and X-ray Scattering

The design of a new class of materials, called organic molecules of intrinsic microporosity (OMIMs), incorporates awkward, concave shapes to prevent efficient packing of molecules, resulting in microporosity. This work presents predictive molecular simulations and experimental wide-angle X-ray scattering (WAXS) for a series of biphenyl-core OMIMs with varying end-group geometries. Development of the utilized simulation protocol was based on comparison of several simulation methods to WAXS patterns. In addition, examination of the simulated structures has facilitated the assignment of WAXS features to specific intra- and intermolecular distances, making this a useful tool for characterizing the packing behavior of this class of materials. Analysis of the simulations suggested that OMIMs had greater microporosity when the molecules were the most shape-persistent, which required rigid structures and bulky end groups. The simulation protocol presented here allows for predictive, presynthesis screening of OMIMs and similar complex molecules to enhance understanding of their structures and aid in future design efforts.

Thermal properties of supercritical carbon dioxide by Monte Carlo simulations

We present simulation results for the volume expansivity, isothermal compressibility, isobaric heat capacity, Joule-Thomson coefficient and speed of sound for carbon dioxide (CO 2 ) in the supercritical region, using the fluctuation method based on Monte Carlo simulations in the isothermal-isobaric ensemble. We model CO 2 as a quadrupolar two-center Lennard-Jones fluid with potential parameters reported in the literature, derived from vapor-liquid equilibria (VLE) of CO 2 . We compare simulation results with an equation of state (EOS) for the two-center Lennard-Jones plus point quadrupole (2CLJQ) fluid and with a multiparametric EOS adjusted to represent CO 2 experimental data. It is concluded that the VLE-based parameters used to model CO 2 as a quadrupolar two-center Lennard-Jones fluid (both simulations and EOS) can be used with confidence for the prediction of thermodynamic properties, including those of industrial interest such as the speed of sound or Joule-Thomson coefficient, for CO 2 in the supercritical region, except in the extended critical region.

Analysis of force fields and BET theory for polymers of intrinsic microporosity

A detailed force field analysis for polymers of intrinsic microporosity (PIMs) was carried out in this study. The generalised amber force field (GAFF) with united atom transferable potential for phase equilibria (TraPPE-UA), and the atomistic polymer consistent force field were evaluated. Analysis carried out with PIM-1 showed that the use of GAFF for bonded interactions and TraPPE-UA for non-bonded interactions yielded a simulated sample that compared best with available experimental data (wide-angle X-ray scattering and nitrogen adsorption at 77 K). In addition, Brunauer–Emmett–Teller surface areas, calculated from simulated nitrogen isotherms as pseudo-experimental data, showed that this common method failed to measure the geometric surface area of this type of material. These findings are expected to facilitate the predictive screening of different PIM functionalities.

The depletion attraction between Pairs of colloid particles in polymer solution

NVT Monte Carlo simulations were used to assess the effective interaction between pairs of colloid particles dissolved in non-adsorbing polymer solutions. The polymers were represented as freely-jointed-hard-sphere chains composed of 10, 20, or 30 segments. The size of the interacting colloid particles was similar to or smaller than the radius of gyration of the polymers. Results show a short-range colloid–colloid depletion attraction. At low polymer concentration, this attraction slowly decays to zero at increasing separations. At higher polymer concentration, the depletion attraction is coupled to a mid-range repulsion, especially for solutions of short, stiff polymers. From the simulated forces, osmotic second virial coefficients were computed for colloids as a function of polymer concentration. The calculated osmotic second virial coefficients exhibit a non-monotonic dependence on polymer concentration, in qualitative agreement with experimental results. The simulated colloid–colloid potentials of mean force were used, within a perturbation theory, to calculate fluid–fluid and fluid–solid coexistence curves. The colloids are treated as a pseudo one-component system, and the polymers in solution are considered only through the effective pair potential between the dissolved colloids. When long flexible polymers are dissolved in solution, the phase diagram for small colloid particles shows a fluid–fluid coexistence curve at low colloid packing fraction, and a fluid–solid coexistence curve at higher packing fraction. As the size of the colloid particles increases, the molecular weight of the polymer decreases, or the polymer concentration in solution increases, the fluid–fluid coexistence curve becomes metastable with respect to the fluid–solid coexistence curve.

Polymer ultrapermeability from the inefficient packing of 2D chains

The promise of ultrapermeable polymers, such as poly(trimethylsilylpropyne) (PTMSP), for reducing the size and increasing the efficiency of membranes for gas separations remains unfulfilled due to their poor selectivity. We report an ultrapermeable polymer of intrinsic microporosity (PIM-TMN-Trip) that is substantially more selective than PTMSP. From molecular simulations and experimental measurement we find that the inefficient packing of the two-dimensional (2D) chains of PIM-TMN-Trip generates a high concentration of both small (<0.7 nm) and large (0.7-1.0 nm) micropores, the former enhancing selectivity and the latter permeability. Gas permeability data for PIM-TMN-Trip surpass the 2008 Robeson upper bounds for O2/N2, H2/N2, CO2/N2, H2/CH4 and CO2/CH4, with the potential for biogas purification and carbon capture demonstrated for relevant gas mixtures. Comparisons between PIM-TMN-Trip and structurally similar polymers with three-dimensional (3D) contorted chains confirm that its additional intrinsic microporosity is generated from the awkward packing of its 2D polymer chains in a 3D amorphous solid. This strategy of shape-directed packing of chains of microporous polymers may be applied to other rigid polymers for gas separations.

Accurate CO2 Joule–Thomson inversion curve by molecular simulations

We present simulation of the Joule–Thomson inversion curve (JTIC) for carbon dioxide using two different approaches based on Monte Carlo (MC) simulations in the isothermal–isobaric ensemble. We model carbon dioxide using a two-center Lennard–Jones (LJ) plus point quadrupole moment (2CLJQ) potential. We show that a precision of four significant figures in ensemble averages of thermodynamic quantities of interest is needed to obtain accurately the JTIC. The agreement between the experimental data, Wagner equation of state (EOS) and our simulations results indicates that the 2CLJQ potential represents an excellent balance between simplicity and accuracy in modeling of carbon dioxide. Additionally, we calculate the JTIC using the BACKONE EOS (that uses the same intermolecular potential as in our simulations) and show that the BACKONE EOS performs very well in predicting the JTIC for carbon dioxide.