Using Enhanced Sampling Simulations to Study the Conformational Space of Chiral Aromatic Peptoid Monomers

Peptoids, or N-substituted glycines, are peptide-like materials that form a wide variety of secondary structures owing to their enhanced flexibility and a diverse collection of possible side chains. Compared to that of peptides, peptoids have a substantially more complex conformational landscape. This is mainly due to the ability of the peptoid amide bond to exist in both cis- and trans-conformations. This makes conventional molecular dynamics simulations and even some enhanced sampling approaches unable to sample the complete energy landscapes. In this article, we present an extension to the CGenFF-NTOID peptoid atomistic forcefield by adding parameters for four side chains to the previously available collection. We employ explicit solvent well-tempered metadynamics simulations to optimize our forcefield parameters and parallel bias metadynamics to study the cis-trans isomerism for SN1-phenylethyl (s1pe) and SN1-naphthylethyl (s1ne) peptoid monomers, the free energy minima generated from which are validated with available experimental data. In the absence of experimental data, we supported our atomistic simulations with ab initio calculations. This work represents an important step toward the computational design of peptoid-based materials.

A perspective on the microscopic pressure (stress) tensor: History, current understanding, and future challenges

The pressure tensor (equivalent to the negative stress tensor) at both microscopic and macroscopic levels is fundamental to many aspects of engineering and science, including fluid dynamics, solid mechanics, biophysics, and thermodynamics. In this Perspective, we review methods to calculate the microscopic pressure tensor. Connections between different pressure forms for equilibrium and nonequilibrium systems are established. We also point out several challenges in the field, including the historical controversies over the definition of the microscopic pressure tensor; the difficulties with many-body and long-range potentials; the insufficiency of software and computational tools; and the lack of experimental routes to probe the pressure tensor at the nanoscale. Possible future directions are suggested.

DFT Analysis of Organotin Catalytic Mechanisms in Dehydration Esterification Reactions for Terephthalic Acid and 2,2,4,4-Tetramethyl-1,3-cyclobutanediol

Polyesters synthesized from 2,2,4,4-tetramethyl-1,3-cyclobutanediol (TMCD) and terephthalic acid (TPA) are improved alternatives to toxic polycarbonates based on bisphenol A. In this work, we use ωB97X-D/LANL2DZdp calculations, in the presence of a benzaldehyde polarizable continuum model solvent, to show that esterification of TMCD and TPA will reduce and subsequently dehydrate a dimethyl tin oxide catalyst, becoming ligands on the now four-coordinate complex. This reaction then proceeds most plausibly by an intramolecular acyl-transfer mechanism from the tin complex, aided by a coordinated proton donor such as hydronium. These findings are a key first step in understanding polyester synthesis and avoiding undesirable side reactions during production.

SAFT-γ-Mie Cross-Interaction Parameters from Density Functional Theory-Predicted Multipoles of Molecular Fragments for Carbon Dioxide, Benzene, Alkanes, and Water

Determining unlike-pair interaction parameters, whether for group contribution equation of state or molecular simulations, is a challenge for the prediction of thermodynamic properties. As the number of components and their respective complexity increase, it becomes impractical to fit all the unlike interactions. Lorentz-Berthelot combining rules work well for systems, where the main interactions are dispersion forces, but they do not account for electrostatics. In this work, we derive predictive combining rules within the SAFT-γ-Mie framework. In the resulting model, the unlike-pair interactions account for the effect of ionization energies, partial charges, dipole moments, and quadrupole moments. We then estimate these properties for molecular fragments using density functional theory calculations and demonstrate their use to obtain realistic cross-interaction energies without the need for experimental data. An open-source python package, Multipole Approach to Predictively Scale Cross-Interactions, is included to facilitate use of the methods presented in this work. A good qualitative agreement was obtained for all phase equilibria calculations of binary mixtures containing carbon dioxide with propane, hexane, benzene, and water, as well as mixtures of hexane and benzene. Finally, we discuss future improvements to our methodology, including the use of physical insights when fitting self-interaction parameters.

Can we define a unique microscopic pressure in inhomogeneous fluids?

The estimation of a microscopic pressure tensor in an adsorbed thin film on a planar surface remains a challenge in both experiment and theory. While the normal pressure is well-defined for a planar surface, the tangential pressure at a point is not uniquely defined at the nanoscale. We report a new method that allows us to calculate the local pressure tensor and its spatial integral using an arbitrary contour definition of the "virial-route" local pressure tensor. We show that by integrating the local tangential pressure over a small region of space, roughly the range of the intermolecular forces, it is possible to define a coarse-grained tangential pressure that appears to be unique and free from ambiguities in the definition of the local pressure tensor. We support our argument by presenting the results for more than ten types of contour definitions of the local pressure tensor. By defining the coarse-grained tangential pressure, we can also find the effective thickness of the adsorbed layer and, in the case of a porous material, the statistical pore width. The coarse-grained in-layer and in-pore tangential pressures are determined for Lennard-Jones argon adsorbed in realistic carbon slit pores, providing a better understanding of the pressure enhancement for strongly wetting systems.

Effect of Poly(vinyl butyral) Comonomer Sequence on Adhesion to Amorphous Silica: A Coarse-Grained Molecular Dynamics Study

Modulating a comonomer sequence, in addition to the overall chemical composition, is the key to unlocking the true potential of many existing commercial copolymers. We employ coarse-grained molecular dynamics (MD) simulations to study the behavior of random-blocky poly(vinyl butyral-co-vinyl alcohol) (PVB) melts in contact with an amorphous silica surface, representing the interface found in laminated safety glass. Our two-pronged coarse-graining approach utilizes both macroscopic thermophysical data and all-atom MD simulation data. Polymer-polymer nonbonded interactions are described by the fused-sphere SAFT-γ Mie equation of state, while bonded interactions are derived using Boltzmann inversion to match the bond and angle distributions from all-atom PVB chains. Spatially dependent polymer-surface interactions are mapped from a hydroxylated all-atom amorphous silica slab model and all-atom monomers to an external potential acting on the coarse-grained sites. We discovered an unexpected complex relationship between the blockiness parameter and the adhesion energy. The adhesion strength between PVB copolymers with intermediate VA content and silica was found to be maximal for random-blocky copolymers with a moderately high degree of blockiness rather than for diblock copolymers. We attribute this to two main factors: (1) changes in morphology, which dramatically alter the number of VA beads interacting with the surface and (2) a non-negligible contribution of vinyl butyral (VB) monomers to adhesion energy because of their preference to adsorb to zones with low hydroxyl density on the silica surface.

Microscopic Pressure Tensor in Cylindrical Geometry: Pressure of Water in a Carbon Nanotube

The microscopic pressure tensor plays an important role in understanding the mechanical stability, transport, and high-pressure phenomena of confined phases. The lack of an exact formulation to account for the long-range Coulombic contribution to the local pressure tensor in cylindrical geometries prevents the characterization of molecular fluids confined in cylindrical pores. To address this problem, we first derive the local cylindrical pressure tensor for Lennard-Jones fluids based on the Harasima (H) definition, which is expected to be compatible with the Ewald summation method. The test of the H-definition pressure equations in a homogeneous system shows that the radial and azimuthal pressure have unphysical radial dependence near the origin, while the axial pressure gives physically meaningful values. We propose an alternative contour definition that is more appropriate for cylindrical geometry and show that it leads to physically realistic results for all three pressure tensor components. With this definition, the radial and azimuthal pressures are of Irving-Kirkwood (IK) type, and the axial pressure is of Harasima type. Because of the practical interest in the axial pressure, we develop a Harasima/Ewald (H/E) method for calculating the long-range Coulombic contribution to the local axial pressure for rigid molecules. As an application, the axial pressure profile of water inside and outside a (20, 20) single-wall carbon nanotube is determined. The H/E method is compared to the IK method, which assumes a spherically truncated Coulombic potential. Detailed analysis of the pressure profile by both methods shows that the water confined in the nanotube is in a stretched state overall in the axial direction.

Conformal Sites Theory for Adsorbed Films on Energetically Heterogeneous Surfaces

We present a conformal sites theory for a solid substrate whose surface is both geometrically and energetically heterogeneous and that interacts with an adsorbed film. The theory is based on a perturbation expansion for the grand potential of a real system with a rough surface about that of a reference system with an ideal reference surface, thus mapping the real system onto a much simpler interfacial system. The expansion is in powers of the intermolecular potential parameters, and leads to mixing rules for the potential parameters of the reference system. Grand canonical Monte Carlo simulations for the adsorption of argon at 87.3 K, carbon dioxide at 273 K, and water vapor at 298 K on heterogeneous carbon surfaces are investigated to explore the limits of applicability of the theory. Simulation results indicate that the theory works well with typical asymmetry of the potential parameters in the force field. However, care should be taken when applying the theory to strongly associating fluids and in the low-pressure region where the active surface sites play an important role. The conformal sites theory can be used to predict the adsorption properties and to characterize the solid substrate by taking advantage of the corresponding states principle. Other possible applications are also discussed.

Understanding and Controlling Food Protein Structure and Function in Foods: Perspectives from Experiments and Computer Simulations

The structure and interactions of proteins play a critical role in determining the quality attributes of many foods, beverages, and pharmaceutical products. Incorporating a multiscale understanding of the structure-function relationships of proteins can provide greater insight into, and control of, the relevant processes at play. Combining data from experimental measurements, human sensory panels, and computer simulations through machine learning allows the construction of statistical models relating nanoscale properties of proteins to the physicochemical properties, physiological outcomes, and tastes of foods. This review highlights several examples of advanced computer simulations at molecular, mesoscale, and multiscale levels that shed light on the mechanisms at play in foods, thereby facilitating their control. It includes a practical simulation toolbox for those new to in silico modeling.

Bottom-Up Approach to the Coarse-Grained Surface Model: Effective Solid-Fluid Potentials for Adsorption on Heterogeneous Surfaces

Coarse-grained surface models with a low-dimension positional dependence have great advantages in simplifying the theoretical adsorption model and speeding up molecular simulations. In this work, we present a bottom-up strategy, developing a new two-dimensional (2D) coarse-grained surface model from the "bottom-level" atomistic model, for adsorption on highly heterogeneous surfaces with various types of defects. The corresponding effective solid-fluid potential consists of a 2D hard wall potential representing the structure of the surface and a one-dimensional (1D) effective area-weighted free-energy-averaged (AW-FEA) potential representing the energetic strength of the substrate-adsorbate interaction. Within the conventional free-energy-averaged (FEA) framework, an accessible-area-related parameter is introduced into the equation of the 1D effective solid-fluid potential, which allows us not only to obtain the energy information from the fully atomistic system but also to get the structural dependence of the potential on any geometric defect on the surface. Grand canonical Monte Carlo simulations are carried out for argon adsorption at 87.3 K to test the validity of the new 2D surface model against the fully atomistic system. We test four graphitic substrates with different levels of geometric roughness for the top layer, including the widely used reference solid substrate Cabot BP-280. The simulation results show that adding one more dimension to the traditional 1D surface model is essential for adsorption on the geometrically heterogeneous surfaces. In particular, the 2D surface model with the AW-FEA solid-fluid potential significantly improves the adsorption isotherm and density profile over the 1D surface model with the FEA solid-fluid potential over a wide range of pressure. The method to construct an effective solid-fluid potential for an energetically heterogeneous surface is also discussed.

Spectroscopic and Rheological Cross-Analysis of Polyester Polyol Cure Behavior: Role of Polyester Secondary Hydroxyl Content

The sol-gel transition of a series of polyester polyol resins possessing varied secondary hydroxyl content and reacted with a polymerized aliphatic isocyanate cross-linking agent is studied to elucidate the effect of molecular architecture on cure behavior. Dynamic rheology is utilized in conjunction with time-resolved variable-temperature Fourier-transform infrared spectroscopy to examine the relationship between chemical conversion and microstructural evolution as functions of both time and temperature. The onset of a percolated microstructure is identified for all resins, and apparent activation energies extracted from Arrhenius analyses of gelation and average reaction kinetics are found to depend on the secondary hydroxyl content in the polyester polyols. The similarity between these two activation energies is explored. Gel point suppression is observed in all the resin systems examined, resulting in significant deviations from the classical gelation theory of Flory and Stockmayer. The magnitude of these deviations depends on secondary hydroxyl content, and a qualitative model is proposed to explain the observed phenomena, which are consistent with results previously reported in the literature.

Pressure Enhancement in Confined Fluids: Effect of Molecular Shape and Fluid-Wall Interactions

Recently, several experimental and simulation studies have found that phenomena that normally occur at extremely high pressures in a bulk phase can occur in nanophases confined within porous materials at much lower bulk phase pressures, thus providing an alternative route to study high-pressure phenomena. In this work, we examine the effect on the tangential pressure of varying the molecular shape, strength of the fluid-wall interactions, and pore width, for carbon slit-shaped pores. We find that, for multisite molecules, the presence of additional rotational degrees of freedom leads to unique changes in the shape of the tangential pressure profile, especially in larger pores. We show that, due to the direct relationship between the molecular density and the fluid-wall interactions, the latter have a large impact on the pressure tensor. The molecular shape and pore size have a notable impact on the layering of molecules in the pore, greatly influencing both the shape and scale of the tangential pressure profile.

Perovskite-structured AMnxB1−xO3 (A = Ca or Ba; B = Fe or Ni) redox catalysts for partial oxidation of methane

High oxygen carrying capacity, lack of loosely bound lattice oxygen, and preferential surface segregation of Ba make BaMn_xB_1−xO₃ (B = Ni or Fe) based redox catalysts suitable for chemical looping reforming of methane with high syngas yield and coke resistance.

Molecular simulation of homogeneous nucleation of crystals of an ionic liquid from the melt

The homogeneous nucleation of crystals of the ionic liquid [dmim(+)][Cl(-)] from its supercooled liquid phase in the bulk (P = 1 bar, T = 340 K, representing a supercooling of 58 K) was studied using molecular simulations. The string method in collective variables [Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] was used in combination with Markovian milestoning with Voronoi tessellations [Maragliano et al., J. Chem. Theory Comput. 5, 2589-2594 (2009)] and order parameters for molecular crystals [E. E. Santiso and B. L. Trout, J. Chem. Phys. 134, 064109 (2011)] to sketch a minimum free energy path connecting the supercooled liquid and the monoclinic crystal phases, and to determine the free energy and the rates involved in the homogeneous nucleation process. The physical significance of the configurations found along this minimum free energy path is discussed with the help of calculations based on classical nucleation theory and with additional simulation results obtained for a larger system. Our results indicate that, at a supercooling of 58 K, the liquid has to overcome a free energy barrier of the order of 60 kcal/mol and to form a critical nucleus with an average size of about 3.6 nm, before it reaches the thermodynamically stable crystal phase. A simulated homogeneous nucleation rate of 5.0 × 10(10) cm(-3) s(-1) was obtained for our system, which is in reasonable agreement with experimental and simulation rates for homogeneous nucleation of ice at similar degrees of supercooling. This study represents our first step in a series of studies aimed at understanding the nucleation and growth of crystals of organic salts near surfaces and inside nanopores.

Design of linear ligands for selective separation using a genetic algorithm applied to molecular architecture

Continuous purification of chemical reaction products through adsorption-based operations during workup may present advantages over batch chromatography or crystallization. In pharmaceutical syntheses, however, the desired product is often structurally similar to byproducts or unconverted reactant, so that identifying a suitable adsorption medium is challenging. We developed an in silico screening process to design organic ligands which, when chemically bound to a solid surface, would constitute an effective adsorption for a pharmaceutically relevant mixture of reaction products. This procedure employs automated molecular dynamics simulations to evaluate potential ligands, by measuring the difference in adsorption energy of two solutes which differed by one functional group. Then, a genetic algorithm was used to iteratively improve a population of such ligands through selection and reproduction steps. This procedure identified chemical designs of the surface-bound ligands that were outside the set we considered using chemical intuition. The ligand designs achieved selectivity by exploiting phenyl-phenyl stacking which was sterically hindered in the case of one solution component. The ligand designs had selectivity energies of 0.8-1.6 kcal/mol in single-ligand, solvent-free simulations, if entropic contributions to the relative selectivity are neglected. We believe this molecular evolution technique presents a useful method for the directed exploration of chemical space or for molecular design, when the chemical properties of interest can be efficiently evaluated through simulations.

Separation of chemical reaction intermediates by metal-organic frameworks

HPLC columns custom-packed with metal-organic framework (MOF) materials are used for the separation of four small intermediates and byproducts found in the commercial synthesis of an important active pharmaceutical ingredient in methanol. In particular, two closely related amines can be separated in the methanol reaction medium using MOFs, but not with traditional C18 columns using an optimized aqueous mobile phase. Infrared spectroscopy, UV-vis spectroscopy, X-ray diffraction, and thermogravimetric analysis are used in combination with molecular dynamic simulations to study the separation mechanism for the best-performing MOF materials. It is found that separation with ZIF-8 is the result of an interplay between the thermodynamic driving force for solute adsorption within the framework pores and the kinetics of solute diffusion into the material pores, while the separation with Basolite F300 is achieved because of the specific interactions between the solutes and Fe(3+) sites. This work, and the exceptional ability to tailor the porous properties of MOF materials, points to prospects for using MOF materials for the continuous separation and synthesis of pharmaceutical compounds.

A general set of order parameters for molecular crystals

Crystallization is fundamental to many aspects of physics and chemistry in addition to being of technological relevance, for example, in the chemical, food, and pharmaceutical industries. However, the design of crystalline materials and crystallization processes is often challenging due to the many variables that can influence the process. As a part of an effort to gain a molecular-level understanding of the way molecules aggregate and organize themselves into crystal structures, in this work we present a new method to construct order parameters suitable for the study of crystallization and polymorph transformations in molecular systems. Our order parameters can be systematically defined for complex systems using information that can be obtained from simple molecular dynamics simulations of the crystals. We show how to construct the order parameters for the study of three different systems: the formation of α-glycine crystals in solution, the crystallization of benzene from the melt, and the polymorph transformation of terephthalic acid. Finally, we suggest how these order parameters could be used to study order-disorder transitions in molecular systems.

Sequestration and selective oxidation of carbon monoxide on graphene edges

The versatility of carbon nanostructures makes them attractive as possible catalytic materials, as they can be synthesized in various shapes and chemically modified by doping, functionalization, and the creation of defects in the nanostructure. Recent research has shown how the properties of carbon nanostructures can be exploited to enhance the yield of chemical reactions such as the thermal decomposition of water (Kostov et al 2005 Phys. Rev. Lett. 95) and the dissociation of methane into carbon and hydrogen (Huang et al 2008 J. Chem. Phys. at press). In this work, we consider the carbon-mediated partial sequestration and selective oxidation of carbon monoxide (CO), both in the presence and absence of hydrogen. Using first-principles calculations we study several reactions of CO with carbon nanostructures, where the active sites can be regenerated by the deposition of carbon decomposed from the reactant (CO) to make the reactions self-sustained. Using statistical mechanics, we also study the conditions under which the conversion of CO to graphene and carbon dioxide is thermodynamically favorable, both in the presence and in the absence of hydrogen. These results are a first step toward the development of processes for the carbon-mediated partial sequestration and selective oxidation of CO in a hydrogen atmosphere.

Theoretical study of kinetics of zipping phenomena in biomimetic polymers

In this work we use theory to obtain a mathematical expression for a time correlation function c(l,t) that provides insight into the zipping phenomena along a polymer going through a conformational transition. The polymer is modeled as an Ising-like chain with each segment being in one of two states: bound (+1) or unbound (-1). The time correlation function c(l,t) predicts the correlation between the state of the jth polymer segment at time 0 and the state of the (j+/-l)th polymer segment at time t . The expressions for c(0,t) , c(1,t), and c(2,t) obtained from our theory are dependent on the values of k0 and k1, where 2k0 is the rate coefficient for one segment changing from an unbound state to a bound state when both the neighboring segments are in an unbound state, and 2k1 is the rate coefficient for one segment changing from an unbound state to a bound state when both the neighboring segments are in a bound state. The ratio k1/k0 is an indication of the extent of cooperativity of binding adjacent segments on the polymer. We observe that c(0,t), c(1,t), and c(2,t) decay to 0 (no correlation) more slowly and the maximum values of c(1,t) and c(2,t) are lower for low values of k1/k0 as compared to high values of k1/k0. This is because at low values of k1/k0 the consecutive binding of adjacent segments along the polymer occurs slowly, while at high values of k1/k0 the cooperativity of binding adjacent segments is high and the segments along the polymer bind in a fast zipping mechanism.

Effect of confinement by porous carbons on the unimolecular decomposition of formaldehyde

As part of an effort to understand the effect of confinement by porous carbons on chemical reactions, we have carried out density functional theory calculations on the unimolecular decomposition of formaldehyde within graphitic carbons. Our results show that the interactions with the carbon walls result in a lowering of the reaction barrier. For larger pores, there is also a shift of the equilibrium towards the formation of carbon monoxide and hydrogen at low temperatures. This trend is reversed for small pore sizes.

Dissociation of water on defective carbon substrates

Using calculations from first principles, we found that water can dissociate over defective sites in graphene or nanotubes following many possible reaction pathways, some of which have activation barriers lower than half the value for the dissociation of bulk water. This reduction is caused by spin selection rules that allow the system to remain on the same spin surface throughout the reaction.

Molecular modeling of freezing of simple fluids confined within carbon nanotubes

We report Monte Carlo simulation results for freezing of Lennard-Jones carbon tetrachloride confined within model multiwalled carbon nanotubes of different diameters. The structure and thermodynamic stability of the confined phases, as well as the transition temperatures, were determined from parallel tempering grand canonical Monte Carlo simulations and free-energy calculations. The simulations show that the adsorbate forms concentric molecular layers that solidify into defective quasi-two-dimensional hexagonal crystals. Freezing in such concentric layers occurs via intermediate phases that show remnants of hexatic behavior, similar to the freezing mechanism observed for slit pores in previous works. The adsorbate molecules in the inner regions of the pore also exhibit changes in their properties upon reduction of temperature. The structural changes in the different regions of adsorbate occur at temperatures above or below the bulk freezing point, depending on pore diameter and distance of the adsorbate molecules from the pore wall. The simulations show evidence of a rich phase behavior in confinement; a number of phases, some of them inhomogeneous, were observed for the pore sizes considered. The multiple transition temperatures obtained from the simulations were found to be in good agreement with recent dielectric relaxation spectroscopy experiments for CCl(4) confined within multiwalled carbon nanotubes.