@article{jani_farias_jain_houston_velev_santiso_hsiao_khan_2024, title={Isothermal Titration Calorimetry Reveals Entropy-Driven Bisphenol A Epoxy Resin Adhesion to Metal Oxide Surfaces}, volume={1}, ISSN={["1520-5835"]}, url={https://doi.org/10.1021/acs.macromol.3c02440}, DOI={10.1021/acs.macromol.3c02440}, abstractNote={Polymer-coated metals are ubiquitous in multiple industries as a corrosion protection strategy. Particularly in food and beverage packaging, bisphenol A (BPA)-based epoxy coatings provide an excellent barrier and strong adhesion to metals. There is, however, a need to design safer, alternative coatings with similar adhesion as BPA-epoxies due to environmental and health concerns associated with BPA. Limited critical information exists on epoxy-metal interactions and the effect of interfacial functional group concentration on overall adhesion due to the constraints of most experimental methods, which typically probe the interface only within a few nanometers in situ. Herein, we use isothermal titration calorimetry (ITC) and molecular dynamics simulations to characterize the thermodynamics of epoxy-metal oxide binding in the liquid phase and identify the influence of epoxy resin structure and metal oxide surface chemistry in dictating the binding process. Across a series of epoxy resins and three metal oxides, we reveal a previously unreported dominant role of entropy in the binding process, primarily facilitated by the release of bound solvent molecules from the epoxy/metal interface with possible contributions from dispersive OH–π interactions between the benzene rings of the resin and the –OH groups on the metal oxide surface. Enthalpy-favored hydrogen bonding between the –OH groups of the resin and the metal oxide plays a supporting role in the binding, with its participation dependent on the interfacial –OH group concentration. ITC therefore offers key molecular insights into the relative functional group contributions to the adhesion mechanism and informs the rational design of next-generation polymer coatings.}, journal={MACROMOLECULES}, author={Jani, Pallav K. and Farias, Barbara V. and Jain, Rakshit Kumar and Houston, Katelyn R. and Velev, Orlin D. and Santiso, Erik E. and Hsiao, Lilian C. and Khan, Saad A.}, year={2024}, month={Jan} }
 @article{shi_smith_santiso_gubbins_2023, title={A perspective on the microscopic pressure (stress) tensor: History, current understanding, and future challenges}, volume={158}, ISSN={["1089-7690"]}, DOI={10.1063/5.0132487}, abstractNote={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.}, number={4}, journal={JOURNAL OF CHEMICAL PHYSICS}, author={Shi, Kaihang and Smith, Edward R. and Santiso, Erik E. and Gubbins, Keith E.}, year={2023}, month={Jan} }
 @article{joshipura_nguyen_quinn_yang_morales_santiso_daeneke_truong_dickey_2023, title={An atomically smooth container: Can the native oxide promote supercooling of liquid gallium?}, volume={26}, ISSN={["2589-0042"]}, url={https://doi.org/10.1016/j.isci.2023.106493}, DOI={10.1016/j.isci.2023.106493}, abstractNote={Metals tend to supercool—that is, they freeze at temperatures below their melting points. In general, supercooling is less favorable when liquids are in contact with nucleation sites such as rough surfaces. Interestingly, bulk gallium (Ga) can significantly supercool, even when it is in contact with heterogeneous surfaces that could provide nucleation sites. We hypothesized that the native oxide on Ga provides an atomically smooth interface that prevents Ga from directly contacting surfaces, and thereby promotes supercooling. Although many metals form surface oxides, Ga is a convenient metal for studying supercooling because its melting point of 29.8°C is near room temperature. Using differential scanning calorimetry (DSC), we show that freezing of Ga with the oxide occurs at a lower temperature (−15.6 ± 3.5°C) than without the oxide (6.9 ± 2.0°C when the oxide is removed by HCl). We also demonstrate that the oxide enhances supercooling via macroscopic observations of freezing. These findings explain why Ga supercools and have implications for emerging applications of Ga that rely on it staying in the liquid state.}, number={4}, journal={ISCIENCE}, author={Joshipura, Ishan D. and Nguyen, Chung Kim and Quinn, Colette and Yang, Jiayi and Morales, Daniel H. and Santiso, Erik and Daeneke, Torben and Truong, Vi Khanh and Dickey, Michael D.}, year={2023}, month={Apr} }
 @article{jain_hall_santiso_2023, title={Using Enhanced Sampling Simulations to Study the Conformational Space of Chiral Aromatic Peptoid Monomers}, volume={19}, ISSN={["1549-9626"]}, DOI={10.1021/acs.jctc.3c00803}, abstractNote={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.}, number={24}, journal={JOURNAL OF CHEMICAL THEORY AND COMPUTATION}, author={Jain, Rakshit Kumar and Hall, Carol K. and Santiso, Erik E.}, year={2023}, month={Nov}, pages={9457–9467} }
 @article{sattor_pervaje_pasquinelli_khan_santiso_2022, title={Multiscale Constitutive Modeling of the Mechanical Properties of Polypropylene Fibers from Molecular Simulation Data}, volume={1}, ISSN={["1520-5835"]}, url={https://doi.org/10.1021/acs.macromol.1c00630}, DOI={10.1021/acs.macromol.1c00630}, abstractNote={We present a multiscale approach to create a constitutive model that predicts the mechanical properties of polypropylene fibers based on chemical and physical characteristics. The development of this method relies on validation with experimental stress–strain curves from nine different isotactic polypropylene (iPP) fibers with their varying molecular weight characteristics, Hermans orientation factors, and crystallinity. Complementary molecular models were built by using molecular dynamics (MD) simulations with united atom models. Tensile deformation simulations adapting a quasi-static procedure resulted in stress–strain curves that aligned well with the experimentally measured ones. A neural network model was trained on the MD simulation data to create correlations that predict parameters for a chosen constitutive model that describes the mechanical properties of the polypropylene fibers. This computational approach is amenable to be applied to polymer fiber systems and aims to aid in the design of polymeric materials to achieve targeted mechanical properties.}, number={3}, journal={MACROMOLECULES}, publisher={American Chemical Society (ACS)}, author={Sattor, Amulya K. and Pervaje, Amulya K. and Pasquinelli, Melissa A. and Khan, Saad A. and Santiso, Erik E.}, year={2022}, month={Jan} }
 @article{shi_santiso_gubbins_2021, title={Can we define a unique microscopic pressure in inhomogeneous fluids?}, volume={154}, ISSN={["1089-7690"]}, DOI={10.1063/5.0044487}, abstractNote={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.}, number={8}, journal={JOURNAL OF CHEMICAL PHYSICS}, author={Shi, Kaihang and Santiso, Erik E. and Gubbins, Keith E.}, year={2021}, month={Feb} }
 @article{clark_thacker_mcgill_miles_westmoreland_efimenko_genzer_santiso_2021, title={DFT Analysis of Organotin Catalytic Mechanisms in Dehydration Esterification Reactions for Terephthalic Acid and 2,2,4,4-Tetramethyl-1,3-cyclobutanediol}, volume={125}, ISSN={["1520-5215"]}, url={https://doi.org/10.1021/acs.jpca.1c00850}, DOI={10.1021/acs.jpca.1c00850}, abstractNote={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.}, number={23}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, publisher={American Chemical Society (ACS)}, author={Clark, Jennifer A. and Thacker, Pranav J. and McGill, Charles J. and Miles, Jason R. and Westmoreland, Phillip R. and Efimenko, Kirill and Genzer, Jan and Santiso, Erik E.}, year={2021}, month={Jun}, pages={4943–4956} }
 @article{clark_santiso_2021, title={SAFT-gamma-Mie Cross-Interaction Parameters from Density Functional Theory-Predicted Multipoles of Molecular Fragments for Carbon Dioxide, Benzene, Alkanes, and Water}, volume={125}, ISSN={["1520-5207"]}, DOI={10.1021/acs.jpcb.1c00851}, abstractNote={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.}, number={15}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Clark, Jennifer A. and Santiso, Erik E.}, year={2021}, month={Apr}, pages={3867–3882} }
 @article{shi_santiso_gubbins_2020, title={Conformal Sites Theory for Adsorbed Films on Energetically Heterogeneous Surfaces}, volume={36}, ISSN={["0743-7463"]}, DOI={10.1021/acs.langmuir.9b03633}, abstractNote={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 (GCMC) 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.}, number={7}, journal={LANGMUIR}, author={Shi, Kaihang and Santiso, Erik E. and Gubbins, Keith E.}, year={2020}, month={Feb}, pages={1822–1838} }
 @article{walker_genzer_santiso_2020, title={Effect of Poly(vinyl butyral) Comonomer Sequence on Adhesion to Amorphous Silica: A Coarse-Grained Molecular Dynamics Study}, volume={12}, ISSN={["1944-8252"]}, DOI={10.1021/acsami.0c10747}, abstractNote={Modulating a comonomer sequence, in addition to 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 molecular dynamics 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 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 ran a series of interfacial coarse-grained MD simulations for PVB melts, systematically varying overall chemical composition and block length distribution. We discovered an unexpectedly complex relationship between blockiness parameter and adhesion energy. For intermediate vinyl alcohol (VA) content, adhesion strength to the silica slab was found to be maximal not for diblock copolymers, but rather random-blocky copolymers with a moderately high degree of blockiness. 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, due to their preference to adsorb to zones with low hydroxyl density on the silica surface.}, number={42}, journal={ACS APPLIED MATERIALS & INTERFACES}, author={Walker, Christopher C. and Genzer, Jan and Santiso, Erik E.}, year={2020}, month={Oct}, pages={47879–47890} }
 @article{smith_fabiani_wang_ramesh_khan_santiso_silva_gorman_menegatti_2020, title={Exploring the physicochemical and morphological properties of peptide‐hybridized dendrimers (
            DendriPeps
            ) and their aggregates}, volume={58}, ISSN={2642-4150 2642-4169}, url={http://dx.doi.org/10.1002/pol.20200277}, DOI={10.1002/pol.20200277}, abstractNote={Abstract}, number={16}, journal={Journal of Polymer Science}, publisher={Wiley}, author={Smith, Ryan J. and Fabiani, Thomas and Wang, Siyao and Ramesh, Srivatsan and Khan, Saad and Santiso, Erik and Silva, Fernando Luis Barroso and Gorman, Christopher and Menegatti, Stefano}, year={2020}, month={Jul}, pages={2234–2247} }
 @article{walker_genzer_santiso_2020, title={Extending the fused-sphere SAFT-gamma Mie force field parameterization approach to poly(vinyl butyral) copolymers}, volume={152}, ISSN={["1089-7690"]}, DOI={10.1063/1.5126213}, abstractNote={SAFT-γ Mie, a molecular group-contribution equation of state with foundations in the statistical associating fluid theory framework, is a promising means for developing accurate and transferable coarse-grained force fields for complex polymer systems. We recently presented a new approach for incorporating bonded potentials derived from all-atom molecular dynamics simulations into fused-sphere SAFT-γ Mie homopolymer chains by means of a shape factor parameter, which allows for bond distances less than the tangent-sphere value required in conventional SAFT-γ Mie force fields. In this study, we explore the application of the fused-sphere SAFT-γ Mie approach to copolymers. In particular, we demonstrate its capabilities at modeling poly(vinyl alcohol-co-vinyl butyral) (PVB), an important commercial copolymer widely used as an interlayer in laminated safety glass applications. We found that shape factors determined from poly(vinyl alcohol) and poly(vinyl butyral) homopolymers do not in general correctly reproduce random copolymer densities when standard SAFT-γ Mie mixing rules are applied. However, shape factors optimized to reproduce the density of a random copolymer of intermediate composition resulted in a model that accurately represents density across a wide range of chemical compositions. Our PVB model reproduced copolymer glass transition temperature in agreement with experimental data, but heat capacity was underpredicted. Finally, we demonstrate that atomistic details may be inserted into equilibrated fused-sphere SAFT-γ Mie copolymer melts through a geometric reverse-mapping algorithm.}, number={4}, journal={JOURNAL OF CHEMICAL PHYSICS}, author={Walker, Christopher C. and Genzer, Jan and Santiso, Erik E.}, year={2020}, month={Jan} }
 @article{raghuvanshi_zhu_ramezani_menegatti_santiso_mason_rodgers_janka_abolhasani_2020, title={Highly Efficient 1-Octene Hydroformylation at Low Syngas Pressure: From Single-Droplet Screening to Continuous Flow Synthesis}, volume={10}, ISSN={["2155-5435"]}, DOI={10.1021/acscatal.0c01515}, abstractNote={We present a reconfigurable flow chemistry strategy for facile transition between accelerated screening and continuous synthesis of linear aldehydes through homogeneous rhodium-catalyzed hydroformy...}, number={14}, journal={ACS CATALYSIS}, author={Raghuvanshi, Keshav and Zhu, Cheng and Ramezani, Mahdi and Menegatti, Stefano and Santiso, Erik E. and Mason, Dawn and Rodgers, Jody and Janka, Mesfin E. and Abolhasani, Milad}, year={2020}, month={Jul}, pages={7535–7542} }
 @article{shi_shen_santiso_gubbins_2020, title={Microscopic Pressure Tensor in Cylindrical Geometry: Pressure of Water in a Carbon Nanotube}, volume={16}, ISSN={["1549-9626"]}, DOI={10.1021/acs.jctc.0c00607}, abstractNote={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. Due to 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 axial pressure profile by both methods shows that the water confined in the nanotube is in a stretched state overall in the axial direction.}, number={9}, journal={JOURNAL OF CHEMICAL THEORY AND COMPUTATION}, author={Shi, Kaihang and Shen, Yifan and Santiso, Erik E. and Gubbins, Keith E.}, year={2020}, month={Sep}, pages={5548–5561} }
 @article{schneible_shi_young_ramesh_he_dowdey_dubnansky_libya_gao_santiso_et al._2020, title={Modified gaphene oxide (GO) particles in peptide hydrogels: a hybrid system enabling scheduled delivery of synergistic combinations of chemotherapeutics}, volume={8}, ISSN={["2050-7518"]}, DOI={10.1039/d0tb00064g}, abstractNote={Composite material enabling the delivery of synergistic combination of doxorubicin and gemcitabine against breast cancer with molar and kinetic precision.}, number={17}, journal={JOURNAL OF MATERIALS CHEMISTRY B}, author={Schneible, John D. and Shi, Kaihang and Young, Ashlyn T. and Ramesh, Srivatsan and He, Nanfei and Dowdey, Clay E. and Dubnansky, Jean Marie and Libya, Radina L. and Gao, Wei and Santiso, Erik and et al.}, year={2020}, month={May}, pages={3852–3868} }
 @article{hijes_shi_noya_santiso_gubbins_sanz_vega_2020, title={The Young-Laplace equation for a solid-liquid interface}, volume={153}, ISSN={["1089-7690"]}, DOI={10.1063/5.0032602}, abstractNote={The application of the Young–Laplace equation to a solid–liquid interface is considered. Computer simulations show that the pressure inside a solid cluster of hard spheres is smaller than the external pressure of the liquid (both for small and large clusters). This would suggest a negative value for the interfacial free energy. We show that in a Gibbsian description of the thermodynamics of a curved solid–liquid interface in equilibrium, the choice of the thermodynamic (rather than mechanical) pressure is required, as suggested by Tolman for the liquid–gas scenario. With this definition, the interfacial free energy is positive, and the values obtained are in excellent agreement with previous results from nucleation studies. Although, for a curved fluid–fluid interface, there is no distinction between mechanical and thermal pressures (for a sufficiently large inner phase), in the solid–liquid interface, they do not coincide, as hypothesized by Gibbs.}, number={19}, journal={JOURNAL OF CHEMICAL PHYSICS}, author={Hijes, P. and Shi, K. and Noya, E. G. and Santiso, E. E. and Gubbins, K. E. and Sanz, E. and Vega, C.}, year={2020}, month={Nov} }
 @article{silva_carloni_cheung_cottone_donnini_foegeding_gulzar_jacquier_lobaskin_mackernan_et al._2020, title={Understanding and Controlling Food Protein Structure and Function in Foods: Perspectives from Experiments and Computer Simulations}, volume={11}, ISSN={["1941-1421"]}, DOI={10.1146/annurev-food-032519-051640}, abstractNote={ 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. }, journal={ANNUAL REVIEW OF FOOD SCIENCE AND TECHNOLOGY, VOL 11}, author={Silva, Fernando Luis and Carloni, Paolo and Cheung, David and Cottone, Grazia and Donnini, Serena and Foegeding, E. Allen and Gulzar, Muhammad and Jacquier, Jean Christophe and Lobaskin, Vladimir and MacKernan, Donal and et al.}, year={2020}, pages={365–387} }
 @article{weiser_santiso_2019, title={A CGenFF-based force field for simulations of peptoids with both cis and trans peptide bonds}, volume={40}, ISSN={["1096-987X"]}, DOI={10.1002/jcc.25850}, abstractNote={Peptoids, or poly‐n‐substituted glycines, are peptide‐like polymers composed of a flexible backbone decorated with diverse chemical side chains. Peptoids can form a variety of self‐assembling structures based on the type and sequence of the side chains attached to their backbones. All‐atom molecular dynamics simulations have been useful in predicting the conformational structures of proteins and will be valuable tools for identifying combinations of peptoid side chains that may form interesting folded structures. However, peptoid models must address a major degree of freedom not common in proteins – the cis/trans isomerization of the peptide bond. This work presents CHARMM general force field (CGenFF) parameters developed to accurately represent peptoid conformational behavior, with an emphasis on a correct representation of both the cis and trans isomers of the peptoid backbone. These parameters are validated against experimental and quantum mechanics data and used to simulate three peptoid side chains in explicitly solvated systems. © 2019 Wiley Periodicals, Inc.}, number={22}, journal={JOURNAL OF COMPUTATIONAL CHEMISTRY}, author={Weiser, Laura J. and Santiso, Erik E.}, year={2019}, month={Aug}, pages={1946–1956} }
 @article{shi_santiso_gubbins_2019, title={Bottom-Up Approach to the Coarse-Grained Surface Model: Effective Solid–Fluid Potentials for Adsorption on Heterogeneous Surfaces}, volume={35}, ISSN={0743-7463 1520-5827}, url={http://dx.doi.org/10.1021/ACS.LANGMUIR.9B00440}, DOI={10.1021/ACS.LANGMUIR.9B00440}, abstractNote={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.}, number={17}, journal={Langmuir}, publisher={American Chemical Society (ACS)}, author={Shi, Kaihang and Santiso, Erik E. and Gubbins, Keith E.}, year={2019}, month={Apr}, pages={5975–5986} }
 @article{walker_genzer_santiso_2019, title={Development of a fused-sphere SAFT-gamma Mie force field for poly(vinyl alcohol) and poly(ethylene)}, volume={150}, ISSN={["1089-7690"]}, DOI={10.1063/1.5078742}, abstractNote={SAFT-γ Mie, a group-contribution equation of state rooted in Statistical Associating Fluid Theory, provides an efficient framework for developing accurate, transferable coarse-grained force fields for molecular simulation. Building on the success of SAFT-γ Mie force fields for small molecules, we address two key issues in extending the SAFT-γ Mie coarse-graining methodology to polymers: (1) the treatment of polymer chain rigidity and (2) the disparity between the structure of linear chains of tangent spheres and the structure of the real polymers. We use Boltzmann inversion to derive effective bond-stretching and angle-bending potentials mapped from all-atom oligomer molecular dynamics (MD) simulations to the coarse-grained sites and a fused-sphere version of SAFT-γ Mie as the basis for non-bonded interactions. The introduction of an overlap parameter between Mie spheres leads to a degeneracy when fitting to monomer vapor-liquid equilibria (VLE) data, which we resolve by matching polymer density from coarse-grained MD simulation with that from all-atom simulation. The result is a chain of monomers rigorously parameterized to experimental VLE data and with structural detail consistent with all-atom simulations. We test our approach on atactic poly(vinyl alcohol) and polyethylene and compare the results for SAFT-γ Mie models with structural detail mapped from the Optimized Potentials for Liquid Simulations (OPLS) and Condensed-phase Optimized Molecular Potentials for Atomistic Simulation Studies (COMPASS) all-atom force fields.}, number={3}, journal={JOURNAL OF CHEMICAL PHYSICS}, author={Walker, Christopher C. and Genzer, Jan and Santiso, Erik E.}, year={2019}, month={Jan} }
 @inbook{trout_chadwick_chen_santiso_2019, edition={3rd}, title={Molecular Modeling in Crystallization}, booktitle={Handbook of Industrial Crystallization}, publisher={Cambridge University Press}, author={Trout, B.L. and Chadwick, K. and Chen, J. and Santiso, E.E.}, editor={Myerson, A. and Erdemir, D. and Lee, A.Y.Editors}, year={2019}, month={Jul} }
 @article{pervaje_walker_santiso_2019, title={Molecular simulation of polymers with a SAFT-gamma Mie approach}, volume={45}, ISSN={["1029-0435"]}, DOI={10.1080/08927022.2019.1645331}, abstractNote={ABSTRACT We review the group contribution Statistical Associating Fluid Theory with Mie interaction potentials (SAFT-γ Mie) approach for building coarse-grained models for molecular simulation of polymeric systems. In this top-down method, force field parameters for coarse-grained polymer models can be derived from thermodynamic information on constituent monomer units using the SAFT-γ Mie equation of state (EoS). This strategy can facilitate high-throughput computational screening of polymeric materials, with a corresponding states correlation expediting the force field fitting. Accurate and transferable non-bonded parameters linked to macroscopic thermodynamic data allow for calculation of properties beyond those obtainable from the EoS alone. To overcome limitations of SAFT-γ Mie regarding polymer chain stiffness and branching, hybrid top-down/bottom-up approaches have combined non-bonded parameters from SAFT-γ Mie with bond-stretching and angle-bending potentials from higher-resolution force fields. Our review critically evaluates the performance of recent SAFT-γ Mie polymer models, highlighting the strengths and weaknesses in the context of other equation of state and coarse-graining methods.}, number={14-15}, journal={MOLECULAR SIMULATION}, author={Pervaje, Amulya K. and Walker, Christopher C. and Santiso, Erik E.}, year={2019}, month={Oct}, pages={1223–1241} }
 @article{clark_santiso_frischknecht_2019, title={Morphology and proton diffusion in a coarse-grained model of sulfonated poly(phenylenes)}, volume={151}, ISSN={["1089-7690"]}, DOI={10.1063/1.5116684}, abstractNote={A coarse-grained model previously used to simulate Nafion using dissipative particle dynamics (DPD) is modified to describe sulfonated Diels-Alder poly(phenylene) (SDAPP) polymers. The model includes a proton-hopping mechanism similar to the Grotthuss mechanism. The intramolecular parameters for SDAPP are derived from atomistic molecular dynamics (MD) simulation using the iterative Boltzmann inversion. The polymer radii of gyration, domain morphologies, and cluster distributions obtained from our DPD model are in good agreement with previous atomistic MD simulations. As found in the atomistic simulations, the DPD simulations predict that the SDAPP nanophase separates into hydrophobic polymer domains and hydrophilic domains that percolate through the system at sufficiently high sulfonation and hydration levels. Increasing sulfonation and/or hydration leads to larger proton and water diffusion constants, in agreement with experimental measurements in SDAPP. In the DPD simulations, the proton hopping (Grotthuss) mechanism becomes important as sulfonation and hydration increase, in qualitative agreement with experiment. The turning on of the hopping mechanism also roughly correlates with the point at which the DPD simulations exhibit clear percolated, hydrophilic domains, demonstrating the important effects of morphology on proton transport.}, number={10}, journal={JOURNAL OF CHEMICAL PHYSICS}, author={Clark, Jennifer A. and Santiso, Erik E. and Frischknecht, Amalie L.}, year={2019}, month={Sep} }
 @article{mishra_li_li_santiso_2019, title={Oxygen Vacancy Creation Energy in Mn-Containing Perovskites: An Effective Indicator for Chemical Looping with Oxygen Uncoupling}, volume={31}, ISSN={["1520-5002"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85061650487&partnerID=MN8TOARS}, DOI={10.1021/acs.chemmater.8b03187}, abstractNote={Chemical looping with oxygen uncoupling (CLOU) is a novel process for carbon dioxide capture from coal combustion. Designing a metal oxide oxygen carrier with suitable oxygen release and uptake (redox) properties represents one of the most critical aspects for CLOU. The current work aims to correlate oxygen vacancy creation energy of metal oxide oxygen carriers with their redox properties. Oxygen vacancy creation energies of CaMnO3−δ, Ca0.75Sr0.25MnO3−δ, CaMn0.75Fe0.25O3−δ, and BaMnO3−δ were determined through density functional theory (DFT) calculations. The effect of the Hubbard U correction on the ground state magnetic configurations and vacancy creation energies was investigated, along with the effect of lattice oxygen coordination environment. It was determined that Hubbard U only slightly changes the relative differences in vacancy creation energies between the Mn-containing perovskites investigated. Therefore, ranking of oxygen vacancy creation energies among the various oxides can be determined us...}, number={3}, journal={CHEMISTRY OF MATERIALS}, author={Mishra, Amit and Li, Tianyang and Li, Fanxing and Santiso, Erik E.}, year={2019}, month={Feb}, pages={689–698} }
 @article{tilly_pervaje_inglefield_santiso_spontak_khan_2019, title={Spectroscopic and Rheological Cross-Analysis of Polyester Polyol Cure Behavior: Role of Polyester Secondary Hydroxyl Content}, volume={4}, ISSN={["2470-1343"]}, url={https://doi.org/10.1021/acsomega.8b02766}, DOI={10.1021/acsomega.8b02766}, abstractNote={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.}, number={1}, journal={ACS OMEGA}, publisher={American Chemical Society (ACS)}, author={Tilly, Joseph C. and Pervaje, Amulya K. and Inglefield, David L. and Santiso, Erik E. and Spontak, Richard J. and Khan, Saad A.}, year={2019}, month={Jan}, pages={932–939} }
 @article{liu_cao_kulkarni_wood_santiso_2019, title={Understanding Polymorph Selection of Sulfamerazine in Solution}, volume={19}, ISSN={["1528-7505"]}, DOI={10.1021/acs.cgd.9b00576}, abstractNote={Polymorphism can have a significant impact on important physical and chemical properties of pharmaceutical products. Empirical screening of polymorphs by using different solvent systems is often la...}, number={12}, journal={CRYSTAL GROWTH & DESIGN}, author={Liu, Chengxiang and Cao, Fengjuan and Kulkarni, Samir A. and Wood, Geoffrey P. F. and Santiso, Erik E.}, year={2019}, month={Dec}, pages={6925–6934} }
 @article{king_theofanis_lemaire_santiso_parsons_2018, title={Ab initio analysis of nucleation reactions during tungsten atomic layer deposition on Si(100) and W(110) substrates}, volume={36}, ISSN={["1520-8559"]}, DOI={10.1116/1.5044740}, abstractNote={Novel insight into the mechanisms that govern nucleation during tungsten atomic layer deposition is presented through a detailed analysis using density functional theory. Using the calculated energetics, the authors suggest the most probable series of reactions that lead to monolayer formation on desired growth surfaces, Si(100) and W(110), during sequential doses of WF6 and SiH4. From this analysis, they conclude that a relatively high-energy barrier exists for initial nucleation of WF6 on a silicon substrate; therefore, the system is limited to physical adsorption and is only capable of accessing nucleation pathways once the reaction barrier is energetically accessible. During early doses of WF6, the initial silicon surface acts as the reductant. Results from this half-reaction provide support for the noncoalesced growth of initial W layers since nucleation is shown to require a 2:1 ratio of silicon to WF6. In addition, the release of H2 is significantly favored over HF production leading to the formation of fluorine-contaminated silicon sites; etching of these sites is heavily supported by the absence of fluorine observed in experimentally deposited films as well as the high volatility of silicon-subfluorides. In the second half-reaction, SiH4 plays the multipurpose role of stripping fluorine atoms from W, displacing any adsorbed hydrogen atoms, and depositing a silicon-hydride layer. Saturation of the previously formed W layer with silicon-hydrides is a crucial step in depositing the consecutive layer since these surface species act as the reductants in the succeeding dose of WF6. The SiH4 half-reaction reaches a limit when all fluorine atoms are removed as silicon-subfluorides (SiFxHy) and tungsten sites are terminated with silicon-hydrides. The WF6 dose reaches a limit in early doses when the reductant, i.e., the surface, becomes blocked due to the formation of a planar network of fluorine-containing tungsten intermediates and in later cycles when the reductant, i.e., adsorbed silicon-hydrides, is etched entirely from the surface. Overall, the calculated energetics indicate that WFxHy, SiFx, and H2 molecules are the most probable by-products released during the ALD process. Results from this work contribute significantly to the fundamental understanding of atomic layer growth of tungsten using silicon species as reducing agents and may be used as a template for analyzing novel ALD processes.}, number={6}, journal={JOURNAL OF VACUUM SCIENCE & TECHNOLOGY A}, author={King, Mariah J. and Theofanis, Patrick L. and Lemaire, Paul C. and Santiso, Erik E. and Parsons, Gregory N.}, year={2018}, month={Nov} }
 @article{clark_santiso_2018, title={Carbon Sequestration through CO2 Foam-Enhanced Oil Recovery: A Green Chemistry Perspective}, volume={4}, ISSN={["2096-0026"]}, DOI={10.1016/j.eng.2018.05.006}, abstractNote={Enhanced oil recovery (EOR) via carbon dioxide (CO2) flooding has received a considerable amount of attention as an economically feasible method for carbon sequestration, with many recent studies focusing on developing enhanced CO2 foaming additives. However, the potential long-term environmental effects of these additives in the event of leakage are poorly understood and, given the amount of additives injected in a typical CO2 EOR operation, could be far-reaching. This paper presents a summary of recent developments in surfactant and surfactant/nanoparticle-based CO2 foaming systems, with an emphasis on the possible environmental impacts of CO2 foam leakage. Most of the surfactants studied are unlikely to degrade under reservoir conditions, and their release can cause major negative impacts on wildlife. With recent advances in the use of additives (e.g., nonionic surfactants, nanoparticles, and other chemicals) the use of harsh anionic surfactants may no longer be warranted. This paper discusses recent advances in producing foaming systems, and highlights possible strategies to develop environmentally friendly CO2 EOR methods.}, number={3}, journal={ENGINEERING}, author={Clark, Jennifer A. and Santiso, Erik E.}, year={2018}, month={Jun}, pages={336–342} }
 @article{shi_gu_shen_srivastava_santiso_gubbins_2018, title={High-density equation of state for a two-dimensional Lennard-Jones solid}, volume={148}, ISSN={0021-9606 1089-7690}, url={http://dx.doi.org/10.1063/1.5029488}, DOI={10.1063/1.5029488}, abstractNote={We present a new equation of state for a two-dimensional Lennard-Jones (2D LJ-EOS) solid at high densities, ρ2D*≥0.9. The new 2D LJ-EOS is of analytic form, consisting of a zero-temperature contribution and vibrational contributions up to and including the second anharmonic term. A detailed analysis of all contributing terms is performed. Comparisons between the 2D LJ-EOS and Monte Carlo simulation results show that the 2D LJ-EOS is very accurate over a wide range of temperatures in the high-density region. A criterion to find the temperature range over which the 2D LJ-EOS is applicable at a certain density is derived. We also demonstrate an application of the equation of state to predict an effective tangential pressure for the adsorbed contact layer near the wall in a slit-pore system. Tangential pressures predicted by this “2D-route” are found to be in qualitative agreement with those found by the more traditional virial route of Irving and Kirkwood.}, number={17}, journal={The Journal of Chemical Physics}, publisher={AIP Publishing}, author={Shi, Kaihang and Gu, Kai and Shen, Yifan and Srivastava, Deepti and Santiso, Erik E. and Gubbins, Keith E.}, year={2018}, month={May}, pages={174505} }
 @article{pervaje_tilly_inglefield_spontak_khan_santiso_2018, title={Modeling Polymer Glass Transition Properties from Empirical Monomer Data with the SAFT-gamma Mie Force Field}, volume={51}, DOI={10.1021/acs.macromol.8b01734}, abstractNote={We apply a recently developed coarse-graining method to build models for polyester polyols, versatile polymers with applications in coatings, by combining models for the component monomers. This strategy employs the corresponding states correlation to the group-contribution SAFT-γ Mie equation of state [Mejia, A.; et al. Ind. Eng. Chem. Res. 2014, 53, 4131–4141] to obtain force-field parameters for the constituent monomer species. Results from simulations agree favorably with experimental values of mass density, glass transition temperature (Tg), and specific heat capacity change at Tg. Further simulations over a range of Mie parameters and polymer chemical compositions yield a correlation that relates the parameters directly to Tg. This correlation is validated by experimental data and can be used as a predictive tool within the tested parameter space to expedite the design of these coating materials.}, number={23}, journal={MACROMOLECULES}, author={Pervaje, Amulya K. and Tilly, Joseph C. and Inglefield, David L. and Spontak, Richard and Khan, Saad and Santiso, Erik E.}, year={2018}, pages={9526–9537} }
 @article{liu_wood_santiso_2018, title={Modelling nucleation from solution with the string method in the osmotic ensemble}, volume={116}, ISSN={["1362-3028"]}, DOI={10.1080/00268976.2018.1482016}, abstractNote={ABSTRACT Direct molecular simulation of nucleation from solution is a challenging task, requiring a combination of ‘rare events’ techniques and methods to control the chemical potential. Rare event methods usually keep the total number of molecules fixed, resulting in artificial free energy profiles due to the depletion of solute from the solution phase. In order to address this issue, we present a new approach that uses the string method in collective variables in the osmotic ensemble to obtain minimum free energy pathways for nucleation at constant supersaturation. Our method does not require using an explicit reservoir of solute molecules, or making additional assumptions about the activity coefficients in the solution. We apply the new method to the crystallisation of sulfamerazine from acetonitrile and methanol solutions, and compare the resulting potential of mean force profiles to those obtained using analytical corrections previously employed in the literature. GRAPHICAL ABSTRACT}, number={21-22}, journal={MOLECULAR PHYSICS}, author={Liu, Chengxiang and Wood, Geoffrey P. F. and Santiso, Erik E.}, year={2018}, pages={2998–3007} }
 @article{gubbins_gu_huang_long_mansell_santiso_shi_sliwinska-bartkowiak_srivastava_2018, title={Surface-Driven High-Pressure Processing}, volume={4}, ISSN={["2096-0026"]}, DOI={10.1016/j.eng.2018.05.004}, abstractNote={The application of high pressure favors many chemical processes, providing higher yields or improved rates in chemical reactions and improved solvent power in separation processes, and allowing activation barriers to be overcome through the increase in molecular energy and molecular collision rates. High pressures—up to millions of bars using diamond anvil cells—can be achieved in the laboratory, and lead to many new routes for chemical synthesis and the synthesis of new materials with desirable thermodynamic, transport, and electronic properties. On the industrial scale, however, high-pressure processing is currently limited by the cost of compression and by materials limitations, so that few industrial processes are carried out at pressures above 25 MPa. An alternative approach to high-pressure processing is proposed here, in which very high local pressures are generated using the surface-driven interactions from a solid substrate. Recent experiments and molecular simulations show that such interactions can lead to local pressures as high as tens of thousands of bars (1 bar = 1 × 105 Pa), and even millions of bars in some cases. Since the active high-pressure processing zone is inhomogeneous, the pressure is different in different directions. In many cases, it is the pressure in the direction parallel to the surface of the substrate (the tangential pressure) that is most greatly enhanced. This pressure is exerted on the molecules to be processed, but not on the solid substrate or the containing vessel. Current knowledge of such pressure enhancement is reviewed, and the possibility of an alternative route to high-pressure processing based on surface-driven forces is discussed. Such surface-driven high-pressure processing would have the advantage of achieving much higher pressures than are possible with traditional bulk-phase processing, since it eliminates the need for mechanical compression. Moreover, no increased pressure is exerted on the containing vessel for the process, thus eliminating concerns about materials failure.}, number={3}, journal={ENGINEERING}, author={Gubbins, Keith E. and Gu, Kai and Huang, Liangliang and Long, Yun and Mansell, J. Matthew and Santiso, Erik E. and Shi, Kaihang and Sliwinska-Bartkowiak, Malgorzata and Srivastava, Deepti}, year={2018}, month={Jun}, pages={311–320} }
 @article{srivastava_santiso_gubbins_barroso da silva_2017, title={Computationally Mapping pKa Shifts Due to the Presence of a Polyelectrolyte Chain around Whey Proteins}, volume={33}, ISSN={0743-7463 1520-5827}, url={http://dx.doi.org/10.1021/acs.langmuir.7b02271}, DOI={10.1021/acs.langmuir.7b02271}, abstractNote={Experimental studies have shown the formation of soluble complexes in the pure repulsive Coulombic regime even when the net charges of the protein and the polyelectrolyte have the same sign ( De Kruif et al. Curr. Opin. Colloid Interface Sci. 2004 , 9 , 340 ; De Vries et al. J. Chem. Phys. 2003 , 118 , 4649 ; Grymonpre et al. Biomacromolecules 2001 , 2 , 422 ; Hattori et al. Langmuir 2000 , 16 , 9738 ). This attractive phenomenon has often been described as "complexation on the wrong side of pI". While one theory assumes the existence of "charged patches" on the protein surface from ion-dipole interactions, thus allowing a polyelectrolyte to bind to an oppositely heterogeneous charged protein region, another theoretical view considers the induced-charge interactions to be the dominant factor in these complexations. This charge regulation mechanism can be described by proton fluctuations resulting from mutual rearrangements of the distributions of the charged groups, due to perturbations of the acid-base equilibrium. Using constant-pH Monte Carlo simulations and several quantitative and visual analysis tools, we investigate the significance of each of these interactions for two whey proteins, α-lactalbumin (α-LA) and lysozyme (LYZ). Through physical chemistry parameters, free energies of interactions, and the mapping of amino acid pKa shifts and polyelectrolyte trajectories, we show the charge regulation mechanism to be the most important contributor in protein-polyelectrolyte complexation regardless of pH, dipole moment, and protein capacitance in a low salt regime.}, number={42}, journal={Langmuir}, publisher={American Chemical Society (ACS)}, author={Srivastava, Deepti and Santiso, Erik and Gubbins, Keith and Barroso da Silva, Fernando Luís}, year={2017}, month={Sep}, pages={11417–11428} }
 @article{j. weiser_e. santiso_2017, title={Molecular modeling studies of peptoid polymers}, volume={4}, ISSN={2372-0484}, url={http://dx.doi.org/10.3934/matersci.2017.5.1029}, DOI={10.3934/matersci.2017.5.1029}, abstractNote={Peptoids, or poly-N-substituted glycines, are synthetic polymers composed of a protein backbone with side chains attached to the nitrogen atoms rather than the α-carbons. Peptoids are biomimetic and protease resistant and have been explored for a variety of applications including pharmaceuticals and coatings. They are also foldamer-type materials that can adopt diverse structures based on the sequences of their side chains. Design of new peptoid sequences may lead to the creation of many interesting materials. Given the large number of possible peptoid side chains, computer models predicting peptoid structure-side chain relationships are desirable. In this paper, we provide a survey of computational efforts to understand and predict peptoid structures. We describe simulations at several levels of theory, along with their assumptions and results. We also discuss some challenges for future peptoid computational research.}, number={5}, journal={AIMS Materials Science}, publisher={American Institute of Mathematical Sciences (AIMS)}, author={J. Weiser, Laura and E. Santiso, Erik}, year={2017}, pages={1029–1051} }
 @article{srivastava_santiso_gubbins_2017, title={Pressure Enhancement in Confined Fluids: Effect of Molecular Shape and Fluid–Wall Interactions}, volume={33}, ISSN={0743-7463 1520-5827}, url={http://dx.doi.org/10.1021/acs.langmuir.7b02260}, DOI={10.1021/acs.langmuir.7b02260}, abstractNote={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.}, number={42}, journal={Langmuir}, publisher={American Chemical Society (ACS)}, author={Srivastava, Deepti and Santiso, Erik E. and Gubbins, Keith E.}, year={2017}, month={Oct}, pages={11231–11245} }
 @article{srivastava_turner_santiso_gubbins_2017, title={The Nitric Oxide Dimer Reaction in Carbon Nanopores}, volume={122}, ISSN={1520-6106 1520-5207}, url={http://dx.doi.org/10.1021/acs.jpcb.7b10876}, DOI={10.1021/acs.jpcb.7b10876}, abstractNote={When confined within nanoporous carbons (activated carbon fibers or carbon nanotubes) having pore widths of about 1 nm, nitric oxide is found to react completely to form the dimer, (NO)2, even though almost no dimers are present in the bulk gas phase in equilibrium with the pore phase. Moreover, the yield of dimer is unchanged upon varying the temperature over the range studied in the experiments. Earlier molecular simulation studies showed a significant increase in dimer formation in carbon nanopores, but the dimer yield was considerably less than that found in the experiments, and decreased rapidly as the temperature was raised. Here, we report an ab initio and molecular simulation study of this reaction in both slit-shaped pores and single-walled carbon nanotubes. The ab initio calculations show that the nitric oxide dimer forms a weak chemical bond with the carbon, and the bonding energy is more than 20 times stronger than the van der Waals energy assumed in the previous studies. When this is accounted for, the predicted dimer yield is in good agreement with the experimental values, as is its temperature dependence. We also report results for the pressure tensor components for this confined reactive mixture. Local tangential pressures near the pore walls are as high as millions of bar, reflecting the strong nanoscale forces.}, number={13}, journal={The Journal of Physical Chemistry B}, publisher={American Chemical Society (ACS)}, author={Srivastava, Deepti and Turner, C. Heath and Santiso, Erik E. and Gubbins, Keith E.}, year={2017}, month={Dec}, pages={3604–3614} }
 @article{wojnilowicz_tortora_bobay_santiso_caruso_micheli_venanzi_menegatti_cavalieri_2016, title={A combined approach for predicting the cytotoxic effect of drug-nanoaggregates}, volume={4}, ISSN={2050-750X 2050-7518}, url={http://dx.doi.org/10.1039/c6tb02105k}, DOI={10.1039/c6tb02105k}, abstractNote={Polymer carriers induce assembly of drugs into nanoaggregates and play a role in tuning the architecture and bioactivity of drug nanoaggregates.}, number={40}, journal={Journal of Materials Chemistry B}, publisher={Royal Society of Chemistry (RSC)}, author={Wojnilowicz, M. and Tortora, M. and Bobay, B. G. and Santiso, E. and Caruso, M. and Micheli, L. and Venanzi, M. and Menegatti, S. and Cavalieri, F.}, year={2016}, pages={6516–6523} }
 @article{he_shen_hung_santiso_2016, title={Heterogeneous nucleation from a supercooled ionic liquid on a carbon surface}, volume={145}, ISSN={["1089-7690"]}, DOI={10.1063/1.4963336}, abstractNote={Classical molecular dynamics simulations were used to study the nucleation of the crystal phase of the ionic liquid [dmim+][Cl−] from its supercooled liquid phase, both in the bulk and in contact with a graphitic surface of D = 3 nm. By combining the string method in collective variables [Maragliano et al., J. Chem. Phys. 125, 024106 (2006)], with Markovian milestoning with Voronoi tessellations [Maragliano et al., J. Chem. Theory Comput. 5, 2589–2594 (2009)] and order parameters for molecular crystals [Santiso and Trout, J. Chem. Phys. 134, 064109 (2011)], we computed minimum free energy paths, the approximate size of the critical nucleus, the free energy barrier, and the rates involved in these nucleation processes. For homogeneous nucleation, the subcooled liquid phase has to overcome a free energy barrier of ∼85 kcal/mol to form a critical nucleus of size ∼3.6 nm, which then grows into the monoclinic crystal phase. This free energy barrier becomes about 42% smaller (∼49 kcal/mol) when the subcooled liquid phase is in contact with a graphitic disk, and the critical nucleus formed is about 17% smaller (∼3.0 nm) than the one observed for homogeneous nucleation. The crystal formed in the heterogeneous nucleation scenario has a structure that is similar to that of the bulk crystal, with the exception of the layers of ions next to the graphene surface, which have larger local density and the cations lie with their imidazolium rings parallel to the graphitic surface. The critical nucleus forms near the graphene surface separated only by these layers of ions. The heterogeneous nucleation rate (∼4.8 × 1011 cm−3 s−1) is about one order of magnitude faster than the homogeneous rate (∼6.6 × 1010 cm−3 s−1). The computed free energy barriers and nucleation rates are in reasonable agreement with experimental and simulation values obtained for the homogeneous and heterogeneous nucleation of other systems (ice, urea, Lennard-Jones spheres, and oxide glasses).}, number={21}, journal={JOURNAL OF CHEMICAL PHYSICS}, author={He, Xiaoxia and Shen, Yan and Hung, Francisco R. and Santiso, Erik E.}, year={2016}, month={Dec} }
 @article{he_shen_hung_santiso_2016, title={Homogeneous Nucleation of [dmim(+)][Cl-] from its Supercooled Liquid Phase: A Molecular Simulation Study}, ISBN={["978-981-10-1126-9"]}, ISSN={["2364-5083"]}, DOI={10.1007/978-981-10-1128-3_7}, abstractNote={We have used molecular simulations to study the homogeneous nucleation of the ionic liquid [dmim+][Cl−] from its bulk supercooled liquid at 340 K. Our combination of methods include the string method in collective variables (Maragliano et al., J. Chem. Phys. 125:024106, 2006), Markovian milestoning with Voronoi tessellations (Maragliano et al J Chem Theory Comput 5:2589, 2009), and order parameters for molecular crystals (Santiso and Trout J Chem Phys 134:064109, 2011). The minimum free energy path, the approximate size of the critical nucleus, the free energy barrier and the rates involved in the homogeneous nucleation process were determined from our simulations. Our results suggest that the subcooled liquid (58 K of supercooling) has to overcome a free energy barrier of ~85 kcal/mol, and has to form a critical nucleus of size ~3.4 nm; this nucleus then grows to form the monoclinic crystal phase. A nucleation rate of 6.6 × 1010 cm−3 s−1 was determined from our calculations, which agrees with values observed in experiments and simulations of homogeneous nucleation of subcooled water.}, journal={FOUNDATIONS OF MOLECULAR MODELING AND SIMULATION}, author={He, Xiaoxia and Shen, Yan and Hung, Francisco R. and Santiso, Erik E.}, year={2016}, pages={107–123} }
 @inbook{santiso_2016, title={Introduction to Bash Scripting}, ISBN={9781498745048 9781498745062}, url={http://dx.doi.org/10.1201/9781315382395-5}, DOI={10.1201/9781315382395-5}, booktitle={Introduction to Scientific and Technical Computing}, publisher={CRC Press}, author={Santiso, E.E.}, editor={Willmore, F. and Jankowski, E. and Colina, C.Editors}, year={2016}, month={Aug}, pages={55–69} }
 @inbook{santiso_2016, title={Operating Systems Overview}, ISBN={9781498745048 9781498745062}, url={http://dx.doi.org/10.1201/9781315382395-2}, DOI={10.1201/9781315382395-2}, booktitle={Introduction to Scientific and Technical Computing}, publisher={CRC Press}, author={Santiso, E.E.}, editor={Willmore, F. and Jankowski, E. and Colina, C.Editors}, year={2016}, month={Aug}, pages={1–29} }
 @article{mishra_galinsky_he_santiso_li_2016, title={Perovskite-structured AMn(x)B(1-x)O(3) (A = Ca or Ba; B = Fe or Ni) redox catalysts for partial oxidation of methane}, volume={6}, ISSN={["2044-4761"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84975156629&partnerID=MN8TOARS}, DOI={10.1039/c5cy02186c}, abstractNote={High oxygen carrying capacity, lack of loosely bound lattice oxygen, and preferential surface segregation of Ba make BaMnxB1−xO3 (B = Ni or Fe) based redox catalysts suitable for chemical looping reforming of methane with high syngas yield and coke resistance.}, number={12}, journal={CATALYSIS SCIENCE & TECHNOLOGY}, author={Mishra, Amit and Galinsky, Nathan and He, Feng and Santiso, Erik E. and Li, Fanxing}, year={2016}, pages={4535–4544} }
 @article{santiso_trout_2015, title={A general method for molecular modeling of nucleation from the melt}, volume={143}, ISSN={["1089-7690"]}, DOI={10.1063/1.4934356}, abstractNote={Crystallization is one of the fundamental phase transition processes, and it is also important practically, for example, in the chemical, food, and pharmaceutical industries. Despite its importance, however, our basic understanding of crystallization, and especially crystal nucleation, at the molecular level is still incomplete. In this work, we present a general molecular simulation approach that can be used to investigate the nucleation of crystals from a subcooled liquid. Our method combines a previously proposed general method to construct structure-based order parameters [E. E. Santiso and B. L. Trout, J. Chem. Phys. 134, 064109 (2011)] with the string method in collective variables [L. Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] to obtain a minimum free energy path connecting the liquid and solid basins. We then use Markovian milestoning with Voronoi tessellations [E. Vanden-Eijnden and M. Venturoli, J. Chem. Phys. 130, 194101 (2009); L. Maragliano et al., J. Chem. Theory Comput. 5, 2589–2594 (2009)] to obtain the free energy profile along the path and the nucleation kinetics. We illustrate the application of this method to the nucleation of Benzene-I crystals from the melt, and compare the results to those previously found using transition path sampling [M. Shah et al., J. Phys. Chem. B 115, 10400–10412 (2011)].}, number={17}, journal={JOURNAL OF CHEMICAL PHYSICS}, author={Santiso, Erik E. and Trout, Bernhardt L.}, year={2015}, month={Nov} }
 @article{herdes_santiso_james_eastoe_muller_2015, title={Modelling the interfacial behaviour of dilute light-switching surfactant solutions}, volume={445}, DOI={10.1016/j.jcis.2014.12.040}, abstractNote={The direct molecular modelling of an aqueous surfactant system at concentrations below the critical micelle concentration (pre-cmc) conditions is unviable in terms of the presently available computational power. Here, we present an alternative that combines experimental information with tractable simulations to interrogate the surface tension changes with composition and the structural behaviour of surfactants at the water-air interface. The methodology is based on the expression of the surface tension as a function of the surfactant surface excess, both in the experiments and in the simulations, allowing direct comparisons to be made. As a proof-of-concept a coarse-grained model of a light switching non-ionic surfactant bearing a photosensitive azobenzene group is considered at the air-water interface at 298 K. Coarse-grained molecular dynamic simulations are detailed based on the use of the SAFT force field with parameters tuned specifically for this purpose. An excellent agreement is obtained between the simulation predictions and experimental observations; furthermore, the molecular model allows the rationalization of the macroscopic behaviour in terms of the different conformations of the cis and trans surfactants at the surface.}, journal={Journal of Colloid and Interface Science}, author={Herdes, C. and Santiso, Erik E. and James, C. and Eastoe, J. and Muller, E. A.}, year={2015}, pages={16–23} }
 @article{he_shen_hung_santiso_2015, title={Molecular simulation of homogeneous nucleation of crystals of an ionic liquid from the melt}, volume={143}, ISSN={["1089-7690"]}, DOI={10.1063/1.4931654}, abstractNote={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 × 1010 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.}, number={12}, journal={JOURNAL OF CHEMICAL PHYSICS}, author={He, Xiaoxia and Shen, Yan and Hung, Francisco R. and Santiso, Erik E.}, year={2015}, month={Sep} }
 @article{chopade_sarma_santiso_simpson_fry_yurttas_biermann_chen_trout_myerson_et al._2015, title={On the connection between nonmonotonic taste behavior and molecular conformation in solution: The case of rebaudioside-A}, volume={143}, ISSN={0021-9606 1089-7690}, url={http://dx.doi.org/10.1063/1.4937946}, DOI={10.1063/1.4937946}, abstractNote={The diterpene steviol glycoside, rebaudioside A, is a natural high potency non-caloric sweetener extracted from the leaves of Stevia rebaudiana. This compound shows a parabolic change in sweet taste intensity with temperature which contrasts with the general finding for other synthetic or natural sweeteners whose sweet taste increases with temperature. The nonmonotonic taste behavior was determined by sensory analysis using large taste panels. The conformational landscape of rebaudioside A was established at a range of temperatures by means of nuclear magnetic resonance and molecular dynamics simulation. The relationship between various conformations and the observed sweetness of rebaudioside A is described.}, number={24}, journal={The Journal of Chemical Physics}, publisher={AIP Publishing}, author={Chopade, Prashant D. and Sarma, Bipul and Santiso, Erik E. and Simpson, Jeffrey and Fry, John C. and Yurttas, Nese and Biermann, Kari L. and Chen, Jie and Trout, Bernhardt L. and Myerson, Allan S. and et al.}, year={2015}, month={Dec}, pages={244301} }
 @article{sun_sun_price_hughes_ter horst_veesler_lewtas_myerson_pan_coquerel_et al._2015, title={Solvent and additive interactions as determinants in the nucleation pathway: general discussion}, volume={179}, ISSN={1359-6640 1364-5498}, url={http://dx.doi.org/10.1039/c5fd90038g}, DOI={10.1039/c5fd90038g}, abstractNote={Sarah Price opened a general discussion of the paper by Sven Schroeder: I have been generating the thermodynamically plausible crystal structures of organic molecules for many years, and back in 2004 we did a crystal structure prediction (CSP) study on imidazole1 and found that it was relatively straightforward. Following your paper, we have reclassified the low energy structures according to the tilt within the hydrogen-bonded chain and the relative direction of the chains. Although the observed structure was the global minimum, two other structures with a displacement of otherwise identical layers are very close in energy. Do you think that if imidazole had crystallised in one of these alternative structures it would be distinguishable by NEXAFS? This would be a very sensitive test of whether NEXAFS combined with CSP could be used in characterising crystal structures.}, journal={Faraday Discussions}, publisher={Royal Society of Chemistry (RSC)}, author={Sun, Changquan Calvin and Sun, Wenhao and Price, Sarah and Hughes, Colan and Ter Horst, Joop and Veesler, Stéphane and Lewtas, Ken and Myerson, Allan and Pan, Haihua and Coquerel, Gerard and et al.}, year={2015}, pages={383–420} }
 @article{santiso_2014, title={Understanding the effect of adsorption on activated processes using molecular theory and simulation}, volume={40}, ISSN={["1029-0435"]}, DOI={10.1080/08927022.2013.840903}, abstractNote={Most chemical reactions of practical interest are catalysed by porous materials, which can improve reaction rates and equilibrium yields through various interactions with the reacting mixture. Nucleation, another kind of activated process, can also be substantially affected by the presence of a surface or by the confinement within a porous material. There are several different effects that can influence such activated processes, such as the reduced dimensionality of the porous space or the adsorbed layer, physical or chemical interactions with the adsorbate and transport limitations. This paper presents a unifying perspective on the influence of each of these effects on chemical reactions and crystallisation processes through the discussion of selected examples from the literature. The common aspects and the differences between these two different kinds of activated processes are considered in the context of each effect. Finally, some of the important issues that could benefit from the development of new molecular simulations methods are discussed.}, number={7-9}, journal={MOLECULAR SIMULATION}, author={Santiso, Erik E.}, year={2014}, month={Aug}, pages={664–677} }
 @article{santiso_musolino_trout_2013, title={Design of Linear Ligands for Selective Separation Using a Genetic Algorithm Applied to Molecular Architecture}, volume={53}, ISSN={1549-9596 1549-960X}, url={http://dx.doi.org/10.1021/ci400043q}, DOI={10.1021/ci400043q}, abstractNote={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.}, number={7}, journal={Journal of Chemical Information and Modeling}, publisher={American Chemical Society (ACS)}, author={Santiso, Erik E. and Musolino, Nicholas and Trout, Bernhardt L.}, year={2013}, month={Jul}, pages={1638–1660} }
 @article{santiso_herdes_mueller_2013, title={On the Calculation of Solid-Fluid Contact Angles from Molecular Dynamics}, volume={15}, ISSN={["1099-4300"]}, DOI={10.3390/e15093734}, abstractNote={A methodology for the determination of the solid-fluid contact angle, to be employed within molecular dynamics (MD) simulations, is developed and systematically applied. The calculation of the contact angle of a fluid drop on a given surface, averaged over an equilibrated MD trajectory, is divided in three main steps: (i) the determination of the fluid molecules that constitute the interface, (ii) the treatment of the interfacial molecules as a point cloud data set to define a geometric surface, using surface meshing techniques to compute the surface normals from the mesh, (iii) the collection and averaging of the interface normals collected from the post-processing of the MD trajectory. The average vector thus found is used to calculate the Cassie contact angle (i.e., the arccosine of the averaged normal z-component). As an example we explore the effect of the size of a drop of water on the observed solid-fluid contact angle. A single coarse- grained bead representing two water molecules and parameterized using the SAFT-γ Mie equation of state (EoS) is employed, meanwhile the solid surfaces are mimicked using integrated potentials. The contact angle is seen to be a strong function of the system size for small nano-droplets. The thermodynamic limit, corresponding to the infinite size (macroscopic) drop is only truly recovered when using an excess of half a million water coarse-grained beads and/or a drop radius of over 26 nm.}, number={9}, journal={ENTROPY}, author={Santiso, Erik E. and Herdes, Carmelo and Mueller, Erich A.}, year={2013}, month={Sep}, pages={3734–3745} }
 @article{santiso_trout_2011, title={A general set of order parameters for molecular crystals}, volume={134}, ISSN={["1089-7690"]}, DOI={10.1063/1.3548889}, abstractNote={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.}, number={6}, journal={JOURNAL OF CHEMICAL PHYSICS}, author={Santiso, Erik E. and Trout, Bernhardt L.}, year={2011}, month={Feb} }
 @article{chunsrivirot_santiso_trout_2011, title={Binding affinity of a small molecule to an amorphous polymer in a solvent. Part 2: Preferential binding to local sites on a surface}, volume={27}, DOI={10.1021/la202593u}, abstractNote={Crystallization, a separation and purification process, is commonly used to produce a wide range of materials in various industries, and it usually begins with heterogeneous nucleation on a foreign surface in industrial practice and most other circumstances. Recent studies show that amorphous polymeric substrates are useful in controlling crystallization and selectively producing pharmaceutical polymorphs. In our previous publication, we investigated the possible correlation of the binding affinity of one molecule to key binding sites (local binding), and the possibility of using this binding affinity to guide the selection of polymers promoting heterogeneous nucleation. The studied systems were aspirin binding to four nonporous cross-linked polymers in ethanol-water 38 v% mixture. Cross-linked with divinylbenzene (DVB), these polymers were poly(4-acryloylmorpholine) (PAM), poly(2-carboxyethyl acrylate) (PCEA), poly(4-hydroxylbutyl acrylate) (PHBA), and polystyrene (PS). We discovered that the trend of the magnitudes of the average free energies of binding to the best sites is very similar to that of heterogeneous nucleation activities. This Article aims to investigate whether or not local binding to key sites is the important variable to describe heterogeneous nucleation as opposed to the overall/average binding affinity of molecules to a surface, and to investigate the possibility of using the overall binding affinity to guide the selection of polymers. We used the polymer surfaces generated from our previous study to calculate the overall binding affinity of aspirin molecules to the surface as measured by the preferential interaction coefficients of aspirin (1 m) to these polymers. We discovered that the trend of the average preferential interaction coefficients does not correlate as well to that of heterogeneous nucleation activities as the free energies of binding to the best sites. We also computed the average numbers of aspirin molecules associated with the areas of the surfaces' best binding sites and found that they correlate better to heterogeneous nucleation activities than the average preferential interaction coefficients. These results further support that local binding is indicative of heterogeneous nucleation. Moreover, we found a weak trend of the distance order parameters of the aspirin molecules to be similar that of heterogeneous nucleation activities. Our results from the two-part study suggest the importance of local binding to heterogeneous nucleation as well as the possibility of using the binding affinity to the local area (the free energy of binding to the best site and the number of nucleating molecules associated with the area of the best binding site) and the distance order parameters to guide the selection of polymers.}, number={20}, journal={Langmuir}, author={Chunsrivirot, S. and Santiso, Erik E. and Trout, B.L.}, year={2011}, pages={12396–12404} }
 @article{shah_santiso_trout_2011, title={Computer Simulations of Homogeneous Nucleation of Benzene from the Melt}, volume={115}, ISSN={["1520-6106"]}, DOI={10.1021/jp203550t}, abstractNote={Nucleation is the key step in crystallization by which the molecules (or atoms or ions) aggregate together, find the right relative orientations, and start to grow to form the final crystal structure. Since nucleation is an activated step involving a large gap in time scales between molecular motions and the nucleation event itself, nucleation must be studied using rare events methods. We employ a technique developed previously in our group known as aimless shooting [Peters, B.; Trout, B. L. J. Chem. Phys., 2006, 125, 054108], which is based on transition path sampling, to generate reactive trajectories between the disordered and ordered phases of benzene. Using the likelihood maximization algorithm, we analyze the aimless shooting trajectories to identify the key order parameters or collective variables to describe the reaction coordinate for the nucleation of benzene from the melt. We find that the local bond orientation and local relative orientation order parameters are the most important collective variables in describing the reaction coordinate for homogeneous nucleation from the melt, as compared to cluster size and space-averaged order parameters. This study also demonstrates the utility of recently developed order parameters for molecular crystals [Santiso, E. E.; Trout, B. L. J. Chem. Phys., 2011, 134, 064109].}, number={35}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Shah, Manas and Santiso, Erik E. and Trout, Bernhardt L.}, year={2011}, month={Sep}, pages={10400–10412} }
 @article{centrone_santiso_hatton_2011, title={Separation of Chemical Reaction Intermediates by Metal-Organic Frameworks}, volume={7}, ISSN={["1613-6829"]}, DOI={10.1002/smll.201100098}, abstractNote={Abstract}, number={16}, journal={SMALL}, author={Centrone, Andrea and Santiso, Erik E. and Hatton, T. Alan}, year={2011}, month={Aug}, pages={2356–2364} }
 @inbook{santiso_huang_gubbins_kostov_george_nardelli_2010, place={Valencia, CA}, title={Ab Initio Simulations of Chemical Reactions in Nanostructured Carbon Materials}, booktitle={Quantum Chemical Calculations of Surfaces and Interfaces of Materials}, publisher={American Scientific Publishers}, author={Santiso, E.E. and Huang, L. and Gubbins, K.E. and Kostov, M.K. and George, A.M. and Nardelli, M.B.}, editor={Basiuk, V.A. and Ugliengo, P.Editors}, year={2010} }
 @inbook{santiso_huang_gubbins_kostov_george_nardelli_2009, title={Ab initio simulations of chemical reactions in nanostructured carbon materials}, ISBN={1588831388}, booktitle={Quantum chemical calculations of surfaces and interfaces of materials}, publisher={Stevenson Ranch, Calif.: American Scientific Publishers,}, author={Santiso, E. E. and Huang, L. and Gubbins, K. E. and Kostov, M. K. and George, A. M. and Nardelli, M. B.}, editor={V. A. Basiuk and Ugliengo, P.Editors}, year={2009} }
 @article{paul_santiso_nardelli_2009, title={Sequestration and selective oxidation of carbon monoxide on graphene edges}, volume={21}, ISSN={["1361-648X"]}, DOI={10.1088/0953-8984/21/35/355008}, abstractNote={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.}, number={35}, journal={JOURNAL OF PHYSICS-CONDENSED MATTER}, author={Paul, Sujata and Santiso, Erik E. and Nardelli, Marco Buongiorno}, year={2009}, month={Sep} }
 @article{santiso_nardelli_gubbins_2008, title={A remarkable shape-catalytic effect of confinement on the rotational isomerization of small hydrocarbons}, volume={128}, ISSN={["1089-7690"]}, DOI={10.1063/1.2819238}, abstractNote={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 rotational isomerization of three four-membered hydrocarbons: n-butane, 1-butene, and 1,3-butadiene. Our results show that the interactions with the carbon walls cause a dramatic change on the potential energy surface for pore sizes comparable to the molecular dimensions. The porous material enhances or hinders reactions depending on how similar is the shape of the transition state to the shape of the confining material. The structure of the stable states and their equilibrium distributions are also drastically modified by confinement. Our results are consistent with a doubly exponential behavior of the reaction rates as a function of pore size, illustrating how the shape of a catalytic support can dramatically change the efficiency of a catalyst.}, number={3}, journal={JOURNAL OF CHEMICAL PHYSICS}, author={Santiso, Erik E. and Nardelli, Marco Buongiorno and Gubbins, Keith E.}, year={2008}, month={Jan} }
 @article{huang_santiso_nardelli_gubbins_2008, title={Catalytic role of carbons in methane decomposition for CO- and CO(2)-free hydrogen generation}, volume={128}, ISSN={["0021-9606"]}, DOI={10.1063/1.2931456}, abstractNote={Decomposition of methane is an environmentally attractive approach to CO- and CO2-free hydrogen production. Using first principles calculations at the density functional theory level, our studies demonstrate that the defective carbons can be used as catalysts for methane decomposition, without the need for other catalysts, such as transition metals or oxides, and the catalytic sites can be regenerated by the deposition of carbon decomposed from methane, to make the hydrogen production a continuous process. Additionally, since no other gases are produced in the process, the cost of CO2 sequestration and hydrogen purification from CO contamination will be dramatically reduced.}, number={21}, journal={JOURNAL OF CHEMICAL PHYSICS}, author={Huang, Liping and Santiso, Erik E. and Nardelli, Marco Buongiorno and Gubbins, Keith E.}, year={2008}, month={Jun} }
 @article{santiso_nardelli_gubbins_2008, title={Isomerization kinetics of small hydrocarbons in confinement}, volume={14}, ISSN={["1572-8757"]}, DOI={10.1007/s10450-007-9075-8}, number={2-3}, journal={ADSORPTION-JOURNAL OF THE INTERNATIONAL ADSORPTION SOCIETY}, author={Santiso, Erik E. and Nardelli, Marco Buongiorno and Gubbins, Keith E.}, year={2008}, month={Jun}, pages={181–188} }
 @article{santiso_kostov_george_nardelli_gubbins_2007, title={Confinement effects on chemical reactions - Toward an integrated rational catalyst design}, volume={253}, ISSN={["1873-5584"]}, DOI={10.1016/j.apsusc.2006.12.121}, abstractNote={Most chemical reactions of practical interest are carried out in nano-structured materials, which can enhance reactions due to their large specific surface area, their interactions with the reacting mixture and confinement effects. An experimental investigation of the role of each possible catalytic effect is challenging, since experimental measurements reflect an integration over multiple effects. In this work, we present a review of our most recent research on some of the factors that can influence a chemical reaction in confinement through the study of several model systems. We first consider the influence of steric hindrance on the equilibrium and kinetics for the rotational isomerizations of several small hydrocarbons [E.E. Santiso, M. Buongiorno Nardelli, K.E. Gubbins, Proc. Natl. Acad. Sci. U.S.A., (2007), in press]. These examples illustrate how reaction rates can vary doubly exponentially with the dimensions of the confining material (the ‘shape-catalytic’ effect). As a second example, we consider the unimolecular decomposition of formaldehyde on graphitic carbon pores of various sizes [E.E. Santiso, A.M. George, K.E. Gubbins, M. Buongiorno Nardelli, J. Chem. Phys. 125 (2006) 084711]. These results illustrate the influence of electrostatic interactions with the supporting material on the reaction mechanism and equilibrium yield for reactions involving a charge transfer. As a final example, we consider the interaction of a water molecule with a defective carbon substrate as an example of a chemical interaction that can be enhanced through a shape-catalytic effect. We first show using ab initio calculations how a vacancy site on a graphene surface can induce the thermal splitting of water at relatively low temperatures [M.K. Kostov, E.E. Santiso, A.M. George, K.E. Gubbins, M. Buongiorno Nardelli, Phys. Rev. Lett. 95 (2005) 136105]. We then examine the dissociation on a vacancy site on a nanotube surface, which shows the shape-catalytic effect of the surface curvature. These results are a first step toward the design of catalytic materials that take advantage of different enhancing effects simultaneously.}, number={13}, journal={APPLIED SURFACE SCIENCE}, author={Santiso, Erik E. and Kostov, Milen K. and George, Aaron M. and Nardelli, Marco Buongiorno and Gubbins, Keith E.}, year={2007}, month={Apr}, pages={5570–5579} }
 @article{jayaraman_santiso_hall_genzer_2007, title={Theoretical study of kinetics of zipping phenomena in biomimetic polymers}, volume={76}, ISSN={["1550-2376"]}, DOI={10.1103/physreve.76.011915}, abstractNote={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.}, number={1}, journal={PHYSICAL REVIEW E}, author={Jayaraman, Arthi and Santiso, Erik E. and Hall, Carol K. and Genzer, Jan}, year={2007}, month={Jul} }
 @article{hoteit_santiso_firoozabadi_2006, title={An efficient and robust algorithm for the calculation of gas–liquid critical point of multicomponent petroleum fluids}, volume={241}, ISSN={0378-3812}, url={http://dx.doi.org/10.1016/j.fluid.2005.12.019}, DOI={10.1016/j.fluid.2005.12.019}, abstractNote={The calculation of critical points in petroleum fluids and other multicomponent mixtures is important for practical and theoretical reasons. For certain applications, there is a need for the calculation of critical point as many 108 times with the change in composition. There is currently no algorithm that enjoys both robustness and efficiency (that is, speed) to be used for such a purpose. In this work, we propose a simple algorithm that has remarkable efficiency and robustness. It is orders of magnitude faster than the existing algorithms which are known to be robust.}, number={1-2}, journal={Fluid Phase Equilibria}, publisher={Elsevier BV}, author={Hoteit, Hussein and Santiso, Erik and Firoozabadi, Abbas}, year={2006}, month={Mar}, pages={186–195} }
 @article{santiso_firoozabadi_2006, title={Curvature dependency of surface tension in multicomponent systems}, volume={52}, DOI={10.1020/aic.10588}, number={1}, journal={AIChE Journal}, author={Santiso, Erik E. and Firoozabadi, A.}, year={2006}, pages={311–322} }
 @article{santiso_george_gubbins_nardelli_2006, title={Effect of confinement by porous carbons on the unimolecular decomposition of formaldehyde}, volume={125}, ISSN={["1089-7690"]}, DOI={10.1063/1.2220566}, abstractNote={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.}, number={8}, journal={JOURNAL OF CHEMICAL PHYSICS}, author={Santiso, Erik E. and George, Aaron M. and Gubbins, Keith E. and Nardelli, Marco Buongiorno}, year={2006}, month={Aug} }
 @article{santiso_george_turner_kostov_gubbins_buongiorno-nardelli_sliwinska-bartkowiak_2005, title={Adsorption and catalysis: The effect of confinement on chemical reactions}, volume={252}, ISSN={["1873-5584"]}, DOI={10.1016/j.apsusc.2005.02.101}, abstractNote={Confinement within porous materials can affect chemical reactions through a host of different effects, including changes in the thermodynamic state of the system due to interactions with the pore walls, selective adsorption, geometrical constraints that affect the reaction mechanism, electronic perturbation due to the substrate, etc. In this work, we present an overview of some of our recent research on some of these effects, on chemical equilibrium, kinetic rates and reaction mechanisms. We also discuss our current and future directions for research in this area.}, number={3}, journal={APPLIED SURFACE SCIENCE}, author={Santiso, EE and George, AM and Turner, CH and Kostov, MK and Gubbins, KE and Buongiorno-Nardelli, M and Sliwinska-Bartkowiak, M}, year={2005}, month={Oct}, pages={766–777} }
 @article{santiso_firoozabadi_2005, title={Curvature dependency of surface tension in multicomponent systems}, volume={52}, ISSN={0001-1541 1547-5905}, url={http://dx.doi.org/10.1002/aic.10588}, DOI={10.1002/aic.10588}, abstractNote={Abstract}, number={1}, journal={AIChE Journal}, publisher={Wiley}, author={Santiso, Erik and Firoozabadi, Abbas}, year={2005}, pages={311–322} }
 @article{kostov_santiso_george_gubbins_nardelli_2005, title={Dissociation of water on defective carbon substrates}, volume={95}, ISSN={["1079-7114"]}, DOI={10.1103/physrevlett.95.136105}, abstractNote={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.}, number={13}, journal={PHYSICAL REVIEW LETTERS}, author={Kostov, MK and Santiso, EE and George, AM and Gubbins, KE and Nardelli, MB}, year={2005}, month={Sep} }
 @article{santiso_george_sliwinska-bartkowiak_nardelli_gubbins_2005, title={Effect of Confinement on Chemical Reactions}, volume={11}, ISSN={0929-5607 1572-8757}, url={http://dx.doi.org/10.1007/s10450-005-5949-9}, DOI={10.1007/s10450-005-5949-9}, abstractNote={Molecular simulation studies of chemical equilibrium for several reactions in pores of slit-like and cylindrical geometry have shown a significant effect of the confinement on the equilibrium compositions, with differences of several orders of magnitude with respect to the bulk fluid phase in some cases. As a first step towards the calculation of rate constants in confinement, we have studied the reaction mechanisms for several reactions involving small organic molecules in slit-like pores. We show results for the rotational isomerization of 1,3-butadiene and the unimolecular decomposition of formaldehyde obtained using plane wave pseudopotential density functional theory (DFT). These examples show the influence that confinement can have through both geometrical constraints and fluid-wall interactions.}, number={S1}, journal={Adsorption}, publisher={Springer Nature}, author={Santiso, Erik E. and George, Aaron M. and Sliwinska-bartkowiak, Malgorzata and Nardelli, Marco Buongiorno and Gubbins, Keith E.}, year={2005}, month={Jul}, pages={349–354} }
 @article{sliwinska-bartkowiak_hung_santiso_coasne_dudziak_siperstein_gubbins_2005, title={Effect of Confinement on Freezing of CCl4 in Cylindrical Pores}, volume={11}, ISSN={0929-5607 1572-8757}, url={http://dx.doi.org/10.1007/s10450-005-5956-x}, DOI={10.1007/s10450-005-5956-x}, number={S1}, journal={Adsorption}, publisher={Springer Nature}, author={Sliwinska-Bartkowiak, Malgorzata and Hung, Francisco R. and Santiso, Erik E. and Coasne, Benoit and Dudziak, Grazyna and Siperstein, Flor R. and Gubbins, Keith E.}, year={2005}, month={Jul}, pages={391–396} }
 @article{hung_coasne_santiso_gubbins_siperstein_sliwinska-bartkowiak_2005, title={Molecular modeling of freezing of simple fluids confined within carbon nanotubes}, volume={122}, ISSN={["1089-7690"]}, DOI={10.1063/1.1881072}, abstractNote={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.}, number={14}, journal={JOURNAL OF CHEMICAL PHYSICS}, author={Hung, FR and Coasne, B and Santiso, EE and Gubbins, KE and Siperstein, FR and Sliwinska-Bartkowiak, M}, year={2005}, month={Apr} }
 @misc{santiso_gubbins_2004, title={Multi-scale molecular modeling of chemical reactivity}, volume={30}, ISSN={["1029-0435"]}, DOI={10.1080/08927020412331294878}, abstractNote={We present a review of the most widely used methods to model chemical reactions, at both the electronic and atomistic levels. While, in principle, ab initio methods alone should provide the required prediction of reaction mechanisms, yields and rates, in practice this can rarely be achieved due to the intensive nature of the computations and the poor scaling of the computational burden with the number of electrons. In many applications a combination of ab initio and semi-classical atomistic simulations will be needed. Specialized atomistic simulation methods are necessary, since the reactions are themselves rare events, and the free energy landscape for the reaction is often rugged with many possible reaction paths. We provide a survey of these methods, with comments on their applicability and a description of their strengths and weaknesses.}, number={11-12}, journal={MOLECULAR SIMULATION}, author={Santiso, EE and Gubbins, KE}, year={2004}, pages={699–748} }
 @article{santiso_müller_2002, title={Dense packing of binary and polydisperse hard spheres}, volume={100}, ISSN={0026-8976 1362-3028}, url={http://dx.doi.org/10.1080/00268970210125313}, DOI={10.1080/00268970210125313}, abstractNote={The packing of binary and polydisperse unimodal and bimodal ensembles of hard spheres in the limit of high pressure is studied using a sequential addition algorithm. Upon fixing the number of particles, and their size distribution, the average (maximum) packing fraction is determined for systems of up to 20 000 particles. The structures obtained correspond to amorphous states close to the dense random close packing density. Binary distributions obtained are denser than the equivalent monodisperse distribution and agree with the theoretical prediction for an infinite size ratio limit. Unimodal normal and lognormal polydisperse distributions obtained compare favourably with available simulation and experimental data. Results for bimodal lognormal distributions are presented. In all cases it is seen how an increase in polydispersity increases the packing fraction of the system. The results can be employed to gain insight into optimal formulations for dense emulsions.}, number={15}, journal={Molecular Physics}, publisher={Informa UK Limited}, author={Santiso, E and Müller, EA}, year={2002}, month={Aug}, pages={2461–2469} }
 @inbook{iturralde_santiso_morales_1996, title={Mass transfer coefficients for the adsorption of pollutants from aqueous effluents using a pore diffusion model}, volume={1}, booktitle={Chemical industry and environment II}, publisher={Torino: Politecnico di Torino}, author={Iturralde, L. and Santiso, E. and Morales, F.}, editor={N. Piccinini and Delorenzo, R.Editors}, year={1996} }