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At least 865 records · Page 48
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Thermodynamic and Kinetic Roles of H2 in Structure Evolution of Urchin-like Co: A density functional theory study

Small gas molecules working as good capping agents play important roles in controlling the morphologies and surface structures of the metal nanocrystals. In present work, the thermodynamic and kinetic roles of H2 molecule played on the morphology of Co nanocrystal were systematically studied based on density functional theory (DFT). The Gibbs surface free energies (?) of Co(100), Co(110) and Co(111) under different hydrogen surface coverages were investigated by ab initio thermodynamics, based on which i) the phase diagrams of stable H coverage on each plane were obtained; ii) the morphology evolutions of the Co nanocrystals with various surface hydrogen coverages were further predicted by Wulff construction. It was revealed that addition of H2 could change the facet stability generating diverse morphological Co nucleus. The kinetic role of H2 was further explored by DFT during adatom Co surface diffusions under different H coverages (?H), which suggested that except for Co(100) at ?H of 0.56 ML, the surface H would hinder Co surface diffusions. The projected density of state (PDOS) gave a deeper insight that the electronic structures of the Co adatom could be alerted by addition of the surface H, which thereby affected its surface diffusion ability. X. Wang, N. Liu, Q. Zhang, X. Liang, and B. Chen were financially supported by the National Natural Science Foundation of China (No. 21476012, 21571012, and 91534201). D. Mei was supported by the US Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. Computing time was granted by the facility user proposal grand challenge of computational catalysis of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL). EMSL is a national scientific user facility located at Pacific Northwest National Laboratory (PNNL) and sponsored by DOE’s Office of Biological and Environmental Research.

Nanocrystal Co, Surface free energy, Surface diffu↗
DOE OSTI2021

Air separation via a two-step solar thermochemical cycle based on (Ba,La) x Sr 1-x FeO 3-δ : Thermodynamic analysis

A two-step solar thermochemical cycle was considered for air separation to produce N2 based on (Ba,La) x Sr 1-x FeO 3-δ perovskite reduction/oxidation (redox) reactions for A-site fractions of 0 ≤ x ≤ 0.2. The cycle steps encompassed (1) thermal reduction and O 2 release via concentrated solar input and (2) re-oxidation with air to uptake O 2 and produce high-purity N 2 . Thermogravimetry at temperatures between 400 and 1100 °C in atmospheres of 0.005 to 90% O 2 /Ar at 1 bar was performed to measure equilibrium nonstoichiometries. The compound energy formalism was applied to model redox thermodynamics for both Ba 2+ and La 3+ substitution. Non-linear regression was used to determine the empirical parameters based on the thermogravimetric measurements. The model was used to define partial molar reaction enthalpies and entropies and predicted equilibrium oxygen nonstoichiometry as functions of oxide stoichiometry, site fraction, temperature, and O 2 partial pressure. The thermodynamic analysis showed the materials are appealing for air separation at temperatures below 800 °C.

42 ENGINEERING↗
DOE OSTI2022

Leveraging computational thermodynamics to guide SiC-ZrC chemical vapor deposition process development

Here using the CALPHAD approach to understand zirconium carbide deposition, a series of phase equilibria were calculated from a custom thermodynamic database based on a literature source, and the equilibria were used to explore the potential chemical vapor deposition (CVD) processing space in the ZrCl 4 -CH 3 SiCl 3 -CH 4 -H 2 system as a function of pressure, temperature, and gas composition. Several gas ratios were considered. At a given ZrCl 4 :CH 3 SiCl 3 ratio within the range studied, the most important factor was found to be the ratios of CH 4 :ZrCl 4 , wherein the nature of the composition – carbide vs. silicide – could be controlled. A pure binary composition of ZrC and SiC is expected to form by increasing the initial amount of methane and decreasing the amount of hydrogen from values predicted purely based on thermodynamic equilibrium. Rietveld analysis of the x-ray diffractograms from corresponding experimental depositions confirmed that increasing the CH 4 :ZrCl 4 ratio increased the fraction of carbon-containing species (SiC, ZrC) and decreased the fraction of non-carbides (ZrSi, ZrSi 2 , etc.), as predicted from the CALPHAD results.

36 MATERIALS SCIENCE↗
DOE OSTI2012

Thermodynamic analysis on heavy metals partitioning impacted by moisture during the MSW incineration

Highlights: Black-Right-Pointing-Pointer Partitioning of HMs affected by moisture was investigated by thermodynamic analysis. Black-Right-Pointing-Pointer Increase in moisture and in temperature was opposite impact on HMs contribution. Black-Right-Pointing-Pointer The extent of temperature decreased by increase in moisture determines the impact. - Abstract: A thermodynamic calculation was carried out to predict the behavior and speciation of heavy metals (HMs), Pb, Zn, Cu, and Cd, during municipal solid waste (MSW) incineration with the different moisture levels. The calculation was based on the minimization of the total Gibbs free energy of the multi-components and multi-phases closed system reaching chemical equilibrium. The calculation also indicated the reaction directions and tendencies of HMs components. The impacts of chlorine additives (No PVC, 1%PVC, and 5%PVC) and moisture on the behavior of HMs were investigated at different temperature levels in the system (750 Degree-Sign C, 950 Degree-Sign C, and 1150 Degree-Sign C). Furthermore, because the incineration temperature falls down with the increase in moisture in waste, the co-influence of moisture and temperature in combusting MSW on the HMs was also studied with the given chlorine (as 1%PVC + 0.5%NaCl). The results showed that in the non-chlorine system, the impact of the moisture on Pb, Zn, and Cu was not significant, and the ratio of compound transformation was less than 10%, except the Cd compounds at 950 Degree-Sign C and 1150 Degree-Sign C. In the system with low chlorine (as 1%PVC) at constant temperature, the chlorides of HMs (Cd, Pb, Zn, and Cu) transferred to oxides, and when the content of chlorine rose up (as 5%PVC), the ratio of the chlorides of HMs (Cd, Pb, Zn, and Cu) transferring to oxides fell down noticeably. When the moisture varied together with the temperature, the Zn and Cu compounds transferred from chlorides to oxides with increase in moisture as well as decrease in temperature. At the temperature of 700-1000 Degree-Sign C, the impact of temperature on Pb and Cd was little and the moisture was the main factor; while at the temperature of 1000-1200 Degree-Sign C, the impact of increase in moisture and decrease in temperature on Pb and Cd was almost equal and reversed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Thermodynamic and Kinetic Transitions of Liquids in Nanoconfinement

Core principles of chemistry are ubiquitously invoked to shed light on the nature of molecular level interactions in nanoconfined fluids, which play a pivotal role in a wide range of processes in geochemistry, biology, and engineering. A detailed understanding of the physicochemical processes involved in the flow, structural transitions, and freezing or melting behavior of fluids confined within nanometer-sized pores of solid materials is thus of enormous importance for both basic research and technological applications. This Account provides a perspective on new insights into the thermodynamic and kinetic transitions of nanoconfined fluids in their stable and metastable forms. After briefly introducing the unique properties of mesoporous silicas from the SBA, MCM, and FDU families that serve as the confinement matrices, combining highly ordered single and bimodal mesopore architectures with tunable pore sizes in the ~2-15 nm range and narrow size distributions, recent studies on melting/freezing behavior of water confined in these host matrices are reviewed. While differential scanning calorimetry (DSC) reveals a linear relationship between melting point depression and pore size (independent of the pore shape), as predicted by the Gibbs-Thomson relation, variable temperature 2 H wide-line nuclear magnetic resonance (NMR) spectroscopy studies confirm the core-shell model of water and give evidence for a layer-by-layer freezing mechanism, which gives rise to an apparent fragile-to-strong transition in the solidification dynamics. In contrast to the freezing/melting behavior of water, the effect of nanoconfinement on the glass transition of supercooled liquids is nonuniversal and the glass transition temperature T g can either increase or decrease with the dimensionality and extent of confinement. This nonuniversal behavior is exemplified by the two glass-forming molecular liquids, glycerol and ortho-terphenyl (OTP). While glycerol shows an increase in T g and a pronounced slowdown of the rotational dynamics of the constituent molecules due to a change in the molecular packing between the bulk and the confined liquid, OTP displays a linear and confining-media-dependent depression of T g with increased confinement that is strongly influenced by the pore-liquid interface characteristics. This Account concludes with a focus on recent experimental evidence of extreme spatial and dynamical heterogeneity in both freezing and glass transition processes. This discovery was enabled by the unique mesoporous structures of SBA-16 and FDU-5, possessing bimodal architectures with two interconnected pore types of different size and shape (spherical and cylindrical). For the very first time, two melting points for water and two glass transitions for supercooled OTP, corresponding to a specific pore type, were observed. Collectively, these observations strongly suggest a close mechanistic connection between the local fluctuations in the structure and dynamics of nanoconfined liquids. Finally, while the findings reviewed in this Account provide new insights into thermodynamic and kinetic transitions of fluids, there remain many unanswered questions regarding the effects of nanoconfinement on the fundamental properties of fluids, which offer exciting future opportunities in chemical research.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Thermodynamic and Kinetic Modulation of Methylammonium Lead Bromide Crystallization Revealed by In Situ Monitoring

Hybrid organic–inorganic perovskite (HOIP) crystals are promising optoelectronic materials, but little is known about either the thermodynamic and kinetic controls on crystal growth or the underlying growth mechanism(s). Herein, we use fluid cell atomic force microscopy (AFM) and solution nuclear magnetic resonance (NMR) spectroscopy to investigate growth of the model HOIP crystal CH 3 NH 3 PbBr 3 (MAPbBr 3 ) and to determine how formic acid (HCOOH) modulates the thermodynamics and kinetics of growth. The results show that growth of MAPbBr 3 in dimethylformamide (DMF) proceeds through the classical pathway by the spreading of atomic crystal steps generated at screw dislocations on the {100} surface. Temperature dependent step velocity measurements demonstrate that with increasing concentration, HCOOH decreases both the solubility of MAPbBr 3 and the kinetic coefficient (b) of step movement. 1 H-NMR measurements indicate that HCOOH increases the lifetime of the methylammonium (MA + ) ions and promotes the association of MAPbBr 3 , thus tuning the solubility of the perovskite. HCOOH also alters the molecular tumbling motion and bulk diffusion of the MA + ions, possibly via H-bonding. Further, our findings establish a direct correlation between the mesoscale crystal growth kinetics and the molecular-scale interactions between organic additives and constituent ions, providing unprecedented insights for developing predictive syntheses of HOIP crystals with defined size, crystal habit and shape, and defect distribution.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Thermodynamic and Kinetic Barriers Limiting Solid-State Reactions Resolved through In Situ Synchrotron Studies of Lithium Halide Salts

Although halide salts such as LiCl and LiBr are routinely used as a source of Li ions during ion exchange reactions, a detailed understanding of the processes controlling the rates of these reactions is presently lacking. Recently, it has been discovered that the rate limiting barriers for ion exchange are commonly associated with these salts rather than the ceramic target of ion exchange, making it important to quantitatively understand of salt processes. Here it is demonstrated that in situ synchrotron studies of ion exchange reactions can be used to precisely quantify the thermodynamic activation energies associated with these solid state reactions in a manner that can be directly compared with predictions from density functional theory (DFT). While the temperature dependence of the LiCl reaction rate is found to be set by a barrier associated with ion hopping, it was discovered that for LiBr it is also affected by the defect formation energy – an energy found to be substantially lower than predicted by DFT. Furthermore, it is shown that when reaction rates for different relative amounts of reactants are varied, it is possible to identify the rate-limiting reagent and to elucidate an overall scaling relationship that controls the concentration-dependence of the reaction rate. Also, it is demonstrated that global fits across doped and undoped salts can be used to probe both intrinsic and extrinsic vacancy concentrations. This improved understanding of ion exchange mechanisms can be used to accelerate ion exchange reaction rates by orders of magnitude. In conclusion, the techniques demonstrated here can be broadly applied to probe the kinetics and thermodynamics of solid state reactions.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Unraveling the Growth Mechanism of Strongly Confined CsPbBr 3 Perovskite Quantum Dots under Thermodynamic Equilibrium Control

Size-confined lead halide perovskite quantum dots (PQDs) are promising materials for optoelectronic devices. Large quantities of PQDs with high ensemble uniformity are often needed for device fabrication. The thermodynamic-equilibrium-controlled synthesis can produce PQDs with good size and shape uniformity. Unfortunately, scaling up this synthesis often produces unwanted perovskite nanoplatelets (NPLs). To date, the PQD and NPL growth mechanism under thermodynamic equilibrium control remains unexplored. We discovered that the growth of size-confined CsPbBr 3 PQDs is mediated by ultrasmall (~ 2.4 nm) metastable nanoclusters. These nanoclusters can eventually grow into PQDs when sufficient Cs-precursors are provided. Otherwise, the unreacted nanoclusters will self-assemble and fuse into NPLs during the synthesis and/or PQD purification. Furthermore, by controlling the homogeneous growth of nanoclusters, strongly confined (≤ 5 nm) PQDs with high size uniformity can be produced at the gram scale.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2025

Thermodynamic and Kinetic Mechanisms Governing the Synthesis of Nickel-Poor Cathodes

A deeper understanding of the thermodynamics and kinetics governing the lithiation and layering mechanisms of NMC cathode materials (LiNixMnyCozO 2 , where x + y + z = 1) offers valuable insights for enhancing synthesis methods and improving cathode performance. By employing atomistic and mesoscale approaches informed by in situ powder X-ray diffraction (PXRD) experiments, critical parameters for comprehending lithiation and layering processes and reaction rates were identified. The mesoscale approach captured the evolution of the phases and crystallite size observed in the in situ PXRD, revealing the differences in reaction rates with the use of different lithium salts and starting precursors. Ab initio molecular dynamics (AIMD) underscored the importance of vacancies and structural defects in promoting ion mobility and facilitating the nucleation of a layered domain. This nucleation disrupts the symmetry of disordered phases, ultimately creating a strained phase that serves as a buffer between layered and disordered regions. The lithiation and layering processes reflect a dynamic balance between the thermodynamic drive for a low-energy layered structure and the kinetic of diffusion, which is influenced by temperature and lithium vacancy concentration. Overall, reaction mechanisms are driven by the inherent defects of the intermediate phase that differ for NMC cathode materials. The lithium salts impact the rates of lithiation and layering, with a much slower process for Li 2 CO 3 .

25 ENERGY STORAGE↗
DOE OSTI2019

Thermodynamic Ground States of Multifunctional Metal Dodecaborides

A large class of metal dodecaborides (MB 12 ) is currently raising great expectations as multifunctional materials, but their refined structures are not fully resolved, which severely limits the understanding of structure–property relationships. In this paper, we report that the tetragonal tI26 structure is the thermodynamic ground state of ScB 12 , and we predict the tetragonal YB 12 , ZrB 12 , and HfB 12 to be metastable, whereas the cubic cF52 structure is the high-temperature phase of ScB 12 and represents the thermodynamic ground state of YB 12 , ZrB 12 , and HfB 12 . Crystal structures based on experimental synchrotron data are reported for tetragonal ScB 12 and cubic YB 12 , and high-temperature X-ray data prove the phase transformation into cubic ScB 12 . In both types of crystal structures, the most prominent feature is that the boron atoms are linked into a rigid three-dimensional network of interconnected, empty B 12 -cuboctahedra with metal atoms in large cages in form truncated octahedra consisting of 24 boron atoms. It is the uniqueness of these configurations that causes unusual functionalities, i.e., the coexistence of high hardness, low density, and good electrical conductivity. Furthermore, we elucidate that these physical properties are of electronic origins. These findings not only resolve the longstanding structural puzzle of this family of MB 12 but also provide crucial insights into the underlying nature of their remarkable properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Solvation Thermodynamics of Solutes in Water and Ionic Liquids Using the Multiscale Solvation-Layer Interface Condition Continuum Model

We report molecular assembly processes are generally driven by thermodynamic properties in solutions. Atomistic modeling can be very helpful in designing and understanding complex systems, except that bulk solvent is very inefficient to treat explicitly as discrete molecules. The SLIC/CDC multiscale model combines continuum solvent electrostatics based on the solvent layer interface condition (SLIC) with statistical thermodynamic models for hydrogen bonding and nonpolar modes: cavity formation, dispersion interactions, combinatorial mixing (CDC). The SLIC/CDC model predicts Gibbs energies of solvation for a database of 500 solutes in water with average accuracy better than 1 kcal/mol both for experimental measurements and for explicit-solvent molecular dynamics simulations. The separate SLIC/CDC energy mode values agree quantitatively with those computed from explicit-solvent molecular dynamics. The SLIC/SASA multiscale model combines the SLIC continuum electrostatic model with the solvent accessible surface area (SASA) nonpolar energy mode. The SLIC/SASA model predicts Gibbs energies of solvation with better than 1.4 kcal/mol average accuracy in aqueous systems and better than 1.6 kcal/mol average accuracy in ionic liquids. Both models predict solvation entropies, and are the first implicit-solvation models capable of predicting solvation heat capacities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Thermodynamics of Anharmonic Systems: Uncoupled Mode Approximations for Molecules

The partition functions, heat capacities, entropies, and enthalpies of selected molecules were calculated using uncoupled mode (UM) approximations, where the full-dimensional potential energy surface for internal motions was modeled as a sum of independent one-dimensional potentials for each mode. The computational cost of such approaches scales the same with molecular size as standard harmonic oscillator vibrational analysis using harmonic frequencies (HO hf ). To compute thermodynamic properties, a computational protocol for obtaining the energy levels of each mode was established. The accuracy of the UM approximation depends strongly on how the one-dimensional potentials of each modes are defined. If the potentials are determined by the energy as a function of displacement along each normal mode (UM-N), the accuracies of the calculated thermodynamic properties are not significantly improved versus the HO hf model. Significant improvements can be achieved by constructing potentials for internal rotations and vibrations using the energy surfaces along the torsional coordinates and the remaining vibrational normal modes, respectively (UM-VT). For hydrogen peroxide and its isotopologs at 300 K, UM-VT captures more than 70% of the partition functions on average. By con trast, the HO hf model and UM-N can capture no more than 50%. For a selected test set of C2 to C8 linear and branched alkanes and species with different moieties, the enthalpies calculated using the HO hf model, UM-N, and UM-VT are all quite accurate comparing with reference values though the RMS errors of the HO model and UM-N are slightly higher than UM-VT. However, the accuracies in entropy calculations differ significantly between these three models. For the same test set, the RMS error of the standard entropies calculated by UM-VT is 2.18 cal mol -1 K -1 at 1000 K. By contrast, the RMS error obtained using the HO model and UM-N are 6.42 and 5.73 cal mol -1 K -1 , respectively. For a test set composed of nine alkanes ranging from C5 to C8, the heat capacities calculated with the UM-VT model agree with the experimental values to within a RMS error of 0.78 cal mol -1 K -1 , which is less than one-third of the RMS error of the HO hf (2.69 cal mol -1 K -1) and UM-N (2.41 cal mol -1 K -1) models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Using Force Matching To Determine Reactive Force Fields for Water under Extreme Thermodynamic Conditions

We present a method for the creation of classical force fields for water under dissociative thermodynamic conditions by force matching to molecular dynamics trajectories from Kohn–Sham density functional theory (DFT). We apply our method to liquid water under dissociative conditions, where molecular lifetimes are less than 1 ps, and superionic water, where hydrogen ions diffuse at liquid-like rates through an oxygen lattice. We find that, in general, our new models are capable of accurately reproducing the structural and dynamic properties computed from DFT, as well as the molecular concentrations and lifetimes. Overall, our force-matching approach presents a relatively simple way to create classical reactive force fields for a single thermodynamic state point that largely retains the accuracy of DFT while having the potential to access experimental time and length scales.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Reaction Pathways, Thermodynamics, and Kinetics of Cyclopentanone Oxidation Intermediates: A Theoretical Approach

Despite the promising role of cyclopentanone as a bio-derived fuel, thermodynamic and kinetic data are lacking for low temperature oxidation regimes. In this study, ab initio calculations at the CBS-QB3 level explore the subsequent reactivity that results from O 2 -addition to 2- and 3-oxo cyclopentyl radicals, including expected reaction classes such as intra-H migration, HO 2 -elimination, cyclic ether formation and β-scission along with their thermodynamic parameters. Some of the rates are similar to the analogous reactions of cyclopentane, but some other reactions of cyclopentanone are very different. The carbonyl group hinders H-migration from the α’ position but promotes HO 2 -elimination. Enol peroxy formation from some hydroperoxy alkyl radicals of cyclopentanone is unexpectedly important, and so is HO 2 -elimination by β-scission. Our calculations also indicated that at engine relevant conditions the α-RO 2 prefers to go back to reactants 2-oxo cyclopentyl radical and O 2 . Therefore, the reactions resulting from HO2-addition to 2-oxo cyclopentyl is also provided. The lowest barrier channel identified on the singlet surface corresponds to an unexpected intra OH-migration path concerted with ring opening. In conclusion, this valuable information will advance the construction of improved kinetic models for the oxidation of cylopentanone.

09 BIOMASS FUELS↗
DOE OSTI2023

Structure–Thermodynamic Relationship of a Polysaccharide Gel (Alginate) as a Function of Water Content and Counterion Type (Na vs Ca)

Biofilms are the predominant mode of microbial life on Earth, and so a deep understanding of microbial communities-and their impacts on environmental processes-requires a firm understanding of biofilm properties. Because of the importance of biofilms to their microbial inhabitants, microbes have evolved different ways of engineering and reconfiguring the matrix of extracellular polymeric substances (EPS) that constitute the main non-living component of biofilms. This ability makes it difficult to distinguish between the biotic and abiotic origins of biofilm properties. An important route toward establishing this distinction has been the study of simplified models of the EPS matrix. This study builds on such efforts by using atomistic simulations to predict the nanoscale (≤10 nm scale) structure of a model EPS matrix and the sensitivity of this structure to interpolymer interactions and water content. To accomplish this, we use replica exchange molecular dynamics (REMD) simulations to generate all-atom configurations of ten 3.4 kDa alginate polymers at a range of water contents and Ca–Na ratios. Simulated systems are solvated with explicitly modeled water molecules, which allows us to capture the discrete structure of the hydrating water and to examine the thermodynamic stability of water in the gels as they are progressively dehydrated. Our primary findings are that (i) the structure of the hydrogels is highly sensitive to the identity of the charge-compensating cations, (ii) the thermodynamics of water within the gels (specific enthalpy and free energy) are, surprisingly, only weakly sensitive to cation identity, and (iii) predictions of the differential enthalpy and free energy of hydration include a short-ranged enthalpic term that promotes hydration and a longer-ranged (presumably entropic) term that promotes dehydration, where short and long ranges refer to distances shorter or longer than ~0.6 nm between alginate strands.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Maximum Entropy Theory of Multiscale Coarse-Graining via Matching Thermodynamic Forces: Application to a Molecular Crystal (TATB)

The MSCG/FM (multiscale coarse-graining via force-matching) approach is an efficient supervised machine learning method to develop microscopically informed coarse-grained (CG) models. Here we present a theory based on the principle of maximum entropy (PME) enveloping the existing MSCG/FM approaches. This theory views the MSCG/FM method as a special case of matching the thermodynamic forces from the extended ensemble described by the set of thermodynamic (relevant) system coordinates. This set may include CG coordinates, the stress tensor, applied external fields, and so forth, and may be characterized by nonequilibrium conditions. Following the presentation of the theory, we discuss the consistent matching of both bonded and nonbonded interactions. The proposed PME formulation is used as a starting point to extend the MSCG/FM method to the constant strain ensemble, which together with the explicit matching of the bonded forces is better suited for coarse-graining anisotropic media at a submolecular resolution. The theory is demonstrated by performing the fine coarse-graining of crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), a well-known insensitive molecular energetic material, which exhibits highly anisotropic mechanical properties.

1,3,5-triamino-2,4,6-trinitrobenzene↗
DOE OSTI2024

Thermodynamically Optimized Machine-Learned Reaction Coordinates for Hydrophobic Ligand Dissociation

Ligand unbinding is mediated by its free energy change, which has intertwined contributions from both energy and entropy. It is important, but not easy, to quantify their individual contributions to the free energy profile. We model hydrophobic ligand unbinding for two systems, a methane particle and a C 60 fullerene, both unbinding from hydrophobic pockets in all-atom water. Using a modified deep learning framework, we learn a thermodynamically optimized reaction coordinate to describe the hydrophobic ligand dissociation for both systems. Interpretation of these reaction coordinates reveals the roles of entropic and enthalpic forces as the ligand and pocket sizes change. In both cases, we observe that the free-energy barrier to unbinding is dominated by entropy considerations. Furthermore, the process of methane unbinding is driven by methane solvation, while fullerene unbinding is driven first by pocket wetting and then fullerene wetting. For both solutes, the direct importance of the distance from the binding pocket to the learned reaction coordinate is present, but low. Furthermore, our framework and subsequent feature important analysis thus give useful thermodynamic insight into hydrophobic ligand dissociation problems that are otherwise difficult to glean.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis

We report that replica-exchange molecular dynamics (REMD) has been proven to efficiently improve the convergence of free energy perturbation (FEP) calculations involving considerable reorganization of their surrounding. We previously introduced the FEP/(λ,H)-REMD algorithm for ligand binding, in which replicas along the alchemical thermodynamic coupling axis λ were expanded as a series of Hamiltonian boosted replicas along a second axis to form a two-dimensional (2D) replica-exchange exchange map [Jiang, W.; Roux, B., J. Chem. Theory Comput. 2010, 6 (9), 2559-2565]. Aiming to achieve a similar performance at a lower computational cost, we propose here a modified version of this algorithm in which only the end-states along the alchemical axis are augmented by boosted replicas. The reduced FEP/(λ,H)-REMD method with one-dimensional (1D) unbiased alchemical thermodynamic coupling axis λ is implemented on the basis of generic multiple copy algorithm (MCA) module of the biomolecular simulation program NAMD. The flexible MCA framework of NAMD enables a user to design customized replica-exchange patterns through Tcl scripting in the context of a highly parallelized simulation program without touching the source code. Two Hamiltonian tempering boosting scheme were examined with the new algorithm: a first one based on potential energy rescaling of a pre-identified “solute”, and a second one via the introduction of flattening torsional free energy barriers. As two illustrative examples with reliable experiment data, the absolute binding free energies of pxylene and n-butylbenzene to the nonpolar cavity of the L99A mutant of T4 lysozyme were calculated. Lastly, the tests demonstrate that the new protocol efficiently enhances the sampling of torsional motions for backbone and side chains around the binding pocket and accelerates the convergence of the free energy computations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗