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In this paper we investigate the adequacy of deep learning force field models for modeling amorphous bodies. A polymer with the studied physical properties, polyphenylene sulfide, was chosen as a test substance. The simulation results shows that the forces predicted by neural networks acting on polymer atoms are significantly different from the forces calculated by ab initio molecular dynamics methods. A qualitative comparison with the force field model of a simpler compound, black phosphorene, shows that feedforward neural networks are unsuitable for modeling complex amorphous substances. [ABSTRACT FROM AUTHOR]

Covalent adaptable networks and vitrimers are novel polymers with dynamic reversible bond exchange reactions for crosslinks, enabling them to modulate their properties between those of thermoplastics and thermosets. They have been gathering interest as materials for their recycling and self-healing properties. In this review, we discuss different molecular simulation efforts that have been used over the last decade to investigate and understand the nanoscale and molecular behaviors of covalent adaptable networks and vitrimers. In particular, molecular dynamics, Monte Carlo, and a hybrid of molecular dynamics and Monte Carlo approaches have been used to model the dynamic bond exchange reaction, which is the main mechanism of interest since it controls both the mechanical and rheological behaviors. The molecular simulation techniques presented yield sufficient results to investigate the structure and dynamics as well as the mechanical and rheological responses of such dynamic networks. The benefits of each method have been highlighted. The use of other tools such as theoretical models and machine learning has been included. We noticed, amongst the most prominent results, that stress relaxes as the bond exchange reaction happens, and that at temperatures higher than the glass transition temperature, the self-healing properties are better since more bond BERs are observed. The lifetime of dynamic covalent crosslinks follows, at moderate to high temperatures, an Arrhenius-like temperature dependence. We note the modeling of certain properties like the melt viscosity with glass transition temperature and the topology freezing transition temperature according to a behavior ruled by either the Williams–Landel–Ferry equation or the Arrhenius equation. Discrepancies between the behavior in dissociative and associative covalent adaptable networks are discussed. We conclude by stating which material parameters and atomistic factors, at the nanoscale, have not yet been taken into account and are lacking in the current literature. [ABSTRACT FROM AUTHOR]

Fullerenes, particularly C60, exhibit unique properties that make them promising candidates for various applications, including drug delivery and nanomedicine. However, their interactions with biomolecules, especially proteins, remain not fully understood. This study implements both explicit and implicit C60 models into the UNRES coarse-grained force field, enabling the investigation of fullerene–protein interactions without the need for restraints to stabilize protein structures. The UNRES force field offers computational efficiency, allowing for longer timescale simulations while maintaining accuracy. Five model proteins were studied: FK506 binding protein, HIV-1 protease, intestinal fatty acid binding protein, PCB-binding protein, and hen egg-white lysozyme. Molecular dynamics simulations were performed with and without C60 to assess protein stability and investigate the impact of fullerene interactions. Analysis of contact probabilities reveals distinct interaction patterns for each protein. FK506 binding protein (1FKF) shows specific binding sites, while intestinal fatty acid binding protein (1ICN) and uteroglobin (1UTR) exhibit more generalized interactions. The explicit C60 model shows good agreement with all-atom simulations in predicting protein flexibility, the position of C60 in the binding pocket, and the estimation of effective binding energies. The integration of explicit and implicit C60 models into the UNRES force field, coupled with recent advances in coarse-grained modeling and multiscale approaches, provides a powerful framework for investigating protein–nanoparticle interactions at biologically relevant scales without the need to use restraints stabilizing the protein, thus allowing for large conformational changes to occur. These computational tools, in synergy with experimental techniques, can aid in understanding the mechanisms and consequences of nanoparticle–biomolecule interactions, guiding the design of nanomaterials for biomedical applications. [ABSTRACT FROM AUTHOR]

Neural network force fields have significantly advanced ab initio atomistic simulations across diverse fields. However, their application in the realm of magnetic materials is still in its early stage due to challenges posed by the subtle magnetic energy landscape and the difficulty of obtaining training data. Here we introduce a data-efficient neural network architecture to represent density functional theory total energy, atomic forces, and magnetic forces as functions of atomic and magnetic structures. Our approach incorporates the principle of equivariance under the three-dimensional Euclidean group into the neural network model. Through systematic experiments on various systems, including monolayer magnets, curved nanotube magnets, and moiré-twisted bilayer magnets of CrI3, we showcase the method's high efficiency and accuracy, as well as exceptional generalization ability. The work creates opportunities for exploring magnetic phenomena in large-scale materials systems. [ABSTRACT FROM AUTHOR]

Bio-based semicrystalline polylactide (PLA) has a growing value as a substitute for fossil-based polyesters in technical applications and as a biocompatible material in medicine. The complexity of the behavior of PLA, determined by the presence of different stereoisomers, the role of electrostatic interactions, and its slow crystallization rate, makes computer simulations an important tool to discover new approaches to control the properties of PLA-based materials. The goal of this review is to summarize the efforts to simulate PLA materials with different levels of detail, including the quantum mechanical approach, all-atom modeling, and coarse-grained particle models. We focus on the validation of the models and the ways to cross-check the results with other simulation and experimental data. Special attention is devoted to the simulations of PLA in the presence of water, which provide insights into molecular mechanisms of hydrolytic degradation of PLA, especially at the initial stage, when the structural changes can not yet be detected by experimental methods. Ultimately, the selection of the appropriate simulation methods can facilitate material design, by combining the throughput and level of detail necessary for the job. [ABSTRACT FROM AUTHOR]

We selected 145 reference organic molecules that include model fragments used in computer-aided drug design. We calculated 158 conformational energies and barriers using force fields, with wide applicability in commercial and free softwares and extensive application on the calculation of conformational energies of organic molecules, e.g. the UFF and DREIDING force fields, the Allinger's force fields MM3-96, MM3-00, MM4-8, the MM2-91 clones MMX and MM+, the MMFF94 force field, MM4, ab initio Hartree–Fock (HF) theory with different basis sets, the standard density functional theory B3LYP, the second-order post-HF MP2 theory and the Domain-based Local Pair Natural Orbital Coupled Cluster DLPNO-CCSD(T) theory, with the latter used for accurate reference values. The data set of the organic molecules includes hydrocarbons, haloalkanes, conjugated compounds, and oxygen-, nitrogen-, phosphorus- and sulphur-containing compounds. We reviewed in detail the conformational aspects of these model organic molecules providing the current understanding of the steric and electronic factors that determine the stability of low energy conformers and the literature including previous experimental observations and calculated findings. While progress on the computer hardware allows the calculations of thousands of conformations for later use in drug design projects, this study is an update from previous classical studies that used, as reference values, experimental ones using a variety of methods and different environments. The lowest mean error against the DLPNO-CCSD(T) reference was calculated for MP2 (0.35 kcal mol−1), followed by B3LYP (0.69 kcal mol−1) and the HF theories (0.81–1.0 kcal mol−1). As regards the force fields, the lowest errors were observed for the Allinger's force fields MM3-00 (1.28 kcal mol−1), ΜΜ3-96 (1.40 kcal mol−1) and the Halgren's MMFF94 force field (1.30 kcal mol−1) and then for the MM2-91 clones MMX (1.77 kcal mol−1) and MM+ (2.01 kcal mol−1) and MM4 (2.05 kcal mol−1). The DREIDING (3.63 kcal mol−1) and UFF (3.77 kcal mol−1) force fields have the lowest performance. These model organic molecules we used are often present as fragments in drug-like molecules. The values calculated using DLPNO-CCSD(T) make up a valuable data set for further comparisons and for improved force field parameterization. [ABSTRACT FROM AUTHOR]

An Online tool for Fragment-based Molecule Parametrization (OFraMP) is described. OFraMP is a web application for assigning atomic interaction parameters to large molecules by matching sub-fragments within the target molecule to equivalent sub-fragments within the Automated Topology Builder (ATB, atb.uq.edu.au) database. OFraMP identifies and compares alternative molecular fragments from the ATB database, which contains over 890,000 pre-parameterized molecules, using a novel hierarchical matching procedure. Atoms are considered within the context of an extended local environment (buffer region) with the degree of similarity between an atom in the target molecule and that in the proposed match controlled by varying the size of the buffer region. Adjacent matching atoms are combined into progressively larger matched sub-structures. The user then selects the most appropriate match. OFraMP also allows users to manually alter interaction parameters and automates the submission of missing substructures to the ATB in order to generate parameters for atoms in environments not represented in the existing database. The utility of OFraMP is illustrated using the anti-cancer agent paclitaxel and a dendrimer used in organic semiconductor devices. OFraMP applied to paclitaxel (ATB ID 35922). [ABSTRACT FROM AUTHOR]

We present a new benchmark set consisting of 16 large non-covalently bound systems (LNCI16) ranging from 380 up to 1988 atoms and featuring diverse interaction motives. Gas-phase interaction energies are calculated with various composite DFT, semi-empirical quantum mechanical (SQM), and force field (FF) methods and are evaluated using accurate DFT reference values. Of the employed QM methods, PBEh-3c proves to be the most robust for large systems with a relative mean absolute deviation (relMAD) of 8.5% with respect to the reference interaction energies. r2 SCAN-3c yields an even smaller relMAD, at least for the subset of complexes for which the calculation could be converged, but is less robust for systems with smaller HOMO–LUMO gaps. The inclusion of Fock-exchange is therefore important for the description of very large non-covalent interaction (NCI) complexes in the gas phase. GFN2-xTB was found to be the best performer of the SQM methods with an excellent result of only 11.1% deviation. From the assessed force fields, GFN-FF and GAFF achieve the best accuracy. Considering their low computational costs, both can be recommended for routine calculations of very large NCI complexes, with GFN-FF being clearly superior in terms of general applicability. Hence, GFN-FF may be routinely applied in supramolecular synthesis planning. 1 Introduction 2 The LNCI16 Benchmark Set 3 Computational Details 4 Generation of Reference Values 5 Results and Discussion 6 Conclusions [ABSTRACT FROM AUTHOR]

This paper is on determination of the thermal conductivities of several hydrocarbon base oils by means of non-equilibrium molecular dynamics simulations using two different force fields. It aims to explore a simulation-based method for lubricant molecular design and analysis concerning heat transfer in electrical vehicle lubrication. Argon was analyzed as a reference for method evaluation, and the results reveal that the calculated conductivity strongly depends on the size of the computational domain. However, for hydrocarbon base oils, the dependence on computation domain size is less prominent as the domain size increases. The method of direct calculation in a sufficiently large computation domain and that of reciprocal extrapolation with data calculated in a much smaller domain are both applicable, and each has a certain value in oil conductivity calculation. The calculated conductivities show certain overpredictions when compared with experimentally measured results, and the overprediction factor is related to number of carbon atoms of the liquid molecules. The results reveal that the thermal conductivity of a single-chain hydrocarbon liquid is linearly proportional to the number of carbon atoms. While each additional branch increases thermal conductivity slightly, the presence of multiple branches reduces it from the ideal linear relationship. A set of equations was formulated to correlate hydrocarbon liquid thermal conductivity with molecular characteristics in terms of number of carbon atoms and number of branches. [ABSTRACT FROM AUTHOR]

Dynamic adaptation is an error-driven process of adjusting planned motor actions to changes in task dynamics (Shadmehr, 2017). Adapted motor plans are consolidated into memories that contribute to better performance on re-exposure. Consolidation begins within 15 min following training (Criscimagna-Hemminger and Shadmehr, 2008), and can be measured via changes in resting state functional connectivity (rsFC). For dynamic adaptation, rsFC has not been quantified on this timescale, nor has its relationship to adaptative behavior been established. We used a functional magnetic resonance imaging (fMRI)-compatible robot, the MR-SoftWrist (Erwin et al., 2017), to quantify rsFC specific to dynamic adaptation of wrist movements and subsequent memory formation in a mixed-sex cohort of human participants. We acquired fMRI during a motor execution and a dynamic adaptation task to localize brain networks of interest, and quantified rsFC within these networks in three 10-min windows occurring immediately before and after each task. The next day, we assessed behavioral retention. We used a mixed model of rsFC measured in each time window to identify changes in rsFC with task performance, and linear regression to identify the relationship between rsFC and behavior. Following the dynamic adaptation task, rsFC increased within the cortico-cerebellar network and decreased interhemispherically within the cortical sensorimotor network. Increases within the cortico-cerebellar network were specific to dynamic adaptation, as they were associated with behavioral measures of adaptation and retention, indicating that this network has a functional role in consolidation. Instead, decreases in rsFC within the cortical sensorimotor network were associated with motor control processes independent from adaptation and retention. [ABSTRACT FROM AUTHOR]

We present a new software package called M-Chem that is designed from scratch in C++ and parallelised on shared-memory multi-core architectures to facilitate efficient molecular simulations. Currently, M-Chem is a fast molecular dynamics (MD) engine that supports the evaluation of energies and forces from two-body to many-body all-atom potentials, reactive force fields, coarse-grained models, combined quantum mechanics molecular mechanics (QM/MM) models, and external force drivers from machine learning, augmented by algorithms that are focused on gains in computational simulation times. M-Chem also includes a range of standard simulation capabilities including thermostats, barostats, multi-timestepping, and periodic cells, as well as newer methods such as fast extended Lagrangians and high quality electrostatic potential generation. At present M-Chem is a developer friendly environment in which we encourage new software contributors from diverse fields to build their algorithms, models, and methods in our modular framework. The long-term objective of M-Chem is to create an interdisciplinary platform for computational methods with applications ranging from biomolecular simulations, reactive chemistry, to materials research. [ABSTRACT FROM AUTHOR]

Bimanual in-phase and anti-phase coordination modes represent two basic movement patterns with distinct characteristics—homologous muscle contraction and non-homologous muscle contraction, respectively. A method to understand the contribution of each limb to the overall coordination pattern involves detuning (Δω) the natural eigenfrequency of each limb. In the present experiment, we experimentally broke the symmetry between the two upper limbs by adding elastic and viscous force fields using a Kinarm robot exoskeleton. We measured the effect of this symmetry breaking on coordination stability as participants performed bimanual in-phase and anti-phase movements using their left and right hand in 1:1 frequency locking mode. Differences between uncoupled frequencies were manipulated via the application of viscous & elastic force fields and using fast and slow oscillation frequencies with a custom task developed using the Kinarm robotic exoskeleton. The effects of manipulating the asymmetry between the limbs were measured through the mean and variability of relative phase (ϕ) from the intended modes of 0 ° or 180 °. In general, participants deviated less from intended phase irrespective of coordination mode in all matched conditions, except for when elastic loads are applied to both arms in the anti-phase coordination. Second, we found that when force fields were mismatched participants exhibited a larger deviation from the intended phase. Overall, there was increased phase deviation during anti-phase coordination. Finally, participants exhibited higher variability in relative phase in mismatched force conditions compared to matched force conditions, with overall higher variability during anti-phase coordination mode. We extend previous research by demonstrating that symmetry breaking caused by force differences between the limbs disrupts stability in each coordination mode. [ABSTRACT FROM AUTHOR]

Atomic-level understanding of the dynamic feature of host–guest interactions remains a central challenge in supramolecular chemistry. The remarkable guest binding behavior of the Cucurbiturils family of supramolecular containers makes them promising drug carriers. Among Cucurbit[n]urils, Cucurbit[8]uril (CB8) has an intermediate portal size and cavity volume. It can exploit almost all host–guest recognition motifs formed by this host family. In our previous work, an extensive computational investigation of the binding of seven commonly abused and structurally diverse drugs to the CB8 host was performed, and a general dynamic binding picture of CB8-guest interactions was obtained. Further, two widely used fixed-charge models for drug-like molecules were investigated and compared in great detail, aiming at providing guidelines in choosing an appropriate charge scheme in host-guest modelling. Iterative refitting of atomic charges leads to improved binding thermodynamics and the best root-mean-squared deviation from the experimental reference is 2.6 kcal/mol. In this work, we focus on a thorough evaluation of the remaining parts of classical force fields, i.e., the bonded interactions. The widely used general Amber force fields are assessed and refitted with generalized force-matching to improve the intra-molecular conformational preference, and thus the description of inter-molecular host–guest interactions. The interaction pattern and binding thermodynamics show a significant dependence on the modelling parameters. The refitted system-specific parameter set improves the consistency of the modelling results and the experimental reference significantly. Finally, combining the previous charge-scheme comparison and the current force-field refitting, we provide general guidelines for the theoretical modelling of host–guest binding. [ABSTRACT FROM AUTHOR]

The manufacturing of high-modulus, high-strength fibers is of paramount importance for real-world, high-end applications. In this respect, carbon nanotubes represent the ideal candidates for realizing such fibers. However, their remarkable mechanical performance is difficult to bring up to the macroscale, due to the low load transfer within the fiber. A strategy to increase such load transfer is the introduction of chemical linkers connecting the units, which can be obtained, for example, using carbon ion-beam irradiation. In this work, we investigate, via molecular dynamics simulations, the mechanical properties of twisted nanotube bundles in which the linkers are composed of interstitial single carbon atoms. We find a significant interplay between the twist and the percentage of linkers. Finally, we evaluate the suitability of two different force fields for the description of these systems: the dihedral-angle-corrected registry-dependent potential, which we couple for non-bonded interaction with either the AIREBO potential or the screened potential ReboScr2. We show that both of these potentials show some shortcomings in the investigation of the mechanical properties of bundles with carbon linkers. [ABSTRACT FROM AUTHOR]

Solving the dendrite growth problem is critical for the development of lithium metal anode for high‐capacity batteries. In this work, a machine learning force field model in combination with a self‐consistent continuum solvation model is used to simulate the morphology evolution of dendrites in a working electrolyte environment. The dynamic evolution of the dendrite morphology can be described in two stages. In the first stage, the energy reduction of the surface atoms induces localized reorientation of the originally single‐crystal dendrite and the formation of multiple domains. In the second stage, the energy reduction of internal atoms drives the migration of grain boundaries and the slipping of crystal domains. The results indicate that the formation of multiple domains might help to stabilize the dendrite, as a higher temperature trajectory in a single crystal dendrite without domains shows a higher dendrite collapsing rate. Several possible modes of morphological evolutions are also investigated, including surface diffusion of adatoms and configuration twists from [100] exposed surfaces to [110] exposed surfaces. In summary, reducing the surface and grain boundary energy drives the morphology evolution. Based on the analysis of these driving forces, some guidelines are suggested for designing a more stable lithium metal anode. [ABSTRACT FROM AUTHOR]

[Display omitted] • Enhanced stability and bio-compatibility of BNNTs make them excellent 1D candidates for drug delivery applications. • DFT and MD offer a new paradigm for identifying the potential of nanocarriers beyond experimental methods. • DFT provides detailed insights into the interaction mechanisms of drug molecules with BNNTs. • MD simulations offer a comprehensive understanding of the dynamic behavior of drug-BNNT complex. Exploring diverse nanocarriers in targeted drug delivery research is vital for optimizing therapeutic efficacy and minimizing adverse effects, thus improving treatment outcomes across various medical conditions. Boron Nitride Nanotubes (BNNTs) have emerged as one of the most promising one-dimensional nanostructures for drug delivery, owing to their unique structural and chemical properties. Herein, the authors explore and review the potential of BNNTs as drug delivery vehicles through the use of computational techniques, including Density Functional Theory (DFT) and Molecular Dynamics (MD) simulations. These simulation techniques yield valuable insights into drug encapsulation, transportation, and release mechanisms through a range of calculations, encompassing adsorption, thermodynamics, electronic characteristics, and chemical interactions. Employing both DFT and MD simulations in drug delivery studies, offers a distinct advantage by providing detailed insights into atomic-level interactions, and exploring dynamic processes from drug loading or encapsulation to drug release, which may be difficult to achieve solely through experimental means. This concise review offers an overview of findings and obstacles delineated in the use of BNNTs, as well as its various analogues for drug delivery. [ABSTRACT FROM AUTHOR]

• The simulation cell describes the physicochemical aspects of the hydrogen production. • The surface of calcite keeps hydrogen strongly bonded and the asphaltene helps to keep them in static equilibrium of forces. • The hydrogen is released from limestone rock surface by the asphaltene- zwitterionic liquids (ZL) system. A theoretical model is presented to describe the processes of release and desorption of molecular hydrogen from the depths of calcite rock oil fields via surfactants such as zwitterionic liquids. This model is based on molecular mechanics and dynamics, for which we built a supercell with a calcite crystalline unit cell in order to model the {1,0,4} surface and volume of the calcite rock; 42 H 2 molecules adsorbed and interacting strongly with the calcite surface stone were analyzed in this work; the effect of crude oil is simulated with an asphaltene macromolecule model. Finally, a branched geminal zwitterionic liquid (ZL) molecule is applied to initiate the process of hydrogen desorption and release. The aqueous medium of the oil field is simulated by the dielectric constant of water. The most stable molecules were obtained using forcite computational code. While the interaction energies were calculated by classical molecular mechanics using Dreiding force field. The dynamics of the H 2 desorption and release process from calcite rock of oil well is studied using the classical molecular dynamics. The purpose of the work is to theoretically demonstrate that ZL substances are capable of releasing and desorb hydrogen from the calcite surface in the depths of oil fields. The results indicate that ZL polar groups form cation-π interactions with the asphaltene benzene rings structure, and that, the carbonated chains of the former trap the latter to release molecular hydrogen. Finally, the aqueous medium desorbs hydrogen from the calcite surface and transports it to the surface of the oil field. [ABSTRACT FROM AUTHOR]

We present a polarisable force field parametrisation for amino acid-based ionic liquids based on the Amoeba framework. The force field has been obtained using accurate ab initio data and has been conceived to be as compatible as possible with the existing Amoeba parametrisation. We present here a validation mainly carried out using reference ab initio calculations and we show how the parametrisation is able to provide the structural features of the fluids to an excellent extent as well as to reproduce the intermolecular interaction energies. [ABSTRACT FROM AUTHOR]

A class of radial, polynomial cutoff functions f c n (r) for short-ranged pair potentials or related expressions is proposed. Their derivatives up to order n and n + 1 vanish at the outer cutoff r c and an inner radius r i , respectively. Moreover, f c n (r ≤ r i ) = 1 and f c n (r ≥ r c ) = 0. It is shown that the used order n can qualitatively affect results: stress and bulk moduli of ideal crystals are unavoidably discontinuous with density for n = 0 and n = 1, respectively. Systematic errors on energies and computing times decrease by 20–50% for Lennard-Jones with n = 2 or n = 3 compared to standard cutting procedures. Another cutoff function turns out beneficial to compute Coulomb interactions using the Wolf summation, which is shown to not properly converge when local charge neutrality is obeyed only in a stochastic sense. However, for all investigated homogeneous systems with thermal noise (ionic crystals and liquids), the modified Wolf summation, despite being infinitely differentiable at r c , converges similarly quickly as the original summation. Finally, it is discussed how to reduce the computational burden of numerically exact Monte Carlo simulations using the Wolf summation even when it does not properly converge. [ABSTRACT FROM AUTHOR]

Machine learning (ML) has been an important arsenal in computational biology used to elucidate protein function for decades. With the recent burgeoning of novel ML methods and applications, new ML approaches have been incorporated into many areas of computational biology dealing with protein function. We examine how ML has been integrated into a wide range of computational models to improve prediction accuracy and gain a better understanding of protein function. The applications discussed are protein structure prediction, protein engineering using sequence modifications to achieve stability and druggability characteristics, molecular docking in terms of protein–ligand binding, including allosteric effects, protein–protein interactions and protein-centric drug discovery. To quantify the mechanisms underlying protein function, a holistic approach that takes structure, flexibility, stability, and dynamics into account is required, as these aspects become inseparable through their interdependence. Another key component of protein function is conformational dynamics, which often manifest as protein kinetics. Computational methods that use ML to generate representative conformational ensembles and quantify differences in conformational ensembles important for function are included in this review. Future opportunities are highlighted for each of these topics. [ABSTRACT FROM AUTHOR]

[Display omitted] • Complete vibrational assignments of all species and its harmonic scaled force constants are reported. • NBO and AIM calculations support the higher stability of monohydrate dimer due to the six H bonds interactions. • The monohydrated dimer reveals a higher solvation energy in aqueous solution. • The monohydrate dimer is the most reactive species, as revealed by the lowest gap value. • Anhydrous and monohydrate species evidence by NBO calculations a very important delocalization of electrons. Experimental FT-IR, FT-Raman and UV spectra have been combined with hybrid B3LYP/6–311++G** calculations and the scaled quantum mechanical force field (SQMFF) methodology to study structural and vibrational properties of monohydrated dimer (MD) of violuric acid in gas and aqueous media. Complete vibrational assignments and its scaled force constants are reported together with the corresponding to anhydrous and monohydrate monomer. From four anhydrous C1, C2, C3, C4 monomers, C4 is the most stable in both media. In solution, the initial structure of C2 change to the tautomeric species most stable C4. The MD reveals a higher solvation energy while natural bond orbital (NBO) and atoms in molecules (AIM) calculations support the higher stability of this species due to the six H bonds interactions and to its higher expansion of volume in solution. The MD is the most reactive species, as revealed by the lowest gap value and by high global electrophilicity and most negative global nucleophilicity indexes. Very good concordances are observed among the predicted IR, Raman, 13C NMR and UV spectra and the corresponding experimental ones. Comparisons of predicted 13C NMR and electronic spectra with the experimental one show that those three species of violuric acid could be present in aqueous solution. Similar f(νC=O) and f(νC-O) force constants for the three species are justified by the important delocalization of electrons evidenced in anhydrous and monohydrate species by NBO calculations. [ABSTRACT FROM AUTHOR]

Dipalmitoylphosphatidylcholine is a phospholipid of major importance for biological systems. Molecular dynamics simulation investigations of this lipid focused on their behavior at human body temperature (≈ 37 °C or 310 K). For some applications, however, it is necessary to study its properties at room temperature (≈ 25 °C or 298 K). A small difference in temperature at this range is responsible for a phase transition in the lipid bilayer. Therefore, molecular dynamics simulations are carried out applying six different force fields from the GROMOS family to compare the less ordered phase (liquid-crystalline phase) with a more ordered phase (gel phase) of the hydrated bilayer of dipalmitoylphosphatidylcholine formed at 323 K and 298 K, respectively. The analysis of the bilayer structural quantities is used to evaluate order and packing at the two temperatures. The area per lipid and deuterium order parameter results are in agreement with simulation results from the literature and are also compared with experimental data. These parameters, however, do not provide a clear picture of the low-temperature gel phase present in the simulations using the force fields from the GROMOS family. To address this, a strategy for computing the lipid phase nematic order parameter is proposed, and a reference gel phase is simulated using the CHARMM36 force field for comparison. The results are consistent with other structural quantities but reveal a level of order that is below the expected for an ordered gel phase for the GROMOS force fields. Visual inspection of the simulation trajectories suggests the presence of a ripple phase. Overall, the GROMOS 54A8 provides the best performance among the tested GROMOS force fields for both investigated temperatures, even lacking a proper representation of the ordered gel phase. [Display omitted] • Among the GROMOS family, 54A8 is the one that provides the best agreement with the APL and deuterium order parameter experimental data for DPPC bilayer. • None of the force fields from GROMOS family reproduce the structure expected for DPPC bilayers at 298 K. • The nematic order parameter seems to be a more adequate quantity to evaluate lipid bilayer phase. [ABSTRACT FROM AUTHOR]

We introduce TUPÃ, a Python‐based algorithm to calculate and analyze electric fields in molecular simulations. To demonstrate the features in TUPÃ, we present three test cases in which the orientation and magnitude of the electric field exerted by biomolecules help explain biological phenomena or observed kinetics. As part of TUPÃ, we also provide a PyMOL plugin to help researchers visualize how electric fields are organized within the simulation system. The code is freely available and can be obtained at https://mdpoleto.github.io/tupa/. [ABSTRACT FROM AUTHOR]

In this article, two main approaches to the prediction of thermal conductivities by molecular dynamics (MD) simulations are discussed, namely non-equilibrium molecular dynamics simulations (NEMD) and the application of the Green–Kubo formula, i.e., EMD. NEMD methods are more affected by size effects than EMD methods. The thermal conductivities of silicone rubbers in special were found as a function of the degree of crosslinking. Moreover, the thermal conductivities of thermoplastic polyurethane as function of the mass fraction of soft segments were obtained by those MD simulations. All results are in good agreement with data from the experimental literature. After the analysis of normalized heat flux autocorrelation functions, it has been revealed that heat in the polymers is mainly transferred by low-frequency phonons. Simulation details as well as advantages and disadvantages of the single methods are discussed in the article. [ABSTRACT FROM AUTHOR]

Carbon force fields are widely used for obtaining structural properties of carbon nanomaterials. We evaluate the performance of a wide range of carbon force fields for obtaining molecular structures of prototypical C60 fullerenes. The reference geometries are optimized using the hybrid B3LYP-D3BJ density functional. The Gaussian approximation potential (GAP-20) machine-learning-based force field attains a root-mean-square deviation (RMSD) of merely 0.014 Å over a set of 29 unique C–C bond distances. This represents a significant improvement over traditional empirical force fields, which result in RMSDs ranging between 0.023 (LCBOP-I) and 0.073 (EDIP) Å. Performance of the GAP-20 force field is on par with that of the PM6 and AM1 semiempirical methods. Moreover, the GAP-20 force field attains a mean signed deviation of 0.003 Å indicating it is free of systematic bias toward underestimating or overestimating the fullerene bond distances. We therefore recommend the GAP-20 force field for optimizing the equilibrium structures of fullerenes and nanotubes. [ABSTRACT FROM AUTHOR]

The synthetic cyclohexenecarboxylate ester antiviral Oseltamivir (O) have been theoretically studied by B3LYP/6–311 + + G** calculations to estimate its reactivity and behaviour in gas and aqueous media. The most stable structure obtained in above media is consistent with that reported experimental for Oseltamivir phosphate. The solvation energy value of (O) in aqueous media is between the predicted for antiviral Idoxuridine and Ribavirin. Besides, (O) containing a NH2 group and NH group reveals lower solvation energy compared with other antiviral agents with an NH2 group, such as Ribavirin, Cidofovir, and Brincidofovir. Atomic charges on N and O atoms in acceptors and donor groups reveal different behaviours in both media, while the natural bond orbital (NBO) studies show a raised stability of (O) in aqueous solution. This latter resulted is in concordance with the lower reactivity evidenced in water. Frontier orbital studies have revealed that (O) in gas phase has a very similar gap value to antiviral Cidofovir used against the ebola disease, while Chloroquine in the two media are more reactive than (O). This study will allow to identify (O) by using vibrational spectroscopy because the 144 vibration modes expected have been assigned using the harmonic force fields calculated from the scaled mechanical force field methodology (SQMFF). Scaled force constants for (O) in the mentioned media are also reported for first time. Due to hydration of the C = O and NH2 groups by solvent molecules, the calculations in solution produce variations not only in the IR wavenumbers bands, but also in their intensities. [ABSTRACT FROM AUTHOR]

[Display omitted] • Complete vibrational assignments of 216 vibration modes of cholesterol in gas phase and ethanol solution are reported. • AIM calculations predicted intra-molecular interactions between CH 3 /CH 3 , CH 3 /CH 2 and CH 2 /CH 2 groups. • NBO studies predicted that the OH group and the four fused rings play important roles in the stability of cholesterol. • Electronic spectra at different ethanol concentrations suggest that positions of maxima increase with the solution concentration. • Frontier orbitals predicted low reactivity of cholesterol in ethanol probably due to its high ω value in this medium. In this investigation, the experimental FT-IR and FT-Raman spectra of cholesterol in the solid phase and in ethanol solution have been combined with the B3LYP/6–311++G** calculations and the scaled quantum mechanical force field (SQMFF) methodology, normal internal coordinates and transferable scaling factors to obtain the complete vibrational assignments of 216 vibration modes expected. Hence, complete vibrational assignments for that steroid of greatest biological importance are reported for first time in gas phase and ethanol solution together with its scaled force constants. Changes in the positions of some bands and in force constants values are observed in the different media due to the predicted intra-molecular interactions between CH 3 /CH 3 , CH 3 /CH 2 and CH 2 /CH 2 groups by atoms in molecules (AIM) calculations. The 1H- and 13C NMR chemical shifts of normal and deuterated cholesterol in aqueous solution confirm that the H atom of OH group is involved in the formation of H bonds in solution. Studies of experimental electronic spectra of cholesterol in different concentrations of ethanol revealed that the positions of peaks maxima increase conform increase the solution concentration. The natural bond orbital (NBO) analyses reveal that the polar OH group and the four fused rings play important roles in the stability and properties of cholesterol than the large hydrophobic moiety. Frontier orbitals predicted low reactivity of cholesterol in ethanol probably due to its high ω value in this medium. [ABSTRACT FROM AUTHOR]

Cellular membranes are composed of a wide diversity of lipid species in varying proportions and these compositions are representative of the organism, cellular type and organelle to which they belong. Because models of these molecular systems simulated by MD steadily gain in size and complexity, they are increasingly representative of specific compositions and behaviors of biological membranes. Due to the number of lipid species involved, of force fields and topologies and because of the complexity of membrane objects that have been simulated, LIMONADA has been developed as an open database allowing to handle the various aspects of lipid membrane simulation. LIMONADA presents published membrane patches with their simulation files and the cellular membrane it models. Their compositions are then detailed based on the lipid identification from LIPID MAPS database plus the lipid topologies and the force field used. LIMONADA is freely accessible on the web at https://limonada.univ-reims.fr/. [ABSTRACT FROM AUTHOR]

Enzymology is concerned with the study of enzyme structure, function, regulation and kinetics. It is an interdisciplinary subject that can be treated as an exclusive sphere of exhaustive inquiry within mathematical, physico‐chemical and biological sciences. Hence, teaching of enzymology, in general, and enzyme kinetics, in particular, should be undertaken in an interdisciplinary manner for a holistic appreciation of this subject. Further, analogous examples from everyday life should form an integral component of the teaching for an intuitive grasp of the subject matter. Furthermore, simulation‐based appreciation of enzyme kinetics should be preferred over simplifying assumptions and approximations of traditional enzyme kinetics teaching. In this Words of Advice, I outline the domain depth of enzymology across the various disciplines and provide initial ideas on how appropriate analogies can provide firm insights into the subject. Further, I demonstrate how an intuitive feel for the subject can help not only in grasping abstract concepts but also extending it in experimental design and subsequent interpretation. Use of simulations in grasping complex concepts is also advocated given the advantages this medium offers over traditional approaches involving images and molecular models. Furthermore, I discuss the merits of incorporating the historical backdrop of major discoveries in enzymological teaching. We, at AstraZeneca, have experimented with this approach with the desired outcome of generating interest in the subject from people practising diverse disciplines. [ABSTRACT FROM AUTHOR]

Properties and functions of various ZnO materials are intensively investigated in biological systems for diagnostics, therapy, health risks assessment as well as bactericidal and decontamination purposes. Herein, the interface between ZnO and biological environment is studied by characterizing adsorption of bovine serum albumin (BSA) and fetal bovine serum (FBS) using atomic force microscopy with CF4‐treated tips. Similar molecular morphologies (thickness around 2 nm) yet different binding forces to ZnO (10–25 nN) are observed. These observations are corroborated by atomic scale simulations of BSA on (0001) ZnO surface using force‐field method and showing rearrangements of Zn surface atoms. Such binding may have an impact also on other properties of ZnO–BSA complex. [ABSTRACT FROM AUTHOR]

Background: Many people with incomplete spinal cord injury (iSCI) have the ability to maneuver while walking. However, neuromuscular impairments create challenges to maintain stability. How people with iSCI maintain stability during walking maneuvers is poorly understood. Thus, this study compares maneuver performance in varying external conditions between persons with and without iSCI to better understand maneuver stabilization strategies in people with iSCI.Methods: Participants with and without iSCI walked on a wide treadmill and were prompted to perform lateral maneuvers between bouts of straight walking. Lateral force fields applied to the participants' center of mass amplified or attenuated the participants' movements, thereby increasing the capability of the study to capture behavior at varied levels of challenge to stability.Results: By examining metrics of stability, step width, and center of mass dynamics, distinct strategies emerged following iSCI. The minimum margin of stability (MOSmin) on each step during maneuvers indicated persons with iSCI generally adapted to amplified and attenuated force fields with increased stability compared to persons without iSCI, particularly using increased step width and reduced center of mass excursion on maneuver initiation. In the amplified field, however, persons with iSCI had a reduced MOSmin when terminating a maneuver, likely due to the challenge of the force field opposing the necessary lateral braking. Persons without iSCI were more likely to rely on or oppose the force field when appropriate for movement execution. Compared to persons with iSCI, they reduced their MOSmin to initiate maneuvers in the attenuated and amplified fields and increased their MOSmin to arrest maneuvers in the amplified field.Conclusions: The different force fields were successful in identifying relatively subtle strategy differences between persons with and without iSCI. Specifically, persons with iSCI adopted increased step width and reduction in center of mass excursion to increase maneuver stability in the amplified field. The amplified field may provoke practice of stable and efficient initiation and arrest of walking maneuvers. Overall, this work allows better framing of the stability mechanisms used following iSCI to perform walking maneuvers. [ABSTRACT FROM AUTHOR]

Many molecular simulation methods use force fields to help model and simulate molecules and their behavior in various environments. Force fields are sets of functions and parameters used to calculate the potential energy of a chemical system as a function of the atomic coordinates. Despite the widespread use of force fields, their inadequacies are often thought to contribute to systematic errors in molecular simulations. Furthermore, different force fields tend to give varying results on the same systems with the same simulation settings. Here, we present a pipeline for comparing the geometries of small molecule conformers. We aimed to identify molecules or chemistries that are particularly informative for future force field development because they display inconsistencies between force fields. We applied our pipeline to a subset of the eMolecules database, and highlighted molecules that appear to be parameterized inconsistently across different force fields. We then identified over-represented functional groups in these molecule sets. The molecules and moieties identified by this pipeline may be particularly helpful for future force field parameterization. [ABSTRACT FROM AUTHOR]

Complete vibrational assignments have been performed for free base, cationic, and hydrochloride species derived from antiviral adamantadine by a combination of hybrid B3LYP with the 6‐31G* and 6‐311++G** basis sets and the scaled quantum force field methodology. Normal internal coordinates and scaling factors were used to obtain the harmonic force fields and scaled force constants of three species in gas phase and in aqueous solution. Bond lengths and angles of cationic and hydrochloride species show very good concordances with experimental amantadinium azide. The cationic species reveals a higher solvation energy value compared with antiviral agents; however, brincidofovir, the antiviral used for Ebola disease, presents a higher reactivity in contrast to adamantadine. A positive value of Mulliken charge on N1 of hydrochloride species in solution could justify the ionic character of the H29···Cl30 bond as it is possible to observe by bond order and atoms in molecules calculations. The hydrochloride species is the most reactive in both media, while the cationic species is the least reactive. High electrophilicity and nucleophilicity indices of cationic species in both media justify its higher hydration. Good concordances were observed between experimental and predicted 1H and 13C NMR and electronic spectra. In solution, the three species are present as demonstrated by the experimental ultraviolet‐visible spectrum of hydrochloride amantadine. [ABSTRACT FROM AUTHOR]

Many key industrial processes, from electricity production, conversion, and storage to electrocatalysis or electrochemistry in general, rely on physical mechanisms occurring at the interface between a metallic electrode and an electrolyte solution, summarized by the concept of an electric double layer, with the accumulation/depletion of electrons on the metal side and of ions on the liquid side. While electrostatic interactions play an essential role in the structure, thermodynamics, dynamics, and reactivity of electrode-electrolyte interfaces, these properties also crucially depend on the nature of the ions and solvent, as well as that of the metal itself. Such interfaces pose many challenges for modeling because they are a place where quantum chemistry meets statistical physics. In the present review, we explore the recent advances in the description and understanding of electrode-electrolyte interfaces with classical molecular simulations, with a focus on planar interfaces and solvent-based liquids, from pure solvent to water-in-salt electrolytes. [ABSTRACT FROM AUTHOR]

Quantum chemistry in the form of density functional theory (DFT) calculations is a powerful numerical experiment for predicting intermolecular interaction energies. However, no chemical insight is gained in this way beyond predictions of observables. Energy decomposition analysis (EDA) can quantitatively bridge this gap by providing values for the chemical drivers of the interactions, such as permanent electrostatics, Pauli repulsion, dispersion, and charge transfer. These energetic contributions are identified by performing DFT calculations with constraints that disable components of the interaction. This review describes the second-generation version of the absolutely localized molecular orbital EDA (ALMO-EDA-II). The effects of different physical contributions on changes in observables such as structure and vibrational frequencies upon complex formation are characterized via the adiabatic EDA. Example applications include red- versus blue-shifting hydrogen bonds; the bonding and frequency shifts of CO, N2, and BF bound to a [Ru(II)(NH3)5]2 + moiety; and the nature of the strongly bound complexes between pyridine and the benzene and naphthalene radical cations. Additionally, the use of ALMO-EDA-II to benchmark and guide the development of advanced force fields for molecular simulation is illustrated with the recent, very promising, MB-UCB potential. [ABSTRACT FROM AUTHOR]

Ab initio molecular dynamics (AIMD) has become a popular simulation technique but long simulation times are often hampered due to its high computational effort. Alternatively, classical molecular dynamics (MD) based on force fields may be used, which, however, has certain shortcomings compared to AIMD. In order to alleviate that situation, a trajectory-based machine learning (TrajML) approach is introduced for the construction of force fields by learning from AIMD trajectories. Only nuclear trajectories are required, which can be obtained by other methods beyond AIMD as well. We developed an easy-to-use MD machine learning package (TrajML MD) for instant modelling of the force field and system-focussed prediction of molecular configurations for MD trajectories. It consumes similar computational resources as classical MD but can simulate complex systems with a higher accuracy due to the targeted learning on the system of interest. [ABSTRACT FROM AUTHOR]

Molecular Dynamics (MD) was used to determine the accuracy of different force fields on predicting the elastic modulus of single crystal aluminum through nanoindentation tests. In this work, nanoindentation was performed using three different types of force fields (EAM, MEAM and ReaxFF) and the resulting elastic modulus was compared to the value obtained using elastic constants from standard small strain tensile simulations. When the predicted modulus of each force field was compared to the modulus via elastic constants, the ReaxFF resultant moduli were similar to that of nanoindentation, but for EAM and MEAM the two methods produced significantly different values. Therefore, even if a force field is parameterised for elastic modulus, it does not guarantee the force field will accurately predict the modulus from other procedures. As well, two different methods for calculating modulus from indentation curves were compared: The Hertz approximation and the Oliver and Pharr (O&P) method. For EAM and MEAM force fields, the Hertz method significantly under predicted modulus while the O&P method was in better agreement with the experimental modulus. [ABSTRACT FROM AUTHOR]

Social impact assessment (SIA) is experiencing both evolutionary and revolutionary forces for change. Using the example of New South Wales, Australia, forces for change include community pressure and shifting expectations, industry desire for clarity and certainty, departmental leadership, a collaborative approach to policy development, and perceived legitimacy of the guideline itself. Inhibiting these forces are general resistance to change, a concern around costs of good SIA, unfamiliarity with social sciences, and insufficient practitioner capacity. The recent Rocky Hill judgement, which highlights concepts such as community cohesion, sense of place, and distributive equity, may accelerate change. However, there is also a need to build capacity among SIA practitioners, and afford sufficient time and budget to meet the standard of leading-practice guidelines. At the same time, unfolding trends such as the climate change and extinction crises, the gendered nature of development, ever-widening inequalities, and 'post-truth' discourses may catalyse more revolutionary change in SIA practice – changes that paradoxically may enable SIA to reclaim its social-science principles and the overarching goal of sustainable social development. [ABSTRACT FROM AUTHOR]

Intrinsically disordered proteins (IDPs) are a class of proteins without stable three-dimensional structures under physiological conditions. IDPs exhibit high dynamic nature and could be described by structural ensembles. As one of the most widely used tools, molecular dynamics (MD) simulation could provide the atomic descriptions of the structural ensemble of IDPs. However, the accuracy of the MD simulation largely depends on the accuracy of the force field. In this paper, we compared the structural ensembles of the activation domain 1 (AD1) in p53 tumor suppressor obtained from the widely used force fields, AMBER99SB-ILDN, CHARMM27, CHARMM36m with different water models. The results show that CHARMM36m generates more extended conformations than other force fields, while CHARMM27 prefers to sample the α -helical structure. Moreover, the chemical shifts obtained by CHARMM36m are the closest to the experimental measurements. These results indicate that the CHARMM36m force field performs best in characterizing the structure properties of p53 AD1. Water models are also critical to describe the structural ensemble of IDPs. TIP4P water model can obtain more extended conformations and produce more local helical conformations than the TIP3P model in our simulation. In addition, we also compare the chemical shifts predicted by different chemical shift predicting programs with experimental measurements, the results show that SHIFTX2 obtains the best performance in the chemical shifts prediction. • CHARMM36m force field achieves the best performance in the simulation of p53 AD1. • SHFITX2 is the most accurate chemical shift calculation tool. • AMBER99SB-ILDN generates more heterogeneous conformations than the other force fields. [ABSTRACT FROM AUTHOR]

[Display omitted] • Structures of cyclic dimers and tetramer of adenine were studied by DFT calculations. • The characteristics of N-H···N interactions were studied by NBO and AIM calculations. • Complete vibrational assignments of cyclic dimers are presented. • Vibronic bands are observed in the electronic spectra. • Different scaled force constants values show the cyclic dimers of adenine. In this work, three different cyclic dimers and a tetramer of adenine taken from the experimental structure determined by X-ray diffraction have been studied by combination of experimental FT-IR, FT-Raman and UV–Visible spectra with hybrid B3LYP/6–311++G** and scaled quantum mechanical force field (SQMFF) calculations in order to perform the complete assignments of bands observed in the vibrational spectra. The characteristics of different N-H···N interactions of those three cyclic structures together with the group of IR bands observed between 2865 and 2599 cm−1 have been elucidated considering the tetrameric structure. The cyclic dimers and the tetramer of adenine confirm that the bands observed between 2865 and 2599 cm−1 are not due to N-H···N interactions but to bands of combination, as was previously suggested. The experimental available deuterated IR and terahertz spectra have allowed the complete assignments of regions of higher and lower wavenumbers. Good correlations were acquired comparing the theoretical IR, Raman and UV spectra of three species and the tetramer with the analogous experimental ones, suggesting the presence of all species in both phases. Vibronic bands are observed in the electronic spectra when adenine concentration is increased in aqueous solution evidencing the presence of monomer, tautomers and dimers, as reported by different studies. Similar characteristics of H bonds interactions are predicted for dimers 1 and 2 but different from the dimer 3, as revealed by using NBO and AIM calculations. Different scaled force constants values were found for the cyclic dimers 1 and 2, as compared to the corresponding to dimer 3. [ABSTRACT FROM AUTHOR]

• Prediction of thermomechanical properties of fluoropolymers is at its infancy. • Atomistic force fields for fluoropolymers are parametrized for oligomers. • Atomistic forcefields are tested for accuracy and transferability to longer chains. • Large variability in predicted properties of different force fields are discussed. Copolymers of vinylidene fluoride (VDF) and hexafluoropropylene (HFP) make up the largest volume of fluoroelastomers sales. Within this family, Viton A (VDF/HFP 60/40 wt%, 66% fluorine) is most important commercially. Determination of thermomechanical properties of such fluorinated polymers is still limited to experimentation or empirical models, while computational prediction of their physical properties is still at its infancy. Considerable efforts have been made to develop molecular force fields for the prediction of properties of various crystalline as well as amorphous fluorinated substances. These force fields were parametrized based on small molecules or oligomers, hence their transferability to longer and more complex (i.e. copolymer) chain architectures must be tested. In this work, thermodynamic, structural, and mechanical properties of the Viton A fluoroelastomer are evaluated using atomistic molecular dynamics (MD) simulations for several force fields and compared with available experimental data. Differences in molecular structure of the chains modeled by different force fields are shown to substantially influence thermodynamic and mechanical behavior. OPLS-derived force fields give rise to extended chains that are more mobile and result in softer material that lack in molecular structure. Other force fields rely on strong nonbonded interactions that interfere with chain dynamics and mechanics. PCFF is shown to most satisfactorily predict structural properties and thermal volumetric behavior around T g , demonstrating relatively successful transferability to long linear polymer chains. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

A key component to enhancing reproducibility in the molecular simulation community is reducing ambiguity in the parameterization of molecular models used to perform a study. Ambiguity in molecular models often stems from inadequate usage documentation of molecular force fields and the fact that force fields are not typically disseminated in a format that is directly usable by software. Specifically, the lack of a generally applicable scheme for the annotation of the rules of a particular force field and a general purpose tool for performing automated parameterization (i.e., atom-typing) based on these rules, may lead to errors in model parameterization that are not easily identified. Here, we present Foyer, an open-source Python tool that enables users to define and apply force field atom-typing rules in a format that is both human- and machine-readable and provides a framework for force field dissemination, thus eliminating ambiguity in atom-typing and improving reproducibility. Foyer defines force fields in an XML format, where SMARTS strings are used to define the chemical context of a particular atom type and "overrides" are used to set rule precedence, rather than a rigid hierarchical scheme. Herein we describe the underlying methodology and force field annotation scheme of the Foyer software, demonstrate its application in several use-cases, and discuss specific aspects of the Foyer approach that are designed to improve reproducibility. [ABSTRACT FROM AUTHOR]

• Ionic conductivities of LiCl at elevated temperature are reported. • Transference numbers of Li+ and Cl− become comparable at high concentration. • This may be resulted from ion-specific concentration dependence of mobility. Lithium chloride LiCl is widely used as a prototype system to study the strongly dissociated 1-1 electrolyte solution. Here, we combined experimental measurements and classical molecular dynamics simulations to study the ion conduction in this system. Ionic conductivities were reported at both 20 °C and 50 °C from experiments and compared to results from molecular dynamics simulations. The main finding of this work is that transference numbers of Li+ and Cl− become comparable at high concentration. This phenomenon is independent of the force fields employed in the simulation and may be resulted from the ion-specific concentration dependence of mobility. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations were performed to systematically compare four all-atom classical ionic liquid force fields and provide recommendations for the appropriate selection of an ionic liquid force field for the calculation of Henry's constants of gases. Four solutes of varying polarity, viz., CH 4 , CO 2 , NH 3 , and SO 2 were investigated. The ionic liquids considered in this work contain the same cation, 1- n -butyl-3-methylimidazolium [C 4 mim]+ paired with four different anions chloride Cl−, methylsulfate [MeSO 4 ]-, dicyanamide [DCA]-, and bis(trifluoromethanesulfonyl)imide [NTf 2 ]-. The calculations were performed at three temperatures of 333, 353, and 373 K to enable the computation of enthalpies and entropies of absorption. Based on a comparison of the predicted results with those available in the literature, it was observed that the recently developed virtual-site ionic liquid force field tends to exhibit an overall better agreement with the published data in comparison to other force fields. Our results further indicate that, in general, SO 2 is the most soluble gas due to the strongest interaction with ionic liquids, followed by NH 3 , CO 2 and CH 4. [ABSTRACT FROM AUTHOR]

Abstract The three steps systematic parameterization procedure, 3SSPP, to develop force fields of polar liquids proposed by our group (J. Chem. Theory Comput. 2015 , 11, 68 3) is reviewed. The method allows obtaining independently the charge distribution and Lennard-Jones parameters of pure components if the experimental dielectric constant, surface tension and liquid density are used as target properties. Different methods to determine the partial atomic charges from electronic structure calculations of isolated polar molecules are analyzed. It is shown that the charge distribution plays an important role in several properties of pure components and binary mixtures, including solubility. Molecular dynamics simulations of 12 typical polar liquids in aqueous solutions show that the TraPPE-UA force field, in general, underestimates the experimental solubility in a liquid-liquid equilibrium at room conditions. The 3SSPP is used to reparameterize the TraPPE-UA non-bonding parameters of liquid 1-propanol, 2-pentanone and methyl acetate using scaled atomic charges from the Hirshfeld partition scheme. The new parameters predict the correct solubility of 1-propanol in water but fail to reproduce that of the other two molecules. The new parameterization procedure, 4SSPP, is extended to include the solubility as a target property. The solubility is reproduced by modifying the charge distribution obtained for the pure components keeping constant the molecular dipole moment and Lennard-Jones parameters. The method is applied to 2-pentanone and methyl acetate as pure components and their mixtures with water. The target properties of the pure components are almost unaffected after the refining process of the charge distribution. The liquid-vapor phase diagram is also determined for a single component. The results show that the use of an explicit solvent, water in this case, in a simulation is a good way to improve, with a small additional computational cost, the force field parameters of pure components to be used in computer simulations in multicomponent systems. The new parameters are used to obtain the liquid density of 1-propanol/methanol and methyl acetate/methanol mixtures and excellent agreement with experimental data is found. [ABSTRACT FROM AUTHOR]

Abstract In this work, the potassium 5-Br-2-isonicotinoyltrifluoroborate salt (B-ITFB) have been experimentally characterized by using FT-IR, FT-Raman and Ultravioleta-visible spectra while Ab-initio calculations in gas and in aqueous solution phases were employed to predict their structural and vibrational properties. Here, the results were compared with those reported for the potassium 2-isonicotinoyltrifluorborate salt (ITFB) in order to know the impact of Br on the 2-isonicotinoyl ring and its effects on the properties of B-ITFB. Potential energy surface using B3LYP/6-311++G** calculations has revealed two conformers for B-ITFB with C 1 symmetries where only one of them presents the minimum energy. The incorporation of Br in the 5 position of isonicotinoyl ring generates: (i) a change in the symmetry from C S in ITFB to C 1 in B-ITFB, (ii) a decreasing in the solvation energy due to higher size of Br, (iii) notable reduction in the Mulliken charges on all the C atoms of ring and, especially, on the C11 atom of trifluoroborate group in both media, (v) smaller bond order values, (vi) an important inductive acceptor effect, (vii) a decreasing in the electron density distribution, specifically in solution and (viii) a smaller reactivity and low electrophilicity and nucleophilicity indexes, as compared with ITFB. On the other hand, for B-ITFB the force fields in both media, the complete assignments of 45 normal vibration modes and the force constants are reported for first time. Graphical abstract Image 1 Highlights • B-ITFB was characterized by using FT-IR, FT-Raman and Ultravioleta-visible spectra. • A change in the symmetry it is observed for B-ITFB by DFT calculations. • The incorporation of Br in the ring generates decreasing in the solvation energy. • The Br atom in the ring generates an important inductive acceptor effect. • The force fields, complete assignments and force constants are reported for B-ITFB. [ABSTRACT FROM AUTHOR]

Abstract Refrigeration has become essential in our society and for our standard of living. Though environmental issues regarding the refrigerants that circulate in heating, ventilation and air conditioning (HVAC&R) cycles have resulted in enormous consequences for this technology sector. Twice in the last three decades, phase-out regulations got effective for established refrigerants, which has necessitated the adoption of suitable replacements, related to the need for data on the thermophysical properties of potential alternative working fluids. In this context, molecular simulation has emerged as important compliment to experimental studies, and we here provide an overview on molecular modelling approaches and simulation studies on different generations of refrigerants, though with focus on the current fourth generation of working fluids, i.e. hydrofluoroolefins (HFO). Due to increasing difficulties in meeting all different selection criteria for a specific application by a single component refrigerant, blends are becoming more and more important. We here present recent simulation results for vapor-liquid equilibria of different binary mixtures based on the newly introduced compound trifluoroethene (HFO-1123) as demonstrative example of the benefit of molecular simulation to provide information on mixtures for which no experimental data are available yet. We also discuss studies on conformational isomers and the development of equations of state as further research topics in which molecular simulations are already playing an important role in complementing experimental studies. Finally we highlight some future research directions in which simulation studies can be expected to make an important contribution to the understanding and theoretical modeling of refrigerant properties. [ABSTRACT FROM AUTHOR]

Investigations on the relative energy of two least-strain conformers for bicyclo[3.3.1]nonane 1, bicyclo[3.3.1]nonan-9-one 2, and their heteroanalogues: 3,7-dimethyl-3,7-diazabicyclo[3.3.1]nonane 3, 3,7-dimethyl-3,7-diazabicyclo[3.3.1]nonan-9-one 4 were performed using the calculations from the first principles (ab initio, DFT) as well as by semiempirical (NDDO, DFTB) and empirical (molecular mechanics, MM) techniques. For these quite simple structures, serious discrepancies in results of modeling between methods of different origins were revealed. Nonempirical calculations state that the "double chair" (CC) form is the most favorable for carbobicyclic structures 1 and 2, while 3,7-dimethyl-3,7-diaza compounds 3 and 4 are in general more prone to adopt the "chair-boat" (CB) conformation. The classical rationalization of these quantum chemistry results leads to the hypothesis similar to one that underlies the Gillespie VSEPR concept, namely that the 3,7-repulsion of lone electron pairs is stronger than the corresponding interaction of hydrogen atoms of C-H bonds. The semiempirical NDDO calculations retain the qualitative correspondence of the results to those of the ab initio calculations, while the results of more recent DFTB approaches are closer to MM in their qualitative inconsistency with high-level ab initio methods. In particular, for 4 the relative energy of CC is severely underestimated, erroneously predicting the predominance of this form over CB. The origin of this failure could lie in the relatively coarse parameterization of common force fields when concerning the subtle interplay between different types of interatomic interactions and could be recovered, although only partially, by the proper choice of the charge scheme to use the atomic-centered charges in the explicit account for the non-valency interactions in the Coulombic form. [ABSTRACT FROM AUTHOR]

Abstract Over the past decade, the Mie λ-6 (generalized Lennard-Jones) potential has grown in popularity due to its improved accuracy for predicting vapor-liquid coexistence densities and pressure compared to the traditional Lennard-Jones 12-6 potential. This manuscript explores the hypothesis that greater accuracy in characterizing the coexistence properties may lead to greater accuracy for viscosity predictions. Four united-atom force fields are considered in detail: the Transferable Potentials for Phase Equilibria (TraPPE-UA and the recently developed TraPPE-2) model of Siepmann and coworkers, the Transferable Anisotropic Mie (TAMie) model of Gross and coworkers, the fourth generation anisotropic-united-atom (AUA4) model of Ungerer and coworkers, and the model of Potoff and coworkers. Equilibrium molecular dynamics simulations are analyzed using the Green-Kubo method for viscosity characterization. Simulations are performed for linear alkanes with two to twenty-two carbons and branched alkanes with four to eight carbons. Simulation conditions follow the saturated liquid from reduced temperatures of 0.5–0.85 and along the 293 K isotherm in the dense liquid region. In general, the more accurate force fields for coexistence properties do indeed predict viscosity more accurately. For saturated liquids, both Mie-based potential models (Potoff and TAMie) provide roughly 10% accuracy for linear alkanes, while deviations are between 20 and 50% for TraPPE-UA. For branched alkanes, the performance is slightly diminished, but Potoff still provides roughly 15–20% accuracy, while the TAMie force field results in deviations of 20–40%, and TraPPE-UA has deviations of approximately 25–60%. The AUA4 deviations are 10–20% for ethane and 30–60% for 2,2-dimethylpropane, the only compounds tested with the AUA4 force field. The TraPPE-2 deviations for ethane are similar to those using the original TraPPE force field, namely, between 10 and 20%. The percent deviations for each compound and force field tend to increase with decreasing temperature, with the exception of the Potoff deviations for propane, which are nearly constant to the triple point temperature. For compressed liquids, the Mie-based potential models perform better once again than the Lennard-Jones-based force fields, but tend to over estimate the viscosity at very high densities. As the Potoff and TAMie models also tend to over estimate the pressure at high densities, a fortuitous cancellation of errors leads to predictions of viscosity with respect to pressure that are accurate to within about 10%. The comparison with experimental viscosity data is limited to pressures below 200 MPa for most normal and branched alkanes. However, accurate predictions are obtained for propane near 1000 MPa with the Potoff force field. [ABSTRACT FROM AUTHOR]