Search

Molecular representation learning is a crucial task to accelerate drug discovery and materials design. Graph neural networks (GNNs) have emerged as a promising approach to tackle this task. However, most of them do not fully consider the intramolecular interactions, i.e. bond stretching, angle bending, torsion, and nonbonded interactions, which are critical for determining molecular property. Recently, a growing number of 3D-aware GNNs have been proposed to cope with the issue, while these models usually need large datasets and accurate spatial information. In this work, we aim to design a GNN which is less dependent on the quantity and quality of datasets. To this end, we propose a force field-inspired neural network (FFiNet), which can include all the interactions by incorporating the functional form of the potential energy of molecules. Experiments show that FFiNet achieves state-of-the-art performance on various molecular property datasets including both small molecules and large protein-ligand complexes, even on those datasets which are relatively small and without accurate spatial information. Moreover, the visualization for FFiNet indicates that it automatically learns the relationship between property and structure, which can promote an in-depth understanding of molecular structure., (© 2023. The Author(s).)

Hydration free energies of small molecules are commonly used as benchmarks for solvation models. However, errors in predicting hydration free energies are partially due to the force fields used and not just the solvation model. To address this, we have used the 3D reference interaction site model (3D-RISM) of molecular solvation and existing benchmark explicit solvent calculations with a simple element count correction (ECC) to identify problems with the non-bond parameters in the general AMBER force field (GAFF). 3D-RISM was used to calculate hydration free energies of all 642 molecules in the FreeSolv database, and a partial molar volume correction (PMVC), ECC, and their combination (PMVECC) were applied to the results. The PMVECC produced a mean unsigned error of 1.01±0.04kcal/mol and root mean squared error of 1.44±0.07kcal/mol, better than the benchmark explicit solvent calculations from FreeSolv, and required less than 15 s of computing time per molecule on a single CPU core. Importantly, parameters for PMVECC showed systematic errors for molecules containing Cl, Br, I, and P. Applying ECC to the explicit solvent hydration free energies found the same systematic errors. The results strongly suggest that some small adjustments to the Lennard-Jones parameters for GAFF will lead to improved hydration free energy calculations for all solvent models.

Charge scaling as an effective solution to the experiment-computation disagreement in molecular modelling of ionic liquids (ILs) could bring the computational results close to the experimental reference for various thermodynamic properties. According to the large-scale benchmark calculations of mass density, solvation, and water-ILs transfer-free energies in our series of papers, the charge-scaling factor of 0.8 serves as a near-optimal option generally applicable to most ILs, although a system-dependent parameter adjustment could be attempted for further improved performance. However, there are situations in which such a charge-scaling treatment would fail. Namely, charge scaling cannot really affect the simulation outcome, or minimally perturbs the results that are still far from the experimental value. In such situations, the vdW radius as an additional adjustable parameter is commonly tuned to minimize the experiment-calculation deviation. In the current work, considering two ILs from the quinuclidinium family, we investigate the impacts of this vdW-scaling treatment on the mass density and the solvation/partition thermodynamics in a fashion similar to our previous charge-scaling works, i.e., scanning the vdW-scaling factor and computing physical properties under these parameter sets. It is observed that the mass density exhibits a linear response to the vdW-scaling factor with slopes close to -1.8 g/mL. By further investigating a set of physiochemically relevant temperatures between 288 K and 348 K, we confirm the robustness of the vdW-scaling treatment in the estimation of bulk properties. The best vdW-scaling parameter for mass density would worsen the computation of solvation/partition thermodynamics, and a marginal decrease in the vdW-scaling factor is considered as an intermediate option balancing the reproductions of bulk properties and solvation thermodynamics. These observations could be understood in a way similar to the charge-scaling situation. i.e., overfitting some properties (e.g., mass density) would degrade the accuracy of the other properties (e.g., solvation free energies). Following this principle, the general guideline for applying this vdW-tuning protocol is by using values between the density-derived choice and the solvation/partition-derived solution. The charge and current vdW scaling treatments cover commonly encountered ILs, completing the protocol for accurate modelling of ILs with fixed-charge force fields.

Machine-learning (ML) models offer the potential to rapidly evaluate the vast inorganic crystalline materials space to efficiently find materials with properties that meet the challenges of our time. Current ML models require optimized equilibrium structures to attain accurate predictions of formation energies. However, equilibrium structures are generally not known for new materials and must be obtained through computationally expensive optimization, bottlenecking ML-based material screening. A computationally efficient structure optimizer is therefore highly desirable. In this work, we present an ML model capable of predicting the crystal energy response to global strain by using available elasticity data to augment the dataset. The addition of global strains improves our model's understanding of local strains too, significantly improving the accuracy of energy predictions on distorted structures. This allows us to construct an ML-based geometry optimizer, which we used for improving the predictions of formation energy for structures with perturbed atomic positions., Competing Interests: The authors declare no competing interests., (© 2022 The Author(s).)

The first attempt to describe water dates back to 1933 with the Bernal–Fowler model and it would take another forty years before the first computer simulation of liquid water by Barker and Watts in 1969. Since then, over a hundred different water models have been proposed. Despite being widely studied, water remains poorly understood. Examining the evolution of water models, we identified three distinct philosophies in water modelling, namely the employment of effective point charges in pioneering empirical models, the incorporation of polarization to describe many-body inductive effects and the extensive use of ab initio calculations to describe short-range effects. In doing so, we can appraise the current understanding of water and identify attributes that a water model should possess to capture the intricate interactions between water molecules.

In the present work, we have studied the structural, topological and spectroscopic properties of five cyclic and of open chain species derived from tricyclic bisguanidine compound in gas and aqueous phases combining the DFT calculations with the experimental infrared and 1 H NMR, 13 C NMR and UV–visible spectra. These species are members of the saxitoxin family and they were recently synthesized by Tsuchiya et al. (Chemistry. A European Journal, 21 (2015) 7835–7840). Here, the self consistent reaction force (SCRF) calculations were employed in aqueous medium to study the solvation energies by using the polarized continuum (PCM) and solvation (SM) models. All the calculations were performed with the 6-31G* and 6-311++G** basis sets. The atomic charges, electrostatic potentials, bond order, stabilization energy, topological properties suggest the structural connection between the cyclic cationic and saxitoxin species while the electrophilicity and nucleophilicity indexes could be one of the explanations for the Na v blocking activities of these species. The complete vibrational assignments for all the species are reported. The predicted spectra present a reasonable concordance with the corresponding experimental ones. [ABSTRACT FROM AUTHOR]

Deriving molecular structure from $$^3J$$ -couplings obtained from NMR experiments is a challenge due to (1) the uncertainty in the Karplus relation $$^3J(\theta )$$ connecting a $$^3J$$ -coupling value to a torsional angle $$\theta $$ , (2) the need to account for the averaging inherent to the measurement of $$^3J$$ -couplings, and (3) the sampling road blocks that may emerge due to the multiple-valuedness of the inverse function $$\theta (^3J)$$ of the function $$^3J(\theta )$$ . Ways to properly handle these issues in structure refinement of biomolecules are discussed and illustrated using the protein hen egg white lysozyme as example. [ABSTRACT FROM AUTHOR]

Comparison of three variants of the GROMOS force field for carbohydrates, 53A6 GLYC , 56A6 CARBO_R and a small modification of the latter, referred to as 56A6 CARBO_R+ , has been conducted by examining the standard binding free enthalpy of linear alcohols from 1-butanol to 1-dodecanol to α -cyclodextrin in aqueous solution. The double decoupling approach was employed to calculate the standard binding free enthalpy of 1-hexanol, while for all other compounds relative binding free enthalpies for pairs of alcohols differing by two carbon atoms were calculated from twin-system enveloping distribution sampling simulations. While all three force fields slightly overestimate the magnitude of the standard binding free enthalpy of 1-hexanol the 53A6 GLYC and 56A6 CARBO_R+ parameter sets are a little closer to the experimental data than 56A6 CARBO_R . For relative binding free enthalpies no significant difference between the force fields was observed. All three force fields support those experimental measurements that found a distinct increase in the binding affinity with increasing number of carbon atoms even for longer chain lengths up to 1-dodecanol. [ABSTRACT FROM AUTHOR]

New equations for torque and atomic force are derived for use in flexible molecule force fields with atomic multipoles. The expressions are based on Cartesian tensors with arbitrary multipole rank. The standard method for rotating Cartesian tensor multipoles and calculating torque is to first represent the tensor with n indexes and 3 n redundant components. In this work, new expressions for directly rotating the unique ( n + 1)( n + 2)/2 Cartesian tensor multipole components Θ pqr are given by introducing Cartesian tensor rotation matrix elements X( R). A polynomial expression and a recursion relation for X( R) are derived. For comparison, the analogous rotation matrix for spherical tensor multipoles are the Wigner functions D( R). The expressions for X( R) are used to derive simple equations for torque and atomic force. The torque and atomic force equations are applied to the geometry optimization of small molecule crystal unit cells. In addition, a discussion of computational efficiency as a function of increasing multipole rank is given for Cartesian tensors. © 2016 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

The construction of a novel protein force field called FFLUX, which uses topological atoms, is founded on high-rank and fully polarizable multipolar electrostatics. The machine learning method kriging successfully predicts multipole moments of a given atom with as only input the nuclear coordinates of the atoms surrounding this given atom. Thus, trained kriging models accurately capture the polarizable multipolar electrostatics of amino acids. Here we show that successful kriging models can also be constructed for non-electrostatic energy contributions. As a result, the full potential energy surface of the (molecular) system trained for can be predicted by the corresponding set of atomic kriging models. In particular, we report on the performance of kriging models for each atom's (A) (1) total atomic energy (EIQAA), (2) intra-atomic energy (EintraA) (both kinetic and potential energy), (3) exchange energy ( V X C A A ′ ) and (4) electrostatic energy ( V cl A A ′ ) of atom A with the rest of the system (A′), and (5) interatomic energy ( V inter A A ′ ). The total molecular energy can be reconstructed from the kriging predictions of these atomic energies. For the three case studies investigated (i.e. methanol, N-methylacetamide and peptide-capped glycine), the molecular energies were produced with mean absolute errors under 0.4, 0.8 and 1.1 kJ mol−1, respectively. [ABSTRACT FROM AUTHOR]

A non-polarizable force field based on atomic multipoles fit to reproduce experimental crystal properties and ab initio gas-phase dimers is described. The Ewald method is used to calculate both long-range electrostatic and 1/ r6 dispersion energies of crystals. The dispersion energy of a crystal calculated by a cutoff method is shown to converge slowly to the exact Ewald result. A method for constraining space-group symmetry during unit-cell optimization is derived. Results for locally optimizing 4427 unit cells including volume, cell parameters, unit-cell r.m.s.d. and CPU timings are given for both flexible and rigid molecule optimization. An algorithm for randomly generating rigid molecule crystals is described. Using the correct experimentally determined space group, the average and maximum number of random crystals needed to find the correct experimental structure is given for 2440 rigid single component crystals. The force field energy rank of the correct experimental structure is presented for the same set of 2440 rigid single component crystals assuming the correct space group. A complete crystal prediction is performed for two rigid molecules by searching over the 32 most probable space groups. [ABSTRACT FROM AUTHOR]

Computational protein design depends on an energy function and an algorithm to search the sequence/conformation space. We compare three stochastic search algorithms: a heuristic, Monte Carlo (MC), and a Replica Exchange Monte Carlo method (REMC). The heuristic performs a steepest-descent minimization starting from thousands of random starting points. The methods are applied to nine test proteins from three structural families, with a fixed backbone structure, a molecular mechanics energy function, and with 1, 5, 10, 20, 30, or all amino acids allowed to mutate. Results are compared to an exact, 'Cost Function Network' method that identifies the global minimum energy conformation (GMEC) in favorable cases. The designed sequences accurately reproduce experimental sequences in the hydrophobic core. The heuristic and REMC agree closely and reproduce the GMEC when it is known, with a few exceptions. Plain MC performs well for most cases, occasionally departing from the GMEC by 3-4 kcal/mol. With REMC, the diversity of the sequences sampled agrees with exact enumeration where the latter is possible: up to 2 kcal/mol above the GMEC. Beyond, room temperature replicas sample sequences up to 10 kcal/mol above the GMEC, providing thermal averages and a solution to the inverse protein folding problem. © 2016 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Biological membranes display a great diversity in lipid composition and lateral structure that is crucial in a variety of cellular functions. Simulations of membranes have contributed significantly to the understanding of the properties, functions and behaviour of membranes and membrane–protein assemblies. This success relies on the ability of the force field used to describe lipid–lipid and lipid–environment interactions accurately, reproducibly and realistically. In this review, we present some recent progress in lipid force-field development and validation strategies. In particular, we highlight how a range of properties obtained from various experimental techniques on lipid bilayers and membranes, can be used to assess the quality of a force field. We discuss the limitations and assumptions that are inherent to both computational and experimental approaches and how these can influence the comparison between simulations and experimental data. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov. [ABSTRACT FROM AUTHOR]

The currently available force field parameters for modified RNA residues in AMBER show significant deviations in conformational properties from experimental observations. The examination of the transferability of the recently revised torsion parameters revealed that there was an overall improvement in the conformational properties for some of the modifications but the improvements were still insufficient in describing the sugar pucker preferences ( J. Chem. Inf. Model. 2014, 54, 1129-1142). Here, we report an approach for the development and fine tuning of the AMBER force field parameters for 2-thiouridine, 4-thiouridine, and pseudouridine with diverse conformational preferences. The χ torsion parameters were reparameterized at the individual nucleoside level. The effect of combining the revised γ torsion parameter and modifying the Lennard-Jones σ parameters were also tested by directly comparing the conformational preferences obtained from our extensive molecular dynamics simulations with those from experimental observations. © 2016 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

The prediction of mutation-induced free-energy changes in protein thermostability or protein-protein binding is of particular interest in the fields of protein design, biotechnology, and bioengineering. Herein, we achieve remarkable accuracy in a scan of 762 mutations estimating changes in protein thermostability based on the first principles of statistical mechanics. The remaining error in the free-energy estimates appears to be due to three sources in approximately equal parts, namely sampling, force-field inaccuracies, and experimental uncertainty. We propose a consensus force-field approach, which, together with an increased sampling time, leads to a free-energy prediction accuracy that matches those reached in experiments. This versatile approach enables accurate free-energy estimates for diverse proteins, including the prediction of changes in the melting temperature of the membrane protein neurotensin receptor 1. [ABSTRACT FROM AUTHOR]

The structures of α- and β-maltose anhydrous and their corresponding monohydrated species were studied combining the FT-IR, FT-Raman and HATR spectra with DFT calculations. The four structures were optimized in gas and aqueous solution by using the hybrid B3LYP/6-31G* method. The self-consistent force field (SCRF) calculations together with the polarized continuum (PCM) model were used to study the systems in solution while the solvation energies were computed using the solvation model (SM). The calculated structural and vibrational properties could explain the anomerization of maltose in solution, as was reported in the literature while the natural bond orbital (NBO) analyses for those species support clearly the mutarotation equilibria between both forms in solution, evidencing the anhydrous forms the equilibrium: α (45%) ⇔ β (55%), similar to that experimentally reported at 20 °C. Bands of all the species observed in the vibrational spectra support the presence of the anomeric species of maltose in solution while the presence of dimeric species justify the intense IR bands observed in the higher wavenumbers region. The similar gap values for maltose and lactose probably justify that these sugars are reducing sugars while the high values in sucrose could explain that it is a non-reducing sugar. On the other hand, the sweeteners cyclamate and saccharine are most reactive in solution than the sugars maltose, lactose and sucrose, as expected due to their ionic characteristics. The predicted vibrational spectra for the four species of maltose show reasonable concordances with the corresponding experimental ones. The f(δC-O-C) force constants of the glycosidic bonds follow the tendency: maltose > lactose > sucrose. [ABSTRACT FROM AUTHOR]

This review discusses the use of molecular modeling tools, together with existing experimental findings, to provide a complete atomic-level description of enzyme dynamics and function. We focus on functionally relevant conformational dynamics of enzymes and the protonation states of substrates. The conformational fluctuations of enzymes usually play a crucial role in substrate recognition and catalysis. Protein dynamics can be altered by a tiny change in a molecular system such as different protonation states of various intermediates or by a significant perturbation such as a ligand association. Here we review recent advances in applying atomistic molecular dynamics (MD) simulations to investigate allosteric and network regulation of tryptophan synthase (TRPS) and protonation states of its intermediates and catalysis. In addition, we review studies using quantum mechanics/molecular mechanics (QM/MM) methods to investigate the protonation states of catalytic residues of β-Ketoacyl ACP synthase I (KasA). We also discuss modeling of large-scale protein motions for HIV-1 protease with coarse-grained Brownian dynamics (BD) simulations. [ABSTRACT FROM AUTHOR]

All-atom simulations are used to derive effective parameters for a coarse-grained description of the crystalline cellulose $$\hbox {I}\alpha$$ . In this description, glucose monomers are represented by the C4 atoms and non-bonded interactions within the cellulose sheets and between the sheets by effective Lennard-Jones interactions. The parameters are determined by two methods: the Boltzmann inversion and through monitoring of the energies associated with changes of the coarse-grained degrees of freedom. We find that the stiffness-related parameters for cellulose $$\hbox {I}\alpha$$ are nearly the same as for $$\hbox {I}\beta$$ allomorph. However, the non-bonded terms are placed differently and are weaker leading to an overall lower energy, and free energy, of $$\hbox {I}\beta$$ compared to $$\hbox {I}\alpha$$ . We apply the coarse-grained description to determine amorphous transition states for the room-temperature conversion process between the $$\hbox {I}\alpha$$ and $$\hbox {I}\beta$$ allomorphs and to characterize the interface between the crystalline forms of the allomorphs. [ABSTRACT FROM AUTHOR]

Friction stir welding (FSW) is a solid-state process based on friction welding. In this study, the numerical simulation of the flow pattern for 2024 aluminum rod FSW was carried out using DEFORM-3D finite-element software. The temperature field and effective strain simulated welding with two 2024 aluminum rods at a rotational speed of 1800 rpm and a feed rate of the FSW of 0.2 mm/s. The rotation of the aluminum rods was stopped when the temperature at the contact surface exceeded the crystallization temperature of the materials; normal force was applied at the contact surface of the aluminum rod. The three-dimensional (3-D) material flow model of FSW resulted in numerical simulations that indicated that FSW can reduce residual stress in the materials and enhance the tensile strength of the weld surface. [ABSTRACT FROM AUTHOR]

Molecular dynamics (MD) simulations have become a central tool for investigating various biophysical questions with atomistic detail. While many different proxies are used to qualify MD force fields, most are based on largely structural parameters such as the root mean square deviation from experimental coordinates or nuclear magnetic resonance (NMR) chemical shifts and residual dipolar couplings. NMR derived Lipari-Szabo squared generalized order parameter ( O2) values of amide NH bond vectors of the polypeptide chain were also often employed for refinement and validation. However, with a few exceptions, side chain methyl symmetry axis order parameters have not been incorporated into experimental reference sets. Using a test set of five diverse proteins, the performance of several force fields implemented in the NAMDD simulation package was examined. It was found that simulations employing explicit water implemented using the TIP3 model generally performed significantly better than those using implicit water in reproducing experimental methyl symmetry axis O2 values. Overall the CHARMM27 force field performs nominally better than two implementations of the Amber force field. It appeared that recent quantum mechanics modifications to side chain torsional angles of leucine and isoleucine in the Amber force field have significantly hindered proper motional modeling for these residues. There remained significant room for improvement as even the best correlations of experimental and simulated methyl group Lipari-Szabo generalized order parameters fall below an R2 of 0.8. [ABSTRACT FROM AUTHOR]

In this work, pectin isolated from citrus peel with a degree of esterification of 76% was characterized by Fourier Transform Infrared (FTIR) and Fourier Transform Raman (FT-Raman) spectroscopies. Structural studies were carried out taking into account their partial degree of esterification and considering the polygalacturonic acid chain as formed by two different subunits, one with both COOH and COO CH 3 groups (Ac) and the other one as constituted by two subunits with two COO CH 3 groups (Es). Their structural properties, harmonic frequencies, force fields and force constants in gas and aqueous solution phases were calculated by using the hybrid B3LYP/6-31G ∗ method. Then, their complete vibrational analyses were performed by using the IR and Raman spectra accomplished with the scaled quantum mechanical (SQM) methodology. Reactivities and behaviors in both media were predicted for Ac and Es by using natural bond orbital (NBO), atoms in molecules (AIM), and frontier orbitals calculations. We report for first time the complete assignments of those two different units of polygalacturonic acid chain which are the 132 normal vibration modes of Ac and the 141 normal vibration modes of Es, combining the normal internal coordinates with the SQM methodology. In addition, three subunits were also studied. Reasonable correlations between the experimental and theoretical spectra were obtained. Thus, this work would allow the quick identification of pectin by using infrared and Raman spectroscopies and also provides new insight into the interactions that exist between subunits of a large pectin chain. [ABSTRACT FROM AUTHOR]

Carotenoids are important actors both in light-harvesting (LH) and in photoprotection functions of photosynthetic pigment-protein complexes. A deep theoretical investigation of this multiple role is still missing owing to the difficulty of describing the delicate interplay between electronic and nuclear degrees of freedom. A possible strategy is to combine accurate quantum mechanical (QM) methods with classical molecular dynamics. To do this, however, accurate force-fields (FF) are necessary. This article presents a new FF for the different carotenoids present in LH complexes of plants. The results show that all the important structural properties described by the new FF are in very good agreement with QM reference values. This increased accuracy in the simulation of the structural fluctuations is also reflected in the description of excited states. Both the energy order and the different nature of the lowest singlet states are preserved during the dynamics when the new FF is used, whereas an unphysical mixing is found when a standard FF is used. © 2016 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Metal-organic frameworks (MOFs) are attracting much attention as promising materials for gas separation. Given the large number of design possibilities in the MOF materials space, it is desirable to efficiently characterize their performance prior to their experimental synthesis. This Perspective focuses on some of the works that have been put forth in developing new methods that accurately describe the thermodynamics of gas uptake in MOFs by making use of a few selected ab initio calculations. We provide a future outlook toward a full ab initio description of these properties using efficient sampling strategies in conjunction with faster and more accurate quantum methods. © 2015 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

A new all-atom first-principles force field (FF) is constructed for the bimetallic, four-bladed zinc paddlewheel (ZPW) motif. Zinc-ligand interactions are described via Morse functions and the angular geometry at the metal centers is modeled with a pure ligand-ligand repulsion term. The ZPW-FF is principally based on 15 DFT-optimized model systems of general formula ZnPR.nL, where ZnP is the base Zn2(O2CR)4 unit, R=H, CH3 or CF3, L=NH3 or pyridine, and n = 0, 1 or 2. It correctly generates the distorted tetrahedral coordination of the uncapped [Zn2(O2CR)4] species in their ground states as well as giving reasonable structures and energies for the higher symmetry D4h transition state conformations. The zinc-ligand Morse function reference distance, r0, is further refined against 30 complexes located in the Cambridge Structural Database and this FF is applied to pore models of t h e f l e x i b l e me t a l - o rganic framework (MOF) [Zn(bdc)2(dabco)]n (bdc = 1,4-benzendicarboxylate; dabco =1,4-diazabicyclo(2.2.2)octane). A single pore model reproduces the unit cell of the evacuated MOF system while a 3×3 grid model is necessary to provide good agreement with the observed pronounced structural changes upon adsorption of either dimethylformamide or benzene. [ABSTRACT FROM AUTHOR]

In this work we predict the key adsorption properties for hydrogen storage applications by investigating a series of recently synthesized zirconium based MOFs. These MOFs consist of an inorganic brick (Zr 6 O 4 (OH) 4 (CO 2 ) 12 ) that binds to organic linkers (1,4-benzene-dicarboxylate and 4,4′-biphenyl-dicarboxylate) to form the two MOFs: UiO-66 and UiO-67. Particular attention has been paid to the performance of different classical force fields to describe the interactions between H 2 and the solid materials. It is found that combinations of several commonly used H 2 potentials in combination with the DREIDING force field give consistently good agreement with experimental adsorption data at 77 K, 95 K, and 110 K. The performance of the different force fields and hydrogen potentials is evaluated and discussed in terms of the physical interactions they describe. All tested force fields clearly underestimate adsorption at 296 K. Possible reasons for this discrepancy with experimental results are discussed and suggestions on how to improve the adsorption simulations are given. [ABSTRACT FROM AUTHOR]

Quantifying an atom's transferability, in a force field context, demands a quantitative understanding of how an atom ‘experiences’ the surrounding environment both intra-atomically and inter-atomically. Here we investigate the intra-atomic (EintraA) viewpoint through the study of the atoms Cα, Hα, N, O, and S in a series of ‘mono’-, tri- and penta-peptides. The remaining inter-atomic viewpoint consists of an electrostatic (via multipole moments), exchange and correlation components respectively, of which the electrostatic component has been previously reported. Together these four energy components, as calculated from the Interacting Quantum Atoms (IQA) partitioning approach, express the foundation of the Quantum Chemical Topological Force Field (QCTFF). In order to have transferability within a force field, smaller sample systems must be calculated and developed as representative of larger target systems. The Cα, Hα, N, O and S atoms in a tri-peptide are energetically comparable to those in their penta-peptide configurations, within 2.1 kJ/mol in absolute value (1 exception). Across all five elements, this energy difference ison average∼0.3 kJ/mol. On average, the tri-peptide sample systems represent a ∼8.2 Å atomic horizon around the central atoms of interest. Thus, both the previous knowledge of the ∼10.3 Å horizon sphere and ∼0.4 kJ/mol error required by the electrostatic multipole moments, determine how two of the four key QCTFF energy components are affected by an atom's molecular environment. [ABSTRACT FROM PUBLISHER]

We introduce a force field for the description of the mackinawite/water interface, which we derive by refining, and consistently merging with the SPC/Fw model of water, a set of existing interatomic potentials for the mineral. The thermal behaviour predicted for bulk mackinawite is in good agreement with experiment. The adsorption of water on the low-index surfaces of mackinawite reproduces results from density functional theory calculations at different water coverages, while the behaviour of water intercalated into the mineral is also remarkably similar to that from ab initio results. The force field is therefore suitable to model bulk mackinawite and its surfaces in an aqueous environment. [ABSTRACT FROM AUTHOR]

In the present work, the structural, topological and vibrational properties of four members of the N-benzylamides series derived from Maca ( Lepidium meyenii ) whose names are, N-benzylpentadecanamide, N-benzylhexadecanamide, N-benzylheptadecanamide and N-benzyloctadecanamide, were studied combining the FTIR, FT-Raman and 1 H and 13 C-NMR spectroscopies with density functional theory (DFT) and ONION calculations. Furthermore, the N-benzylacetamide, N-benzylpropilamide and N-benzyl hexanamide derivatives were also studied in order to compare their properties with those computed for the four macamides. These seven N -benzylamides series have a common structure, C 8 H 8 NO-R, being R the side chain [–(CH 2 ) n –CH 3 ] with a variable n number of CH 2 groups. Here, the atomic charges, molecular electrostatic potentials, stabilization energies, topological properties of those macamides were analyzed as a function of the number of C atoms of the side chain while the frontier orbitals were used to compute the gap energies and some descriptors in order to predict their reactivities and behaviors in function of the longitude of the side chain. Here, the force fields, the complete vibrational assignments and the corresponding force constants were only reported for N -benzylacetamide, N -benzyl hexanamide and N-benzylpentadecanamide due to the high number of vibration normal modes that present the remains macamides. [ABSTRACT FROM AUTHOR]

This work is framed within the Eighth Industrial Fluid Properties Simulation Challenge, with the aim of assessing the capability of molecular simulation methods and force fields to accurately predict adsorption in porous media for systems of relevant practical interest. The current challenge focuses on predicting adsorption isotherms of n-perfluorohexane in the certified reference material BAM-P109 standard activated carbon. A temperature of T ¼ 273 K and pressures of p=p0 ¼ 0:1, 0.3, and 0.6 relative to the bulk saturation pressure p0 (as predicted by the model) are the conditions selected in this challenge. In our methodology we use coarse-grained intermolecular models and a top-down technique where an accurate equation of state is used to link the experimental macroscopic properties of a fluid to the force-field parameters. The state-of-the-art version of the statistical associating fluid theory (SAFT) for potentials of variable range as reformulated in the Mie group contribution incarnation (SAFT-γ Mie) is employed here. The parameters of the SAFT-γ Mie force field are estimated directly from the vapour pressure and saturated liquid density data of the pure fluids using the equation of state, and further validated by molecular dynamic simulations. The coarse-grained intermolecular potential models are then used to obtain the adsorption isotherm kernels for argon, carbon dioxide, and n-perfluorohexane in graphite slit pores of various widths using Grand Canonical Monte Carlo simulations. A unique and fluid-independent pore size distribution curve with total micropore volume of 0.5802 cm³/g is proposed for the BAM-P109. The pore size distribution is obtained by applying a non-linear regression procedure over the adsorption integral equation to minimise the quadratic error between the available experimental adsorption isotherms for argon and carbon dioxide and purpose-built Grand Canonical Monte Carlo kernels. The predicted adsorption levels of n-perfluorohexane at 273 K in BAM-P109 are 72.75±0.01, 73.82±0.01, and 75.44± 0.05 cm³/g at Standard Temperature and Pressure (STP) conditions for p=p0 ¼ 0:1, 0.3, and 0.6, respectively. [ABSTRACT FROM AUTHOR]

Gibbs ensemble Monte Carlo simulations were used to calculate absorption isotherms of water in three imidazolium-based ionic liquids (ILs) with different degrees of hydrophobicity: 1- n -butyl-3-methylimidazolium hexafluorophosphate ([C 4 mim][PF 6 ]), 1- n -butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide ([C 4 mim][Tf2N]) and 1- n -butyl-3-methylimidazolium chloride ([C 4 mim][Cl]). An evaluation of several water models and various IL force fields was conducted. The selected water models are the TIP5P, TIP4P2005 and a collection of three site models based on the SPC geometry but with different sets of fixed partial charges. These partial charges are consistent with water surrounded by different electrostatic environments, and crudely account for polarizability. In the case of the IL force fields, net partial charges of ±1.0e were used. In addition, scaled charges of ±0.9e and ±0.8e were used to account for polarization and charge transfer. It is found that most water models tested with the full charge [C 4 mim][PF 6 ] and [C 4 mim][Cl] force field overestimate the solubility, but the agreement is reasonably good with [C 4 mim][Tf2N]. Attempts at improving the results by either scaling the charges on the IL or on water were made, but no combination was able to reproduce experimental phase behavior satisfactorily. The main conclusion of the study is that, to consistently model water absorption in ILs, force fields that include effects such as polarization are likely necessary. [ABSTRACT FROM AUTHOR]

The retrieval of motor memory requires a previous memory encoding and subsequent consolidation of the specific motor memory. Previous work showed that motor memory seems to rely on different memory components (e.g., implicit, explicit). However, it is still unknown if explicit components contribute to the retrieval of motor memories formed by dynamic adaptation tasks and which neural correlates are linked to memory retrieval. We investigated the lower and higher gamma bands of subjects' electroencephalography during encoding and retrieval of a dynamic adaptation task. A total of 24 subjects were randomly assigned to a treatment and control group. Both groups adapted to a force field A on day 1 and were re-exposed to the same force field A on day 3 of the experiment. On day 2, treatment group learned an interfering force field B whereas control group had a day rest. Kinematic analyses showed that control group improved their initial motor performance from day 1 to day 3 but treatment group did not. This behavioral result coincided with an increased higher gamma band power in the electrodes over prefrontal areas on the initial trials of day 3 for control but not treatment group. Intriguingly, this effect vanished with the subsequent re-adaptation on day 3. We suggest that improved re-test performance in a dynamic motor adaptation task is contributed by explicit memory and that gamma bands in the electrodes over the prefrontal cortex are linked to these explicit components. Furthermore, we suggest that the contribution of explicit memory vanishes with the subsequent re-adaptation while task automaticity increases. [ABSTRACT FROM AUTHOR]

We introduce a simple but computationally very efficient harmonic force field, which works for all fullerene structures and includes bond stretching, bending, and torsional motions as implemented into our open-source code Fullerene. This gives accurate geometries and reasonably accurate vibrational frequencies with root mean square deviations of up to 0.05 Å for bond distances and 45.5 cm−1 for vibrational frequencies compared with more elaborate density functional calculations. The structures obtained were used for density functional calculations of Goldberg-Coxeter fullerenes up to C980. This gives a rather large range of fullerenes making it possible to extrapolate to the graphene limit. Periodic boundary condition calculations using density functional theory (DFT) within the projector augmented wave method gave an energy difference between −8.6 and −8.8 kcal/mol at various levels of DFT for the reaction C60→graphene (per carbon atom) in excellent agreement with the linear extrapolation to the graphene limit (−8.6 kcal/mol at the Perdew-Burke-Ernzerhof level of theory). © 2015 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

We introduce a simple but computationally very efficient harmonic force field, which works for all fullerene structures and includes bond stretching, bending, and torsional motions as implemented into our open-source code Fullerene. This gives accurate geometries and reasonably accurate vibrational frequencies with root mean square deviations of up to 0.05 Å for bond distances and 45.5 cm−1 for vibrational frequencies compared with more elaborate density functional calculations. The structures obtained were used for density functional calculations of Goldberg-Coxeter fullerenes up to C980. This gives a rather large range of fullerenes making it possible to extrapolate to the graphene limit. Periodic boundary condition calculations using density functional theory (DFT) within the projector augmented wave method gave an energy difference between −8.6 and −8.8 kcal/mol at various levels of DFT for the reaction C60→graphene (per carbon atom) in excellent agreement with the linear extrapolation to the graphene limit (−8.6 kcal/mol at the Perdew-Burke-Ernzerhof level of theory). © 2015 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Proteins play diverse and vital roles in biology, which are dominated by their three-dimensional structures. The three-dimensional structure of a protein determines its functions and chemical properties. Protein secondary structures, including α-helices and β-sheets, are key components of the protein architecture. Molecular interactions, in particular hydrogen bonds, play significant roles in the formation of protein secondary structures. Precise and quantitative estimations of these interactions are required to understand the principles underlying the formation of three-dimensional protein structures. In the present study, we have investigated the molecular interactions in α-helices and β-sheets, using ab initio wave function-based methods, the Hartree-Fock method (HF) and the second-order Møller-Plesset perturbation theory (MP2), density functional theory, and molecular mechanics. The characteristic interactions essential for forming the secondary structures are discussed quantitatively. [ABSTRACT FROM AUTHOR]

The paper primarily deals with the development of an interaction potential (force field) for a realistic description of atom-by-atom ZrO 2 growth. Owing to the fact that for many metal oxides including ZrO 2 only full-charge (Zr +4 and O −2 ) interaction potentials are available, special attention is paid to the effect of the Zr and O elemental charges. Parameters of the short-range part of the interaction potential leading to experimental lattice parameters and formation energies have been identified in a wide range of elemental charges. Molecular dynamics simulations of ZrO 2 growth reveal that the structures grown using the presently available full-charge interaction potentials are in contradiction with an experiment (the atoms have too low coordination numbers). Simulations using a wide range of newly fitted full-charge and partial-charge interaction potentials reveal that the results depend (in addition to the fitting procedure) on the elemental charges. Correct partial charges and potential parameters leading to experimentally relevant structures (with correct coordination numbers) have been identified and used. [ABSTRACT FROM AUTHOR]

Force field accuracy is still one of the "stalemates" in biomolecular modeling. Model systems with high quality experimental data are valuable instruments for the validation and improvement of effective potentials. With respect to protein-ligand binding, organic host-guest complexes have long served as models for both experimental and computational studies because of the abundance of binding affinity data available for such systems. Binding affinity data collected for cyclodextrin (CD) inclusion complexes, a popular model for molecular recognition, is potentially a more reliable resource for tuning energy parameters than hydration free energy measurements. Convergence of binding free energy calculations on CD host-guest systems can also be obtained rapidly, thus offering the opportunity to assess the robustness of these parameters. In this work, we demonstrate how implicit solvent parameters can be developed using binding affinity experimental data and the binding energy distribution analysis method (BEDAM) and validated using the Grid Inhomogeneous Solvation Theory analysis. These new solvation parameters were used to study protein-ligand binding in two drug targets against the HIV-1 virus and improved the agreement between the calculated and the experimental binding affinities. This work illustrates how benchmark sets of high quality experimental binding affinity data and physics-based binding free energy models can be used to evaluate and optimize force fields for protein-ligand systems. [ABSTRACT FROM AUTHOR]