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Force fields are actively used to study RNA. Development of accurate force fields relies on a knowledge of how the variation of properties of molecules depends on their structure. Detailed scrutiny of RNA’s conformational preferences is needed to guide such development. Towards this end, minimum energy structures for each of a set of 16 small RNA-derived molecules were obtained by geometry optimization at the HF/6-31G(d,p), B3LYP/apc-1, and MP2/cc-pVDZ levels of theory. The number of minima computed for a given fragment was found to be related to both its size and flexibility. Atomic electrostatic multipole moments of atoms occurring in the [HO-P(O3)-CH2-] fragment of 30 sugar-phosphate-sugar geometries were calculated at the HF/6-31G(d,p) and B3LYP/apc-1 levels of theory, and the transferability of these properties between different conformations was investigated. The atomic multipole moments were found to be highly transferable between different conformations with small standard deviations. These results indicate necessary elements of the development of accurate RNA force fields. [ABSTRACT FROM AUTHOR]

Understanding the ways of interaction of a drug with a biological target is crucial in the pharmacology field. One methodology that allows the simulation of new drugs under in vitro conditions is the classical molecular dynamics (MD) method. However, MD simulations in systems containing metallodrugs are challenging due to the lack of specific parameters found in the literature. In this work, we propose and model a new possible anticancer platinum(II) complex: cis‐dichloro(2‐aminomethylpyridine)platinum(II) bonded to 2‐(4′‐amino‐2′‐hydroxyphenyl)benzothiazole (AHBT). The developed model consists of a new set of AMBER force field parameters based on density functional theory (DFT) calculations. The extensive validation of the parameter set shows that it adequately describes the structural properties of the complex. Overall, we expect this work to contribute significantly to future MD simulations of Pt(II) complexes in biological targets that are still not well explored, mainly due to the few parameters found in the literature. [ABSTRACT FROM AUTHOR]

The possible effect of plastic nanoparticles of waste origin on biological systems is still unclear and could pose a severe threat. Model studies at the molecular level are urgently needed in order to help reveal the interplay between these particles and biological systems, and thereby to indicate the direction of further research. In the present study, simulated annealing molecular dynamics is adjusted and applied to generate an array of conformations for a sample peptide oligoalanine possibly binding to polyethylene and nylon 6,6 nanoplastics. The resulting structures, with a diameter of up to 5 nm, were investigated with the aid of static quantum chemical calculations. The obtained data unequivocally show that both plastic nanoparticles influence the relative stability of α‐helix, β‐hairpin, and other conformations strongly. Polyethylene nanoparticle increases the stability of the helical foldamer. Nylon 6,6 nanoplastic offers strong plastic‐peptide interactions on its surface, making the unfolding of the peptide thermodynamically highly favorable. These results further underscore that nanoplastics can do significant molecular‐level damage to living organisms via facilitating the misfolding and denaturation of proteins. Furthermore, it is apparent that plastics can have very different effects on living matter depending upon their composition, and hence experiments with any single kind of plastics (eg, polystyrene) should not be considered generally valid for all nanoplastics. [ABSTRACT FROM AUTHOR]

FFLUX is a biomolecular force field under construction, based on Quantum Chemical Topology (QCT) and machine learning (kriging), with a minimalistic and physically motivated design. A detailed analysis of the forces within the kriging models as treated in FFLUX is presented, taking as a test example a liquid water model. The energies of topological atoms are modeled as 3Natoms‐6 dimensional potential energy surfaces, using atomic local frames to represent the internal degrees of freedom. As a result, the forces within the kriging models in FFLUX are inherently N‐body in nature where N refers to Natoms. This provides a fuller picture that is closer to a true quantum mechanical representation of interactions between atoms. The presented computational example quantitatively showcases the non‐negligible (as much as 9%) three‐body nature of bonded forces and angular forces in a water molecule. We discuss the practical impact on the pressure calculation with N‐body forces and periodic boundary conditions (PBC) in molecular dynamics, as opposed to classical force fields with two‐body forces. The equivalence between the PBC‐related correction terms in the general virial equation is shown mathematically. [ABSTRACT FROM AUTHOR]

In the current work we report on our participation in the SAMPL7 challenge calculating absolute free energies of the host–guest systems, where 2 guest molecules were probed against 9 hosts-cyclodextrin and its derivatives. Our submission was based on the non-equilibrium free energy calculation protocol utilizing an averaged consensus result from two force fields (GAFF and CGenFF). The submitted prediction achieved accuracy of 1.38 kcal / mol in terms of the unsigned error averaged over the whole dataset. Subsequently, we further report on the underlying reasons for discrepancies between our calculations and another submission to the SAMPL7 challenge which employed a similar methodology, but disparate ligand and water force fields. As a result we have uncovered a number of issues in the dihedral parameter definition of the GAFF 2 force field. In addition, we identified particular cases in the molecular topologies where different software packages had a different interpretation of the same force field. This latter observation might be of particular relevance for systematic comparisons of molecular simulation software packages. The aforementioned factors have an influence on the final free energy estimates and need to be considered when performing alchemical calculations. [ABSTRACT FROM AUTHOR]

As part of the SAMPL7 host–guest binding challenge, the AMOEBA force field was applied to calculate the absolute binding free energy for 16 charged organic ammonium guests to the TrimerTrip host, a recently reported acyclic cucurbituril-derived clip host structure with triptycene moieties at its termini. Here we report binding free energy calculations for this system using the AMOEBA polarizable atomic multipole force field and double annihilation free energy methodology. Conformational analysis of the host suggests three families of conformations that do not interconvert in solution on a time scale available to nanosecond molecular dynamics (MD) simulations. Two of these host conformers, referred to as the "indent" and "overlap" structures, are capable of binding guest molecules. As a result, the free energies of all 16 guests binding to both conformations were computed separately, and combined to produce values for comparison with experiment. Initial ranked results submitted as part of the SAMPL7 exercise had a mean unsigned error (MUE) from experimental binding data of 2.14 kcal/mol. Subsequently, a rigorous umbrella sampling reference calculation was used to better determine the free energy difference between unligated "indent" and "overlap" host conformations. Revised binding values for the 16 guests pegged to this umbrella sampling reference reduced the MUE to 1.41 kcal/mol, with a correlation coefficient (Pearson R) between calculated and experimental binding values of 0.832 and a rank correlation (Kendall τ) of 0.65. Overall, the AMOEBA results demonstrate no significant systematic error, suggesting the force field provides an accurate energetic description of the TrimerTrip host, and an appropriate balance of solvation and desolvation effects associated with guest binding. [ABSTRACT FROM AUTHOR]

Molecular electronic structure, IR, UV, and NMR spectra of the most popular cathinone, known as mephedrone or 4-methylmethcathinone (4-MMC), is studied thoroughly by quantum chemical calculation in terms of the density functional theory (DFT). Geometry optimization of 4-MMC and its hydrochloride complex is performed with the B3LYP functional, and all vibrational frequencies are analyzed in all details. On this background, the IR and Raman spectra are interpreted. The importance of low-frequency terahertz and Raman spectra is stressed for distinguishing of various MMC isomers. The UV spectrum is calculated by time-dependent DFT method which allows complete interpretation of intense absorption bands at 270 and 210 nm as combinations of various ππ*, nπ*, and charge transfer excitations in amino-phenyl moieties. Very informative analysis of UV absorption and NMR spectra provides useful details on the structure-activity relationship for mephedrone molecule. [ABSTRACT FROM AUTHOR]

Modular organization of the spinal motor system is thought to reduce the cognitive complexity of simultaneously controlling the large number of muscles and joints in the human body. Although modular organization has been confirmed in the hindlimb control system of several animal species, it has yet to be established in the forelimb motor system or in primates. Expanding upon experiments originally performed in the frog lumbar spinal cord, we examined whether costimulation of two sites in the macaque monkey cervical spinal cord results in motor activity that is a simple linear sum of the responses evoked by stimulating each site individually. Similar to previous observations in the frog and rodent hindlimb, our analysis revealed that in most cases (77% of all pairs) the directions of the force fields elicited by costimulation were highly similar to those predicted by the simple linear sum of those elicited by stimulating each site individually. A comparable simple summation of electromyography (EMG) output, especially in the proximal muscles, suggested that this linear summation of force field direction was produced by a spinal neural mechanism whereby the forelimb motor output recruited by costimulation was also summed linearly. We further found that the force field magnitudes exhibited supralinear (amplified) summation, which was also observed in the EMG output of distal forelimb muscles, implying a novel feature of primate forelimb control. Overall, our observations support the idea that complex movements in the primate forelimb control system are made possible by flexibly combined spinal motor modules. [ABSTRACT FROM AUTHOR]

Alkanes are a fundamental part in empirical force fields (FF) not only due to their technological relevance, but also due to the prevalence of alkane moieties in organic molecules, e.g., compounds containing a saturated carbon chain. Therefore, a good description of alkane interactions is crucial for determining the quality of a FF. In this study, the performance of 12 empirical force fields (FF) was evaluated in the context of reproducing liquid properties of alkanes. More specifically, n-octane was chosen as a reference compound since it is a liquid in a broad temperature range and it has numerous experimental data for thermodynamic, transport, and structural properties, as well as for their temperature dependencies. A normalized root-mean-square deviation (NRMSD) analysis was used to rank the force fields in their ability to reproduce the experimental data. Five out of the six best force fields considered were united-atom models. The GROMOS force field showed the smallest deviation in terms of NRMSD, followed by TRAPPE-EH, NERD, CHARMM-UA, TRAPPE-UA, and OPLS-UA. This overall better performance of the united-atom force fields indicates that complexity does not always bring quality. [ABSTRACT FROM AUTHOR]

The use of molecular simulation has been growing in the field of engineering, fueled not just by the advances in computational power but also on the availability of reliable software. One potential use of molecular simulation is related to the screening of materials for a specific application. The reliability of molecular simulation results depends on the trustworthiness of the force field used, which for engineering purposes should be as simple as possible. This work provides an evaluation of the potential accuracy cost of using simple generic force fields to predict the adsorption of CO2, CH4, N2 and their mixtures on MFI. We employed the GCMC technique for this investigation. Different models and force fields to describe adsorbates and adsorbent were tested. The force fields performances were estimated through comparison with available adsorption experimental data. Transferability was evaluated on the prediction of pure and mixtures adsorption on CHA, LTA and FER. The results showed that a simple force field presented similar performance when compared to a more sophisticated one. [ABSTRACT FROM AUTHOR]

We illustrate a series of molecular dynamics simulations of lipid membranes using the coarse-grained model, SPICA force field. The force field was designed to reproduce the experimental thermodynamic quantities such as surface tension, density, and solvation free energy, and simultaneously the molecular distribution functions calculated from all-atom molecular simulations. Further, the elastic properties and line tension of lipid membranes are well reproduced, which guarantees a reasonable morphology of lipid aggregates. The molecular library now includes several different lipids as well as cholesterols. Large scale simulations and free energy calculations are described to show the performance of the SPICA force field. [ABSTRACT FROM AUTHOR]

Flavin containing molecules form a group of important cofactors that assist a wide range of enzymatic reactions. Flavins use the redox‐active isoalloxazine system, which is capable of one‐ and two‐electron transfer reactions and can exist in several protonation states. In this work, molecular mechanics force field parameters compatible with the CHARMM36 all‐atom additive force field were derived for biologically important flavins, including riboflavin, flavin mononucleotide, and flavin adenine dinucleotide. The model was developed for important protonation and redox states of the isoalloxazine group. The partial charges were derived using the CHARMM force field parametrization strategy, where quantum mechanics water–solute interactions are used to target optimization. In addition to monohydrate energies and geometries, electrostatic potential around the compound was used to provide additional restraints during the charge optimization. Taking into account the importance of flavin‐containing molecules special attention was given to the quality of bonded terms. All bonded terms, including stiff terms and torsion angle parameters, were parametrized using exhaustive potential energy surface scans. In particular, the model reproduces well the butterfly motion of isoalloxazine in the oxidized and reduced forms as predicted by quantum mechanics in gas phase. The model quality is illustrated by simulations of four flavoproteins. Overall, the presented molecular mechanics model will be of utility to model flavin cofactors in different redox states. © 2019 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Actual CTAB and SB3-12 surfactant force field models fail to reproduce one of the most important thermodynamic property of those molecules, the surface tension. Molecular dynamics simulations were conducted to construct new force fields of the cationic surfactant, Cetyl Trimethyl Ammonium Bromide (CTAB), and the non-ionic, cocoamidopropyl betaine, surfactants using united atom models. By scaling the Lennard Jones parameters, the well depth potential (ε) and the intermolecular distance (σ), we constructed an united atom model of the cationic and the betaine surfactants. The new models were tested with actual experiments reported in the literature. With the correct parameters, surface tensions of both surfactants were calculated at different temperatures and different areas per molecule. Electrostatic properties and micelle structures were also calculated with the new set of parameters and radius of gyrations, i.e. micelle radius, were evaluated showing good affinity with experimental data. The new force fields were proved with two different water models, TIP4P/ε and SPC/E, having good agreement with actual experiments [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations are more frequently being utilised to predict macroscale mechanical properties as a result of atomistic defects. However, the interatomic force field can significantly affect the resulting mechanical properties. While several studies exist which demonstrate the ability of various force fields to predict mechanical properties, the investigation into which is most accurate for the investigation of vacancies is limited. To obtain meaningful predictions of mechanical properties, a clear understanding of force field parameterisation is required. As such, the current study evaluates various many-body force fields to demonstrate the reduction in mechanical properties of iron and iron–chromium due to the presence of vacancies while undergoing room temperature atomistic uniaxial tension. Reduction was normalised in each case with the zero-vacancy elastic modulus, removing the need to predict an accurate nominal elastic modulus. Comparisons were made to experimental data and an empirical model from literature. It was demonstrated that accurate fitting to vacancy formation and migration energy allowed for accurate predictions. In addition, bond-order based force fields showed enhanced predictions regardless of fitting procedure. Overall, these findings highlight the need to understand capabilities and limitations of available force fields, as well as the need for enhanced parameterisation of force fields. [ABSTRACT FROM AUTHOR]

The parametrization of classical nonbonded models of metal ions has been widely addressed in the recent years. Despite the continuous development of novel and more physically inspired functional forms, the 12‐6 Lennard‐Jones plus Coulomb potential is still the most adopted force field in molecular dynamics (MD) codes, owing to its simple form and easy implementation. However, due to the integer formal charge, unpolarizable force fields of ions may suffer from overestimated interatomic electrostatic interactions, leading to nonphysical clustering or repulsion between such full charges. The electronic continuum correction (ECC) can fix this problem through a simple inclusion of solvent polarization effects via ionic charge rescaling. In this work, the development of novel nonbonded models for mono, divalent, and highly charged metal ions is presented. For each metal species, the ionic charge has been scaled, according to the ECC. Lennard‐Jones parameters have been optimized using experimental structural and thermodynamic properties as target quantities. Performances of the proposed models are discussed and compared with the literature data, while transferability attitudes among different and well‐known water models are evaluated. © 2019 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

The topmost polyamide (PA) layer of the thin‐film‐composite reverse osmosis (RO) membrane is the most important part in the membrane‐based RO technology. With the aid of molecular dynamics simulations, many PA layer‐related features in the RO process can be revealed. With many novel types of PA RO membranes out of trimesoyl chloride/m‐phenylenediamine monomers developed in the laboratory, a convenient model building tool for these PA layer systems is urgently needed to conduct the theoretical analysis. Here, we develop a new universal toolkit for constructing PA RO membranes, named as MembrFactory, which combines flexibility of force fields and membrane compositions. A key characteristic of our approach is the use of monomers as the starting state, and the final membrane model was obtained automatically by stepwise reaction between the functional groups on the monomers. The reliability of MembrFactory has been validated by constructing several common PA RO membranes. © 2019 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

The pressure-dependent viscosity of 2,2,4-trimethylhexane is predicted using all-atom TEAM force field and the non-equilibrium periodic perturbation (PP) method. The viscosities predicted using the PP method do not show Newtonian plateau in the precision range of prediction for high-viscosity fluids. Using four alkane molecules as test cases, we found that our previously published force field, developed for ambient pressure conditions, is inaccurate for predicting viscosities under elevated pressures. Two approaches were attempted to enhance the pressure transferability of the force field: one involves moving the non-bond interaction site of hydrogen closer to that of attached carbon, which smooths the van der Waals (vdW) surface of molecule, and the other involves replacing the LJ-12-6 function by LJ-9-6, making the repulsion softer. Both approaches enhanced the pressure transferability; however, the former works well below 500 MPa, while the latter is valid under pressures up to 1 GPa. [ABSTRACT FROM AUTHOR]

[Display omitted] • We have employed the method of atomic cluster expansion (ACE) combined with first-principles density functional theory (DFT) calculations for machine learning, and successfully obtained the force field of the binary Fe-Co alloy. • Using ACE force field, the molecular dynamics simulation of Fe-Co alloy was carried out and the temperature related phase transformation range of Fe-Co alloy was correctly predicted. • The ACE force field is able to predict well the phase transition hysteresis behavior, which contributes to the development of the force field of Fe-Co and the use of molecular dynamics to simulate the physical properties of such alloy materials. The force field describing the calculated interaction between atoms or molecules is the key to the accuracy of many molecular dynamics (MD) simulation results. Compared with traditional or semi-empirical force fields, machine learning force fields have the advantages of faster speed and higher precision. We have employed the method of atomic cluster expansion (ACE) combined with first-principles density functional theory (DFT) calculations for machine learning, and successfully obtained the force field of the binary Fe-Co alloy. Molecular dynamics simulations of Fe-Co alloy carried out using this ACE force field predicted the correct phase transition range of Fe-Co alloy. [ABSTRACT FROM AUTHOR]

We reproduced the simulations described in Wang et al. (2018) and found we could not obtain the results reported. The root cause was identified to be incorrect atom masses in the original simulation files. As a consequence, the potential does not reproduce the experimental glass density – and presumably, other structural properties – and should be considered with great caution. [ABSTRACT FROM AUTHOR]

It has been known that classical molecular simulations of concentrated aqueous electrolyte solutions are limited by the ability of microscopic models (force fields) to predict the correct values of salt solubility, which also requires their ability to faithfully model crystalline salts. Previous simulation studies have often focused on the solubility of anhydrous crystalline salts, but virtually never on crystalline hydrates, except for hydrohalite, NaCl⋅2H 2 O, despite there are at least 23 experimentally known different hydrates that can precipitate from alkali-halide solutions. This work attempts to fill this gap in hydrate simulation studies by systematically investigating the ability of the best force fields selected to qualitatively capture the stability of the individual phases of various alkali-halide hydrates and to quantitatively predict their lattice parameters. First, we show that the nonpolarizable force fields studied often fail to model hydrates containing the Li+ cations, whereas the polarizable force fields recently refined by us are able to model all the hydrates except for LiCl⋅H 2 O. Second, we further refine our FFs for Li+ to yield stable LiCl⋅H 2 O. Third, our simulations clarify the positions of the Li+ cations in the β phases of LiBr⋅H 2 O and LiI⋅H 2 O, whose distributions were previously described only as stochastic. As a byproduct, a simple and reliable simulation methodology suitable also for complex polarizable models and nonorthorhombic crystal lattices is proposed and tested, based on simulations of finite crystals floating in vacuum. • Current nonpolarizable force fields often fail to predict lithium halide hydrates. • Refined polarizable force fields predict well the structure of alkali metal halide hydrates. • Hydrate precipitation from solutions should not be overlooked despite the absence of ion pairing. [ABSTRACT FROM AUTHOR]

• DFT-D predicts bulk and surface properties of gypsum accurately. • The INTERFACE force field results in a good agreement with DFT-D and experiment. • Changing partial charges of CLAYFF to those of the INTERFACE improves its performance. A crucial step in atomistic simulations of interfacial phenomena is confirming the thermodynamic consistency of the force field. This can be achieved by investigating the ability of the force field in predicting the bulk and surface properties of all components in the system. In this work, our focus is on the interfacial properties of gypsum, the calcium sulfate dihydrate (CaSO 4 ·2H 2 O), which is the most abundant calcium sulfate in the earth crust. The performance of classical force fields was tested by comparing their results with those calculated with dispersion-corrected density functional theory (DFT-D) method as well as experimentally reported data. The DFT-D method implemented to study gypsum and showed a promising performance by reproducing experimentally reported bulk and surface properties. We showed that properties calculated using classical force fields are highly dependent on ionic partial charges. Substituting the original ionic partial charges in the CLAYFF force field with those of the INTERFACE force field improved the calculated bulk and surface properties significantly. CLAYFF with augmented partial charges and INTERFACE force fields showed the best overall performance in reproducing bulk and surface properties of gypsum. [ABSTRACT FROM AUTHOR]

Previous studies have shown that cerebellar transcranial direct current stimulation (tDCS) leads to faster adaptation of arm reaching movements to visuomotor rotation and force field perturbations in healthy subjects. The first aim of the present study was to confirm a stimulation-dependent effect on motor adaptation. Second, we investigated whether tDCS effects differ depending on onset, that is, before or at the beginning of the adaptation phase. A total of 120 healthy and right-handed subjects (60 women, mean age 23.2 ± SD 2.7 yr, range 18-31 yr) were tested. Subjects moved a cursor with a manipulandum to one of eight targets presented on a vertically orientated screen. Three baseline blocks were followed by one adaptation block and three washout blocks. Sixty subjects did a force field adaptation task (FF), and 60 subjects did a visuomotor adaptation task (VM). Equal numbers of subjects received anodal, cathodal, or sham cerebellar tDCS beginning either in the third baseline block or at the start of the adaptation block. In FF and VM, tDCS and the onset of tDCS did not show a significant effect on motor adaptation (all P values >0.05). We were unable to support previous findings of modulatory cerebellar tDCS effects in reaching adaptation tasks in healthy subjects. Prior to possible application in patients with cerebellar disease, future experiments are needed to determine which tDCS and task parameters lead to robust tDCS effects. NEW & NOTEWORTHY Transcranial direct current stimulation (tDCS) is a promising tool to improve motor learning. We investigated whether cerebellar tDCS improves motor learning in force field and visuomotor tasks in healthy subjects and what influence the onset of stimulation has. We did not find stimulation effects of tDCS or an effect of onset of stimulation. A reevaluation of cerebellar tDCS in healthy subjects and at the end of the clinical potential in cerebellar patients is demanded. [ABSTRACT FROM AUTHOR]

Highlights • The enthalpies of sublimation of CH 3 ReO 3 and Re 2 (CO) 10 were measured by Calvet microcalorimetry. • The molecular and crystal structure of CH 3 ReO 3 was determined by X-ray diffraction. • An all-atom force field (FF) for organometallic compounds was extended to rhenium species. • MD simulations using that FF predicted Δ sub H m o and unit cell parameters with a maximum deviation of ∼3%. Abstract The standard (p ° = 0.1 MPa) molar enthalpies of sublimation, at 298.15 K, of methyltrioxorhenium(VII), Δ sub H m o [CH 3 ReO 3 ] = 70.2 ± 0.4 kJ mol−1, and dirhenium decacarbonyl, Δ sub H m o [Re 2 (CO) 10 ] = 97.4 ± 0.9 kJ mol−1, corresponding to well characterized crystalline phases, were determined by Calvet microcalorimetry. These results, along with structural information obtained in this work by single crystal X-ray diffraction for CH 3 ReO 3 , or previously reported for Re 2 (CO) 10 , tetramethylammonium perrhenate(VII), [N 1111 ][ReO 4 ], and hexamethylrhenium(VI), Re(CH 3) 6 , were used to extend our previously developed all-atom force field for organometallic compounds, to rhenium species. The new parametrization was able to reproduce the enthalpies of sublimation and unit cell parameters of the test set with maximum absolute deviations of 3.3 kJ⋅mol−1 and <3.8%, respectively. The transferability of the interaction (ε) and atomic diameter (σ) parameters of the Lennard-Jones (12–6) potential function, observed for first and second-row transition metals, was also found to be valid for rhenium and tungsten (third-row metals). [ABSTRACT FROM AUTHOR]

Valence Shell Electron Pair Repulsion (VSEPR) theory, commonly taught in introductory chemistry courses, provides a basis for understanding the molecular structures of molecules of the type XY , where X is a central atom surrounded by m Y ligands. While VSEPR is generally thought of only as a qualitative theory, Bartell and coworkers constructed a semi-quantitative model potential to address the physical underpinnings of VSEPR by introducing a points-on-a-sphere (POS) potential such that all X-Y bonds are of fixed length and all atoms Y repel each other. More than forty years ago, this simple model was shown to be effective in reproducing relative quadratic and cubic bending force constants for a variety of binary XY compounds when compared to values computed with semi-empirical and fairly primitive methods. The work presented here endeavours to go beyond the model used in the early investigations by Bartell and coworkers. Specifically, stretching force constants are clearly omitted from any POS model with a fixed radius, and are (primitively) included here by treating all X-Y bonds as simple (and equivalent) Morse oscillators. With the additional degrees of freedom in the parametrization that come from the Morse potential, the resulting model was investigated. The degree to which this simple mechanical model can reproduce quadratic and cubic force fields for PF is studied here, as well as how it works for a more difficult problem – the energetics and transition state properties for the intermediate in the (Berry) pseudorotation process that interchanges axial and equatorial fluorines in this prototype molecule. The five parameter Morse-POS model is shown to be do quite well in describing the quadratic and cubic force fields, as well as the pseudorotation process, a fairly impressive feat given the naivete of the model. [ABSTRACT FROM AUTHOR]

We propose a general strategy to remediate force‐field artifacts in describing pairwise interactions among similar molecules M in the vicinity of another chemical species, C, like water molecules interacting at short distance from a monoatomic ion. This strategy is based on introducing a three‐body potential energy term that alters the pairwise interactions among M‐type molecules when they lie at short range from the species C. In other words the species C is the center of a space domain where the pairwise interactions among the molecules M is altered. Here, we apply it to improve the description of the water interactions provided by the polarizable water model TCPE/2013 in the vicinity of halides, from F− to At−, and of the prototypical carboxylate anion CH3COO−. We show the accuracy and the transferability of such an approach to investigate not only the hydration process of single anions but also of a salt solution NH4+/Cl‐ in aqueous phase. This strategy can be used to remediate the drawbacks of any kind of force fields. © 2019 Wiley Periodicals, Inc. A general strategy is proposed to remediate force‐field artifacts in describing solvent pairwise interactions in the vicinity of a solute, based on introducing a three‐body potential energy term that alters the solvent pairwise interactions in a space domain centered at the solute. It is used to improve the description of the water interactions provided by the polarizable water model TCPE/2013 in the vicinity of halides, from F− to At−, and of the carboxylate anion CH3COO−. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations, which take place on the atomistic scale, are now being used to predict the influence of atomistic processes on macro-scale mechanical properties. However, there is a lack of clear understanding on which potential should be used when attempting to obtain these properties. Moreover, many MD studies that do test mechanical properties do not actually simulate the macro-scale laboratory tension tests used to obtain them. As such, the purpose of the current study was to evaluate the various types of potentials for their accuracy in predicting the mechanical properties of iron from an atomistic uniaxial tension test at room temperature. Results demonstrated that while EAM and MEAM potentials all under predicted the elastic modulus at room temperature, the Tersoff and ReaxFF potentials were significantly more accurate. Unlike EAM and MEAM, both the Tersoff and ReaxFF potentials are bond order based. Therefore, these results demonstrate the importance of considering bonding between atoms when modelling tensile tests. In addition, the ReaxFF potential also accurately predicted the Poisson's ratio, allowing for complete characterisation of the material's behaviour. Overall, these findings highlight the need to understand the capabilities and limitations of each potential before application to a problem outside of the initial intended use. [ABSTRACT FROM AUTHOR]

Abstract Carquejyl acetate (CA), the main component of the essential oil from Baccharis trimera was isolated and characterized by using Fourier Transform infrared (FT-IR) and Raman (FT-Raman), Ultraviolet–Visible (UV–Visible), Electronic Circular Dichroism (ECD), Mass, Hydrogen and Carbon Nuclear Magnetic Resonance (1H- and 13C NMR) and 2D 1H-1H gCOSY, 1H-13CgHSQC, 1H-13CgHMBC spectroscopies. Two conformers were found in the potential energy surface (PES) for CA in gas and aqueous solution phases by using the hybrid B3LYP method with the 6-31G* and 6-311++G** basis sets and, only one of them, C2 , was the most stable and with higher populations in both phases. Natural bond orbital (NBO) studies evidence the high stability of CA as compared with carquejol while atoms in molecules (AIM) analyses reveals the different characteristics of the H bonds formed showing CA higher topological properties. The gap values suggest that carquejol is most reactive than CA while higher values in the global electrophilicity and nucleophilicity indexes are observed for C2 , as compared with carquejol. Very good correlations between the experimental FTIR, FT-Raman, UV–Visible and 1H and 13C NMR spectra with their theoretical counterparts were found. The ECD spectrum predicted for C2 reveals the absolute configuration of CA. The complete assignment of the 84 normal vibration modes of CA is presented. Graphical abstract Image 1 Highlights • FTIR, FTRaman, and ECD spectra for Carquejil acetate were reported. • The solvation energies and the solvent effects were studied by using the PCM model. • The NBO and AIM studies show the higher stability of CA as compared with carquejol. • The ECD spectrum predicted for C2 reveals the absolute configuration of CA. • The influence of acetate group on C2 is evidenced through NPA and MK charges. [ABSTRACT FROM AUTHOR]

Abstract FT-IR, FT-Raman and ultraviolet–visible spectroscopies were used to characterize the potassium 5-hydroxypentanoyltrifluoroborate salt (HTFB) while the theoretical structures of this salt in gas and aqueous solution phases were studied by using hybrid B3LYP/6-311++G** calculations and the self consistent reaction field (SCRF) and solvation (SM) models because these models consider the solvent effects. Good concordance were obtained among the predicted 1H-, 13C and 19F-NMR chemical shifts for HTFB in aqueous solution with the corresponding experimental available data for this salt in CDCl 3. The corrected solvation energy by using ZPVE and non electrostatic terms is higher for this salt (−103.73 kJ/mol) than those reported for furoyl (−84.72 kJ/mol) and isonicotinoyl (−95.05 kJ/mol). Evidently, the side chain in HTFB increase the solubility of this salt in water, as compared with furoyl and isonicotinoyl. The NBO analyses show that the potassium 2-isonicotinoyltrifluorborate salt in both media is most stable than hydroxypentanoyl and furoyl salts and, in particular, the side chain in HTFB generates a diminishing of its stability in aqueous solution. Probably, this low stability of HTFB in solution is due to the higher solvation energy and to the n→σ∗ transitions no observed in the other salts. The AIM studies support the high stability of isonicotinoyl than the other two salts and, also, reveal the ionic characteristics of the K --O and K --F interactions observed in those three salts. The comparisons of the gap values for the three species suggest that the most reactive salt is isonicotinoyl while furoyl salt is the less reactive. The descriptors show the importance of study these salts in different media because the values in solution are slightly different in the three salts from those computed in gas phase. In addition, the harmonic force fields and the scaled internal force constants for the salt in both media are reported together to their complete vibrational assignments. Graphical abstract Image 1 Highlights • HTFB was characterized by FT-IR, FT-Raman and UV–Vis spectroscopies. • The HTFB structure was studied by using hybrid B3LYP/6-311++G** calculations. • The corrected solvation energy is higher in HTFB than the FTFB and ITFB salts. • The NBO analyses show that the side chain in HTFB decrease its stability in solution. • The AIM reveal the ionic characteristics of the Ke--O and Ke--F interactions. [ABSTRACT FROM AUTHOR]

Abstract Molecular dynamics simulations can be applied to explore the complex liquid phase behavior of lipid-based formulations and the gastrointestinal tract lumen. In order for the results from these simulations to be of value, the manner in which molecules interact with both aqueous and oil phases present needs to be as correct as possible. An existing molecular dynamics force field, GROMOS 53a6, was demonstrated to poorly reproduce the partitioning of straight-chain alcohol and short-chain polyethylene glycol (PEG) molecules between octanol and water phase (logP), with the molecules too hydrophobic. Force field parameters for Lennard-Jones interactions between CH2 and CH3 with water oxygen were adjusted to reproduce the experimental octanol logP, with all other Lennard-Jones and force field parameters left untouched. This parameter set, called 53a6 DBW , was subsequently used to recalculate straight-chain alcohol and short-chain PEG molecules, with significant improvement in the values obtained. Simulations of a nonionic surfactant in water, octaethylene glycol monocaprylate, were also performed to observe the aggregation behavior. 53a6 DBW demonstrated significant improvements in water interactions with the PEG chains, well hydrating the PEG groups, and allowing the formation of micelles. Further improvements and evaluation of the improved parameter set are ongoing. [ABSTRACT FROM AUTHOR]

Abstract A β -amyloid self-assembly is related to the changing the structure of the β -amyloid from the helix to the sheet. This structural change is one of the main reasons for developing Alzheimer's disease. Usually, the addition of non-polar solvents to water is used to study the role of hydrophobic forces in the self-assembly behavior. However, adding non-polar solvents also causes unwanted structural changes. Here, by changing the Lennard-Jones potential repulsion expression, structural changes in Amyloid β -peptide (1-40) (A β 40) have been studied using molecular dynamics simulation. For this purpose, in the Lennard-Jones potential n = 6 and m = 8 , 9, 10, 11, 12 were placed in attractive and repulsion terms, respectively. Then this change in the potential was applied to the GROMOS96 and OPLS-AA/L force fields. Molecular dynamics simulations of A β 40 were performed based on these 10 potentials. The results show that the change in the Lennard-Jones repulsion term in both of the applied force fields does not have a regular impact on the structure and dynamics of the A β 40. For example, with the change of m = 12 to m = 11 in the GROMOS96 force field, the diffusion coefficient of A β 40 decreases, while with the change of m = 11 to m = 10, the diffusion coefficient increases in this force field. The change zones in the secondary and tertiary structures are also different. However, the results indicate that the OPLS AA/L force field is more sensitive to the change in the Lennard-Jones potential repulsion term. Highlights • A new method was presented for studying A β -amyloid self-assembles. • The change zones in the secondary and tertiary structures are different. • The percentage of turn secondary structure in the LJ 6-12 has the highest value. • Sensitivity of the OPLS-AA/L force field to the potential change is more. [ABSTRACT FROM AUTHOR]

Refinement is the last step in protein structure prediction pipelines to convert approximate homology models to experimental accuracy. Protocols based on molecular dynamics (MD) simulations have shown promise, but current methods are limited to moderate levels of consistent refinement. To explore the energy landscape between homology models and native structures and analyze the challenges of MD-based refinement, eight test cases were studied via extensive simulations followed by Markov state modeling. In all cases, native states were found very close to the experimental structures and at the lowest free energies, but refinement was hindered by a rough energy landscape. Transitions from the homology model to the native states require the crossing of significant kinetic barriers on at least microsecond time scales. A significant energetic driving force toward the native state was lacking until its immediate vicinity, and there was significant sampling of off-pathway states competing for productive refinement. The role of recent force field improvements is discussed and transition paths are analyzed in detail to inform which key transitions have to be overcome to achieve successful refinement. [ABSTRACT FROM AUTHOR]

The analysis of remote sensing (RS) images, which is often accomplished using unsupervised image classification techniques, requires an effective method to determine an appropriate number of classification clusters. This paper proposes a preliminary analytical method to evaluate the input parameters for unsupervised RS image classification. Our approach involves first analysing the colour spaces of RS images based on the human visual perception theory. This enables the initial number of clusters and their corresponding centres to be automatically established based on the interaction of different forces in our supposed force field. The proposed approach can automatically determine the appropriate initial number of clusters and their corresponding centres for unsupervised image classification. A comparison of the experimental results with those of existing methods showed that the proposed method can considerably facilitate unsupervised image classification for acquiring accurate results efficiently and effectively without any prior knowledge. [ABSTRACT FROM AUTHOR]

Available estimates indicate that 30–40 % of all proteins need at least one metal ion to perform their biological function. Therefore, they are called metalloproteins. The correct biosynthesis of metalloproteins requires living organisms to be able to cope with issues such as the limited bioavailability or the potential cytotoxicity of several essential metals. Thus, organisms have developed complex machineries that guarantee the proper intracellular concentration and distribution among compartments of each metal, i.e. metal homeostasis. To understand how the different proteins responsible for metal homeostasis carry out their function, it is necessary to investigate their three‐dimensional (3D) structure and mobility at the atomic level. Nuclear magnetic resonance spectroscopy is one of the main experimental techniques providing this information. Computer simulations of molecular dynamics (MD) complement experimental information by showing how the 3D structure fluctuates over time and as a function of environmental conditions, with the possibility of exploring a wider range of timescales and conditions than usually amenable to experiment. Here we review numerous applications of MD for the investigation of the structure and dynamics of metalloproteins, and we also mention some technical aspects related to the parametrization of metals in commonly used force fields. Molecular dynamics simulations complement experimental information providing an atomistic view on biological functions. Here we discuss some applications to the study of metalloproteins, from the determination of their 3D structures, to their role in metal storage, transport and metal‐dependent transcriptional regulation. Some technical aspects related to the parametrization of metal ions are also mentioned. [ABSTRACT FROM AUTHOR]

We present a new force field for zinc ion to be used in classical Molecular Dynamics. Such model has been developed according to an optimization procedure by fitting experimental quantities taken from the literature. The metal ion electrostatic charge has been scaled by a factor 0.75, according to a recently proposed polarization model which considers the electronic screening effects due to the surrounding environment. Zinc interatomic interactions have been modeled by means of the Waldman‐Hagler combination rule. It is demonstrated that the proposed force field for zinc is transferable from water solution to protein catalytic sites, offering in both the considered cases good performances in the reproduction of experimental quantities usually addressed in soft matter computer simulations. A new force field for zinc ion, based on the standard Lennard‐Jones plus Coulomb potential, is presented. The ion point charge has been scaled to consider the electronic screening effects due to the environment. Structural and thermodynamic properties in water solution and protein metal centers have been calculated by means of molecular simulations, showing a fair agreement with experimental data. [ABSTRACT FROM AUTHOR]

The key to nanoscale control of physical, chemical, and biological processes lies in well‐founded models of noncovalent binding. Atomistic simulations probe the free‐energy surface underlying molecular assembly processes in solution. Two examples of noncovalent binding studied by molecular dynamics simulations are discussed, the dimerization of a water‐soluble perylene bisimide derivative in aqueous solution with a focus on the influence of solvent composition on the aggregation strength and the binding of 1‐butanol to α‐cyclodextrin at infinite dilution with the focus on the determination of method‐independent binding free energies. The association of molecular building blocks in a given solvent depends in a complex manner on the solvent composition. Molecular dynamics simulations provide a molecular‐level understanding of the various driving forces. In this work, two examples of noncovalent binding are studied and some aspects of force field validation are illustrated. [ABSTRACT FROM AUTHOR]

Recent computational theories and behavioral observations suggest that motor learning is supported by multiple adaptation processes, operating on different timescales, but direct neural evidence is lacking. We tested this hypothesis by applying transcranial magnetic stimulation over motor cortex in 16 human subjects during a validated reach adaptation task. Motor-evoked potentials (MEPs) and cortical silent periods (CSPs) were recorded from the biceps brachii to assess modulations of corticospinal excitability as indices for corticospinal plasticity. Guided by a two-state adaptation model, we show that the MEP reflects an adaptive process that learns quickly but has poor retention, while the CSP correlates with a process that responds more slowly but retains information well. These results provide a physiological link between models of motor learning and distinct changes in corticospinal excitability. Our findings support the relationship between corticospinal gain modulations and the adaptive processes in motor learning. NEW & NOTEWORTHY Computational theories and behavioral observations suggest that motor learning is supported by multiple adaptation processes, but direct neural evidence is lacking. We tested this hypothesis by applying transcranial magnetic stimulation over human motor cortex during a reach adaptation task. Guided by a two-state adaptation model, we show that the motor-evoked potential reflects a process that adapts and decays quickly, whereas the cortical silent period reflects slow adaptation and decay. [ABSTRACT FROM AUTHOR]

As part of the SAMPL6 host-guest blind challenge, the AMOEBA force field was applied to calculate the absolute binding free energy for a cucurbit[8]uril host complexed with 14 diverse guests, ranging from small, rigid structures to drug molecules. The AMOEBA results from the initial submission prompted an investigation into aspects of the methodology and parameterization employed. Lessons learned from the blind challenge include: a double annihilation scheme (electrostatics and van der Waals) is needed to obtain proper sampling of guest conformations, annihilation of key torsion parameters of the guest are recommended for flexible guests, and a more thorough analysis of torsion parameters is warranted. When put in to practice with the AMOEBA model, the lessons learned improved the MUE from 2.63 to 1.20 kcal/mol and the RMSE from 3.62 to 1.68 kcal/mol, respectively. Overall, the AMOEBA protocol for determining absolute binding free energies benefitted from participation in the SAMPL6 host-guest blind challenge and the results suggest the implementation of the methodology in future host-guest calculations. [ABSTRACT FROM AUTHOR]

Abstract: The study on the polymerization of fibrinogen molecules into fibrin monomers and eventually a stable, mechanically robust fibrin clot is a persistent and enduring topic in the field of thrombosis and hemostasis. Despite many research advances in fibrin polymerization, the change in the structure of fibrin clots and its influence on the formation of a fibrous protein network are still poorly understood. In this paper, we develop a new computational method to simulate fibrin clot polymerization using dissipative particle dynamics simulations. With an effective combination of reactive molecular dynamics formularies and many body dissipative particle dynamics principles, we constructed the reactive dissipative particle dynamics (RDPD) model to predict the complex network formation of fibrin clots and branching of the fibrin network. The 340 kDa fibrinogen molecule is converted into a spring-bead coarse-grain system with 11 beads using a topology representing network algorithm, and using RDPD, we simulated polymerization and formation of the fibrin clot. The final polymerized structure of the fibrin clot qualitatively agrees with experimental results from the literature, and to the best of our knowledge this is the first molecular-based study that simulates polymerization and structure of fibrin clots.Graphical abstract: [ABSTRACT FROM AUTHOR]

Intrinsically disordered proteins (IDPs) are closely related to various human diseases. Because IDPs lack certain tertiary structure, it is difficult to use X‐ray and NMR methods to measure their structures. Therefore, molecular dynamics simulation is a useful tool to study the conformer distribution of IDPs. However, most generic protein force fields were found to be insufficient in simulations of IDPs. Here, we report our development for the CHARMM community. Our residue‐specific IDP force field (CHARMM36IDPSFF) was developed based on the base generic force field with CMAP corrections for all 20 naturally occurring amino acids. Multiple tests show that the simulated chemical shifts with the newly developed force field are in quantitative agreement with NMR experiment and are more accurate than the base generic force field. Comparison of J‐couplings with previous work shows that CHARMM36IDPSFF and its corresponding base generic force field have their own advantages. In addition, CHARMM36IDPSFF simulations also agree with experiment for SAXS profiles and radii of gyration of IDPs. Detailed analysis shows that CHARMM36IDPSFF can sample more diverse and disordered conformers. These findings confirm that the newly developed force field can improve the balance of accuracy and efficiency for the conformer sampling of IDPs. [ABSTRACT FROM AUTHOR]

It is presented a straightforward procedure based on the CLAYFF force field to perform molecular dynamics (MD) computer simulations with the GROMACS open source package of layered double hydroxide (LDH) materials with different intercalated anions. This procedure enables running very long simulations of systems where all atomic positions are allowed to move freely, while maintaining the integrity of the LDH structure intact. Therefore, it has the potential to model different important applications of LDH involving ion-exchange and interlayer equilibrium processes in diverse areas as drug delivery, water purification, and corrosion protection. The magnesium-aluminium based LDH with a metallic ratio 2:1 (Mg 2 Al) was chosen to validate our computer simulation framework, because of the comprehensive experimental and computational studies reported in the literature devoted to the understanding of the structure of Mg 2 Al LDH. Potential parameters from the literature were used to model the Mg 2 Al LDH with different intercalated anions using a new set of atomic point charges calculated with the DDEC6 formalism. Once the model was validated through careful comparisons of the simulated and experimental structures, the procedure was adapted to the Zn 2 Al LDH materials. Lennard-Jones parameters had to be developed for zinc (II) cations and calibrated using the experimental structural data found in the literature for Zn 2 Al LDH and the height of the galleries determined experimentally in this work for Zn 2 Al with intercalated nitrate anions. The consistency of the model is proved by carrying out MD simulations to reproduce in the computer the typical experimental conditions in which the Zn 2 Al LDH is immersed in a sodium chloride water solution to act as a nanotrap for aggressive anions in corrosion protection applications. The LDH structure is maintained in the MD simulation in which the LDH is free to move alongside the solution and allowing a natural anion exchange between the LDH and the solution as well as dehydration/hydration of the basal space. [ABSTRACT FROM AUTHOR]

In many important processes in chemistry, physics, and biology the nuclear degrees of freedom cannot be described using the laws of classical mechanics. At the same time, the vast majority of molecular simulations that employ wide-coverage force fields treat atomic motion classically. In light of the increasing desire for and accelerated development of quantum mechanics (QM)-parameterized interaction models, we reexamine whether the classical treatment is sufficient for a simple but crucial chemical species: alkanes. We show that when using an interaction model or force field in excellent agreement with the "gold standard" QM data, even very basic simulated properties of liquid alkanes, such as densities and heats of vaporization, deviate significantly from experimental values. Inclusion of nuclear quantum effects via techniques that treat nuclear degrees of freedom using the laws of classical mechanics brings the simulated properties much closer to reality. [ABSTRACT FROM AUTHOR]

The infrared and Raman spectra of N -carbamoyl-L-proline, C 6 H 10 N 2 O 3 [(2 S )-1-carbamoylpyrrolidine-2-carboxylic acid] were obtained and interpreted with the help of DFT calculations. Six relatively stable molecular conformers were predicted by theory, being one of these similar to the conformer present in the crystal whose X-ray study was already known. The vibrational study was based in that conformer. The experimental vibrational data and assignments were used as basis for the definition of the Scaled Quantum Mechanics (SQM) force field for the molecule. The Potential Energy Distribution (P.E.D.), which revealed the complex nature of many molecular vibrations, and a set of internal force constants were calculated from this SQM force field. [ABSTRACT FROM AUTHOR]

In many important processes in chemistry, physics, and biology the nuclear degrees of freedom cannot be described using the laws of classical mechanics. At the same time, the vast majority ofmolecular simulations that employ wide-coverage force fields treat atomic motion classically. In light of the increasing desire for and accelerated development of quantum mechanics (QM)-parameterized interaction models, we reexamine whether the classical treatment is sufficient for a simple but crucial chemical species: alkanes. We show that when using an interaction model or force field in excellent agreement with the "gold standard" QM data, even very basic simulated properties of liquid alkanes, such as densities and heats of vaporization, deviate significantly from experimental values. Inclusion of nuclear quantum effects via techniques that treat nuclear degrees of freedom using the laws of classical mechanics brings the simulated properties much closer to reality. [ABSTRACT FROM AUTHOR]

Transferable force fields allow the prediction of physical properties for substances with scarce or absent experimental data. For substances with a comprehensive experimental database, however, transferable force fields produce results with higher errors than desired, because the transferable force fields are designed to represent a compromise in correlating the properties of many substances. For applications in chemical engineering, where requirements for accurate vapor pressure correlations and predictions exist, the results from transferable force fields are sometimes insufficient. We individualize the transferable anisotropic Mie force field (TAMie) for 38 substances of various chemical families, by introducing a correction parameter that scales all van der Waals energy parameters ε i of the considered substance. We find markedly reduced deviations, mainly in the description of vapor pressures while the errors in liquid density do not change significantly. For polar species, the improvement in vapor pressure is typically a factor four in absolute average deviation to experimental data, when compared to the original TAMie force field. The improved description of pure substances enables more reliable predictions of phase equilibria in binary mixtures. The concept of individualizing substances that are well-characterized by experimental data within a transferable force field is appealing, because the ability to predict mixtures with substances that are not covered by experimental data is preserved. [ABSTRACT FROM AUTHOR]

In this work, 2-isopropenyl-3-methylphenol, hereafter referred to as carquejiphenol (CARP), a minor component of “carqueja” essential oil, was synthesized starting from carquejol and characterized by using Fourier Transform infrared (FT-IR) and Raman (FT-Raman) spectroscopies, Ultraviolet–Visible (UV–Visible) spectroscopy, Electron Impact Mass spectrometry (EI-MS), Hydrogen and Carbon Nuclear Magnetic Resonance ( 1 H- and 13 C-NMR) and 2D 1 H 1 H gCOSY, 1 H 13 C gHSQC, 1 H 13 C gHMBC experiments. A very good correlation between the predicted FTIR, FTRaman, UV–visible and 1 H 13 C-NMR spectra for monomer and dimer of CARP by using theoretical B3LYP/6-31G* and 6-311++G** calculations with the corresponding experimental ones was observed. The solvation energies for CARP were predicted by using both levels of calculations and considering the solvent effects with the polarised continuum and solvation models. The increase in volume in solution supports the H bonds formation due to the presence in its structure of an OH group, as revealed by atoms in molecules (AIM) analysis. A high stability for CARP was found by using natural bond orbital (NBO) and AIM studies, while the investigation of the frontier orbitals reveals that CARP is more reactive than carquejol and N-(3,4-dimethoxybenzyl)-hexadecanamide but less reactive than the sesquiterpene lactone cnicin. The proximity of both the electrophilicy and nucleophilicity index of CARP with those obtained respectively for carquejol and for N-(3,4-dimethoxybenzyl)-hexadecanamide, suggests that CARP could probably present pharmacological properties. The scaled quantum mechanical force field (SQMFF) methodology was used to compute the harmonic force fields and to perform the complete vibrational analysis. In this way, 63 normal modes of vibration were assigned and compared with other terpene substances. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations are employed to investigate the aggregation behavior at the late stages of silica production in a colloidal solution to find new insights into the structures and dynamics of the produced aggregates and pores. The implemented theoretical investigations used the Amorphous cell and Forcite modules, and Dreiding force field of Materials Studio package. The key thermodynamic parameters, mean squared displacements, and radial distribution functions were calculated. Results revealed that aggregation occurred in the late stages due to the negative value of Gibbs free energy. Diameters of the generated “aggregates and pores” continuously increased while the number of “aggregates and pores” first increased and then decreased. Furthermore, the volume of pores first rose and then fell as the reaction proceeded. Variations of reactant numbers had the noticeable influence on the pores and aggregates topologies. The number of aggregates and pores had an upward trend while their diameters slightly reduced when more effective molecules were involved in the aggregation process. In addition, the shape of the aggregates examined and found that the predominant shapes of the aggregates were spherical. [ABSTRACT FROM AUTHOR]

The optimisation of a peptide-capped glycine using the novel force field FFLUX is presented. FFLUX is a force field based on the machine-learning method kriging and the topological energy partitioning method called Interacting Quantum Atoms. FFLUX has a completely different architecture to that of traditional force fields, avoiding (harmonic) potentials for bonded, valence and torsion angles. In this study, FFLUX performs an optimisation on a glycine molecule and successfully recovers the target density-functional-theory energy with an error of 0.89 ± 0.03 kJ mol−1. It also recovers the structure of the global minimum with a root-mean-squared deviation of 0.05 Å (excluding hydrogen atoms). We also show that the geometry of the intra-molecular hydrogen bond in glycine is recovered accurately. [ABSTRACT FROM AUTHOR]

The potassium 2-isonicotinoyltrifluorborate salt has been characterized by using FT-IR, FT-Raman and UV–Visible spectroscopies while its structural properties were studied by using B3LYP/6-31G* and B3LYP/6-311++G** calculations in gas and aqueous solution phases. Four conformers with C S and C 1 symmetries were found in the potential energy surfaces but only one of them presents the minimum energy. Two dimeric species of this salt were also optimized in accordance to the layered architectures suggested for trifluoroborate potassium salts in the solid phase. Here, the experimental Raman bands at 796, 748 and 676 cm −1 clearly support the presence of both dimers. On the other hand, the 2-isonicotinoyltrifluorborate anion was optimized because its presence is expected in solution. Reasonable correlations were observed between the predicted FTIR, Raman and UV–visible spectra with the corresponding experimental ones. The solvation energies for the salt in aqueous solution were predicted by using both methods. Here, it is observed that the change of furane by pyridine ring generates an increase in the solvation energies of the potassium 2-isonicotinoyltrifluorborate salt in relation to potassium 3-furoyltrifluoroborate salt. The study of the charges has revealed that there is an effect of the size of the basis set on the Mulliken charges while the AIM analyses suggest that the F⋯H and O⋯K interactions are also strongly dependent of the medium and the size of the basis sets. The bond orders for the F and K atoms evidence their higher ionic characteristics in solution with both basis sets. The NBO and AIM results clearly support the higher stability of this salt in both media. The studies by using the frontier orbitals indicate that the change of furane by pyridine ring decreases the reactivity of this salt by using 6-31G* basis set but increases when the other one is employed. Another effect of change of furane by pyridine ring is observed in the increase of the f(νC O) and f(νBF 3 ) force constants. In addition, the force fields for the salt in both media were reported together to their complete vibrational assignments and force constants by using both levels of theory. [ABSTRACT FROM AUTHOR]

We present a molecular mechanics-based approach to model the isolated zigzag BNNTs bonds by an (energy-)equivalent piezoelectric beam element. The harmonic DREIDING force field is employed for bonded and nonbonded interatomic interactions. To investigate the effectiveness of the proposed method we predict the elastic modulus and piezoelectric coefficients of BNNTs and demonstrate good accuracy compared to quantum mechanics predictions. Subsequently, we study the influence of some input parameters such as the tube diameter, aspect ratio and chirality. Finally, our approach is validated by comparison to data from the literature. [ABSTRACT FROM AUTHOR]

Aim. To parameterize a modified chained residue and use a newborn topology for molecular dynamics simulation. Method. To deal with the problem, a series of ab initio and semi-empirical methods were combined. The RESP (Restrained ElectroStatic Potential) program, which fits molecular electrostatic potential (MEP) at molecular surfaces using an atom-centered point charge model. All parameters were quantum mechanically calculated and processed with R.E.D.III server. Results. The method of molecular dynamics has potential advantages, like its capability to explore large systems, and disadvantages, like not being feasible to run on fly without a preliminary prepared topologies for identification of each molecule. In an attempt to find a balance between both features speed and accuracy and apply the approach in a computational study, a functional mechanism of prolyl-tRNA synthetase from E.faecalis was investigated. In addition, a well validated protocol of topology preparation for non-canonical structure was developed. Conclusions. Computational approaches like molecular dynamics simulation and molecular docking had now become a strong in silico methods to study biological processes. The major benefits of this methods are expensiveness and speed. It also a strong competitor of quantum modeling approach. However, there is a need to include new structures that are not exist in the GROMACS library is associated with the growing use of different types of modified amino and nucleic acids (DNA derivatives and RNAs) both in fundamental studies in molecular biology, molecular biophysics, etc., and in applied research related to the search for new drugs. The obtained data well correlate with the experimental data. [ABSTRACT FROM AUTHOR]