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Background: Force fields are used in a wide variety of contexts for classical molecular simulation, including studies on protein-ligand binding, membrane permeation, and thermophysical property prediction. The quality of these studies relies on the quality of the force fields used to represent the systems. Methods: Focusing on small molecules of fewer than 50 heavy atoms, our aim in this work is to compare nine force fields: GAFF, GAFF2, MMFF94, MMFF94S, OPLS3e, SMIRNOFF99Frosst, and the Open Force Field Parsley, versions 1.0, 1.1, and 1.2. On a dataset comprising 22,675 molecular structures of 3,271 molecules, we analyzed force field-optimized geometries and conformer energies compared to reference quantum mechanical (QM) data. Results: We show that while OPLS3e performs best, the latest Open Force Field Parsley release is approaching a comparable level of accuracy in reproducing QM geometries and energetics for this set of molecules. Meanwhile, the performance of established force fields such as MMFF94S and GAFF2 is generally somewhat worse. We also find that the series of recent Open Force Field versions provide significant increases in accuracy. Conclusions: This study provides an extensive test of the performance of different molecular mechanics force fields on a diverse molecule set, and highlights two (OPLS3e and OpenFF 1.2) that perform better than the others tested on the present comparison. Our molecule set and results are available for other researchers to use in testing., Competing Interests: Competing interests: DLM serves on the scientific advisory board for OpenEye Scientific Software and is an Open Science Fellow with Silicon Therapeutics., (Copyright: © 2020 Lim VT et al.)

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

In the field of molecular simulation for drug design, traditional molecular mechanic force fields and quantum chemical theories have been instrumental but limited in terms of scalability and computational efficiency. To overcome these limitations, machine learning force fields (MLFFs) have emerged as a powerful tool capable of balancing accuracy with efficiency. MLFFs rely on the relationship between molecular structures and potential energy, bypassing the need for a preconceived notion of interaction representations. Their accuracy depends on the machine learning models used, and the quality and volume of training data sets. With recent advances in equivariant neural networks and high‐quality datasets, MLFFs have significantly improved their performance. This review explores MLFFs, emphasizing their potential in drug design. It elucidates MLFF principles, provides development and validation guidelines, and highlights successful MLFF implementations. It also addresses potential challenges in developing and applying MLFFs. The review concludes by illuminating the path ahead for MLFFs, outlining the challenges to be overcome and the opportunities to be harnessed. This inspires researchers to embrace MLFFs in their investigations as a new tool to perform molecular simulations in drug design. [ABSTRACT FROM AUTHOR]

Background: Force fields are used in a wide variety of contexts for classical molecular simulation, including studies on protein-ligand binding, membrane permeation, and thermophysical property prediction. The quality of these studies relies on the quality of the force fields used to represent the systems. Methods: Focusing on small molecules of fewer than 50 heavy atoms, our aim in this work is to compare nine force fields: GAFF, GAFF2, MMFF94, MMFF94S, OPLS3e, SMIRNOFF99Frosst, and the Open Force Field Parsley, versions 1.0, 1.1, and 1.2. On a dataset comprising 22,675 molecular structures of 3,271 molecules, we analyzed force field-optimized geometries and conformer energies compared to reference quantum mechanical (QM) data. Results: We show that while OPLS3e performs best, the latest Open Force Field Parsley release is approaching a comparable level of accuracy in reproducing QM geometries and energetics for this set of molecules. Meanwhile, the performance of established force fields such as MMFF94S and GAFF2 is generally somewhat worse. We also find that the series of recent Open Force Field versions provide significant increases in accuracy. Conclusions: This study provides an extensive test of the performance of different molecular mechanics force fields on a diverse molecule set, and highlights two (OPLS3e and OpenFF 1.2) that perform better than the others tested on the present comparison. Our molecule set and results are available for other researchers to use in testing.

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. [ABSTRACT FROM AUTHOR]

Deep eutectic solvents (DESs) are binary or ternary mixtures of compounds that possess significant melting point depressions relative to the pure isolated components. The discovery of DESs has been a major breakthrough with multiple fields benefitting from their low cost and tunable physiochemical properties. However, tailoring DESs for specific applications through their practically unlimited synthetic combinations can be as much a hindrance as a benefit given the expense and time‐required to perform large‐scale experimental measurements. This emphasizes the need for fast computational tools capable of making accurate predictions of DES physiochemical properties exclusively from molecular structure. Yet, these systems are not trivial to model or simulate at the atomic level given their exceedingly nonideal behaviors, asymmetry of components, and the complexity of their molecular electrostatic interactions. Despite the challenge, computational reports featuring quantum mechanical (QM) methods have provided significant understanding into the relationship between the melting point depression and the unique and complex hydrogen bond network present in DESs. Classical molecular dynamics (MD) methods have examined bulk‐phase solvent organization in conjunction with thermodynamic and transport properties. Machine learning (ML) algorithms have shown great potential as structure–property prediction tools. Overall, this review highlights computational accomplishments that have meaningfully advanced our understanding of DESs and strives to give the reader a sense of the overall strengths and drawbacks of the methodologies employed while hinting at promises of advances to come. This article is categorized under:Software > Simulation Methods [ABSTRACT FROM AUTHOR]

The absolute binding free energies and binding enthalpies of twelve host-guest systems in the SAMPL5 blind challenge were computed using our attach-pull-release (APR) approach. This method has previously shown good correlations between experimental and calculated binding data in retrospective studies of cucurbit[7]uril (CB7) and β-cyclodextrin (βCD) systems. In the present work, the computed binding free energies for host octa acid (OA or OAH) and tetra-endo-methyl octa-acid (TEMOA or OAMe) with guests are in good agreement with prospective experimental data, with a coefficient of determination (R2) of 0.8 and root-mean-squared error of 1.7 kcal/mol using the TIP3P water model. The binding enthalpy calculations achieve moderate correlations, with R2 of 0.5 and RMSE of 2.5 kcal/mol, for TIP3P water. Calculations using the newly developed OPC water model also show good performance. Furthermore, the present calculations semi-quantitatively capture the experimental trend of enthalpy-entropy compensation observed, and successfully predict guests with the strongest and weakest binding affinity. The most populated binding poses of all twelve systems, based on clustering analysis of 750 ns molecular dynamics (MD) trajectories, were extracted and analyzed. Computational methods using MD simulations and explicit solvent models in a rigorous statistical thermodynamic framework, like APR, can generate reasonable predictions of binding thermodynamics. Especially with continuing improvement in simulation force fields, such methods hold the promise of making substantial contributions to hit identification and lead optimization in the drug discovery process.

[Display omitted] • Anhydrous, mono, di and trihydrate species were studied by using DFT calculations. • Mapped MEP surfaces show increase in the energies values from anhydrous to trihydrate. • Complete vibrational assignments of all the species are reported. • NBO studies reveal that the trihydrate in the gas phase is the most stable species. • The dihydrate is the most reactive species in gas phase and the anhydrous in solution. Theoretical structures of anhydrous (A), mono (M), di (D) and trihydrate (T) species of bronchodilator theophylline agent have been studied by using hybrid B3LYP/6–311++G** calculations to analyse the role of water molecules in its properties, reactivities and behaviours. The dipole moments increase with the number of water molecules (N) while the volumes (V) and solvation energies evidence behaviours lineal with N. D species shows higher V contraction, as T while A and M show slight V expansions. MEP surfaces show increase in energy from A to T. NBO studies reveal that T is most stable in the gas phase while A in solution. Gap values show that D is the most reactive species in gas phase while A in solution. Complete assignments of all the species and their scaled force constants are reported including librations of water molecules. [ABSTRACT FROM AUTHOR]

In the present work, the structural, topological and vibrational properties of five members of the series C 8 H 13 N 3 O 5 PO R (R H, (CH 2) 3 O CH 2 CH 3 , (CH 2) 3 O (CH 2) 7 CH 3 , (CH 2) 3 O (CH 2) 13 CH 3 and (CH 2) 3 O (CH 2) 15 CH 3), where the first and the latter members are the two potential antiviral agents, cidofovir and brincidofovir, respectively, were studied by using density functional theory (DFT), natural bond orbital (NBO), atoms in molecules theory (AIM), frontier orbitals and molecular electrostatic potential (MEP) calculations and the hybrid B3LYP/6-31G∗ method. Here, the changes in the properties were followed modifying the side chain from cidofovir to brincidofovir. This study reveals clearly the differences in the properties when they change the longitude of the side chain. The high dipole moment value of brincidofovir together with the large side chain could explain the ability of brincidofovir to traverse biological membranes more rapidly than cidofovir while the low bond order that presents the PO R bond in brincidofovir probably supports the quick removal of its side chain inside the cell. The frontier orbitals predicted a high reactivity and a higher electrophilicity index for brincidofovir, as compared with cidofovir. The complete assignment of the 90 vibration modes of cidofovir was proposed. [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]

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]

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]

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 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]

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]

Abstract: Structural characterization of liquid pyrrole has been obtained by performing classical molecular dynamics simulations with a new parameterization of electrostatic interactions. Despite the relatively simple molecular structure of pyrrole, a correct and accurate representation of its intermolecular interactions in bulk phase is a challenging task, since these are affected at short range by the quadrupole–quadrupole term. This new parameterization permits not only to correctly describe the liquid structure but also to obtain macroscopic properties in excellent agreement with experiments. [ABSTRACT FROM AUTHOR]

In this study, three anhydrous species of trehalose and their dihydrated form were studied using the Fourier Transform Infrared (FTIR) and Raman spectroscopy combined with theoretical calculations derived from the theory of the functional of the density (DFT). Here, the structural and vibrational properties were predicted using the hybrid B3LYP/6-31G ∗ method. The complete vibrational assignments were performed using the scaled mechanical force fields (SQMFF) methodology and their internal normal coordinates. The natural bond orbital (NBO) and atoms in molecules (AIM) calculations predicted high stabilities for the dihydrated species in gas and aqueous solution phases. The little variation observed in the dipole moment for the dihydrated species in solution could be related to a small perturbation of water hydration shell and short hydrogen bonds, as revealed by NBO and AIM studies. The lower volume expansion, low solvation energy and the higher nucleophilicity index observed for trehalose species in solution, in relation to maltose and sucrose could probably explain that different water molecules are around of trehalose/water mixtures generating higher “rigidity” in trehalose, as was experimentally reported in the literature. On the other hand, the low f ( νO – H ) H2O force constant value for trehalose, as compared with maltose and lactose could justify the very fragile character from the trehalose/water system to the temperature and concentration changes, as was experimentally observed from viscosity and Raman scattering studies. [ABSTRACT FROM AUTHOR]

Dieldrin was characterized by using Fourier Transform infrared (FT-IR) and Raman (FT-Raman), Ultraviolet–Visible (UV–Visible) spectroscopies. The structural and vibrational properties for dieldrin in gas phase and in aqueous solution were computed combining those experimental spectra with hybrids B3LYP and WB97XD calculations by using the 6-31G* and 6-311++G** basis sets. Here, the experimental available Hydrogen and Carbon Nuclear Magnetic Resonance ( 1 H and 13 C NMR) for dieldrin were also used and compared with those predicted by calculations. The B3LYP/6-311++G** method generates the most stable structures while the results have demonstrated certain dependence of the volume and dipole moment values with the method, size of the basis set and, with the studied media. The lower solvation energy for dieldrin (−32.94 kJ/mol) is observed for the higher contraction volume (−2.4 Å 3 ) by using the B3LYP/6-31G* method. The NBO studies suggest a high stability of dieldrin in gas phase by using the WB97XD/6-31G* method due to the n→π* and n*→π* interactions while the AIM analyses support this high stability by the C18⋯H26 and C14⋯O7 contacts. The different topological properties observed in the R5 ring suggest that probably this ring plays a very important role in the toxics properties of dieldrin. The frontier orbitals show that when dieldrin is compared with other toxics substances the reactivity increases in the following order: CO < STX < dieldrin < C 6 Cl 6

The p -xylylenediaminium bis(nitrate) compound have been synthesized and then, it was characterized by using Fourier Transform infrared (FT-IR) in the solid phase and, by using the Ultraviolet–Visible (UV–Visible) and Hydrogen and Carbon Nuclear Magnetic Resonance ( 1 H- and 13 C-NMR) spectra in aqueous solution and in dimethylsulfoxide solvent. In this work, two monodentate and bidentate coordination modes were considered for the nitrate ligands in both media in order to study the structural and vibrational properties of that salt. Hence, the natural bond orbital (NBO), atoms in molecules (AIM), Merz-Kollman (MK) charges, molecular electrostatic potentials (MEP) and frontier orbitals studies were performed for p -xylylenediaminium bis(nitrate) and their cation and anion species taking into account for the salt those two coordination modes for the nitrate ligands. The intermolecular interactions of this salt were also evaluated by Hirshfeld surface analysis. The B3LYP calculations performed by using the hybrid method and the 6-311G* and 6-311++G** basis sets generate monodentate and bidentate structures with C i and C 2 symmetries, respectively. The force fields and the force constants values for these two structures were also computed and their complete vibrational assignments were performed by using those both levels of theory. The strong band at 1536 cm −1 , the bands between 2754 and 2547 cm −1 and the bands between 1779 and 1704 cm −1 support clearly the presence of the dimeric species while the IR bands at 1986/1856 cm −1 could justify the presence of the bidentate species in the solid phase. [ABSTRACT FROM AUTHOR]

Carquejol and its acetate are monoterpenoids based on the rare o -menthane skeleton and distinctive components of the essential oil from Baccharis trimera . Carquejol was 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 ( 1 H and 13 C NMR) and 2D 1 H 1 H gCOSY, 1 H 13 CgHSQC, 1 H 13 CgHMBC spectroscopies. Due to the chirality of this monoterpenoid, six different structures were analysed, of which only four showed higher populations and minimal energies. The natural bond orbital (NBO), atoms in molecules (AIM), Merz-Kollman (MK) charges, molecular electrostatic potentials (MEP) and frontier orbitals studies were performed in order to evaluate their structural, electronic, topological and vibrational properties. All calculations were performed by using the hybrid B3LYP method and the 6-31G* and 6-311++G** basis sets. The comparison of the experimental ECD spectra with the corresponding theoretical ones confirm the (4S,5R) configuration assigned to carquejol. The force fields for the most stable configurations were computed by using those two levels of theory and the complete vibrational assignments for the two conformations of carquejol are reported. The different orientations and directions of the dipole moments of the two structures and the proximity in the nucleophilic indexes with those reported for other terpenes could justify in part the potential biological properties reported for carquejol. The MEP surfaces for both structures reveal that the nucleophilic and electrophilic sites of higher reactivity are principally centred on the OH groups. [ABSTRACT FROM AUTHOR]

We investigated the effect of fluorinated molecules on dipalmitoylphosphatidylcholine (DPPC) bilayers by force-field molecular dynamics simulations. In the first step, we developed all-atom force-field parameters for additive molecules in membranes to enable an accurate description of those systems. On the basis of this force field, we performed extensive simulations of various bilayer systems containing different additives. The additive molecules were chosen to be of different size and shape, and they included small molecules such as perfluorinated alcohols, but also more complex molecules. From these simulations, we investigated the structural and dynamic effects of the additives on the membrane properties, as well as the behavior of the additive molecules themselves. Our results are in good agreement with other theoretical and experimental studies, and they contribute to a microscopic understanding of interactions, which might be used to specifically tune membrane properties by additives in the future. [ABSTRACT FROM AUTHOR]

We have synthesized 3,3′,4,4′ Tetrachloroazoxybenzene (TCAOB) and, later, characterized it by using infrared, Raman, 1 H, 13 C NMR and UV–visible spectroscopies. The structural, topological and vibrational properties of four Cis and three Trans isomers were theoretically predicted by using the hybrid B3LYP together with the 6-31G* and 6-311++G** basis sets. The 69 normal modes of vibration for all TCAOB isomers were assigned by using the scaled quantum mechanical force field (SQMFF) procedure and their experimental vibrational spectra and normal internal coordinates. The high stabilities of all Cis and Trans isomers are supported by the π→π* , n→σ*, n→π* and π*→π* electronic transitions calculated by NBO studies while the AIM analyses reveal for the Trans forms the existence of intra-molecular C H⋯O hydrogen bonds, as suggested by the broad IR band observed in the higher wavenumbers region. The low gap energy for the Trans I isomer supports their higher reactivity probably due to the repulsion of the more electronegative Cl and O atoms as a consequence of their proximities. In addition, the force constants for all Cis and Trans isomers were calculated by using both levels of theory. Here, the comparisons of the predicted IR, Raman, NMR and ultraviolet–visible spectra with the corresponding experimental ones demonstrate good concordances. The existence of the N O groups in all TCAOB isomers support the differences in their properties, as compared with those reported for TCAB. [ABSTRACT FROM AUTHOR]

In this work, the structural, topological and vibrational properties of the monomer and three dimers of the 2-(4-nitrophenyl)-4H-3,1-benzoxazin-4-one (NPB) derivative were studied combining the experimental FTIR and FT-Raman spectra in the solid phase with DFT calculations. Here, Natural Bond Orbital (NBO), Atoms in Molecules (AIM) and HOMO and LUMO calculations were performed by using the hybrid B3LYP/6-31G*and B3LYP/6-311++G** methods in order to compute those properties and to predict their reactivities. The comparisons with the properties reported for the chlorinated (Cl-PB) and methylated (CH 3 -PB) derivatives at the same levels of theory can be clearly justified by the activating (CH 3 ) and deactivating (NO 2 and Cl) characteristics of the different groups linked to oxaxin rings. The NBO and AIM studies evidence the following stability orders: Cl-PB > NO 2 -PB > CH 3 -PB in very good concordance with the f(νC23-X26) force constants values. The frontier orbitals analyses reveal that the Cl-PB and NO 2 -PB derivatives have good stabilities and high chemical hardness while CH 3 -PB has a higher chemical reactivity. On the other hand, the complete vibrational assignments for monomer and dimers species of NPB were presented. The presence of the IR bands at 1574 and 1037 cm −1 and, of the Raman bands at 1571 and 1038 cm −1 support clearly the presence of the different dimeric species proposed for NPB. [ABSTRACT FROM AUTHOR]

In this work, three monomeric forms of arabinitol, usually named arabitol, and their dimeric species have been structural and vibrationally studied by using the micro-Raman spectra in the solid phase accomplished with theoretical calculations based on the theory of the functional of the density (DFT). The hybrid B3LYP method was used for all the calculations together with the 6-31G* and 6-311++g** basis sets. Two different L structures with minima energies were predicted in accordance to the two polymorphic structures revealed by recent X-ray diffraction experiments. The studies by natural bond orbital (NBO) calculations reveals high stabilities of the L form as compared with the D one but the topological properties by using the atoms in molecules (AIM) suggest a higher stability of the D form due to a strong H bond interactions. The scaled mechanical force fields (SQMFF) procedure was used to perform the complete vibrational assignments for the monomeric forms and their dimer. On the other hand, the similarity in the gap values computed for the three forms of arabitol with those observed for sucrose, trehalose, maltose and lactose in gas phase at the same level of theory could partially explain the sweetening property of this alcohol. In addition, the influences of the size of the basis set on some properties were evidenced. [ABSTRACT FROM AUTHOR]

The structural and vibrational properties of the α-adrenergic agonist clonidine hydrochloride agent and their anionic and dimeric species were studied combining the experimental FT-IR and Raman spectra in solid phase with ab-initio calculations based on the density functional theory (DFT). All the calculations were performed by using the hybrid B3LYP with the 6-31G* and 6-311++G** basis sets. The structural properties for those species were studied employing the Natural Bond Orbital (NBO), Atoms in Molecules theory (AIM) and frontier orbitals calculations. The complete assignments of the FTIR and Raman spectra were performed combining the DFT calculations with the Pulay's Scaled Quantum Mechanics Force Field (SQMFF) methodology. Very good concordances between the theoretical and experimental spectra were found. In addition, the force constants for those three species were computed and compared with the values reported for similar antihypertensive agents. The ionic nature of the H→Cl bond and the high value of the LP(1)N4 → LP*(1)H18 charge transfer could explain the high reactivity of clonidine hydrochloride in relation to other antihypertensive agent and the strong shifthing of the band assigned to the N H stretching mode linked to the H Cl bond toward lower wavenumbers. [ABSTRACT FROM AUTHOR]

N -(3,4-dimethoxybenzyl)-hexadecanamide (DMH) was characterized by using Fourier Transform infrared (FT-IR) and Raman (FT-Raman), Ultraviolet- Visible (UV-Visible) and Hydrogen and Carbon Nuclear Magnetic Resonance ( 1 H and 13 C NMR) spectroscopies. The structural, electronic, topological and vibrational properties were evaluated in gas phase and in n -hexane employing ONIOM and self-consistent force field (SCRF) calculations. The atomic charges, molecular electrostatic potentials, stabilization energies and topological properties of DMH were analyzed and compared with those calculated for N -(3,4-dimethoxybenzyl)-acetamide (DMA) in order to evaluate the effect of the side chain on the properties of DMH. The reactivity and behavior of this alkamide were predicted by using the gap energies and some descriptors. Force fields and the corresponding force constants were reported for DMA only in gas phase and n -hexane due to the high number of vibration normal modes showed by DMH, while the complete vibrational assignments are presented for DMA and both forms of DMH. The comparisons between the experimental FTIR, FT-Raman, UV-Visible and 1 H and 13 C NMR spectra with the corresponding theoretical ones showed a reasonable concordance. [ABSTRACT FROM AUTHOR]

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]

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]

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]

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]

In this work, the structural, topological and vibrational properties of an isothiazole derivatives series with antiviral activities in gas and aqueous solution phases were studied by using DFT calculations. The self consistent reaction field (SCRF) method was combined with the polarized continuum (PCM) model in order to study the solvent effects and to predict their reactivities and behaviours in both media. Thus, the 3-mercapto-5-phenyl-4-isothiazolecarbonitrile (I), 3-methylthio-5-phenyl-4-isothiazolecarbonitrile (II), 3-Ethylthio-5-phenyl-4-isothiazolecarbonitrile (III), S -[3-(4-cyano-5-phenyl)isothiazolyl] ethyl thiocarbonate (IV), 5-Phenyl-3-(4-cyano-5-phenylisothiazol-3-yl) disulphanyl-4-isothiazolecarbonitrile (V) and 1,2-Bis(4-cyano-5-phenylisothiazol-3-yl) sulphanyl Ethane (VI) derivatives were studied by using the hybrid B3LYP/6-31G* method. All the properties were compared and analyzed in function of the different R groups linked to the thiazole ring. This study clearly shows that the high polarity of (I) probably explains its elevated antiviral activity due to their facility to traverse biological membranes more rapidly than the other ones while in the (IV) and (V) derivatives the previous hydrolysis of both bonds increasing their antiviral properties inside the cell probably are related to their low S-R bond order values. In addition, the complete vibrational assignments and force constants are presented. [ABSTRACT FROM AUTHOR]

In the present work, the structural and vibrational properties of the sesquiterpene lactone onopordopicrin (OP) were studied by using infrared spectroscopy and density functional theory (DFT) calculations together with the 6-31G ∗ basis set. The harmonic vibrational wavenumbers for the optimized geometry were calculated at the same level of theory. The complete assignment of the observed bands in the infrared spectrum was performed by combining the DFT calculations with Pulay’s scaled quantum mechanical force field (SQMFF) methodology. The comparison between the theoretical and experimental infrared spectrum demonstrated good agreement. Then, the results were used to predict the Raman spectrum. Additionally, the structural properties of OP, such as atomic charges, bond orders, molecular electrostatic potentials, characteristics of electronic delocalization and topological properties of the electronic charge density were evaluated by natural bond orbital (NBO), atoms in molecules (AIM) and frontier orbitals studies. The calculated energy band gap and the chemical potential ( μ ), electronegativity ( χ ), global hardness ( η ), global softness ( S ) and global electrophilicity index ( ω ) descriptors predicted for OP low reactivity, higher stability and lower electrophilicity index as compared with the sesquiterpene lactone cnicin containing similar rings. [ABSTRACT FROM AUTHOR]

In this work, the structural, electronic and vibrational properties of 6-Nitro-1,3-benzothiazole-2(3 H )-thione and their 2-thiol tautomer were studied by using density functional theory (DFT) and self consistent reaction force (SCRF) calculations in gas phase and, in formamide, aqueous, DMSO and acetone solutions. The solvation energies were computed taking into account the solvent effects by using the polarized continuum (PCM) and solvation (SM) models. The atomic charges, electrostatic potentials, bond order, energy stabilizations, topological properties were calculated together with the gap energies and some descriptors in order to predict the reactivities and behaviour of both tautomers in the different media. The dipole moment and solvation energy values for both forms show different behaviours with the permittivity values of the solvents. The studies by infrared spectroscopy reveal the presence of both tautomers and of the two dimers of thione in the solid phase, as supported by the weak IR bands at 1702, 1525, 1303 and 1292 cm −1 and the shoulder at 915 cm −1 . Moreover, the strong IR band at 3062 cm −1 , the bands of the media intensities at 680 and 466 cm −1 and, the very weak band at 499 cm −1 support the presence of the thione form. The higher electrostatic potentials on the NO 2 group of the thiol tautomer and their low electrophilic index show that thiol is better electron donor than thione while, thione has the highest reactivities in all the solvents and in gas phase than thiol. Here, the complete assignments of the normal vibration modes of thione and thiol in gas phase and in the four solvents are reported for the first time. [ABSTRACT FROM AUTHOR]

In this study 3,3′,4,4′-tetrachloroazobenzene (TCAB) was prepared and then characterized by infrared, Raman, multidimensional nuclear magnetic resonance (NMR) and ultraviolet–visible spectroscopies. The density functional theory (DFT) together with the 6-31G * and 6-311++G ** basis sets were used to study the structures and vibrational properties of the two cis and trans isomers of TCAB. The harmonic vibrational wavenumbers for the optimized geometries were calculated at the same theory levels. A complete assignment of all the observed bands in the vibrational spectra of TCAB was performed combining the DFT calculations with the scaled quantum mechanical force field (SQMFF) methodology. The molecular electrostatic potentials, atomic charges, bond orders and frontier orbitals for the two isomers of TCAB were compared and analyzed. The comparison of the theoretical ultraviolet–visible spectrum with the corresponding experimental demonstrates a good concordance while the calculated 1 H and 13 C chemicals shifts are in good conformity with the corresponding experimental NMR spectra of TCAB in solution. The np®p * transitions for both forms were studied by natural bond orbital (NBO) while the topological properties were calculated by employing Bader ’ s Atoms in the Molecules (AIM) theory. This study shows that the cis and trans isomers exhibit different structural and vibrational properties and absorption bands. [ABSTRACT FROM AUTHOR]

• A new dimeric sesquiterpene lactone was isolated from Mikania parodii Cabrera. • Its structure was established by HR-MS, and 1D and 2D NMR experiments. • Parodiolide was also characterized by FT-IR, FT-Raman, UV-V and ECD spectra. • The predicted solvation energy of parodiolide in methanol is −167.9 kJ/mol. • The ECD spectrum in methanol solution confirms its absolute configuration. A new dimeric sesquiterpene lactone named parodiolide was isolated from Mikania parodii Cabrera. Its structure and relative stereochemistry were established by HR-MS, 1H- and 13C NMR spectroscopy using 1D and 2D experiments in combination with the use of FT-IR, FT-Raman and UV-Visible spectroscopies. The combination of B3LYP/6-31G* calculations with experimental results revealed its structural and topological properties showing a rare spiro connection, and allowed to establish the absolute configuration of its ten chiral centers. The predicted solvation energy of parodiolide in methanol is -167.9 kJ/mol. Mapped MEP surfaces show nucleophilic sites on two lactone rings while on H atoms of C CH 2 and C=C H groups, electrophilic sites are observed. NBO and AIM studies have shown a higher stability of parodiolide in methanol solution while its gap value in the same medium suggest reactivity comparable to other sesquiterpene lactones, such as cnicin and onopordopicrin. The atomic orbitals of the rings contribute to the increase of the gap value, decreasing their reactivity and potency in solution. Very good correlations were observed when the predicted infrared, Raman, NMR and ECD spectra were compared with the corresponding experimental ones. Complete assignments of the vibration normal modes and the main force constants are also reported for paradiolide in both media. Finally, the ECD spectrum in methanol solution confirms the absolute configuration of parodiolide. [Display omitted] [ABSTRACT FROM AUTHOR]

In this study, aqueous solutions at different molar concentrations of sodium cyclamate in water were completely characterized by HATR (Horizontal Attenuated Total Reflectance) and Raman spectroscopies. The theoretical structures of cyclamate ion, the zwitterionic and neutral forms of the cyclamic acid and its dimer were optimized in gas and aqueous solution phases by using the hybrid B3LYP/6-31G* method. The solvent effects for the four species in aqueous solutions were simulated by using self-consistent reaction field (SCRF) calculations employing the integral equation formalism variant (IEFPCM) model. The complete assignments of the vibrational spectra of all the forms of cyclamic acid were performed taking into account the factor group analysis with the Scaled Quantum Mechanics Force Field (SQMFF) methodology. The existence of the zwitterionic and neutral forms of the cyclamic acid and its dimer in a solution of cyclamate in water is evidenced by characteristic bands in the HATR and Raman spectra. The dimerization of cyclamate in aqueous solution was previously reported by conductimetric method. The natural population analysis (NPA) and Merz-Kollman (MK) charges, molecular electrostatic potential (MEP), natural bond orbital (NBO) and atoms in molecules (AIM) calculations predict for all the species the principal donor and acceptor sites for the H bonds formation in aqueous solution. The SQM force fields for the cyclamate ion, the zwitterionic and neutral species of the cyclamic acid were obtained and their corresponding force constants in both phases were reported. Additionally, the solvation energies for those species were reported. [ABSTRACT FROM AUTHOR]

Highlights: [•] Cnicin was characterized by infrared, Raman, NMR and UV–visible spectroscopies. [•] The molecular structure of cnicin has a ten member’s ring with a chair conformation. [•] The γ-lactone ring of cnicin has a half-chair conformation. [•] The NBO and AIM studies show the high stability of cnicin. [•] A complete assignment of the 153 normal vibration modes for cnicin was performed. [Copyright &y& Elsevier]

Highlights: [•] A complete vibrational assignment of sucrose in aqueous medium was performed. [•] Sucrose in aqueous solution was characterized by IR, HATR, and Raman spectroscopies. [•] The solvent effects for all species were studied using the solvation PCM/SMD model. [•] The presence of pure water, sucrose penta-hydrate, and sucrose dihydrate was confirmed. [•] The H bond formation in aqueous solution was studied by NBO and AIM investigation. [Copyright &y& Elsevier]