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The use of tris(4-aminophenyl)amine (TAPA) as central to the synthesis of both polyimines and polyimides and covalent organic frameworks and inorganic cages, among others, has grown in the last few years. The resulting materials exhibit high performance in their area of application. In this contribution, the crystal structures of two TAPA derivatives, triethyl (nitrilotris(benzene-4,1-diyl))tricarbamate (1) and triethyl 2,2′,2″-((nitrilotris(benzene-4,1-diyl))tris(azanediyl))tris(2-oxoacetate) (2), are described. The molecular and supramolecular structures of both compounds were compared between them and with analogous compounds. The analyses of their vibrational and 13C-CPMAS NMR spectroscopies, as well as their thermal stability, were included and corelated with the crystal structure. Hirshfeld surface analysis on the crystal structures of both TAPA derivatives revealed the stabilization of the crystal network via the amide N—H∙∙∙O interactions of dispersive nature in the carbamate, whereas dispersive carbonyl–carbonyl interactions also played a competitive role in the supramolecular arrangement of the oxamate. Interaction energy DFT calculations performed at the B3LYP/6-31G(d,p) level allowed us to estimate the energy contributions and nature of several interactions in terms of the stability of both crystal lattices. [ABSTRACT FROM AUTHOR]

We utilized density functional theory (DFT) to investigate the electronic structure and Raman spectrum of Azinphos-methyl (AzM) (C10H12N3O3PS2) both in isolation and in combination with gold nanoclusters (Aun, n = 2, 4, and 6). The research highlights a significant enhancement in Raman activity with increasing gold atom count from AzM-Au2 to AzM-Au4. The DFT calculations provide a comprehensive analysis of various electronic properties, including HOMO and LUMO energies, gap energy (Eg), ionization potential (IP), and electron affinity (EA), comparing these with experimental results from Liu et al. (2012). We also examined reactivity parameters, electrostatic properties, molecular electrostatic potential (MEP), Natural bond orbital (NBO) analysis, and atoms-in-molecules theory (AIM). The binding energy trends among the (AzM)-Aun complexes revealed a hierarchy: (AzM)-Au2 > (AzM)-Au6 > (AzM)-Au4. Monte Carlo simulations were used to explore AzM interactions with gold nanoparticles (AuNPs) of various shapes and sizes, indicating that increased Raman intensity correlates with higher global electrophilicity and total polarizability. The results suggested that the stability of the complexes improves with more gold atoms, as evidenced by greater charge transfer, interaction energies, and second-order stabilization energies (E2). Among the complexes studied, AzM-Au2 showed the highest stability. Monte Carlo simulations revealed that the right circular cone-shaped structure, especially at 7 nm, demonstrated the most negative adsorption energy, indicating stronger adsorption interactions. This research fills a gap in previous studies on AzM, providing valuable insights and serving as a reference for future work.

The importance of potential use of Linear Free Energy Relationships (LFER, both Hammett and Taft equations) is explored by applying to the binding/interaction energies of the cation-benzene molecular complexes. An intense study of the application of both Hammett and Taft correlations in their various forms in the present study reveals that the substituent effect is not confined to a particular carbon atom of the η-system of benzene but propagated through the entire moiety of the η-system. Possible explanations are provided based on the magnitude of several Hammett and Taft reaction constants (P and p*). [ABSTRACT FROM AUTHOR]

We utilized density functional theory (DFT) to investigate the electronic structure and Raman spectrum of Azinphos-methyl (AzM) (C10H12N3O3PS2) both in isolation and in combination with gold nanoclusters (Aun, n = 2, 4, and 6). The research highlights a significant enhancement in Raman activity with increasing gold atom count from AzM-Au2 to AzM-Au4. The DFT calculations provide a comprehensive analysis of various electronic properties, including HOMO and LUMO energies, gap energy (Eg), ionization potential (IP), and electron affinity (EA), comparing these with experimental results from Liu et al. (2012). We also examined reactivity parameters, electrostatic properties, molecular electrostatic potential (MEP), Natural bond orbital (NBO) analysis, and atomsin-molecules theory (AIM). The binding energy trends among the (AzM)-Aun complexes revealed a hierarchy: (AzM)-Au2 > (AzM)-Au6 > (AzM)-Au4. Monte Carlo simulations were used to explore AzM interactions with gold nanoparticles (AuNPs) of various shapes and sizes, indicating that increased Raman intensity correlates with higher global electrophilicity and total polarizability. The results suggested that the stability of the complexes improves with more gold atoms, as evidenced by greater charge transfer, interaction energies, and second-order stabilization energies (E²). Among the complexes studied, AzM-Au2 showed the highest stability. Monte Carlo simulations revealed that the right circular cone-shaped structure, especially at 7 nm, demonstrated the most negative adsorption energy, indicating stronger adsorption interactions. This research fills a gap in previous studies on AzM, providing valuable insights and serving as a reference for future work. [ABSTRACT FROM AUTHOR]

Context: Molecularly imprinted polymers (MIPs) have promising applications as synthetic antibodies for protein and peptide recognition. A critical aspect of MIP design is the selection of functional monomers and their adequate proportions to achieve materials with high recognition capacity toward their targets. To contribute to this goal, we calibrated a molecular dynamics protocol to reproduce the experimental trends in peptide recognition of 13 pre-polymerization mixtures reported in the literature for the peptide toxin melittin. Methods: Three simulation conditions were tested for each mixture by changing the box size and the number of monomers and cross-linkers surrounding the template in a solvent-explicit environment. Fully atomistic MD simulations of 350 ns were conducted with the AMBER20 software, with ff19SB parameters for the peptide, gaff2 parameters for the monomers and cross-linkers, and the OPC water model. Template-monomer interaction energies under the LIE approach showed significant differences between high-affinity and low-affinity mixtures. Simulation systems containing 100 monomers plus cross-linkers in a cubic box of 90 Å3 successfully ranked the mixtures according to their experimental performance. Systems with higher monomer densities resulted in non-specific intermolecular contacts that could not account for the experimental trends in melittin recognition. The mixture with the best recognition capacity showed preferential binding to the 13–26-α-helix, suggesting a relevant role for this segment in melittin imprinting and recognition. Our findings provide insightful information to assist the computational design of molecularly imprinted materials with a validated protocol that can be easily extended to other templates. [ABSTRACT FROM AUTHOR]

We study a large family of axisymmetric Riesz-type singular interaction potentials with anisotropy in three dimensions. We generalize some of the results of the recent work [J. A. Carrillo and R. Shu, Global minimizers of a large class of anisotropic attractive-repulsive interaction energies in 2D, Comm. Pure Appl. Math. (2023), 10.1002/cpa.22162] in two dimensions to the present setting. For potentials with linear interpolation convexity, their associated global energy minimizers are given by explicit formulas whose supports are ellipsoids. We show that, for less singular anisotropic Riesz potentials, the global minimizer may collapse into one or two-dimensional concentrated measures which minimize restricted isotropic Riesz interaction energies. Some partial aspects of these questions are also tackled in the intermediate range of singularities in which one-dimensional vertical collapse is not allowed. Collapse to lower-dimensional structures is proved at the critical value of the convexity but not necessarily to vertically or horizontally concentrated measures, leading to interesting open problems. [ABSTRACT FROM AUTHOR]

The use of tris(4-aminophenyl)amine (TAPA) as central to the synthesis of both polyimines and polyimides and covalent organic frameworks and inorganic cages, among others, has grown in the last few years. The resulting materials exhibit high performance in their area of application. In this contribution, the crystal structures of two TAPA derivatives, triethyl (nitrilotris(benzene-4,1-diyl))tricarbamate (1) and triethyl 2,2′,2″-((nitrilotris(benzene-4,1-diyl))tris(azanediyl))tris(2-oxoacetate) (2), are described. The molecular and supramolecular structures of both compounds were compared between them and with analogous compounds. The analyses of their vibrational and 13C-CPMAS NMR spectroscopies, as well as their thermal stability, were included and corelated with the crystal structure. Hirshfeld surface analysis on the crystal structures of both TAPA derivatives revealed the stabilization of the crystal network via the amide N—H∙∙∙O interactions of dispersive nature in the carbamate, whereas dispersive carbonyl–carbonyl interactions also played a competitive role in the supramolecular arrangement of the oxamate. Interaction energy DFT calculations performed at the B3LYP/6-31G(d,p) level allowed us to estimate the energy contributions and nature of several interactions in terms of the stability of both crystal lattices.

This work systematically examines the interactions between a single argon atom and the edges and faces of cyclic H 2 O clusters containing three–five water molecules (Ar(H 2 O) n = 3 – 5 ). Full geometry optimizations and subsequent harmonic vibrational frequency computations were performed using MP2 with a triple- ζ correlation consistent basis set augmented with diffuse functions on the heavy atoms (cc-pVTZ for H and aug-cc-pVTZ for O and Ar; denoted as haTZ). Optimized structures and harmonic vibrational frequencies were also obtained with the two-body–many-body (2b:Mb) and three-body–many-body (3b:Mb) techniques; here, high-level CCSD(T) computations capture up through the two-body or three-body contributions from the many-body expansion, respectively, while less demanding MP2 computations recover all higher-order contributions. Five unique stationary points have been identified in which Ar binds to the cyclic water trimer, along with four for (H 2 O) 4 and three for (H 2 O) 5 . To the best of our knowledge, eleven of these twelve structures have been characterized here for the first time. Ar consistently binds more strongly to the faces than the edges of the cyclic (H 2 O) n clusters, by as much as a factor of two. The 3b:Mb electronic energies computed with the haTZ basis set indicate that Ar binds to the faces of the water clusters by at least 3 kJ mol − 1 and by nearly 6 kJ mol − 1 for one Ar(H 2 O) 5 complex. An analysis of the interaction energies for the different binding motifs based on symmetry-adapted perturbation theory (SAPT) indicates that dispersion interactions are primarily responsible for the observed trends. The binding of a single Ar atom to a face of these cyclic water clusters can induce perturbations to the harmonic vibrational frequencies on the order of 5 cm − 1 for some hydrogen-bonded OH stretching frequencies. [ABSTRACT FROM AUTHOR]

Accurate information about interactions between group I metals and nucleic acids is required to understand the roles these metals play in basic cellular functions, disease progression, and pharmaceuticals, as well as to aid the design of new energy storage materials and nucleic acid sensors that target metal contaminants, among other applications. From this perspective, this work generates a complete CCSD(T)/CBS data set of the binding energies for 64 complexes involving each group I metal (Li+, Na+, K+, Rb+, or Cs+) directly coordinated to various sites in each nucleic acid component (A, C, G, T, U, or dimethylphosphate). This data have otherwise been challenging to determine experimentally, with highly accurate information missing for many group I metal-nucleic acid combinations and no data available for the (charged) phosphate moiety. Subsequently, the performance of 61 DFT methods in combination with def2-TZVPP is tested against the newly generated CCSD(T)/CBS reference values. Detailed analysis of the results reveals that functional performance is dependent on the identity of the metal (with increased errors as group I is descended) and nucleic acid binding site (with larger errors for select purine coordination sites). Over all complexes considered, the best methods include the mPW2-PLYP double-hybrid and wB97M-V RSH functionals (<1.6% MPE; <1.0kcal/mol MUE). If more computationally efficient approaches are required, the TPSS and revTPSS local meta-GGA functionals are reasonable alternatives (<2.0% MPE; <1.0 kcal/mol MUE). Inclusion of counterpoise corrections to account for basis set superposition error only marginally improves the computed binding energies, suggesting that these corrections can be neglected with little loss in accuracy when using larger models that are necessary for describing biosystems and biomaterials. Overall, the most accurate functionals identified in this study will permit future works geared towards uncovering the impact of group I metals on the environment and human biology, designing new ways to selectively sense harmful metals, engineering modern biomaterials, and developing improved computational methods to more broadly study group I metal-nucleic acid interactions. [ABSTRACT FROM AUTHOR]

A cyclobenzaprine-tetraphenylborate (CBP-TPB) complex was synthesized, achieving a 78% yield through an anion exchange reaction. The white crystals of the complex were formed in acetonitrile and characterized using a variety of spectroscopic and analytical techniques, including ultraviolet, infrared, mass, elemental, and nuclear magnetic resonance (NMR) spectroscopy, as well as X-ray crystallography. The study employed a comprehensive approach to investigate the structural properties, stability, and behavior of the CBP-TPB complex. The use of crystallographic analysis, Hirshfeld surface analysis, quantum theory of atoms in molecules, noncovalent interaction reduced density gradient, global reactivity descriptors, frontier molecular orbitals, molecular electrostatic potential, and ultraviolet-visible spectroscopy provided valuable insights into the complex's molecular geometries, supramolecular features, and intermolecular interactions. These findings contribute to a better understanding of the CBP-TPB complex's potential applications in fields such as pharmaceuticals and materials science and emphasize the importance of combining theoretical predictions and experimental measurements in understanding molecular properties. The study also demonstrated the potential of density functional theory-based computational methods for predicting NMR spectroscopic parameters. [ABSTRACT FROM AUTHOR]

Interactions between negatively charged aluminosilicate species and positively charged metal cations are critical to many important engineering processes and applications, including sustainable cements and aluminosilicate glasses. In an effort to probe these interactions, here we have calculated the pair-wise interaction energies (i.e., binding energies) between aluminosilicate dimer/trimer and 17 different metal cations Mn+ (Mn+ = Li+, Na+, K+, Cu+, Cu2+, Co2+, Zn2+, Ni2+, Mg2+, Ca2+, Ti2+, Fe2+, Fe3+, Co3+, Cr3+, Ti4+ and Cr6+) using a density functional theory (DFT) approach. Analysis of the DFT-optimized structural representations for the clusters (dimer/trimer + Mn+) shows that their structural attributes (e.g., interatomic distances) are generally consistent with literature observations on aluminosilicate glasses. The DFT-derived binding energies are seen to vary considerably depending on the type of cations (i.e., charge and ionic radii) and aluminosilicate species (i.e., dimer or trimer). A survey of the literature reveals that the difference in the calculated binding energies between different Mn+ can be used to explain many literature observations associated with the impact of metal cations on materials properties (e.g., glass corrosion, mineral dissolution, and ionic transport). Analysis of all the DFT-derived binding energies reveals that the correlation between these energy values and the ionic potential and field strength of the metal cations are well captured by 2nd order polynomial functions (R2 values of 0.99–1.00 are achieved for regressions). Given that the ionic potential and field strength of a given metal cation can be readily estimated using well-tabulated ionic radii available in the literature, these simple polynomial functions would enable rapid estimation of the binding energies of a much wider range of cations with the aluminosilicate dimer/trimer, providing guidance on the design and optimization of sustainable cements and aluminosilicate glasses and their associated applications. Finally, the limitations associated with using these simple model systems to model complex interactions are also discussed.

Hypothesis: Charged particles and like-charged ionic surfactant can co-stabilize oil-in-dispersion emulsions at very low concentrations. The surfactant molecules adsorb at the oil-water interface endowing droplets with charge whereas particles remain dispersed in the aqueous phase forming a thick lamella between droplets. The reduced van der Waals attraction between droplets together with the electric double layer repulsion between droplets and between droplets and particles prevents droplets from flocculation and coalescence., Experiments: n-Decane-in-water emulsions co-stabilized by positively charged alumina nanoparticles (0.0001-0.06 wt%) and cationic surfactant cetyltrimethyl-ammonium bromide (CTAB, 0.002-0.1 mM) were prepared and characterized. Specifically, the minimum particle concentration required for emulsion stabilization as a function of CTAB concentration was determined, which describes a V shaped boundary separating stable emulsions from unstable ones., Findings: A model based on the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory was proposed to calculate the droplet-droplet and droplet-particle interactions. Along the V shaped boundary particles are attracted by droplets at large distance but may form a monolayer between droplets when they approach at small distance. Both the attraction and repulsion between droplets and particles are proportional to the particle number surrounding unit area of droplet interfaces and the repulsion is always larger than the attraction. This together with the droplet-droplet repulsion ensures emulsion stabilization. Increasing CTAB concentration results in high interfacial potential but also high counterion concentration; to compensate, the particle concentration required for emulsion stabilization is initially reduced and subsequently increased yielding the V shaped boundary., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2025 Elsevier Inc. All rights reserved.)

Six isomeric molecules, featuring a minimum of three fluorine atoms on either the benzoyl or aniline side, have been synthesized, crystallized and characterized through single crystal X-ray diffraction (SCXRD). In addition, two other compounds, containing six fluorine atoms, three on each of the benzoyl and aniline side of the benzanilide scaffold have also been characterized through SCXRD. This current study aims to augment the capacity for hydrogen bond formation, specifically involving organic fluorine, by elevating the acidity of the involved hydrogens through the incorporation of highly electronegative fluorine atoms, in the presence of strong N-H⋅⋅⋅O=C H-bonds. Lattice energy calculations and assessment of intermolecular interaction energies elucidate the contributions of electrostatics and dispersion forces in crystal packing. The topological analysis of the electron density is characterized by the presence of bond critical points (BCPs) involving C-H⋅⋅⋅F and F⋅⋅⋅F contacts, thus establishing the bonding nature of these interactions which play a crucial role in the crystal packing in addition to the presence of traditional N-H⋅⋅⋅O=C H-bonds., (© 2024 Wiley-VCH GmbH.)

The amino group of 2‐amino‐5‐(4‐halophenyl)‐1,3,4‐chalcogenadiazole has been replaced with bromo/iodo substituents to obtain a library of four compositionally related compounds. These are 2‐iodo‐5‐(4‐iodophenyl)‐1,3,4‐thiadiazole, C8H4I2N2S, 2‐bromo‐5‐(4‐bromophenyl)‐1,3,4‐selenadiazole, C8H4Br2N2Se, 2‐bromo‐5‐(4‐iodophenyl)‐1,3,4‐selenadiazole, C8H4BrIN2Se, and 2‐bromo‐5‐(4‐iodophenyl)‐1,3,4‐thiadiazole, C8H4BrIN2S. All were isostructural and contained bifurcated Ch...N (Ch is chalcogen) and X...X (X is halogen) interactions forming a zigzag packing motif. The noncovalent Ch...N interaction between the chalcogen‐bond donor and the best‐acceptor N atom appeared preferentially instead of a possible halogen bond to the same N atom. Hirshfeld surface analysis and energy framework calculations showed that, collectively, a bifurcated chalcogen bond was stronger than halogen bonding and this is more structurally influential in this system. [ABSTRACT FROM AUTHOR]

Quantum-chemical results are summarized and analyzed from studying the interactions of NH3 and alkylamines (R)nNH3–n (R = CH3, C2H5, C3H7, C4H9, and n = 1–3) with a series of protic acids of different strengths. Data are obtained on the proton affinity of alkylamines and acid anions. Energy characteristics of molecular complexes and ion pairs formed after acid–base interaction are assessed. It is proposed that the difference between the proton affinity of an acid anion and alkylamine be used to assess the degree of proton transfer in acid–base interactions. [ABSTRACT FROM AUTHOR]

In this study, polyethersulfone (PES) ultrafiltration (UF) membranes were modified with GO, Ag, ZnO, Ag-GO and ZnO-GO nanoparticles to improve carbamazepine removal and fouling prevention by making membrane surfaces more hydrophilic. The fabricated membranes were characterized for surface and cross-sectional morphology, surface roughness and zeta potential, as well as hydrophilicity, functional groups, surface tension parameters and water permeability Thereafter, the membranes were evaluated for their efficiency in removing MgSO4 and carbamazepine as well as antifouling properties. To understand the role of affinity interactions in rejection and fouling, membrane–solute adhesion energies (∆Gslm) were quantified based on the Lifshitz–van der Waals/acid–base method. Unlike previous studies, which have generalized fouling prevention to be due to improvements in hydrophilicity upon adding nanoparticles, this work further explored the role of surface tension components on rejection and fouling prevention. The addition of nanoparticles improved membrane hydrophilicity (77–62°), water permeability (11.9–17.7 Lm−2 h−1 bar−1), mechanical strength (3.46–4.11 N/mm2), carbamazepine rejection (30–85%) and fouling prevention (60–23% flux decline). Rejection and antifouling properties increased as ∆Gslm became more repulsive (i.e., less negative). Membrane modification reduced irreversible fouling, and the fouled membranes were cleaned by flushing with water. Fouling related more to membrane electron donor components (γ−), while the roles of electron acceptor (γ+) and Lifshitz–van der Waals components (γLW) were less important. This work provides more insights into the role of affinity interactions in rejection and fouling and how rejection and fouling mechanisms change with nanoparticle addition.

A cyclobenzaprine-tetraphenylborate (CBP-TPB) complex was synthesized, achieving a 78% yield through an anion exchange reaction. The white crystals of the complex were formed in acetonitrile and characterized using a variety of spectroscopic and analytical techniques, including ultraviolet, infrared, mass, elemental, and nuclear magnetic resonance (NMR) spectroscopy, as well as X-ray crystallography. The study employed a comprehensive approach to investigate the structural properties, stability, and behavior of the CBP-TPB complex. The use of crystallographic analysis, Hirshfeld surface analysis, quantum theory of atoms in molecules, noncovalent interaction reduced density gradient, global reactivity descriptors, frontier molecular orbitals, molecular electrostatic potential, and ultraviolet-visible spectroscopy provided valuable insights into the complex’s molecular geometries, supramolecular features, and intermolecular interactions. These findings contribute to a better understanding of the CBP-TPB complex’s potential applications in fields such as pharmaceuticals and materials science and emphasize the importance of combining theoretical predictions and experimental measurements in understanding molecular properties. The study also demonstrated the potential of density functional theory-based computational methods for predicting NMR spectroscopic parameters.

The synthesis, structure, and spectroscopic characterization of a pincer-type compound; N,N′-di(pyridine-4-yl)-pyridine-3,5-dicarboxamide is described. The tricationic pro-ligand (C20H22N5O2)3+ bearing two pendant alkylated 4-pyridyl arms at the 3,5-positions of the central pyridyl group features three triflate anions (CF3SO3−) in the asymmetric unit. Two of the triflate ligands in the structure are connected to the pincer cation by strong N–H⋯O hydrogen bonds. The central N-methyl moiety is planar to a r.m.s deviation of 0.01, and the two adjacent N-methylpyridine moieties are out of the plane with dihedral angles of 33.62° (3) and 86.08° (3). The molecular packing structure of the compound shows an 18-molecule aggregate in a 3-dimensional supramolecular synthon stabilized by intermolecular N–H⋯O and C–H⋯O contacts. The Hirshfeld surface analysis and fingerprint plots show that the OH/HO contacts resulting from C–H⋯O intermolecular interactions contributed significantly to the overall surface interaction with a total percentage contribution of 35.4%. The pairwise interaction energy calculations were implemented with a Gaussian plugin in Crystal Explorer 17 at the B3LYP/6-31G(d,p) level of theory. Energy profile diagrams and interaction energy values indicate that the crystal structure was stabilized by a combination of electrostatic and dispersion forces in the crystal lattice. The crystal structure of a tricationic pro-ligand N,N′-di(pyridine-4-yl)-pyridine-3,5-dicarboxamide is described. The structures features three triflate anions in the asymmetric unit with two of the triflate ligands in the structure connected to the pincer pro-ligand by strong N–H⋯O hydrogen bonds. Hirshfeld surface interaction and pairwise interaction energies are explored. [ABSTRACT FROM AUTHOR]

In this article we use MP2 and CCSD(T) calculations for the A24 and S66 data sets to explore how midbond functions can be used to generate cost effective counterpoise corrected supramolecular interaction energies of noncovalent complexes. We use the A24 data set to show that the primary role of midbond functions is not to approach the complete basis set limit, but rather to ensure a balanced description of the molecules and the interaction region (unrelated to the basis set superposition error). The need for balance is a consequence of using atom centered basis sets. In the complete basis set limit, the error will disappear, but reaching the complete basis set limit is not feasible beyond small systems. For S66 we investigate the need for increasing the number of midbond centers. Results show that adding a second midbond center increases the accuracy, but the effect is secondary to changing the atom centered basis set. Further, by comparing calculations using the 3s3p2d1f1g midbond set with using aug‐cc‐pVDZ and aug‐cc‐pVTZ as midbond sets, we see that the requirements for the midbond set to be effective, is not just that it contains diffuse functions, but also that high angular momentum functions are included. By comparing two approaches for placing midbond centers we show that results are not particularly sensitive to placement as long as the placement is reasonable. [ABSTRACT FROM AUTHOR]

Aims: The rapid spread of new SARS-CoV-2 variants has highlighted the crucial role played in the infection by mutations occurring at the SARS-CoV-2 spike receptor binding domain (RBD) in the interactions with the human ACE2 receptor. In this context, it urgently needs to develop new rapid tools for quickly predicting the affinity of ACE2 for the SARS-CoV-2 spike RBD protein variants to be used with the ongoing SARS-CoV-2 genomic sequencing activities in the clinics, aiming to gain clues about the transmissibility and virulence of new variants, to prevent new outbreaks and to quickly estimate the severity of the disease in the context of the 3PM. Methods: In our study, we used a computational pipeline for calculating the interaction energies at the SARS-CoV-2 spike RBD/ACE2 protein–protein interface for a selected group of characterized infectious variants of concern/interest (VoC/VoI). By using our pipeline, we built 3D comparative models of the SARS-CoV-2 spike RBD/ACE2 protein complexes for the VoC B.1.1.7-United Kingdom (carrying the mutations of concern/interest N501Y, S494P, E484K at the RBD), P.1-Japan/Brazil (RBD mutations: K417T, E484K, N501Y), B.1.351-South Africa (RBD mutations: K417N, E484K, N501Y), B.1.427/B.1.429-California (RBD mutations: L452R), the B.1.141 (RBD mutations: N439K), and the recent B.1.617.1-India (RBD mutations: L452R; E484Q) and the B.1.620 (RBD mutations: S477N; E484K). Then, we used the obtained 3D comparative models of the SARS-CoV-2 spike RBD/ACE2 protein complexes for predicting the interaction energies at the protein–protein interface. Results: Along SARS-CoV-2 mutation database screening and mutation localization analysis, it was ascertained that the most dangerous mutations at VoC/VoI spike proteins are located mainly at three regions of the SARS-CoV-2 spike "boat-shaped" receptor binding motif, on the RBD domain. Notably, the P.1 Japan/Brazil variant present three mutations, K417T, E484K, N501Y, located along the entire receptor binding motif, which apparently determines the highest interaction energy at the SARS-CoV-2 spike RBD/ACE2 protein–protein interface, among those calculated. Conversely, it was also observed that the replacement of a single acidic/hydrophilic residue with a basic residue (E484K or N439K) at the "stern" or "bow" regions, of the boat-shaped receptor binding motif on the RBD, appears to determine an interaction energy with ACE2 receptor higher than that observed with single mutations occurring at the "hull" region or with other multiple mutants. In addition, our pipeline allowed searching for ACE2 structurally related proteins, i.e., THOP1 and NLN, which deserve to be investigated for their possible involvement in interactions with the SARS-CoV-2 spike protein, in those tissues showing a low expression of ACE2, or as a novel receptor for future spike variants. A freely available web-tool for the in silico calculation of the interaction energy at the SARS-CoV-2 spike RBD/ACE2 protein–protein interface, starting from the sequences of the investigated spike and/or ACE2 variants, was made available for the scientific community at: https://www.mitoairm.it/covid19affinities. Conclusion: In the context of the PPPM/3PM, the employment of the described pipeline through the provided webservice, together with the ongoing SARS-CoV-2 genomic sequencing, would help to predict the transmissibility of new variants sequenced from future patients, depending on SARS-CoV-2 genomic sequencing activities and on the specific amino acid replacement and/or on its location on the SARS-CoV-2 spike RBD, to put in play all the possible counteractions for preventing the most deleterious scenarios of new outbreaks, taking into consideration that a greater transmissibility has not to be necessarily related to a more severe manifestation of the disease. [ABSTRACT FROM AUTHOR]

The crystal and molecular structures of C14H12Cl2, (I), and C14H12Br2, (II), are described. The asymmetric unit of (I) comprises two independent molecules, A and B, each disposed about a centre of inversion. Each molecule approximates mirror symmetry [the Cb—Cb—Ce—Ce torsion angles = −83.46 (19) and 95.17 (17)° for A, and −83.7 (2) and 94.75 (19)° for B; b = benzene and e = ethylene]. By contrast, the molecule in (II) is twisted, as seen in the dihedral angle of 59.29 (11)° between the benzene rings cf. 0° in (I). The molecular packing of (I) features benzene-C—H...π(benzene) and Cl...Cl contacts that lead to an open three-dimensional (3D) architecture that enables twofold 3D–3D interpenetration. The presence of benzene-C—H...π(benzene) and Br...Br contacts in the crystal of (II) consolidate the 3D architecture. The analysis of the calculated Hirshfeld surfaces confirm the influence of the benzene-C—H...π(benzene) and X...X contacts on the molecular packing and show that, to a first approximation, H...H, C...H/H...C and C...X/X...C contacts dominate the packing, each contributing about 30% to the overall surface in each of (I) and (II). The analysis also clearly differentiates between the A and B molecules of (I).

The binary complexes formed between the dihalogens fluorine, chlorine and bromine, and the cyclic ethers oxirane, oxetane, tetrahydrofuran and tetrahydropyran, have been studied by means of ab initio calculations at the second-order level of Møller–Plesset perturbation theory. The properties of interest are the interaction energies, the intermolecular geometries, the perturbations of the intramolecular dihalogen and ether geometries, the wavenumber shifts of the dihalogen and ether molecules, and the variations of the natural atomic charges resulting from complexation. The trends observed are discussed in terms of the physical properties of the interacting monomers, such as the polarizabilities of the dihalogen molecules and the gas phase basicities of the ethers. [ABSTRACT FROM AUTHOR]

The analysis of atom-to-atom and/or residue-to-residue contacts remains a favoured mode of analysing the molecular packing in crystals. In this contribution, additional tools are highlighted as methods for analysis in order to complement the `crystallographer's tool', PLATON [Spek (2009). Acta Cryst. D65, 148–155]. Thus, a brief outline of the procedures and what can be learned by using Crystal Explorer [Spackman & Jayatilaka (2009). CrystEngComm 11, 19–23] is presented. Attention is then directed towards evaluating the nature, i.e. attractive/weakly attractive/repulsive, of specific contacts employing NCIPLOT [Johnson et al. (2010). J. Am. Chem. Soc. 132, 6498–6506]. This is complemented by a discussion of the calculation of energy frameworks utilizing the latest version of Crystal Explorer. All the mentioned programs are free of charge and straightforward to use. More importantly, they complement each other to give a more complete picture of how molecules assemble in molecular crystals.

Herein, we have investigated the key functions of the calix[4]arene, abbreviated as CX [1], and designed its several derivatives by substitution of the functional groups. Molecular geometry provides an intuitive understanding of the effect of functional groups on various physical properties. The addition of the N-β-ketoimine (n = 1–4) ligands has a direct effect on the stretching vibration of the H-bonding interaction. The results showed that all molecules possess absorption bands at 190 nm and in the range between 200 and 300 nm assigned to π–π* and n-π* transitions. HOMO–LUMO energy gap of the CX[4]-N-β-ketoimine, one with chemical hardness of 1.62 eV, has been found to be 3.24 eV calculated at B3LYP/6–31 + G(d) level of theory. This finding explains the good kinetic stability of this compound. The large values of electrophilicity make the current molecules as a good electrophilic species. The atom in molecule (AIM) and the reduced density gradient (RDG) analyses showed the type and the strength of the interactions taking place between Cu2+ and the β-ketoimine ligands. [ABSTRACT FROM AUTHOR]

The properties of the hydrogen-bonded complexes of chloroform and bromoform with ammonia, water, hydrogen fluoride, phosphine, hydrogen sulphide and hydrogen chloride were studied by means of ab initio calculations. The properties of interest were the molecular structures, the interaction energies, the vibrational spectra and the nature of the orbital interactions involved in the formation of the complexes. Of particular interest was the determination of whether the various interactions exhibited red-shifted or blue-shifted hydrogen bond behaviour. The complexes optimized in three distinct structural models, singly bonded, cyclic and cage. The interaction energies, in the main, varied systematically with changes of the haloform and of the partner molecules. Changes of the CH or YH (Y = N, O, F, P, S and Cl) bond lengths correlated in most cases with the interaction energies, subject to some inconsistencies, with opposite behaviour being shown by the two sets. Similarly, the CH and YH stretching wavenumber shifts also displayed a dependence on the interaction energies, tracking with the bond length changes. Based on the diagnostic utility of these structural and spectroscopic properties, the complexes were found to be almost exclusively red-shifted, for binding through both the CH and YH groups. The orbital interactions responsible for the stability of the complexes were determined to be donation from a Y atom lone pair orbital of the partner molecule to a CH σ antibonding orbital and from a X lone pair orbital (X = Cl and Br) of the haloform to a YH σ antibonding orbital. [ABSTRACT FROM AUTHOR]

Calix[n]arenes (abbreviated as CX[n]) are the macro-molecules based on phenol groups with a hydrophobic cavity to encapsulate a gas or small molecules. They are used as molecular vehicles. For instance, these molecules are used in the activation of the solubility of monomers in the specific media and in pharmaceutical drug delivery. The limit of the development of gaseous pollutants will be a vital subject in the future. The polluting gases NO3, NO2, CO2, N2, etc., need cage molecules, such as CX[4], to be encapsulated. In this report, the red shift of the H-bonding interactions of the CX[4]-gas (by adding the gas inside or outside the cavity) is clearly explained by the vibrational analysis. The electronic spectra of the complexes of CX[4] with NO3, NO2, CO2, and N2) exhibit a blue-shift pick in comparison with the ones observed for the CX[4] molecule. The electrophilic and nucleophilic sites of the stable host-guest have been investigated. Additionally, the non-covalent interactions have been calculated based on the reduced density gradient RDG and QTAIM theory. [ABSTRACT FROM AUTHOR]

The intermolecular interactions in the structures of a series of Schiff base ligands have been thoroughly studied. These ligands can be obtained in different forms, namely, as the free base 2‐[(2E)‐2‐(1H‐imidazol‐4‐ylmethylidene)‐1‐methylhydrazinyl]pyridine, C10H11N5, 1, the hydrates 2‐[(2E)‐2‐(1H‐imidazol‐2‐ylmethylidene)‐1‐methylhydrazinyl]‐1H‐benzimidazole monohydrate, C12H12N6·H2O, 2, and 2‐{(2E)‐1‐methyl‐2‐[(1‐methyl‐1H‐imidazol‐2‐yl)methylidene]hydrazinyl}‐1H‐benzimidazole 1.25‐hydrate, C13H14N6·1.25H2O, 3, the monocationic hydrate 5‐{(1E)‐[2‐(1H‐1,3‐benzodiazol‐2‐yl)‐2‐methylhydrazinylidene]methyl}‐1H‐imidazol‐3‐ium trifluoromethanesulfonate monohydrate, C12H13N6+·CF3O3S−·H2O, 5, and the dicationic 2‐{(2E)‐1‐methyl‐2‐[(1H‐imidazol‐3‐ium‐2‐yl)methylidene]hydrazinyl}pyridinium bis(trifluoromethanesulfonate), C10H13N52+·2CF3O3S−, 6. The connection between the forms and the preferred intermolecular interactions is described and further studied by means of the calculation of the interaction energies between the neutral and charged components of the crystal structures. These studies show that, in general, the most important contribution to the stabilization energy of the crystal is provided by π–π interactions, especially between charged ligands, while the details of the crystal architecture are influenced by directional interactions, especially relatively strong hydrogen bonds. In one of the structures, a very interesting example of the nontypical F...O interaction was found and its length, 2.859 (2) Å, is one of the shortest ever reported. [ABSTRACT FROM AUTHOR]

Chiral recognition holds immense significance in both life science and chemistry. Chiral recognition of enantiomers is crucial because one enantiomer is generally more fundamental than its counterpart, which is not only unnecessary but also toxic. Understanding and distinguishing the S and R enantiomers of amino acids is imperative not only for unraveling the intricacies of biological systems but also for designing more effective and selective therapeutic agents. In this research work, the complexes of twisted carbon belt (specifically Möbius cyclacene composed of 15 nitrogen-substituted benzo rings) with S and R enantiomers of amino acids (alanine, proline, serine, and valine) are studied through geometric, thermodynamic, and electronic properties. The values of interaction energy (E int) range from −24.19 to −35.32 kcal mol−1. Two distinct trends of E int are identified, with the belt demonstrating selectivity for S-enantiomers of alanine and serine, and R-enantiomers of proline and valine. Chiral discrimination energy is most pronounced for pro@belt enantiomeric complexes i. e., 4.18 kcal mol−1, among all the designed complexes. Quantum theory of atoms in molecules (QTAIM) and non-covalent interaction index (NCI) analyses are used to study the nature of interactions between carbon belt and amino acids. These analyses reveal van der Waals forces as predominant non-bonding interactions. Furthermore, NCI and QTAIM analyses support that the presence of hydrogen bonding is an eminent reason for the highest chiral discrimination energy of pro@belt complexes. Natural bond orbital (NBO) and electron density difference (EDD) analyses indicate charge transfer from the belt towards amino acids, with S-pro@belt having the maximum charge transfer i. e., −0.059 (e−). Electronic properties show an increase in highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) energy gap upon complexation, along with the presence of HOMO and LUMO densities over the twisted carbon belt. The increase in E H-L is more pronounced for S-ala@belt complex. The density of states (DOS) analysis is conducted to observe the individual contributions of each enantiomer to the overall density of the complexes. Overall, our analyses highlight the sensitivity of carbon belt towards chiral molecules, showing a significant chiral discrimination ability for S and R enantiomers of amino acids, particularly for proline enantiomers. This research contributes valuable insights into chiral recognition and molecular interactions involving carbon belts. [Display omitted] • Möbius carbon belt is investigated as a host for chiral recognition of amino acid enantiomers. • Chiral recognition is mainly driven by van der Waals interactions between amino acids and carbon belt. • NBO and EDD analysis verifies that the charge is mainly transferred from Möbius carbon belt towards amino acids. • The highest E chir between amino acid@carbon belt is observed in case of pro@belt complexes. [ABSTRACT FROM AUTHOR]

Heterocyclic ligands and their metallic complexes are biologically active materials [...]

This paper reports the crystal growth and structure of a newly synthesized hybrid organic-inorganic compound (CH6N3)2[Co (NCS)4].H2O by means of a joint experimental and theoretical study. Single-crystal X-ray diffraction reveals that this compound crystallizes in the noncentrosymmetric P21212 space group. The 3D framework of the crystal structure is formed by hydrogen-bonded cations of (CH6N3)+, [Co (NCS)4]2− anions and water molecules. UV-Visible reveals an indirect allowed optical transition with energy gap Eg = 3.41 eV. The optimized molecular structure, harmonic vibrational frequencies, static and frequency-dependent nonlinear optical (NLO) parameters were calculated by density functional theory with and without dispersion corrections. A good consistency for the structure, as well as IR and Raman spectra, is found between the calculated and experimental results. A detailed interpretation of the vibrational modes was carried out and a total assignment was performed on the basis of the potential energy distribution (PED) contribution. Moreover, the inter-ionic interaction energy was evaluated and a decomposition analysis was performed by localized molecular orbital energy decomposition analysis (LMO-EDA) method. The calculated NLO parameters compared to urea as a reference show that the title compound can be a good candidate for NLO applications. [ABSTRACT FROM AUTHOR]

Hydrogen–hydrogen C─H...H─C bonding between the bay‐area hydrogens in biphenyls, and more generally in congested alkanes, very strained polycyclic alkanes, and cis‐2‐butene, has been investigated by calculation of proton nuclear magnetic resonance (NMR) shifts and atom–atom interaction energies. Computed NMR shifts for all protons in the biphenyl derivatives correlate very well with experimental data, with zero intercept, unit slope, and a root mean square deviation of 0.06 ppm. For some congested alkanes, there is generally good agreement between computed values for a selected conformer and the experimental data, when it is available. In both cases, the shift of a given proton or pair of protons tends to increase with the corresponding interaction energy. Computed NMR shift differences for methylene protons in polycyclic alkanes, where one is involved in a very short contact ("in") and the other is not ("out"), show a rough correlation with the corresponding C─H...H─C exchange energies. The "in" and "in,in" isomers of selected aza‐ and diaza‐cycloalkanes, respectively, are X─H...H─N hydrogen bonded, whereas the "out" and "in,out" isomers display X─H...N hydrogen bonds (X = C or N). Oxa‐alkanes and the "in" isomers of aza–oxa‐alkanes are X─H...O hydrogen bonded. There is a very good general correlation, including both N─H...H─Y (Y = C or N) and N─H...Z (Z = N or O) interactions, for NH proton shifts against the exchange energy. For "in" CH protons, the data for the different C─H...H─Y and C─H...Z interactions are much more dispersed and the overall shift/exchange energy correlation is less satisfactory. [ABSTRACT FROM AUTHOR]

The role of substituents in the enhancement of corrosion inhibition effectiveness in some organic compounds has been the subject of several studies in recent years. Understanding the relationship between corrosion inhibition performance and electronic properties of the molecule shall facilitate the design of efficient inhibitors and reduce the burden of experimental trials involved. In this study, quantum chemical calculations using density functional theory (DFT) method were performed on benzimidazole and its derivatives involving various electron-withdrawing and electron-releasing substituents. Several reactivity indicators, such as frontier orbitals, energy gaps, electronegativity, electrophilicity and global hardness were calculated and correlated with available experimental data. Frontier orbital energy gap predicted 2-nitrobenzimidazole to possess higher anti-corrosion properties, while electronegativity, electrophilicity and global hardness predicted 2-aminobenzimidazole to exhibit higher corrosion inhibition tendency. Results of molecular level interaction studies predicted that the adsorption of the molecules over the iron surface would take place preferentially through the nitrogen atoms of the imidazole ring and the carbon atoms of the benzene ring, resulting in the formation of Fe–N and Fe–C bonds with 2.00–2.40 Å bond distances which lie within the range of the chemisorption interaction. Image 1 • The role of substituent groups on the corrosion inhibitive performance of benzimidazole derivatives was studied using DFT. • Frontier orbitals energy gap analysis predicted 2-nitrobenzimidazole as potential highly effective corrosion inhibitor. • Molecular level interaction studies predicted adsorption of the molecules on Fe surface to occur via chemisorption. • Adsorption occur via nitrogen and carbon atoms of benzene and imidazole with effective bond distances of 2.00–2.40 Å. [ABSTRACT FROM AUTHOR]

Density functional theory calculations were performed to assess the relative interaction energies of plant cell wall components: cellulose, xylan, lignin and pectin. Monomeric and tetramer linear molecules were allowed to interact in four different configurations for each pair of compounds. The M05-2X exchange-correlation functional which implicitly accounts for short- and mid-range dispersion was compared against MP2 and RI-MP2 to assess the reliability of the former for modeling van der Waals forces between these PCW components. Solvation effects were examined by modeling the interactions in the gas phase, in explicit H2O, and in polarized continuum models (PCM) of solvation. PCMs were used to represent water, methanol, and chloroform. The results predict the relative ranges of each type of interaction and when specific configurations will be strongly preferred. Structures and energies are useful as a basis for testing classical force fields and as guidance for coarse-grained models of PCWs. [ABSTRACT FROM AUTHOR]

• NCI quantities to go from DFT interacting energies to CCSD(T)/CBS in weakly bound systems. • DFT errors can be reduced down to 6% at a virtually negligible computational cost. • Promolecular densities can improve DFT interaction energy results. Machine learning has a wide range of applications in chemistry, encompassing the prediction of the structure and properties of a variety of chemical systems (molecules, macromolecules and solids). The idea of using a self-learning algorithm to explore chemical problems is particularly alluring when facing open challenges in theoretical chemistry, such as non-covalent interactions, which are known to be critical for density functional methods. Additionally, the difficulty of predicting accurate non-covalent interaction (NCI) energies lies in their small absolute values, which make even the slightest absolute error severely affect the quality of the calculated result. In this work, we test the possibility of computing accurate interaction energies (at the golden standard CCSD(T)/CBS level) of small non-covalent complexes starting from a DFTD/DZ energy and using descriptors derived from the promolecular density. Calculations on the S66x8 dataset of molecular complexes show that these local descriptors can reduce to one third the mean absolute error of DFT results at a virtually negligible computational cost. [ABSTRACT FROM AUTHOR]

The crystal and mol­ecular structures of C14H12Cl2, (I), and C14H12Br2, (II), are described. The asymmetric unit of (I) comprises two independent mol­ecules, A and B, each disposed about a centre of inversion. Each mol­ecule approximates mirror symmetry [the Cb--Cb--Ce--Ce torsion angles = --83.46 (19) and 95.17 (17)° for A, and --83.7 (2) and 94.75 (19)° for B; b = benzene and e = ethyl­ene]. By contrast, the mol­ecule in (II) is twisted, as seen in the dihedral angle of 59.29 (11)° between the benzene rings cf. 0° in (I). The mol­ecular packing of (I) features benzene-C--H...π(benzene) and Cl...Cl contacts that lead to an open three-dimensional (3D) architecture that enables twofold 3D-3D inter­penetration. The presence of benzene-C--H...π(benzene) and Br...Br contacts in the crystal of (II) consolidate the 3D architecture. The analysis of the calculated Hirshfeld surfaces confirm the influence of the benzene-C--H...π(benzene) and X...X contacts on the mol­ecular packing and show that, to a first approximation, H...H, C...H/H...C and C...X/X...C contacts dominate the packing, each contributing about 30% to the overall surface in each of (I) and (II). The analysis also clearly differentiates between the A and B mol­ecules of (I). [ABSTRACT FROM AUTHOR]

Eight new (–)-(N-[(AA)-(N-phtaloyl)]cytisines (where AA is amino acid: glycine, β-alanine, D,L-valine, L-valine, L-isoleucine, L-leucine, D-leucine and D,L-phenyloalanine), were synthesized and fully spectroscopically characterized (NMR, FTIR and MS). For two of these compounds, N-[glycine-(N-phtaloyl)]cytisine and N-[L-isoleucine-(N-phtaloyl)]cytisine, X-ray crystal structures were obtained and used as the basis for an in-depth analysis of intermolecular interactions and packing energies. The structural geometrical data (weak hydrogen bonds, π···π interactions, etc.) were compared with the energies of interactions and the topological characteristics (electron density, Laplacian at the appropriate critical point) based on the atoms-in-molecules theory. The results suggest that there is no straightforward connection between the geometry of point-to-point interactions and the molecule-to-molecule energies. Additionally, the usefulness of the transfer of multipolar parameters in estimating of critical points’ characteristics have been confirmed.

The functionalization of N-(benzo[d]thiazol-2-yl)benzamide with a nitro (NO2) substituent influences the solid-state arrangement, absorption and fluorescence properties of these compounds. Each of these compounds crystallised in a different crystal system or space group, namely a monoclinic crystal system with P21/n and C2/c space groups for o-NO2 and m-NO2 derivatives, respectively, and an orthorhombic crystal system (Pbcn space group) for p-NO2 derivative. The o-NO2 substituent with intrinsic steric hindrance engendered a distorted geometry. Conversely, the m-NO2 derivate displayed the most planar geometry among the analogues. The solid-state architectures of these compounds were dominated by the N−H···N and C−H···O intermolecular hydrogen bonds and were further stabilised by other weak interactions. The dimer synthons of the compounds were established via a pair of N−H···N hydrogen bonds. These findings were corroborated by a Hirshfeld surface analysis and two-dimensional (2D) fingerprint plot. The interaction energies within the crystal packing were calculated (CE-B3LYP/6-31G(d,p)) and the energy frameworks were modelled by CrystalExplorer17.5. The highly distorted o-NO2 congener synthon relied mainly on the dispersion forces, which included π–π interactions compared to the electrostatic attractions found in m-NO2. Besides, the latter possesses an elevated asphericity character, portraying a marked directionality in the crystal array. The electrostatic and dispersion forces were regarded as the dominant factors in stabilising the crystal packing.

Abstract A liquid-liquid extraction procedure for the removal of fluoridated compounds [i.e., hydrogen fluoride (HF) and organic fluorides (R-F)] from alkylation gasoline (AG) using ionic liquids was studied both experimentally and theoretically. Synthesis and characterization of 1-butyl-3-methylimidazolium bromide, [C 4 MIM][Br], 1-butyl-3-metylimidazolium trifluoroacetate, [C 4 MIM][CF 3 COO], and 1-butyl-3-metylimidazolium bis(trifluoromethanesulphonyl)imide, [C 4 MIM][NTf 2 ], ionic liquids (ILs) and its evaluation in the adsorption of HF and R-F species from organic medium (AG), was determined experimentally. Also the assessment of molecular interactions of HF with IL in the organic media was studied via Hybrid "QM (quantum mechanics)/MM (molecular mechanics)" Molecular Dynamics (MD) calculations. This QM/MM-MD simulations allowed the setting of a series of time equi-spaced HF-IL system configurations to evaluate interaction energies at QM theoretical level between HF and the closest ILs, as well as the mapping of Non-Covalent Interactions (NCI). Experiments indicate that fluoridated ILs are more efficient for HF extraction than brominated ILs. From the calculated interaction energies and NCI mapping it seems that the capacity of the anion of ILs to form hydrogen bonds with HF is the driving force in HF extraction. Graphical abstract QM/MM simulation of [C 4 MIM][NTf 2 ]-HF interaction for removal in organic medium. Unlabelled Image Highlights • Synthesis of ionic liquids (ILs), ([C 4 MIM][Br], [C 4 MIM][CF 3 COO] and [C 4 MIM][NTf 2 ]) • Procedure for the removal of fluoridated compounds from alkylation gasoline using ILs • The assessment of molecular interactions of HF with ILs in AG via hybrid calculations • Correlation between the experimental removal of HF and theoretical energy interactions [ABSTRACT FROM AUTHOR]

Tetrathiafulvalene (TTF) and its derivatives are very well known as electron donors with widespread use in the field of organic conductors and superconductors. Stacking interactions between two neutral TTF fragments were studied by analysing data from Cambridge Structural Database crystal structures and by quantum chemical calculations. Analysis of the contacts found in crystal structures shows high occurrence of parallel displaced orientations of TTF molecules. In the majority of the contacts, two TTF molecules are displaced along their longer C2 axis. The most frequent geometry has the strongest TTF–TTF stacking interaction, with CCSD(T)/CBS energy of −9.96 kcal mol−1. All the other frequent geometries in crystal structures are similar to geometries of the minima on the calculated potential energy surface. Stacking interactions in which two TTF molecules are displaced along their longer C2 axis are dominant in crystal structures. The most frequent geometry has the strongest stacking interaction (−9.96 kcal mol−1), calculated at very accurate CCSD(T)/CBS level. The other frequent geometries in crystal structures are also similar to very stable geometries of the minima on the calculated potential energy surface. [ABSTRACT FROM AUTHOR]

Carbon nanotubes (CNTs) constitute an interesting material for nanomedicine applications because of their unique properties, especially their ability to penetrate membranes, to transport drugs specifically and to be easily functionalized. In this work, the energies of the intermolecular interactions of single-walled CNTs and the anticancer drug doxorubicin (DOX) were determined using the AMBER 12 molecular dynamics MM/PBSA and MM/GBSA methods with the aim of better understanding how the structural parameters of the nanotube can improve the interactions with the drug and to determine which structural parameters are more important for increasing the stability of the complexes formed between the CNTs and DOX. The armchair, zigzag, and chiral nanotubes were finite hydrogen-terminated open tubes, and the DOX was encapsulated inside the tube or adsorbed on the nanotube surface. Pentagon/heptagon bumpy defects and polyethylene glycol (PEG) nanotube functionalization were also studied. The best interaction occurred when the drug was located inside the cavity of the nanotube. Armchair and zigzag nanotubes doped with nitrogen, favored interaction with the drug, whereas chiral nanotubes exhibited better drug interactions when having bumpy defects. The π-π stacking and N-H...π electrostatic interactions were important components of the attractive drug-nanotube forces, enabling significant flattening of the nanotube to favor a dual strong interaction with the encapsulated drug, with DOX-CNT equilibrium distances of 3.1-3.9 Å. These results can contribute to the modeling of new drug-nanotube delivery systems. [ABSTRACT FROM AUTHOR]

Abstract Aggregation onsets of seven different asphaltenes dissolved in model oils, due to the effects of misciblized compressed air or nitrogen injections, were studied through molecular dynamics simulation. Natures of aggregations, cumulative coordination numbers, and interaction energies were investigated. Onset of aggregation processes were highly affected by injected gas concentration. In more cases little differences were observed between using air and pure nitrogen. However, asphaltene aggregation onset was highly affected by its molecular architecture. Asphaltenes with long aliphatic chains and archipelago structure showed low aggregation affinities. Highlights • Molecular Dynamics Simulations were employed to study asphaltene aggregation process during misciblized gas flooding. • Seven different model asphaltenes were used in different concentrations of compressed air and nitrogen. • The differences between the use of compressed air and compressed nitrogen were investigated. • The aggregation onset and interaction energies between asphaltene molecules were investigated. [ABSTRACT FROM AUTHOR]

Density functional theory calculations are used to compute proton nuclear magnetic resonance (NMR) chemical shifts, interatomic distances, atom–atom interaction energies, and atomic charges for partial structures and conformers of α‐D‐glucopyranose, β‐D‐glucopyranose, and α‐D‐galactopyranose built up by introducing OH groups into 2‐methyltetrahydropyran stepwisely. For the counterclockwise conformers, the most marked effects on the NMR shift and the charge on the OH1 proton are produced by OH2, those of OH3 and OH4 being somewhat smaller. This argues for a diminishing cooperative effect. The effect of OH6 depends on the configuration of the hydroxymethyl group and the position, axial or equatorial, of OH4, which controls hydrogen bonding in the 1,3‐diol motif. Variations in the interaction energies reveal that a “new” hydrogen bond is sometimes formed at the expense of a preexisting one, probably due to geometrical constraints. Whereas previous work showed that complexing a conformer with pyridine affects only the nearest neighbour, successive OH groups increase the interaction energy of the N⋯H1 hydrogen bond and reduce its length. Analogous results are obtained for the clockwise conformers. The interaction energies for C―H⋯OH hydrogen bonding between axial CH protons and OH groups in certain conformers are much smaller than for O―H⋯OH bonds but they are largely covalent, whereas those of the latter are predominantly coulombic. These interactions are modified by complexation with pyridine in the same way as O―H⋯OH interactions: the computed NMR shifts of the CH protons increase, the atom–atom distances are shorter, and interaction energies are enhanced. [ABSTRACT FROM AUTHOR]

The occurrence of 3D isostructurality in six halogen substituted N -benzoyl- N -phenylbenzamides has been reported and this feature has been quantitatively analyzed in this study. 4-fluoro- N -(4-fluorobenzoyl) N -(fluorphenyl)benzamide ( 1 ) was observed to be isostructural with 2-fluoro- N -(2-fluorobenzoyl) N -(4-fluorophenyl)benzamide ( 7 ), N -(4-bromophenyl)-2-fluoro- N -(2-fluorobenzoyl)benzamide ( 8 ) and 2-fluoro- N -(2-fluorobenzoyl) N -(4-iodophenyl)benzamide ( 9 ). Similarly, N -(4-chlorophenyl)-4-fluoro- N -(4-fluorobenzoyl)benzamide ( 2 ) and N -(4-bromophenyl)-4-fluoro- N -(4-fluorobenzoyl)benzamide ( 3 ) was observed to be isostructural with each other. It was clearly evident from the analysis of structural similarity that 3D supramolecular construct present in 2/3 [ Set 2 ] were more identical as compared to those observed in 1/7/8/9 [Set 1] . The molecular packing in both sets of isostructural molecules was observed to be governed by the presence of several C H ⋯ O C interactions. In addition to that, C H ⋯ F C and C H ⋯ π interactions also played an important role in the stabilization. However, 2D Fingerprint analysis revealed that the contribution of C H ⋯ F C interaction in a given structure was also dependent on the contribution of other hydrogens bonds involving halogens. [ABSTRACT FROM AUTHOR]