Intermolecular Interaction Energies Research Articles

Impact of edetate sodium on calcium carbonate scaling: Insights from molecular dynamics simulations

In order to mitigate calcium carbonate (CaCO3) scaling in oil and gas wells, antiscaling agents are commonly used. This research employed the molecular dynamics method to simulate the crystallization process of a supersaturated CaCO3 solution, with particular emphasis on examining the influence of the antiscalant edetate sodium (EDTA). Analysis of the spatial distribution of Ca2+ in proximity to CO32− revealed that EDTA effectively impedes the interaction between Ca2+ and CO32−, resulting in a reduction in the mean square displacement and diffusion coefficient of CO32−. The examination of intermolecular interaction energies indicates that the binding energy between Ca2+ and CO32− is approximately −516 kcal mol−1, while the binding energy between Ca2+ and EDTA is estimated at −718 kcal mol−1. These findings suggest that EDTA exhibits a higher affinity for binding with Ca2+ compared to CO32−, consequently hindering the formation of CaCO3.

Synthesis, characterization, biological activity, DFT and Hirshfeld surface studies of Pd(II) and Pt(II)-1-cyclohexyl-3-phenylthiourea and amine ligands

A series of mixed ligand complexes of Pd(II) and Pt(II) of 1-cyclohexyl-3-phenylthiourea and diamine ligands {2,2'-bipyridyl (Bipy) and 1,10-phenanthroline (Phen)} were prepared and characterized by FT-IR, NMR spectroscopy, molar conductivity. Density functional theory (DFT) calculations and biological activity were carried out on the prepared complexes. In vitro antimicrobial activity was investigated against three pathogenic bacteria (Staphylococcus aureus, Bacillus cereus and Escherichia coli). The most active compound 6 was found more active than free ligand and other complexes. The crystal structure of the free ligand was determined by X-ray diffraction (XRD) analysis. Hirshfeld surface analysis was executed for the free ligand by finding and exploring the interatomic contacts that are important considering the supramolecular assembly of the crystal. The mechanical stability or response is prophesied by voids analysis. The supramolecular assembly is significantly uncovered by intermolecular interaction energies calculations performed at of the B3LYP/6-31G(d,p) electron density level. KEY WORDS: Thiourea, Diamine, Crystal structure, DFT, Hirshfeld surface Bull. Chem. Soc. Ethiop. 2025, 39(1), 15-27. DOI: https://dx.doi.org/10.4314/bcse.v39i1.2

Design of Eutectic Solvents with Specified Extraction Properties Based on Intermolecular Interaction Energy.

A new approach to managing the extraction properties of eutectic solvents based on aliphatic alcohols is proposed. Aliphatic alcohols, when functioning as hydrogen bond donors within a eutectic solvent, significantly enhance the solvent's efficiency in extracting metal ions. Conversely, when the alcohol acts as a hydrogen bond acceptor, its extraction properties diminish. Molecular modelling reveals that the extraction efficiency of these alcohols is directly proportional to the intermolecular interaction energy between the components of the eutectic solvent.

Study of substituents-regulated dyeing properties in non-aqueous media systems based on MD simulation and DFT

To investigate the relationship between N-acetoxyethyl group and dyeing properties of disperse dyes in D5 non-aqueous medium dyeing system, the adsorption and diffusion behaviors of three disperse dyes with different structures were studied by molecular dynamics (MD). The diffusion coefficients, the planar distribution densities of dyes in different directions, and the intermolecular interaction energies were calculated. Molecular dynamics simulation (MD) was used to calculate molecules polarity index (MPI). Meanwhile, the practical dyeing experiments also were investigated to compare with simulated results. The results showed that the adsorption and diffusion behavior of disperse dyes with different structures were significantly different. Compared with dye B257, D-1 and D-2 are more easily adsorbed and diffused into the interior of the fiber because of the introduction of polar acetoxyethyl group. Moreover, the diffusion coefficient of D-2 in the fiber was relatively low, indicating that the combination between dye and polyester fiber was stable. XY plane distribution density and MPI revealed that the introduction of acetoxyethyl was beneficial to increase the adsorption amount of dye on the fiber, which was mainly related to the high binding energy between dye molecule and polyester fiber. The results of dyeing experiments showed that the decreased solubility of disperse dyes in the D5 medium was conducive to improving the dyeing rate of disperse dyes. This was consistent with the simulated interaction between dyes and D5. This study will provide a basis for further rapid and accurate development and selection of disperse dyes with high dyeing rate in non-aqueous medium systems.

Local potential energy density – A DFT analysis and the local binding energy in complexes with multiple interactions

A recently developed method, so-called local potential energy density, LPED, provides the binding energy density of intra/intermolecular interactions. The LPED cannot directly give the binding energy of intra/intermolecular interactions. However, it can indirectly give the binding energy through the linear equation between LPED and supramolecular binding energy, SME. In addition, the LPED can be used to obtain the SME of local or individual interactions indirectly for the case of complexes with multiple interactions, which cannot be obtained for any other method to our knowledge. The calculation of the LPED was evaluated with three different levels of theory using density functional methods. The linearity of LPED and SME between the reference level of theory (ωB97X-D/aug-cc-pVTZ) and the other levels of theory are similar among the studied levels of theory. In addition, LPED was used indirectly to obtain the local binding energy of intermolecular interactions of complexes with multiple interactions, such as the EDTA-Ca+2 and the fosfomycin-Ca+2.

On the Potential Energy Surface of the Pyrene Dimer

Knowledge of reliable geometries and associated intermolecular interaction energy () values at key fragments of the potential energy surface (PES) in the gas phase is indispensable for the modeling of various properties of the pyrene dimer (PYD) and other important aggregate systems of a comparatively large size (ca. 50 atoms). The performance of the domain-based local pair natural orbital (DLPNO) variant of the coupled-cluster theory with singles, doubles and perturbative triples in the complete basis set limit [CCSD(T)/CBS] method for highly accurate predictions of the at a variety of regions of the PES was established for a representative set of pi-stacked dimers, which also includes the PYD. For geometries with the distance between stacked monomers close to a value of such a distance in the minimum structure, an excellent agreement between the canonical CCSD(T)/CBS results and their DLPNO counterparts was found. This finding enabled us to accurately characterize the lowest-lying configurations of the PYD, and the physical origin of their stabilization was thoroughly analyzed. The proposed DLPNO-CCSD(T)/CBS procedure should be applied with the aim of safely locating a global minimum of the PES and firmly establishing the pertaining of even larger dimers in studies of packing motifs of organic electronic devices and other novel materials.

Rational analysis of hydrogen bonding interaction in phenazine, 2-hydroxynaphthalene (1:1) cocrystal: from molecular modeling to photophysical properties.

Organic cocrystals have a wide range of applications in the field of optics due to their photo responsive property. We present here a newly synthesized phenazine 2-hydroxynaphthalene (1:1) cocrystal, its structural and theoretical calculations which tend to the nonlinear optical property. In the crystal structure of the title cocrystal, the phenazine and 2-hydroxynaphthalene molecules from one- and two-dimensional supramolecular frameworks via O‒H…N hydrogen bonds and C‒H…N, C‒H…π interaction, respectively. The phenazine molecules from an infinite off-set stacking through π…π interactionin the three-dimensional molecular packing of the title cocrystal. The contribution of intermolecular interaction in the three-dimensional molecular packing and the interaction energy calculation is studied by the Hirshfeld surface analysis. The molecular geometry retrieved from the experimental X-ray diffraction analysis is in good agreement with the theoretically calculated parameters. Further, the molecular electrostatic potential (MEP) and frontier molecular orbital (FMO) analysis have been carried out to study the charge distribution and molecular reactive mechanism. Third-order nonlinear optical property of the cocrystals has been analyzed by Z-scan measurements. The determined nonlinear optical absorption coefficient value 6.442 × 10-05 (m/W) and the nonlinear refractive index value - 5.535 × 10-2 (m/W) suggest that the crystalline solid can be a good choice of potential nonlinear optical material. The crystal structures of phenazine 2-hydroxynaphthalene cocrystal was solved by direct methods procedure using SHELXS program and refined by full-matrix least square procedure on F2 using SHELXL-2018 program on Olex2 software. The computational calculation has been carried out using DFT/B3LYP quantum chemical function with triple zeta 6-311 + + basis set in the ground state molecular stability using Gaussian 09W program suite. The Hirshfeld surface analysis mapping, associated 2D fingerprint plot, and intermolecular molecular interaction energy calculations were carried out using CrystalExplorer (version 21.5) software.

Quantitative evaluation of noncovalent interactions with negative fragmentation approach including basis set superposition error correction

Abstract We propose a negative fragmentation approach (NFA), including counterpoise (CP) correction to basis set superposition error (BSSE) for quantitatively evaluating intra- and intermolecular noncovalent interactions. Noncovalent interactions are widely found in chemistry and biology and are regarded as essential interactions. However, there are few general methods for evaluating these individual intra- and intermolecular interaction energies because of two issues: (i) difficulty in the evaluation of intramolecular interactions due to the interacting sites connected with covalent bonds and (ii) BSSE affecting the quantitative accuracy of interaction analysis. In our scheme, we overcome the issue (i) using the NFA scheme, which can evaluate intra- and intermolecular interactions as a fragment–fragment interaction of interacting sites, and address the issue (ii) using the CP method. Here, NFA including the CP correction was applied to various molecular systems, providing comparable results for intermolecular interactions to supermolecule calculations with the CP correction and also succeeding in the evaluation of intramolecular interactions and its BSSEs. It is notable that our NFA scheme does not require any particular program or a modification of the program codes. These indicate that many researchers can apply our NFA scheme to various molecular systems.

Quantitative Characterization of Fluorine-Centered Noncovalent Interactions in Crystalline Benzanilides.

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.

Electron beam irradiation coupled ultrasound-assisted natural deep eutectic solvents extraction: A green and efficient extraction strategy for proanthocyanidin from walnut green husk

Proanthocyanidin (PAC) is recognized as a potent natural antioxidant that prevents various diseases. As societal awareness increases, eco-friendly and efficient natural product extraction technologies are gaining more attention. In this study, an electron beam irradiation (EBI) coupled with ultrasound-assisted natural deep eutectic solvents (NADES) extraction method was developed to enable the green and highly efficient extraction of PAC from walnut green husk (WGH). NADES, prepared with choline chloride and ethylene glycol, demonstrated excellent extraction capacity and storage stability for PAC. Molecular dynamics simulations elucidated the high compatibility between NADES and PAC, attributed mainly to a higher SASA value (207.85 nm2), a greater number of hydrogen bonds (330.99), an extended hydrogen bonding lifetime (4.54 ps), and lower inter-molecular interaction energy. Based on these findings, the optimal conditions (13 kGy EBI, 42 mL/g liquid-solid ratio, 38 °C extraction temperature, 70 min extraction time) resulted in a maximum PAC extraction yield of 56.34 mg/g. Notably, this yield was 32.93 % higher than that observed in samples not treated with EBI and ultrasound-assisted extraction (UAE). Analysis of tissue morphology, extract functional groups and thermal behavior suggested a possible mechanism for the synergistically enhanced PAC extraction by the EBI-NADES-UAE method. Additionally, the PAC extracted using the NADES by the EBI coupled with ultrasound-assisted method exhibited outstanding antioxidant activity (comparable to Vc), digestive enzyme inhibition (IC50: 17–0.61 mg/mL), and anti-glycation capacity (IC50: 86.49 μg/mL). Overall, this work provided a green and efficient strategy for PAC extraction from WGH, elucidated the extraction mechanism and bioactivities, and offered valuable insights for potential industrial applications.

Optimization of damping function parameters for -D3 and -D4 dispersion models for Hartree-Fock based symmetry-adapted perturbation theory.

Symmetry-adapted perturbation theory (SAPT) directly computes intermolecular interaction energy in terms of electrostatics, exchange-repulsion, induction/polarization, and London dispersion components. In SAPT based on Hartree-Fock ("SAPT0") or based on density functional theory, the most time-consuming step is the computation of the dispersion terms. Previous work has explored the replacement of these expensive dispersion terms with simple damped asymptotic models. We recently examined [Schriber et al. J. Chem. Phys. 154, 234107 (2021)] the accuracy of SAPT0 when replacing its dispersion term with Grimme's popular -D3 correction, reducing the computational cost scaling from O(N5) to O(N3). That work optimized damping function parameters for SAPT0-D3/jun-cc-pVDZ using estimates of the coupled-cluster complete basis set limit [CCSD(T)/CBS] on a 8299 dimer dataset. Here, we explore the accuracy of SAPT0-D3 with additional basis sets, along with an analogous model using -D4. Damping parameters are rather insensitive to basis sets, and the resulting SAPT0-D models are more accurate on average for total interaction energies than SAPT0. Our results are surprising in several respects: (1) improvement of -D4 over -D3 is negligible for these systems, even charged systems where -D4 should, in principle, be more accurate; (2) addition of Axilrod-Teller-Muto terms for three-body dispersion does not improve error statistics for this test set; and (3) SAPT0-D is even more accurate on average for total interaction energies than the much more computationally costly density functional theory based SAPT [SAPT(DFT)] in an aug-cc-pVDZ basis. However, SAPT0 and SAPT0-D3/D4 interaction energies benefit from significant error cancellation between exchange and dispersion terms.

Crystal structure-mechanical property relationship in succinic acid and L- alanine probed by nanoindentation

Establishing structure–mechanical property relationships is crucial for understanding and engineering the performance of pharmaceutical molecular crystals. In this study, we employed nanoindentation, a powerful technique that can probe mechanical properties at the nanoscale, to investigate the hardness and elastic modulus of single crystals of succinic acid and L-alanine. Nanoindentation results reveal distinct mechanical behaviors between the two compounds, with L-alanine exhibiting significantly higher hardness and elastic modulus compared to succinic acid. These differences are attributed to the underlying variations in molecular crystal structures − the three-dimensional bonding network and high intermolecular interaction energies of L-alanine molecules leads to its stiffness compared to the layered and weakly bonded crystal structure of succinic acid. Furthermore, the anisotropic nature of succinic acid is reflected in the directional dependence of the mechanical responses where it has been found that the (111) plane is more resistant to indentation than (100). By directly correlating the nanomechanical properties obtained from nanoindentation with the detailed crystal structures, this study provides important insights into how differences in molecular arrangements can translate into different macroscopic mechanical performance. These findings have implications on the selection of molecular crystals for optimized drug manufacturability.

Effectiveness of Essential Oil Component Cocrystals Against Food Spoilage Bacteria

AbstractImproving food preservation technologies is a key aspect in the struggle to reduce global food waste, and natural antimicrobial substances, such as essential oil (EO) components represent very promising food preserving agent. However, their intrinsic chemico‐physical properties, such as the low melting point, low water solubility and high volatility, pose some practical difficulties in exploiting them for practical applications. Cocrystallization is used to stabilize liquid or volatile EO components providing them whit a crystalline environment, thus improving their potential application as antibacterial agents. Five EO active ingredients (THY = thymol, CAR = carvacrol, EUG = eugenol, CAD = trans‐cinnamaldehyde, and VAN = o‐vanillin) and two coformers (INA = Isonicotinamide, and HBA = 4‐hydroxybenzoic acid) have been combined and the corresponding cocrystals have been studied for their potential inhibiting effect against four food spoilage bacteria (Bacillus thuringiensis, Enterobacter cloacae, Pseudomonas fluorescens, and Serratia marcescens). The structures of the five cocrystals have been used to derive structure‐activity relationships in terms of release energy of the active ingredients form the crystalline environment, and a correlation has been derived with the Intermolecular Interaction Energies of the EO molecules.

Tensor hypercontraction for fully self-consistent imaginary-time GF2 and GWSOX methods: Theory, implementation, and role of the Green's function second-order exchange for intermolecular interactions.

We present an efficient MPI-parallel algorithm and its implementation for evaluating the self-consistent correlated second-order exchange term (SOX), which is employed as a correction to the fully self-consistent GW scheme called scGWSOX (GW plus the SOX term iterated to achieve full Green's function self-consistency). Due to the application of the tensor hypercontraction (THC) in our computational procedure, the scaling of the evaluation of scGWSOX is reduced from O(nτnAO5) to O(nτN2nAO2). This fully MPI-parallel and THC-adapted approach enabled us to conduct the largest fully self-consistent scGWSOX calculations with over 1100 atomic orbitals with only negligible errors attributed to THC fitting. Utilizing our THC implementation for scGW, scGF2, and scGWSOX, we evaluated energies of intermolecular interactions. This approach allowed us to circumvent issues related to reference dependence and ambiguity in energy evaluation, which are common challenges in non-self-consistent calculations. We demonstrate that scGW exhibits a slight overbinding tendency for large systems, contrary to the underbinding observed with non-self-consistent RPA. Conversely, scGWSOX exhibits a slight underbinding tendency for such systems. This behavior is both physical and systematic and is caused by exclusion-principle violating diagrams or corresponding corrections. Our analysis elucidates the role played by these different diagrams, which is crucial for the construction of rigorous, accurate, and systematic methods. Finally, we explicitly show that all perturbative fully self-consistent Green's function methods are size-extensive and size-consistent.

An automated calculation pipeline for differential pair interaction energies with molecular force fields using the Tinker Molecular Modeling Package

An automated pipeline for comprehensive calculation of intermolecular interaction energies based on molecular force-fields using the Tinker molecular modelling package is presented. Starting with non-optimized chemically intuitive monomer structures, the pipeline allows the approximation of global minimum energy monomers and dimers, configuration sampling for various monomer–monomer distances, estimation of coordination numbers by molecular dynamics simulations, and the evaluation of differential pair interaction energies. The latter are used to derive Flory–Huggins parameters and isotropic particle–particle repulsions for Dissipative Particle Dynamics (DPD). The computational results for force fields MM3, MMFF94, OPLS-AA and AMOEBA09 are analyzed with Density Functional Theory (DFT) calculations and DPD simulations for a mixture of the non-ionic polyoxyethylene alkyl ether surfactant C10E4 with water to demonstrate the usefulness of the approach.Scientific ContributionTo our knowledge, there is currently no open computational pipeline for differential pair interaction energies at all. This work aims to contribute an (at least academically available, open) approach based on molecular force fields that provides a robust and efficient computational scheme for their automated calculation for small to medium-sized (organic) molecular dimers. The usefulness of the proposed new calculation scheme is demonstrated for the generation of mesoscopic particles with their mutual repulsive interactions.

Assessing the domain-based local pair natural orbital (DLPNO) approximation for non-covalent interactions in sizable supramolecular complexes.

The titular domain-based local pair natural orbital (DLPNO) approximation is the most widely used method for extending correlated wave function models to large molecular systems, yet its fidelity for intermolecular interaction energies in large supramolecular complexes has not been thoroughly vetted. Non-covalent interactions are sensitive to tails of the electron density and involve nonlocal dispersion that is discarded or approximated if the screening of pair natural orbitals (PNOs) is too aggressive. Meanwhile, the accuracy of the DLPNO approximation is known to deteriorate as molecular size increases. Here, we test the DLPNO approximation at the level of second-order Møller-Plesset perturbation theory (MP2) and coupled-cluster theory with singles, doubles, and perturbative triples [CCSD(T)] for a variety of large supramolecular complexes. DLPNO-MP2 interaction energies are within 3% of canonical values for small dimers with ≲10 heavy atoms, but for larger systems, the DLPNO approximation is often quite poor unless the results are extrapolated to the canonical limit where the threshold for discarding PNOs is taken to zero. Counterpoise correction proves to be essential in reducing errors with respect to canonical results. For a sequence of nanoscale graphene dimers up to (C96H24)2, extrapolated DLPNO-MP2 interaction energies agree with canonical values to within 1%, independent of system size, provided that the basis set does not contain diffuse functions; these cause the DLPNO approximation to behave erratically, such that results cannot be extrapolated in a meaningful way. DLPNO-CCSD(T) calculations are typically performed using looser PNO thresholds as compared to DLPNO-MP2, but this significantly impacts accuracy for large supramolecular complexes. Standard DLPNO-CCSD(T) settings afford errors of 2-6 kcal/mol for dimers involving coronene (C24H12) and circumcoronene (C54H18), even at the DLPNO-CCSD(T1) level.

High-throughput computational screening for optimal solvents in methyl 2-hydroxyisobutyrate-water separation

In the semiconductor industry, the efficacy of methyl 2-hydroxyisobutyrate (HBM) as a photoresist thinner is crucial but often compromised by water contamination. Additionally, the manufacturing process tends to form an azeotrope with water, rendering traditional distillation methods inefficient for purification. This study introduces a novel computational screening approach to identify optimal solvents for the liquid-liquid extraction of HBM, offering a sustainable alternative to conventional distillation. Our three-step sequential screening protocol utilizes molecular dynamics simulations to evaluate intermolecular interaction energy, partition coefficient, and environmental, health, and safety (EHS) parameters. Initially, a comprehensive database of 4919 solvents was screened using molecular dynamics simulations to assess interaction energies and partition coefficients. Solvents that met these energy criteria were further evaluated for their EHS profiles. This process identified seven solvents that optimize extraction efficiency while adhering to stringent environmental and safety standards. Our approach not only enhances the purity and performance of HBM in semiconductor manufacturing but also presents a green, cost-effective solution for other industrial chemical processes requiring refined solvent selection.

Modeling Molecular Study between SDO1/Inhibitors: Search of New Treatments for Amyotrophic Lateral Sclerosis

Background: The Amyotrophic lateral sclerosis (ALS) is a degenerative and most frequent motor neuron disease characterized by the progressive impairment of upper and lower motor neurons. The treatment of the disease is still palliative and limited to the use of only two drugs, riluzole and edaravone, which only prolong survival by a few months. Taking into account the low number of therapy available for this disease, identification of novel therapeutic strategies for ALS is urgently needed. The superoxide dismutase 1 (SOD1) was the first gene in which mutations were found to be causative for the neurodegenerative disease and has been used as a promising target for the ALS treatment. Methods: In this work we used powerful computational tools (in silico method) such as Ligand-based Virtual Screening (SBVS), docking and molecular dynamics techniques to collaborate with the discovery of new candidates for more potent drugs to be used in the ALS disease treatment. Results: Compound 1 shows good stability in the active site of the SOD1 enzyme, with an intermolecular interaction energy of -154.80 kcal/mol. In addition, the presence of some amino acids such as Glu24, Glu21, Pro28, Lys23 and Lys30 is important for to maintain stability of this compound inside SOD1. Conclusion: This study was essential due to a low number of therapy available for this disease until the moment. With this study, it was possible to observe that Compound 1 is the most promising for the design of SOD1 mutant enzyme potential inhibitors. However, experimental tests in the SOD1 mutant to validate the inhibitory effect of Compound 1 will be required.

Revisiting the Most Stable Structures of the Benzene Dimer.

The benzene dimer (BD) is an archetypal model of π∙∙∙π and C-H∙∙∙π noncovalent interactions as they occur in its cofacial and perpendicular arrangements, respectively. The enthalpic stabilization of the related BD structures has been debated for a long time and is revisited here. The revisit is based on results of computations that apply the coupled-cluster theory with singles, doubles and perturbative triples [CCSD(T)] together with large basis sets and extrapolate results to the complete basis set (CBS) limit in order to accurately characterize the three most important stationary points of the intermolecular interaction energy (ΔE) surface of the BD, which correspond to the tilted T-shaped (TT), fully symmetric T-shaped (FT) and slipped-parallel (SP) structures. In the optimal geometries obtained by searching extensive sets of the CCSD(T)/CBS ΔE data of the TT, FT and SP arrangements, the resulting ΔE values were -11.84, -11.34 and -11.21 kJ/mol, respectively. The intrinsic strength of the intermolecular bonding in these configurations was evaluated by analyzing the distance dependence of the CCSD(T)/CBS ΔE data over wide ranges of intermonomer separations. In this way, regions of the relative distances that favor BD structures with either π∙∙∙π or C-H∙∙∙π interactions were found and discussed in a broader context.

Structural and computational exploration of zwitterionic and quinoidal forms in Schiff base compound

The stable NH-form of the Schiff base compound, (Z)-6-(((4-chlorobenzyl) amino) methylene)-2-hydroxycyclohexa-2,4-dienone was synthesized and characterized by FTIR, SEM, EDAX anlysis and X-ray crystallographic analysis. Structural analysis was carried out to examine the NH-form of the halogen-based Schiff base compound. Additionally, an analysis of bond lengths, based on previously reported NH-forms of other Schiff bases, was conducted to distinguish between the zwitterion and quinoid structures. Further, Hirshfeld surface analysis was performed to visualize and quantify intermolecular interactions, supported by shape index, 2D fingerprint plots, and Enrichment ratio analyzes, highlighting the importance of these interactions. Energy frameworks were established to deepen the understanding of crystal packing through the computation of intermolecular interaction energies. QTAIM analysis was performed to visualize and quantify intramolecular interactions, while Density Functional Theory (DFT) studies elucidated molecular properties such as the HOMO-LUMO energy gap and its derivatives. Evaluation of antibacterial activity against S. aureus was conducted via the disc diffusion assay supplemented by molecular docking studies. This comprehensive approach provides valuable structural insights into the NH-form, as well as molecular and biological aspects of (Z)-6-(((4-chlorobenzyl) amino) methylene)-2-hydroxycyclohexa-2,4-dienone.