A Probe to Surface Reactivity, Crystal Structure, and DFT Investigations for Newly Synthesized 4,5-bis(4-Nitrophenyl)-8a-phenyl-decahydro-[1,3]diazino[4,5-d]pyrimidine-2,7-dione: A Combined Theoretical and Experimental Study

The multicomponent reaction of 4-nitrobenzaldehyde with acetophenone and urea in the presence of HCl was investigated, and, as a result, 4,5-bis(4-nitrophenyl)-8a-phenyl-decahydro-[1,3]diazino[4,5-d]pyrimidine-2,7-dione was synthesized. The structure of the synthesized compound was confirmed by the X-ray method. We performed Hirshfeld surfaces (HS) analysis and two-dimensional (2D) fingerprint plots for the studied compound to obtain surface reactivity and intermolecular interactions. The H∙∙∙H interactions were found to be higher, up to 32.2%, while the percentage C∙∙∙O contact was found to be the lowest among the reported interactions for single crystal packing. The energy framework analysis shows the strength of interaction energy within fragments of a single crystal at 3.08 A distances. The DFT study shows structural reactivity and a reduced HOMO-LUMO gap up to 4.0 eV. The NPA study reveals the reactivity and excellent charge transfer within the structure. The TD-DFT study reveals the absorbance in the UV region and excited state parameters during crucial transitions (transitions with maximum oscillator strength). The investigated compound shows excellent optical and nonlinear optical (NLO) properties, as indicated by its polarizability (αo) and hyperpolarizability (βo) values

Geometric, Electronic, and Optoelectronic Properties of Carbon-Based Polynuclear C₃O[C(CN)₂]₂M₃ (where M = Li, Na, and K) Clusters: A DFT Study

Carbon-based polynuclear clusters are designed and investigated for geometric, electronic, and nonlinear optical (NLO) properties at the CAM-B3LYP/6-311++G(d,p) level of theory. Significant binding energies per atom (ranging from −162.4 to −160.0 kcal mol−1) indicate excellent thermodynamic stabilities of these polynuclear clusters. The frontier molecular orbital (FMOs) analysis indicates excess electron nature of the clusters with low ionization potential, suggesting that they are alkali-like. The decreased energy gaps (EH-L) with increased alkali metals size revael the improved electrical conductivity (σ). The total density of state (TDOS) study reveals the alkali metals’ size-dependent electronic and conductive properties. The significant first and second hyperpolarizabilities are observed up to 5.78 × 103 and 5.55 × 106 au, respectively. The βo response shows dependence on the size of alkali metals. Furthermore, the absorption study shows transparency of these clusters in the deep-UV, and absorptions are observed at longer wavelengths (redshifted). The optical gaps from TD-DFT are considerably smaller than those of HOMO-LUMO gaps. The significant scattering hyperpolarizability (βHRS) value (1.62 × 104) is calculated for the C3 cluster, where octupolar contribution to βHRS is 92%. The dynamic first hyperpolarizability β(ω) is more pronounced for the EOPE effect at 532 nm, whereas SHG has notable values for second hyperpolarizability γ(ω)

Color properties and non-covalent interactions in hydrated (Z)-4-(1-cyano-2-(2,4,5-trimethoxyphenyl)-vinyl)pyridin-1-ium chloride salt: Insights from experimental and theoretical studies

The optical charge-transfer (CT) property and the crystal structure of (Z)-4-(1-cyano-2-(2,4,5-trimethoxyphenyl)vinyl)pyridin-1-ium chloride monohydrate salt (I), which belongs to an acrylonitrile family, was studied. The title salt, I, was characterized using different spectroscopy techniques and a single-crystal X-ray diffraction study combined with quantum chemical computations. The results showed that the color properties of I are determined by the CT, changes in bandgap, optical absorption, and various non-covalent interactions. The HOMO-LUMO energy gaps are 5.41 eV and 5.23 eV for the precursor and salt, respectively. It was demonstrated that π-π stacking interactions lead to the formation of intercalated dimers and donor-acceptor interactions assisted by hydrogen bonds; the dimers and interactions are different between the precursor and the salt. The cation moiety is mainly stabilized by N(1)+-H···Cl, and the anion is predominantly stabilized by strong O(1W)– H⋯ Cl− bonds as well as the hydrogen bonds with the MeO group O(2W)–H⋯O(1) and O(2W)–H⋯O(1W). The charge transfer between cation and anion moieties in the structure is established through NBO analysis

Synthesis, crystal structure investigation, and theoretical approaches to discover potential 6-bromo-3-cyanocoumarin as a potent inhibitor MetAP (methionine aminopeptidase) 2

It has been ascertained that trifluoroacetic acid accelerates the Knoevenagel condensation reaction of 5-bromosalicylaldehyde and ethyl ester of cyanoacetic acid. As a result, the 6-bromo-3-cyanocoumarin compound has been synthesized and the structure was eventually confirmed by X-ray analysis. Based on the structure-activity relationship and literature survey we found this compound has a potent inhibitor for MetAP (methionine aminopeptidase) and further we have studied molecular docking to understand the binding interactions and also performed ADME/T studies for this compound. The surface reactivity and intermolecular interactions of the studied compound were investigated by Hirshfeld surface analysis. Energy framework analysis shows the interaction between pair of fragments with neighbor molecules. Furthermore, the DFT study is performed to investigate structural reactivity and stability at B3LY/6-311+G(d,p) functional. The decreased HOMO-LUMO gap (3.97 eV) indicates its higher reactivity and soft nature. Molecular electrostatic potential (MESP) analysis and NBO charges indicate the structure's reactive site and charge transfer. Excited analysis by using the TD-DFT was performed to get excitation energy (ΔE), absorbance, and oscillator strength (fo) of crucial transition. Theoretically predicted values of polarizability (αo) and hyperpolarizability (βo) suggest their excellent optical and Nnar (NLO) properties

X-ray Diffraction, Spectroscopy, Optical Properties, NPA, NBO, FMO, and Hirshfeld Surface Analyses of Two Newly Synthesized Piperidinium Ionic Liquids

The present study elaborates on the synthesis, crystal structure, and computational studies of two new ionic liquids. In the crystal structure, [C5H12N][C21H14ClN2O2S] (4a), the anions form chains along the a-axis direction through C—H···π(ring) interactions. These are connected into layers that run approximately parallel to the ac plane by a variety of hydrogen bonds. In the compound structure, [C5H12N][C18H15N2O2S] (4b), the two ions are primarily associated by an N—H···N hydrogen bond. In the crystal structure, layers parallel to the bc plane are formed by pairs of C—H···O and N—H···S hydrogen bonds and by C—H···π(ring) interactions. A theoretical study reveals that 4a has lower energy than 4b and is more stable. The NBO and DOS studies further confine the liquids’ structural reactivity and electronic properties. The quantum theory of atoms in a molecule (QTAIM) analysis reveals the important non-covalent interactions among the fragments and charge transfer. The global reactivity descriptors indicate their molecular reactivity relationship with the presence of functional groups. The remarkable polarizability (αo) and hyperpolarizability (βo) values indicate their optical and nonlinear optical (NLO) properties. Furthermore, the analysis performed by CrystalExplorer shows the intermolecular interactions and reactive sites between cations and anions in ionic liquids. The 2D fingerprint plots and Hirshfeld surfaces indicate the major interactions of crystals with neighboring elements in crystal packing. For both compounds, the H···H interactions are significantly higher than the other element interactions

Synthesis, crystal structure investigation, Hirshfeld and DFT studies of newly synthesized dihydroisoquinoline derivatives

Isoquinoline and its derivatives, which constitute an important category of heterocyclic compounds and are found in a variety of naturally occurring alkaloids, serve a variety of biological purposes such as a potent agonist for human melatonin receptors 1. This research was conducted in an attempt to develop new dihydroisoquinoline molecules (III and IV). Single-crystal X-ray crystallography study validated their structures. The Hirshfeld surface analysis identifies intermolecular interactions by using a 2-D fingerprint map to recognize each type's relative contribution H⋅⋅⋅H connections are discovered to be dominating. The interaction energies between chemical pairs in crystal structures were found using an energy framework analysis. The DFT investigation demonstrates the electronic stability and reactivity of the compounds using the HOMO-LUMO and global reactivity descriptors, indicating that IV has higher chemical reactivity than III. The derived polarizability (αo) and hyperpolarizability (βo) values were used to calculate the optical and nonlinear optical characteristics of III and IV. The IV's significant βo value (488.94 au) indicates that it has good optical and NLO qualities. Molecular docking simulation using human melatonin receptors 1 was used to better understand the binding interaction mechanism of the title compounds. In addition, ADMET evaluations were performed to establish the therapeutic potential of III and IV

Insights into the crystal structure investigation and virtual screening approach of quinoxaline derivatives as potent against c-Jun N-terminal kinases 1

Quinoxaline derivatives are an important class of heterocyclic compounds in which N replaces one or more carbon atoms of the naphthalene ring and exhibit a wide spectrum of biological activities and therapeutic applications. As a result, we were encouraged to explore a new synthetic approach to quinoxaline derivatives. In this work, we synthesized two new derivatives namely, ethyl 4-(2-ethoxy-2-oxoethyl)-3-oxo-3,4-dihydroquinoxaline-2-carboxylate (2) and 3-oxo-3,4-dihydroquinoxaline-2-carbohydrazide (3) respectively. Their structures were confirmed by single-crystal X-ray analysis. Hirshfeld surface (HS) analysis is performed to understand the nature and magnitude of intermolecular interactions in the crystal packing. Density functional theory using the wb97xd/def2-TZVP method was chosen to explore their reactivity, electronic stability and optical properties. Charge transfer (CT) and orbital energies were analyzed via natural population analysis (NPA), and frontier molecular orbital (FMO) theory. The calculated excellent static hyperpolarizability (βo) indicates nonlinear optical (NLO) properties for 2 and 3. Both compounds show potent activity against c-Jun N-terminal kinases 1 (JNK 1) based on structural activity relationship studies, further subjected to molecular docking, molecular dynamics and ADMET analysis to understand their potential as drug candidates. Communicated by Ramaswamy H. Sarma</p

Synthesis, Crystal Growth, and Computational Investigation of New Tetrahydroisoquinoline Derivatives Potent against Molecule Nitric Oxide Synthases

In the present work, we describe the synthesis of new tetrahydroisoquinoline derivatives and the crystal structures of two of them. Density functional theory (DFT) investigations at the B3LYP/6-31+G(d,p) level provided their structural reactivity and nonlinear optical properties. The low HOMO-LUMO gaps (EH-L) suggest a soft nature and higher reactivity, while calculated global reactivity descriptors provide assessments of their reactivity and electronic stability. The calculated natural bonding molecular orbital (NBO) charges show excellent charge separation (charge transfer) and identify the donor and acceptor parts of the molecules. Density of states (DOS) analyses show the newly generated energy states and reduced band gaps, which impart higher conductive properties. For surface reactivity, 3D MESP surfaces are plotted and show electron-rich sites near the nitrogen atoms of the tetrahydroisoquinoline rings. Nonlinear optical (NLO) properties of the crystals are predicted from calculated polarizability (αo) and hyperpolarizability (βo) values. For IVb, the αo and βo values are 415.53 and 1003.44 au. The remarkable value (1003.44 au) of the hyperpolarizability (βo) shows IVb has excellent NLO properties. Structural activity relationship analysis suggests that nitric oxide synthases are better targets for both compounds, and they were further subjected to molecular docking simulations to understand the binding efficiency. In addition, ADMET analyses were carried out to understand the potential activity of the molecules as drug candidates

XRD/DFT, Hirshfeld surface analysis and molecular modelling simulations for unfolding reactivity of newly synthesized vanillin derivatives: excellent optical, NLO and protein binding efficiency

New vanillin derivatives, namely, ethyl (4-formyl-2-methoxyphenoxy)acetate (2a) and 2-(4-formyl-2-methoxyphenoxy)-N-phenylacetamide (2b), respectively, were synthesized and characterized by NMR (1H and 13C), IR, mass spectra and confirmed by single-crystal X-ray analysis. Hirshfeld surface (HS) analysis was performed to probe intra- and intermolecular interactions and surface reactivity. 2D fingerprint plots (FP) were used to study the nature and percentage contribution of intermolecular interactions leading to the formation of the crystal unit. Density functional theory (DFT) simulations were used to obtain the electronic structure and reactivity of the new molecules. Natural population analysis (NPA) and frontier molecular orbital (FMO) calculations reveal significant charge transfer and a reduced HOMO-LUMO gap up to 4.34 eV for 2b. Bader’s quantum theory of atoms in molecules (QTAIM) study is utilized to understand the surface topological and bonding nature of 2a and 2b. The performed molecular electrostatic potential (MESP) and density of states (DOS) study further suggest sites likely to be attractive to incoming reagents. At the same time, hyperpolarizability (βo) is used to characterize the nonlinear optical properties, and TD-DFT study shows the excitation energy and absorption behavior. In silico studies were performed, including docking, binding free energies (MMBGSA) and molecular dynamics simulations. Compounds 2a and 2b were docked with RdRp of SARS-Cov-2, and the MMBGSA for 2a and 2b were −30.70 and −28.47 kcal/mol, respectively, while MD simulation showed the stability of protein-ligand complexes. Communicated by Ramaswamy H. Sarma</p