FMO Energies Research Articles

Synthesis, molecular structure, experimental and computational studies, nonlinear optical properties of amaranth dye doped L-lysine sulphate (ALLS) semiorganic crystal

A polycrystals of amaranth dye-doped L-lysine sulphate (ALLS) was synthesized and fabricated as a single crystal utilizing the solution-based growth approach and confirmed the orthorhombic structure through XRay diffraction anlaysis. The ALLS molecule was optimized in Gaussian 09 W utilizing the density functional theory (LANL2DZ/DFT) basis. Along with PED, the Fourier transform infrared (FTIR) spectroscopy helps vibrational assignments of ALLS were both theoretically and experimentally suited to one another. The FMO energies of ALLS molecules are used to derive quantum chemical parameters. To study the properties of charges existing at the molecular structure level, DOS, MESP, and MULLIKEN studies were performed. To figure out the compound's NLO activity, hyperpolarisability values are calculated. ELF, LOL, and RDG topological studies were carried out through which the localization and delocalization of electrons were found. MEP gives the relative polarity and the UV absorption gives maximum absorption at 414 nm were recorded. Additionally, ALLS's thermodynamic parameters were calculated. The NLO behaviour of the LLS complex was improved by amaranth dye, and ALLS has been suggested as a suitable compound for the fabrication of NLO devices as an outcome of both experimental and computational results.

New 2-Chloroimidazo[1,2-a]pyridine induced Schiff bases: Synthesis, characterization, antimicrobial and A-498 and A-549 anticancer activity, molecular modeling, in-silico pharmacokinetics, and DFT studies

The novel 1-(2-chloroimidazo[1,2-a]pyridin-3-yl)-N-(substitutedphenyl) methanimines have been synthesized and characterized by spectral (IR, MS, 1H, and 13C NMR) and elemental analysis. Molecular docking studies were conducted with three cancer target proteins (PDB IDs: 1M17, 2OF4, and 3LCK) and assorted microbial target proteins (1KZN, 2XCT, 1D7U, 1BAG, and 1EA1) to explore their binding interactions. Further in-silico target prediction study suggested a 26.7 % probability that VIf acts on kinases. The synthesized analogs were subjected to in-vitro anticancer activity assessments against A-498 (kidney carcinoma) and A-549 (lung carcinoma) cell lines and compound VIf exhibited good inhibition (GI50<10) of the A-498 cell line. Additionally, all analogs showed moderate to good in-vitro antimicrobial activity against S. aureus, B. subtilis, E. coli, K. pneumoniae (bacterial strains), and C. albicans (fungal strain). The optimized geometries, FMO energies, MEP plots, and global reactivity descriptors (µ, ɳ, S, and ω) were achieved employing DFT at B3LYP/6-31G (d) level to explore structural features and probable reactivity and toxicity of the synthesized compounds. Compound VIg exhibited high reactivity (ɳ: 1.8218 eV, S: 0.2744 eV) and low toxicity (ω: 3.2061 eV) among all analogs. These findings collectively underscore the potential of the synthesized compounds, with VIf and VIg standing out as particularly promising candidates for further exploration.

Synthesis, crystal structure, biological evaluation, in silico ADME properties, enzymatic target prediction and molecular docking studies of pyrazolone-azomethine analogs

A series of twelve azomethine analogs (3a-l) of 4-aminoantipyrine (4-AA) were prepared and characterized using FT-IR, 1HNMR and EI mass spectrometric analysis. Analog 3f was obtained as a single crystal, and X-ray diffraction (XRD) data indicated its adoption of a trans configuration around the central azomethine (CN) group, forming monoclinic P2(1)/n symmetry. The unit cell of 3f contains four molecules, and its crystal packing is stabilized through significant intermolecular host-guest CH⋯O, CH⋯π, and π⋯π interactions, resulting in a stacked supramolecular structure. In vitro bactericidal and fungicidal screening of analogs 3a-l was performed against twelve bacterial and five fungal strains, respectively. Most of the analogs demonstrated weak to moderate antimicrobial activities, specifically 3a, 3b, 3e and 3g exhibited highest activity against S. boydii, B. megaterium; S. sonnei and E. coli, respectively and 3c, 3d and 3l showed potent fungicidal activity against A. flavus, C. albicans, and N. crassa, respectively. The results indicate that the antimicrobial potency is largely dependent on the nature of the aromatic ring linked pyrazolone moiety via azomethine (CN) group. DPPH free radical scavenging assay revealed analogs 3e, 3l, 3g, 3k, 3h and 3d had IC50 values of 0.07, 1.19, 2.31, 2.57, 4.04 and 4.07 µg mL−1, respectively, comparable to that of the standard ascorbic acid (IC50 = 4.10 µg mL−1). Docking simulations were conducted to elucidate the binding mode of potent antibacterial analogs (3e and 3g) and antifungal analogs (3d and 3l) within the active sites of KAS (E. coli) and CYP 51 (C. albicans) receptors, respectively. The results revealed strong binding affinities between the studied molecules and the respective proteins. All the tested analogs fulfill the condition of Lipinski's rule of five (ROF) and Veber's rule, and the calculated ADMET profile indicated favorable drug-likeness, pharmacokinetic properties, and drug scores. Ligand-based enzymatic target predictions suggest that analogs 3a-l have potential as inhibitors of kinases, enzymes, proteases, or ligands for Family A GPCR. Finally, DFT calculations using the B3LYP/6-311G(d,p) level of theory provide insights into the FMO energies, global molecular reactivity, and biological properties of the azomethine analogs of 4-AA.

Material of oxo-peroxo-molybdenum (VI) complex involving 4-Furoyl-3-methyl-1-phenyl-2-pyrazoline-5- one: experimental cum theoretical observations

We report here the experimental and theoretical investigation of the bis(4-furoyl-3-methyl-1-phenyl-2-pyrazolin-5-one)oxoperoxomolybdenum(VI) complex molecule. It was prepared by the reaction of (2:1) 4-furoyl-3-methyl-1-phenyl-2-pyrazolin-5-one and [MoO(O)2]2+ in an aqueous ethanol medium. Characterization was performed by elemental analysis, molar conductivity, magnetic measurements, electrochemical analysis, and infrared and electronic spectral studies. Theoretical validation was performed by density functional theory calculations using B3LYP as the LANL2DZ function. The molecular geometry results show a distorted pseudo-pentagonal bipyramidal geometry together with the O7 coordination mode around the Mo(VI) center. The FMO energies allow the determination of the atomic and molecular parameters and also represent the charge transfer across the molecule.

Valeramide and Halo-phenol in a Non-polar Liquid: DFT Based Characterization and Reactivity, Non-covalent Interaction, and Dielectric Relaxation Studies

Valeramide and halogenated phenol in solvent benzene have been studied using DFT. Dielectric relaxation studies have also been undertaken. The wave functional characteristics like reduced density gradient (RDG), electron localization function (ELF), localized orbital locator (LOL) are also evaluated. It has been found that the computed FMO energies accurately depict the characteristics of electron excitation which provide an explanation for the charge transfer. MEP analysis is done to identify electrophilic and nucleophilic sites. The theoretical analysis of the UV-Visible spectrum using the TD-DFT method in solution and the computational investigation of spectroscopic wavenumbers was also carried out (IR, Raman). Thermodynamic properties of title compound at different temperatures was carried out. Various dielectric parameters, like the dielectric constant the dielectric loss at microwave frequency, the static dielectric constant ε0 and the dielectric constant ε∞ at optical frequency, were measured across five distinct molar ratios (i.e. 1:3, 1:2, 1:1, 2:1 and 3:1). While the relaxation time τ2 for group rotation is utilized to identify the steric interaction of the proton donor, Higasi’s single-frequency equation is proven to measure multiple relaxation time τ1 to determine the intensity of hydrogen bonding. At a 1:1 (molar ratio) , the values of relaxation time were found to be high. Molecular docking was done in a supplementary effort to support intermolecular interactions.

Molecular modelling, DFT, molecular dynamics simulations, synthesis and antimicrobial potential studies of heterocyclic nucleoside mimetics

Few N-1-(β-D-ribofuranosyl) heterocyclic mimetics have been designed using in silico techniques, synthesized by Vorbrüggen and Bennua method and subjected to evaluate in vitro antimicrobial activity. The global reactivity descriptors were evaluated using FMO energies data to analyse the chemical properties and biological activity of compounds. Several mode of interactions, binding affinity and 50% effective concentration of compounds were computed by docking simulations against peptide deformylase (PDF) protein, using Discovery Studio v20.1.0.19295. MD simulations were also executed on the best screened compound for a better understanding of binding affinity and stability of compound within the inhibitory binding pocket of PDF by employing GROMACS 2019.6 package. Furthermore, antibacterial screening in combination approaches was carried out for all compounds using standard antibiotics chloramphenicol and kanamycin through broth micro-dilution method. A promising synergistic effect with two-fold to sixteen-fold better inhibitory potency was exhibited by compounds against different wild type human pathogenic bacteria, viz. B. cerus, B. subtilis, S. aureus, E. coli and P. aeruginosa, and one mutant strain of E. coli. Moreover, antifungal screening was also performed for all compounds against four pathogenic fungal species, viz. A. flavus, A. niger, F. oxysporum and C. albicans by two different methods and compound 3 was obtained as the best screened one. The study clearly demonstrated that in silico and in vitro results found in good coherence. Thus, the lead compound could be potentially developed as an antimicrobial agent.

Mild and efficient addition of carbon nucleophiles to condensed pyridines: influence of structure and limits of applicability

A number of azolo- and azinopyridines with varying substituents and annulated heterocycles were synthesized and examined in dearomatization reactions with carbon nucleophiles. Depending on the structure, the resulting covalent σ-adducts were formed either under basefree conditions or in Et3N-promoted process to give functionalized condensed dihydropyridines. Quantum-chemical calculations of the global electrophilicity index derived from FMO energies of azolopyridine series were performed to explain reactivity toward neutral and anionic C-nucleophiles. These values may be useful for qualitative prediction of particular reactivity pattern.

Optimized Geometry, Charge Distributions, Frontier Molecular Orbital Analysis and NLO Efficiency of BIS (4-Methoxyanilinium) Adipate by Quantum Chemical Calculations

In this work, optimized molecular geometry, vibrational and electronic properties of Bis(4-methoxylanilinium) adipate (4MAA) was obtained by Quantum chemical analysis using 6-311++G(d,p) basis sets. The experimental and computation vibrational spectra have been discussed. Experimental spectra of the 4MAA were recorded in the region 4000–400 cm-1. The experimental and computational assignments were found to be in good agreement. FMO energies showed that charge transfer had occurred within the molecule. Mulliken charge distribution of the present compound was studied systematically. Furthermore, the hyperpolarizability calculations were analyzed.

Synthesis, Characterization and DFT Analysis of Benzimidazolylpyrazolylacrylonitrile

A novel heterocyclic molecule possessing two important scaffolds such as pyrazole and benzimidazole was synthesized and the structure of the same was corroborated based on analytical and spectroscopic techniques. The molecular structure of 6 was optimized; FMO energies associated properties were calculated. The hyperpolarizability (βtot) and electric dipole moment (μtot) of 6 were computed. When compared to urea, the β was 7.6 times superior, which validate the target 6 may serve as a candidate for NLO applications.

Spectroscopic Identifications, Molecular Docking, Neuronal Growth and Enzyme Inhibitory Activities of Steroidal Nitro Olefin: Quantum Chemical Study

AbstractFT‐IR, NMR and ultraviolet spectroscopy by means of DFT / B3LYP‐6‐311G(d, p), molecular docking and biological activity of 6‐nitrocolest‐5‐en‐3‐beta‐yl acetate (steroid nitro‐olefin) was reported in this article. The optimized molecular geometric structure and its associated parameters including vibrational frequencies, carbon and 1H NMR data of the title compound in ground electronic state was obtained at DFT approach applying B3LYP/6‐311G(d,p). The ultraviolet absorbance data is obtained at TDB3LYP/6‐311G(d,p) basis set. The present computational data are found in reasonable agreement with the experimental results. Simulated electronic and NMR (1H and 13C) spectra have been reported in solution phase. Parameters like thermodynamic quantities, dipole moment, FMO energies, MEP and global reactivity descriptors of steroid nitro olefin were determined at same level of theory. The neuromodulatory effect of the compound on central nervous system development of rat embryonic hippocampal neurons has been studied. Based on the outcome; compound demonstrated suppression activity despite the promotion of neuronal cytoarchitecture leading to a negative effect on hippocampal neurons. The nature of the compound found to be toxic to the cells. Besides, steroid compound is also used to perform inhibitory activity against acetylcholinesterase (AChE) compared to the reference drug i. e. Galanthamine. The molecular docking of the synthesized compound is carried out with the structure of the acetylcholinesterase (PDB: 1DX6) protein to check the mode of interactions.

Synthesis and Field-Effect Transistor Application of π-Extended Lactam-Fused Conjugated Oligomers obtained by Tandem Direct Arylation.

Five π-extended lactam-fused conjugated oligomers (5FO, 5FS, 4FPO, 4FPS, and R-4FPO) were synthesized by the tandem direct arylation. The intermolecular oxidative direct arylation was applied in the second step. These conjugated oligomers had fine-tuned FMO energies predictable by the theoretical calculation and excellent thermal stabilities. 4FPO and 4FPS bearing tetrafluoropyridine exhibited lower LUMO energy levels (-3.20 eV and -3.39 eV, respectively) compared with others. Based on the X-ray crystallography, 4FPO was found to have a herringbone crystal packing and a considerably large electron transfer integral value (137 meV). 4FPO-based bottom-gate, bottom-contact FET device demonstrated an electron mobility of 5.2×10-3 cm2 V-1 s-1 as a result of an edge-on alignment on the SiO2 substrate.

5-Methyl-2-thiophenecarboxaldehyde: Experimental and TD/DFT study

The 5-Methyl-2-thiophenecarboxaldehyde (MTC) and its derivatives present a wide range of biological activities. In this regard a combined experimental and theoretical analysis for MTC and its derivatives can help to understand the electronic factors involved in the mode of action in biological systems. In the present work we used FT-IR and UV–vis techniques to investigate the spectroscopic properties of MTC. The conformational and vibrational analyses were theoretically explored using DFT calculation at DFT/B3LYP/6–311++G(d,p) level. A full electronic analysis of compound was performed using TD-DFT/B3LYP/6–311++G(d,p) calculations in gas phase and in ethanol solvent with the CPCM model. The NLO parameters (β, γ and χ(3)) and FMO energies for MTC were calculated at the same level of theory. The relation between linear polarizability (α) and refractive index (n) were used to describe the polarization behavior of MTC in ethanol solvent. Our results indicate that MTC can be considered as a candidate to microscopic third−order NLO material.

1H–pyrazole–3–carboxylic acid: Experimental and computational study

The FT–IR and UV–Vis spectra for 1H–pyrazole–3–carboxylic acid (H2pc) were recorded in methanol solvent. The optimized molecular structure, vibrational frequencies and NMR chemical shifts of the title molecule in methanol solvent and gas phase were obtained by using DFT/B3LYP and DFT/HSEh1PBE methods with 6–311++G(d,p) basis set. TD–DFT calculations in methanol solvent and gas phase were used to investigate UV–Vis absorption wavelengths. Furthermore, the NLO parameters and FMO energies of the molecule were calculated by using B3LYP and HSEh1PBE methods with 6–311++G(d,p) basis set. In order to investigate intermolecular hydrogen bonds and π–π interactions, NBO study was fulfilled by the same levels. To sum up, the fact that the title compound used frequently in coordination chemistry field has encouraged us to do experimental and theoretical characterizations of H2pc

Quality Assessment of Predicted Protein Models Using Energies Calculated by the Fragment Molecular Orbital Method.

Protein structure prediction directly from sequences is a very challenging problem in computational biology. One of the most successful approaches employs stochastic conformational sampling to search an empirically derived energy function landscape for the global energy minimum state. Due to the errors in the empirically derived energy function, the lowest energy conformation may not be the best model. We have evaluated the use of energy calculated by the fragment molecular orbital method (FMO energy) to assess the quality of predicted models and its ability to identify the best model among an ensemble of predicted models. The fragment molecular orbital method implemented in GAMESS was used to calculate the FMO energy of predicted models. When tested on eight protein targets, we found that the model ranking based on FMO energies is better than that based on empirically derived energies when there is sufficient diversity among these models. This model diversity can be estimated prior to the FMO energy calculations. Our result demonstrates that the FMO energy calculated by the fragment molecular orbital method is a practical and promising measure for the assessment of protein model quality and the selection of the best protein model among many generated.

Comparative Theoretical Study of 1,3-Dipolar Cycloadditions of Allyl-Anion Type Dipoles to Free and Pt-Bound Nitriles

1,3-Dipolar cycloadditions of a series of 12 allyl-anion type 1,3-dipoles X=Y(+)-Z(-) (X, Z = CH(2), NH, O; Y = N(Me), O) to acetonitrile MeC[triple bond]N, both free and coordinated to Pt(II) and Pt(IV) in the complexes trans-[PtCl(n)(NCMe)(2)] (n = 2, 4), were investigated by theoretical methods. The reactivity increases along the following sequence of dipoles, the first three being inert toward nitriles: ON(Me)O < NHN(Me)O < NHN(Me)NH < CH(2)N(Me)O < OOO approximately NHONH < CH(2)N(Me)NH < NHOO < CH(2)N(Me)CH(2) < CH(2)OCH(2) approximately CH(2)ONH < CH(2)OO. The thermodynamic stability of the cycloaddition products (reaction energies) inversely correlates with the activation energies with exception of dioxadiazoles N=C(Me)OO NH which cannot exist in the uncoordinated state. A complete ortho selectivity of these reactions is predicted. Coordination of MeCN to platinum accelerates the reactions of CH(2)N(Me)CH(2), CH(2)ONH, and particularly CH(2)N(Me)O and CH(2)N(Me)NH and stabilizes the corresponding products. Coordination accelerates the reactions of CH(2)OCH(2), CH(2)OO, and NHONH only slightly and inhibits the reactions of NHOO and OOO. The cycloadditions of nitrones to nitriles are potentially interesting for dynamic combinatorial chemistry. The details of the reaction mechanisms and correlations of activation and reaction energies, synchronicity, and charge transfer vs dipole nature, FMO energies, atomic charges, HSAB properties, distortion energies, and regioisomeric pathways are discussed.

Semiquantitative FMO Analysis of Substituent Effect on the Reaction of Permanganate Ion with Unsymmetrical Alkenes.

The substituent effects on the reactions of permanganate ion with unsymmetrical alkenes are analyzed on the assumption of a concerted (3 + 2) cycloaddition model by using an equation obtained by approximation based on the FMO theory in which development and localization of the frontier molecular orbitals at the reaction sites with progress of the reaction are considered. The Hammett plots are successfully reproduced with the newly obtained rate data for the reactions of trans-chalcone and its derivatives and the data for methyl cinnamates, cinnamate ions, and alkyl vinyl ethers taken from the literature using FMO energies and orbital coefficients calculated by the PM3 method. It was indicated that a factor introduced to the basic equation in order to estimate the extent of localization of the molecular orbitals at the transition state is closely related to the position of the transition state along the reaction path.

Ionic Diels-Alder Reactions

The polar cycloaddition reaction of cationic heteroaromatic dienes, the triazoloisoquinolinium ion 1 and the tetramethoxycarbonylquinolizinium ion 4 with electron-rich dienophiles was studied resembling Diels-Alder reactions with inverse electron demand. This was also substantiated by ab initio calculations of the FMO energies of the reactants; also the regio- and stereochemistry of the cycloadducts obtained are readily explained in terms of FMO theory.