Potential Energy Surface Scan Research Articles

Investigation on molecular and biomolecular spectroscopy of the novel 2BCA molecule to analyse its biological activities and binding interaction with nipah viral protein

The molecule of 2-Biphenyl Carboxylic Acid (2BCA), which contains peculiar features, was explored making use of density functional theory (DFT) and experimental approaches in the area of quantum computational research. The optimised structure, atomic charges, vibrational frequencies, electrical properties, electrostatic potential surface (ESP), natural bond orbital analysis and potential energy surface (PES) were obtained applying the B3LYP approach with the 6–311++ G (d,p) basis set.. The 2BCA molecule was examined for possible conformers using a PES scan. The methods applied for spectral analyses included FT-IR, FT-RAMAN, NMR, and UV–Vis results. Vibrational frequencies for all typical modes of vibration were found using the Potential Energy Distribution (PED) data. The UV–Vis spectrum was simulated using the TD-DFT technique, which is also seen empirically. The Gauge-Invariant Atomic Orbital (GIAO) approach was employed to model and study the 13C and 1H NMR spectra of the 2BCA molecule in a CDCL3 solution. The spectra were then exploited experimentally to establish their chemical shifts. To predict the donor and acceptor interaction, the NBO analysis was used. The electrostatic potential surface was employed to anticipate the locations of nucleophilic and electrophilic sites. Hirshfeld surfaces and their related fingerprint plots are exploited for the investigation of intermolecular interactions. Reduced Density Gradient (RDG) helps to measure and illustrate electron correlation effects, offering precise insights into chemical bonding, reactivity, and the electronic structure of 2BCA. According to Lipinski and Veber’s drug similarity criteria, 2BCA exhibits the typical physicochemical and pharmacokinetic properties that make it a potential oral pharmaceutical candidate. According to the findings of a molecular docking study, the 2BCA molecule has promise as a treatment agent for the Nipah virus (PDB ID: 6 EB9), which causes severe respiratory and neurological symptoms in humans.

Dissociation Constant of Di‐ and Tri‐Basic Solvents Based on Piperazine and Its Derivatives for Post‐Combustion CO2 Capture

AbstractAmine solvents remain popular in the industries for post combustion carbon dioxide (CO2) capture. Dissociation constant of basic amine solvents plays significant role to influence the CO2 absorption. It is thus important to study the dissociation of new amine solvents for assessing their viability for CO2 capture. In the present work, potentiometric titration method is employed to determine the dissociation constants of dibasic (e. g., Piperazine (PZ), 1‐methyl piperazine (1‐MPZ) and tribasic amines (1‐(2‐aminoethyl‐piperazine) (AEPZ) which could be promising for formulating blended solvent system towards enhancing the rate of CO2 absorption. The estimated dissociation constants for the PZ and 1‐MPZ while match well with reported results, the dissociation constants for AEPZ has been determined newly here within the temperature range 298—318 K. In addition, the structural geometric parameters and Natural Bond Order (NBO) calculations of the amine solvents are performed based on Density Functional Theory (DFT). The NBO calculations predict charge distribution on the nitrogen and other elements, and envisage its effect on the pKa values of the amines. Further, potential energy surface (PES) scanning calculations are performed for AEPZ to explain it's ring inversion which is responsible for obtaining a single pKa value in experimental studies.

Development of analytic gradients for the Huzinaga quantum embedding method and its applications to large-scale hybrid and double hybrid DFT forces.

The theory of analytic gradients is presented for the projector-based density functional theory (DFT) embedding approach utilizing the Huzinaga-equation. The advantages of the Huzinaga-equation-based formulation are demonstrated. In particular, it is shown that the projector employed does not appear in the Lagrangian, and the potential risk of numerical problems is avoided at the evaluation of the gradients. The efficient implementation of the analytic gradient theory is presented for approaches where hybrid DFT, second-order Møller-Plesset perturbation theory, or double hybrid DFT are embedded in lower-level DFT environments. To demonstrate the applicability of the method and to gain insight into its accuracy, it is applied to equilibrium geometry optimizations, transition state searches, and potential energy surface scans. Our results show that bond lengths and angles converge rapidly with the size of the embedded system. While providing structural parameters close to high-level quality for the embedded atoms, the embedding approach has the potential to relax the coordinates of the environment as well. Our demonstrations on a 171-atom zeolite and a 570-atom protein system show that the Huzinaga-equation-based embedding can accelerate (double) hybrid gradient computations by an order of magnitude with sufficient active regions and enables affordable force evaluations or geometry optimizations for molecules of hundreds of atoms.

Experimental and Theoretical Approach for the Corrosion Deceleration of Mild Steel in Hydrochloric Acid Medium by Two Sulfonamide Derivatives

AbstractIn the pursuit to find corrosion inhibitors of superior efficacy, N‐(pyrimidin‐2‐yl)‐4‐[(quinazoline‐4‐yl)amino]benzene‐1‐sulfonamide (PQS) and N‐(4‐methylpyrimidin‐2‐yl)‐4‐[(quinazoline‐4‐yl)amino]benzene‐1‐sulfonamide (MQS) are the two new sulfonamides employed, which have decelerating effect on mild steel (MS) corrosion in a medium 0.5 M HCl and were found to have an efficiency of 98.7 % and 96.8 % respectively (303 K for 40 ppm concentration) deliberated through the electrochemical techniques (PDP and EIS). The inhibitory efficacy relies on the temperature of the solution and inhibitor concentration. PQS had greater stability than MQS at higher temperatures which is indicative in the obtained experimental data. The relative adsorption process was in consonance with the Langmuir adsorption isotherm. The SEM, EDS, FT‐IR, and AFM analysis validated PQS and MQS to form a barrier on MS, opposing corrosion. The potential energy surfaces (PES) scan and a theoretical study for PQS and MQS were probed employing density functional theory (DFT) at B3LYP/6‐311+G(d, p) basis set level that explicated the formation of a complex between the sulfonamides and MS. The corrosion inhibition efficiency of PQS and MQS inferred from experimental and theoretical data comply, making them credible corrosion inhibitors.

Isomerization pathway of a C–C sigma bond in a bis(octaazamacrocycle)dinickel(II) complex activated by deprotonation: a DFT study

The anti (a) to syn (s) isomerization pathway of the deprotonated form of the dimer with two nickel(II) 15-membered octaazamacrocyclic units connected via a carbon–carbon (C–C) σ bond was investigated. For the initial anti (a) structure, a deprotonation of one of the bridging (sp3 hybridized) carbon atoms is suggested to allow for an a to s geometry twist. A 360° scan around the bridging C–C dihedral angle was performed first to find an intermediate geometry. Subsequently, the isomerization pathway was explored via individual steps using a series of mode redundant geometry optimizations (internal coordinates potential energy surface scans) and geometry relaxations leading to the s structure. The prominent geometries (intermediates) of the isomerization pathway are chosen and compared to the a and s structures, and geometry relaxations of the protonated forms of selected intermediates are considered.

Probing solution conformations of l-DOPA: Integration of experiment and simulation via vibrational optical activity

l-DOPA plays a critical role as a precursor to dopamine and is a standard treatment for Parkinson's disease. Recent research has highlighted the potential therapeutic advantages of deuterated l-DOPA analogs having a longer biological half-life. For their spectroscopic characterization, the in-detail characterization of l-DOPA itself is necessary. This article presents a thorough examination of the vibrational spectra of l-DOPA, with a particular emphasis on chirally sensitive VOA techniques. We successfully obtained high-quality Raman and ROA spectra of l-DOPA in its cationic form, under low pH conditions, and at a high concentration of 100 mg/ml. These spectra cover a broad spectral range, allowing for precise comparisons with theoretical simulations. We also obtained IR and VCD spectra, but they faced limitations due to the narrow accessible spectral region. Exploration of l-DOPA's conformational landscape revealed its intrinsic flexibility, with multiple coexisting conformations. To characterize these conformations, we employed two methods: one involved potential energy surface scans with implicit solvation, and the other utilized molecular dynamics simulations with explicit solvation. Comparing ROA spectra from different conformer groups and applying spectral decomposition proved crucial in determining the correct conformer ratios. The use of explicit solvation significantly improved the quality of the final simulated spectral profiles. The accurate determination of conformer ratios, rather than solely relying on the number of averaged spectra, played a crucial role in simulation accuracy. In conclusion, our study offers valuable insights into the structure and conformational behavior of l-DOPA and represents a valuable resource for subsequent spectroscopic studies of its deuterated analogs.

FT-IR, FT-raman and UV spectra and ab initio HF and DFT study of conformational analysis, molecular structure and properties of ortho- meta– and para–chlorophenylboronic acid isomers

In this study, the FT-IR, FT-Raman, and UV–Vis spectroscopic properties of three monosubstituted phenylboronic acid derivatives: ortho-chlorophenylboronic acid (o-ClPhBA), meta-chlorophenylboronic acid (m-ClPhBA) and para-chlorophenylboronic acid (p-ClPhBA) molecules are investigated both experimentally and theoretically using Density Functional Theory (B3LYP) and Hartree Fock (HF). In order to find the stable possible conformations of the compounds, the conformational analysis was carried out by running potential energy surface (PES) scan by means of rotation of two structural parameters, the dihedral angles indicated as φ2 (C6–B–O1–H1A) and φ3 (C6–B–O2–H2A), varying from −180° to 180° with an increment of 10° using B3LYP/6-31G level of theory. Also, to determinate the most stable conformer for all the molecules, potential energy curve (PEC) the stable possible conformations on PES scan were investigated as a function of φ1 (C1-C6–B–O1) dihedral angle from 0° up to 180° with an increment of 10° using B3LYP/6–311++G(d,p) and HF/6–311++G(d,p) level of theory. For all the studied compounds, two conformational structures (conformer anti-anti, syn-syn) that did not have imaginary frequency values outside the equilibrium state (conformer anti-syn) were detected theoretically at the both methods.Due to their conformational flexibility, the relative stabilities of the anti-syn, anti-anti, and syn-syn conformers of o-ClPhBA, m-ClPhBA, and p-ClPhBA are 0.0, 4.66, and 6.76 kcal/mol, respectively, at the B3LYP/6–311++G(d,p) level of theory. For the HF/6–311++G(d,p) level of theory, the relative stabilities are 0.00, 4.54, and 6.11 kcal/mol for o-ClPhBA; 0.00, 3.98, and 1.51 kcal/mol for m-ClPhBA; and 0.00, 4.10, and 1.44 kcal/mol for p-ClPhBA, respectively. Some of the determined stable conformations of these molecules are different in symmetry groups. It was observed that the increase in the symmetry was effective in the of molecular properties, especially for vibrational frequencies. The structural parameter, dipole moments (μ), vibrational frequencies, polarizability (α), hyperpolarizability (β), the highest occupied molecular orbital (HOMO), and the lowest unoccupied molecular orbital (LUMO) of the stable conformers were calculated by using Ab initio HF/6–311++G(d,p) and DFT/B3LYP/6–311++G(d,p) level of theory. The assignments of fundamental vibrational modes of the studied molecule were performed based on total energy distribution (TED) analysis.

Multireference and Coupled-Cluster Study of Dimethyltetroxide (MeO4Me) Formation and Decomposition.

Peroxyl radicals (RO2) are important intermediates in the atmospheric oxidation processes. The RO2 can react with other RO2 to form reactive intermediates known as tetroxides, RO4R. The reaction mechanisms of RO4R formation and its various decomposition channels have been investigated in multiple computational studies, but previous approaches have not been able to provide a unified methodology that is able to connect all relevant reactions together. An apparent difficulty in modeling the RO4R formation and its decomposition is the involvement of open-shell singlet electronic states along the reaction pathway. Modeling such electronic states requires multireference (MR) methods, which we use in the present study to investigate in detail a model reaction of MeO2 + MeO2 → MeO4Me, and its decomposition, MeO4Me → MeO + O2 + MeO, as well as the two-body product complexes MeO···O2 + MeO and MeO···MeO + O2. The used MR methods are benchmarked against relative energies of MeO2 + MeO2, MeO4Me, and MeO + MeO + O2, calculated with CCSD(T)/CBS, W2X, and W3X-L methods. We found that the calculated relative energies of the overall MeO2 + MeO2 → MeO4Me → MeO + O2 + MeO reaction are very sensitive to the chosen MR method and that the CASPT2(22e,14o)-IPEA method is able to reproduce the relative energies obtained by the various coupled-cluster methods. Furthermore, CASPT2(22e,14o)-IPEA and W3X-L results show that the MeO···O2 product complex + MeO is lower in energy than the MeO···MeO complex + O2. The formation of MeO4Me is exothermic, and its decomposition is endothermic, relative to the tetroxide. Both the formation and decomposition reactions appear to follow pathways with no saddle points. According to potential energy surface scans of the decomposition pathway, the concerted cleavage of both MeO···O bonds in MeO4Me is energetically preferred over the corresponding sequential decomposition.

Spectroscopic (FT-IR, FT-Raman, NMR and UV–vis), quantum calculation, molecular structure, solvent interaction, ADME and molecular docking investigation on 4-oxo-4h-1-benzopyran-2-carboxylic acid

The present work, spectroscopic and quantum computational study has been carried out for the molecule 4-oxo-4H-1-benzopyran-2-carboxylic acid. The stable conformer of the title molecule was identified using Potential Energy Surface (PES) scan. The structural and geometrical parameters of the stable conformer of the molecule were determined by Density Functional Theory (DFT) using B3LYP method along with the basis set 6-311++G(d,p) through Gaussian 09 W software. The theoretical and experimental investigations such as Vibrational (FT-IR and FT-Raman), UV–visible and NMR analysis were done. The FT-IR were recorded in the region of (4000–400 cm−1) and FT-Raman in the region of (4000–100 cm−1), and the vibrational bands were compared with the theoretical values. Carbon NMR and Proton NMR spectra have been analyzed in DMSO solution. The theoretical chemical shift values were determined using Gauge Independent Atomic Orbital (GIAO) method. The intermolecular and intra-molecular bonding of orbitals and transfer of charge were studied using the Natural Bond Orbital (NBO) analysis. The respective transitional study was done through UV–vis's spectra and theoretical values predicted using TD-DFT (Time Dependent – DFT) method for both gas and solvent (ethanol) state. HOMO (Highest Occupied Molecular Orbital) – LUMO (Lowest Unoccupied Molecular Orbital) energy gap results prove the exchange of charges inside the molecule. Molecular Electrostatic Potential (MEP) is used to identify the nucleophilic and electrophilic sites of the molecule. To check the bioactive nature of the title molecule the drug-likeness was determined. Molecular docking is used to analyze the biological activity of the title molecule. The distribution of torsional angles in a protein structure is viewed by the Ramachandran plots of the molecules.

Energy landscape of perylenediimide chromophoric aggregates.

Understanding the self-assembly of conjugated organic materials at the molecular level is crucial in their potential applications as active components in electronic and optoelectronic devices. The type of aggregation significantly influences the intriguing electronic and optical characteristics differing from their constituent molecules. Perylenediimides (PDIs), electron-deficient molecules exhibiting remarkable n-type semiconducting properties, are among the most explored organic fluorescent materials due to their high fluorescence efficiency, photostability, and optoelectronic properties. PDI derivatives are reported to form well-tailored supramolecular architectures: cofacial with minor slip (H-aggregates), staggered with major slip (J-aggregates), magic angle stacking (M-aggregates), rotated (X-aggregates), rotated orthogonal ((+)-aggregates), etc. H*-aggregates are defined here as an ideal case of H-aggregate with an eclipsed configuration. Although numerous reports regarding the formation and optical properties of various PDI aggregates are known, the key driving force within the PDI units guiding the self-assembly to form distinct aggregate systems remains elusive. To unravel the molecular-level mechanisms behind the self-assembly of PDI units by probing the intermolecular interactions, symmetry-adapted perturbation theory-based energy decomposition, potential energy surface scans, and non-covalent interaction index analyses were employed on PDI dimer models. Quantum theory of atoms in molecules and frontier molecular orbital analyses were implemented on the dimer models to comprehend the effect of heteroatoms and orbital interactions in stabilising the X-aggregates over the other PDI aggregate systems. Competition between the attractive and repulsive non-covalent interactions dictates a stability order of X > H > J > M > (+) > H* for the PDI aggregate system, while in the parent perylene system, the stability order was found to be X > (+) > H > M > J > H*.

Atomistically informed hierarchical modeling for revisiting the constituent structures from heredity and nano-micro mechanics of sheath-core carbon fiber.

To better understand the heterogeneous anisotropic nanocomposite features and provide reliable underlying constitutive parameters of carbon fiber for continuum-level simulations, hierarchical modeling approaches combining quantum chemistry, molecular dynamics, numerical and analytical micromechanics are employed for studying the structure-performance relationships of the precursor-inherited sheath-core carbon fiber layers. A robust debonding force field is derived from energy matching protocols, including bond dissociation enthalpy calculations and rigid-constraint potential energy surface scan. Logistic long range bond stretching curves with exponential parameters and shifted force vdW curves are designed to diminish energy perturbations. The pseudo-crystalline microstructure is proposed and validated using virtual wide angle X-ray diffraction patterns and bond-orientational order parameters. The distribution or alignment features of the nanocomposite microstructures are collected from quantum chemical topology analysis and normal vector extractions. Non-equilibrium tensile loading simulation predicts the decomposed strain energy contributions, principal-axis modulus, strength limit, localized stress, and fracture morphologies of the model. Finally, an atomistically-informed stiffness prediction model combining numerical homogenization and analytical self-consistent Eshelby-Mori-Tanaka-type effective mean field micromechanics theory is proposed, giving a successful estimation of the overall stiffness matrix of the sheath-core carbon fiber system. The hierarchical models in combination with the carbonization reaction template will help in providing efficient and feasible schemes for the synergistic process-performance control of distinct types of carbon fiber.

DFT investigation on the structural and vibrational behaviours of the non-protein amino acids in hybrid explicit/continuum solvent: a case of the zwitterions γ-aminobutyric and α - aminoisobutyric acids.

The influence of hybrid solvation models on the molecular structures and vibrational characteristics of g-aminobutyric acid (GABA) and a-aminoisobutyric acid (AIB) zwitterions was assessed by employing a variety of Density Functional Theory (DFT). The quantum chemical methods included the B3LYP and B3PW91 hybrid functionals and the 6‑311++G(d,p) basis set. The most stable conformation derived from the potential energy surface (PES) scans using the B3LYP/6-311++G(d,p) model chemistry for each studied molecule was predicted within a continuum environment represented by the COSMO and SMD solvation models. The stable structures were subsequently immersed in explicit/COSMO and explicit/SMD hybrid solvation models, where 10 and 8 water molecules were explicitly positioned around the functional groups of the GABA and AIB zwitterions, respectively. The number of water molecules chosen was sufficient to prevent proton transfer among the carboxylate group (COO-) and the ammonium group (NH3+) within each molecule under investigation. After optimizing the geometry of each hydrated complex, the normal vibrational modes were determined. The scaled theoretical frequencies obtained from the various model chemistries were then compared to available experimental data from infrared (IR) and Raman spectroscopy. In the case of GABA and AIB molecules, the comparisons revealed that the B3LYP/6-311++G(d,p) model chemistry yielded wavenumber values that closely matched the experimental IR and Raman data, particularly when the explicit/SMD solvent was employed. The computed results indicate deviations of less than 4% when compared to the experimental data for the two molecules under investigation.

A DFT Study of Solvent and Substituent Effects on the Adsorptive and Photovoltaic Properties of Some Selected Porphyrin Derivatives for DSSC Application.

A DFT/TD-DFT method was employed to study the effects of structural modification and solvent variation on the solubility, adsorptive, and photovoltaic properties of six porphyrins (A-F) obtained by structurally modifying two literature porphyrins A and D. The properties of interest were studied in vacuum, acetonitrile (AcCN), dichloromethane (DCM), dimethyl sulphoxide (DMSO), and ethanol (EtOH) for possible application of the molecules as sensitizers in dye-sensitized solar cells (DSSCs). Electronic absorption properties of the molecules were computed via potential energy surface scan, and thermodynamic data were obtained by DFT calculations in the selected media. Solubility properties of the molecules were mostly enhanced with DMSO as the solvent. The adsorptivity of the molecules onto mesoporous titanium (IV) oxide surface were predicted to be enhanced in the presence of DMSO. Most of the molecules were found to exhibit their highest photovoltaic activity measured in terms of the incidentphoton conversion efficiency (IPCE) in AcCN and DCM, rather than in DMSO due to its high viscosity and the ability to use its oxygen to form the catenating O-Ti4+ bond with the Ti4+ of the TiO2, causing inhibition of electron movement on the semiconductor surface. In general, the computed photovoltaic (PV) properties were found to be enhanced with -CO2H group as the substituent, and in AcCN or DCM as the solvent.

Molecular structure, physicochemical properties, impact of solvents ionization potential, electron occupancy, inhibition constant, and stabilization energy investigations of 4-acetamido benzoic acid

A novel heterocyclic organic compound, 4-Acetamido benzoic acid (4AMBA) had a wide range of applications in the field of drug discovery arena. The molecular structural stability conformation had been carried out using the Molecular Potential Energy Surface (MPES) scan with chosen suitable dihedral angle. For both the calculated and experimental procedures, the identifications of the chemical bonds of pertinent functional groups were investigated using spectral measurements (FT-IR and FT-Raman). The DFT/B3LYP/6–311++G(d,p) basis set, which is a highly compatible technique, was implemented to execute the quantum computational studies. Further, to enhance the molecular (inter and intra) interactions, reactivity regions between the atoms were performed using reactivity sites such as MEP, NBO, NLMO, NHO, and Hirshfeld surface analysis. In addition, the topological analysis for the various solvents and the electronic properties of the appropriate wavelength, the energy gap of the UV–Visible spectrum (both theoretical (various solvents) and experimental), FMO theories (HOMO and LUMO) energies and topological analyses were attained. The significant features that explain the biological behavior of the header composite were computed with the least possible binding energy using protein-ligand interactions with appropriate protein receptors, such as 1J1R, 1G1K, and 1J1Q.

Computational Analysis of Excited State Intramolecular Hydrogen Atom Transfer and Microsolvation Studies on 8-Acetyl-7-hydroxy-4-methylcoumarin using DFT and TDDFT

The computational calculations were carried out on 8-acetyl-7-hydroxy-4-methyl coumarin (AHM) and its water complex AHM+(H2O)4- [AHMH] at ground and excited states by employing density functional theory (DFT)/specific state time-dependent density functional theory (SS-TDDFT). In AHM and AHMH molecules, there is an intramolecular hydrogen bond between hydroxyl group and acetyl group along with inter-molecular hydrogen bonds in the hydrated molecule. The computational studies of molecular structural parameters, molecular electrostatic potential, natural bond orbital (NBO) analysis, the molecular orbital’s and UV-Vis spectra of both the molecules under polar solvents were explored by B3LYP/cc-pVDZ/PCM/EFP1 method. The intramolecular hydrogen atom transpired between hydroxyl to acetyl group in AHM/AHMH molecules from S0→S1 state but not in S0→S3/S0→S2 states even though the S3/S2 states have significant oscillation strengths. This indicates that intramolecular chage transfer (ICT) occurs within the molecules and it confirmed using potential energy surface (PES) scan studies.

Theoretical Investigations of the Crystal Structures and Molecular Energetics of High Quality Silicon Carbide (β-SiC) Precursor Compound 1,4-bis(trimethylsilyl)benzene

Over the last decades, the rapidly growing theoretical methods have revolutionized whole scientific paradigm, developed state-of-art analyses, and created substantial computational platforms through the huge support of outstanding mathematical algorithms. The self-consistent-charge density-functional based tight-binding (SCC-DFTB) scheme is one of them that offers versatile and efficient quantum mechanical calculations with some unique features compatible especially to the crystalline solid even at low computational resources. Its effective parametrizations and computational implementations under the Gaussian standardized interface as an "External program" via the users' script (Gaussian- External methodology; GEM) has added an additional value because of which various in-built high-level Gaussian computations are directly accessible. Herewith, the Gaussian offered geometry optimization algorithms and convergence criteria plus the ModRedundant type relaxed potential energy surface (PES) scanning techniques are assessed through the GEM, and characterized the crystal structures with concerned molecular energetics and PES of the experimentally synthesized 1,4-bis (trimethylsilyl) benzene (1,4-BTMSB) compound; a potential precursor for the high quality Silicon Carbide (β-SiC) coating particles, and an ideal "Internal Standard" for the quantitative spectroscopic analyses. The general results reveal that the 1,4- BTMSB molecules in its unit-cell and crystal lattice experience significant non-bonding interactions that induces them to attain the definite molecular geometry with recognizable ring, angle, torsional, and steric strains. The quantitative analyses of its PES depict that the phenylene ring has to overcome multiple yet unidentical energy barriers with the tallest Ea1= 5.3 kcal/mol in order to undergo internal 2π angular rotation around the 1,4-(C-Si) axes. And, exhibiting such type internal rotation of its phenylene ring is energetically highly probable as this compound is widely employed in coating high temperature reactors, and in quantizing analyte in high energy run spectroscopic facilities. The same quantification is referred here in order to underscore the significance of adopting perfectly closed topological molecular architectures while designing/synthesizing amphidynamic type crystalline free molecular gyrotops and their prototypes.

Quantum computational, spectroscopic, ADMET, molecular docking and dynamics simulation revealing the inhibition of psoralidin against anti-tuberculosis

A linear, three-ring phenolic compound containing a free radical reported pharmacological effects against the anti-tuberculosis (TB) disease. In our study, psoralidin, or 3,9-dihydroxy-2-prenylcoumestan (PSR) compound, was characterized. The bioactive conformer was recognized through the potential energy surface scan (PES) analysis. The optimized and spectroscopic profiles were computed by using the DFT / B3LYP method with the 6–311++G (d,p) basis set, and their outcomes were correlated with the experimental ones. The HOMO-LUMO, MEP, and quantum chemical parameters are also calculated. The screened compounds that confirmed a better drug-likeness score were more thoroughly analyzed for pharmacological properties and Lipinski's rule of 5, and the results were calculated and discussed. The title ligand may block or inhibit the activity of Mycobacterium tuberculosis protein kinase B (PknB), acting as an anti-tuberculosis agent, when it binds at the macromolecule's active site, in accordance with molecular docking analyses. Using the Autodock program, the binding affinity of PSR was calculated as -9.0 kcal/mol. For 100 ns, MD simulations were executed to predict the RMSF, H-bonds, RMSD, and interaction energy analyses.

Density Functional Theory (DFT) Study of Methyl 2-methoxycyclohex-3-ene-1-carboxylate for structure optimization, transition state, vibrational, electronic and PES scan

The current investigation is carried out to study stability of Diels-Alder adduct methyl 2-methoxycyclohex-3-ene-1 where (a) and (e) represent axial and equatorial orientation of group .The region-selective mechanism of Diels-Alder reaction between 1-methoxy 1,3butadiene (1) and methyl acrylate (2) to give methyl 2-methoxycyclohex-3-ene-1-carboxylate (3) is studied using Density Functional Theory (DFT). There are three possible stereo-chemical products possible for this reaction such as axial-axial (a,a), equatorial-equatorial (e,e) and axial-equatorial (a,e). Density Functional Theory was carried out to study the optimized molecular structure and the Potential Energy Surface (PES) Scan. The Frontier Molecular Orbital (FMO) energy calculations were carried out and HOMO LUMO energy gap was calculated to analyse the stability and reactivity. The Molecular Electrostatic Potential (MEP) study was carried out to analyse the surface of the molecule. FTIR spectra show the vibrational analysis of molecule.

Structural (monomer and dimer), spectroscopic (FT-IR, FT-Raman, UV–Vis and NMR) and solvent effect (polar and nonpolar) studies of 2‑methoxy-4-vinyl phenol

The structural aspects of 2‑methoxy-4-vinyl phenol (2M4VP) were examined by analyzing both the monomeric and dimeric forms of the highly stable conformer, which were found through a Potential Energy Surface (PES) scan at 170° with energy minima of 0.191 kcal/mol. Experimental and theoretical methods were employed to investigate the spectroscopic properties, including vibrational assignments, electronic transitions, and chemical shifts. Simulating the frontier molecular orbitals (FMO) in different solvents, both polar and non-polar, provides insights into the energy gap (3.9306 eV in chloroform, 3.9059 eV in water, 3.9054 eV in DMSO, and 3.9086 eV in ethanol) and chemical stability. Furthermore, the Natural Bonding Orbitals (NBO), Mulliken population, and Molecular Electrostatic Potential (MESP) surfaces were carried out to get insights into charge distribution, intra-molecular, inter-molecular interactions, and stabilization energies. The majority of the experimental data exhibit a strong correlation with the theoretical values, thereby confirming the highly stable structure of 2M4VP.

Spectroscopic investigations, quantum chemical, drug likeness and molecular docking studies of methyl 1-methyl-4-nitro-pyrrole-2-carboxylate: A novel ovarian cancer drug

Density functional theory (DFT) calculation was used to analyse the structural and vibrational properties of Methyl 1-Methyl-4-nitro-pyrrole-2-carboxylate (MMNPC) using the cc-pVTZ basis set. The potential energy surface scan and the most stable molecular structure were optimized using Gaussian 09 program. A potential energy distribution calculation was used to calculate and assign vibrational frequencies using the VEDA 4.0 program package. The Frontier Molecular Orbitals (FMOs) were analysed to determine their related molecular properties. Ab initio density functional theory (B3LYP/cc-pVTZ) method with basis set was used to calculate 13C NMR chemical shift values of MMNPC in the ground state. Fukui function and molecular electrostatic potential (MEP) analysis confirmed the bioactivity of the MMNPC molecule. The charge delocalization and stability of the title compound were studied using natural bond orbital analysis. All experimental spectral values from FT-IR, FT-Raman, UV–VIS, and 13C NMR are in good agreement with the value calculated by the DFT. Molecular docking analysis was carried out to find the MMNPC compound that can be used as a potential drug development candidate for ovarian cancer.