Molecular structure and spectroscopic properties of polyaromatic heterocycles by first principle calculations: spectroscopic shifts with the adsorption of thiophene on phyllosilicate surface

Exploring quantum computational, molecular docking, and molecular dynamics simulation with MMGBSA studies of ethyl-2-amino-4-methyl thiophene-3-carboxylate

2-aminothiophenes derivative, Ethyl-2-amino-4-methyl thiophene-3-carboxylate (EAMC) has been synthesized, characterized, and investigated quantum chemically. It was experimentally investigated by different spectroscopic methods like- NMR (1H-NMR and 13C-NMR), FT-IR, and UV-Visible. B3LYP method and 6-311++G(d,p) basis set were employed for optimization of molecular structure and calculation of wave numbers of normal modes of vibrations and various other important parameters. Calculated bond lengths and angles were compared with the experimental bond lengths and Bond Angle Parameters. Optimized bond parameters and experimental bond parameters were found in good agreement. Complete potential energy distribution assignments were done successfully by VEDA. The HOMO/LUMO energy gap emphasizes adequate charge transfer happening within the molecule. A study of donor-acceptor interconnections was done via NBO analysis. MEP surface analysis was done to demonstrate charge distribution and reactive areas qualitatively in the molecule. The degree of relative localization of electrons was analyzed via ELF Diagram. The Fukui function analysis showed possible sites for attacks by different substituents. By using the TD-DFT method and PCM solvent model, the UV-Vis spectrum (gas, methanol, DMSO) and the maximum absorption wavelength was computed and compared with experimental data. 3D and 2D intermolecular interactions in the crystal were analyzed via Hirshfeld surface analysis and fingerprint plots reveal that the EAMC crystal was stabilized by H--H/H--H/C--H bond formation. The molecular docking was done with 7 different protein receptors on the molecule to find the best ligand-protein interactions. Molecular dynamic simulations and MMGBSA calculations were also carried out to find out the best binding of the ligand with the protein.Communicated by Ramaswamy H. Sarma.

The on-and-off dynamics of thiophene on a nickel cluster enables efficient hydrodesulfurization and excellent stability at high temperatures

Despite significant advances in the synthesis and structural determination of atomically precise metal clusters, few studies have explored their catalytic applications in industrially important reactions. Here, we report a thiolate-stabilized Ni cluster for the efficient hydrodesulfurization of thiophene under relatively harsh reaction conditions while maintaining its atomic structure, which was enabled by the on-and-off dynamic state of thiophene on the cluster. Through a combined experimental and theoretical approach, we elucidate the activated structure and the catalytic mechanism. The study highlights the great potential of structurally precise clusters for practical industrial applications.

Molecular Modeling of Adsorption of 5-Aminosalicylic Acid in the Halloysite Nanotube

Halloysite nanotubes are becoming interesting materials for drug delivery. The knowledge of surface interactions is important for optimizing this application. The aim of this work is to perform a computational study of the interaction between 5-aminosalicylic acid (5-ASA) drug and halloysite nanotubes for the development of modified drug delivery systems. The optimization of this nanotube and the adsorption of different conformers of the 5-ASA drug on the internal surface of halloysite in the presence and absence of water were performed using quantum mechanical calculations by using Density Functional Theory (DFT) and methods based on atomistic force fields for molecular modeling, respectively.

A DFT study of the adsorption of glycine in the interlayer space of montmorillonite

The adsorption properties of clay minerals have been widely studied in several technological areas, due to their versatility, absorption capacity and catalytic properties. The interaction of amino acids with clay surfaces can be interesting due to their role in prebiotic scenarios. Different degrees of hydration and the adsorption of the glycine molecule and glycinium cation in the interlayer space of montmorillonite were investigated by means of calculations based on density functional theory (DFT). Our calculations show that the cation exchange of K⁺ by glycinium in the interlayer of hydrated K-montmorillonite is highly possible and exothermic. This supports previous experimental results by explaining the possible adsorption of glycine as a molecule and cation. Glycine is adsorbed in a zwitterionic form in the interlayer without being solvated with water. Besides, glycine and glycinium are highly exothermically adsorbed in the interlayer. The interlayer spacings under different conditions were in agreement with the experimental values. Hydrogen bonds and electrostatic interactions between molecules and surface atoms are responsible for this exothermicity. The IR spectra were calculated and compared with the experimental results showing interesting frequency shifts depending on the intermolecular interactions in the interlayer space of montmorillonite.

Modeling the Adsorption of Oxalate onto Montmorillonite

In this work, a multiscale modeling of the interaction of oxalate with clay mineral surfaces from macroscale thermodynamic equilibria simulations to atomistic calculations is presented. Previous results from macroscopic adsorption data of oxalate on montmorillonite in 0.01 M KNO3 media at 25 °C within the pH range from 2.5 to 9 have been used to develop a surface complexation model. The experimental adsorption edge data were fitted using the triple-layer model (TLM) with the aid of the FITEQL 4.0 computer program. Surface complexation of oxalate is described by two reactions: >AlOH + Ox(2-) + 2H(+) = >AlOxH + H2O (log K = 14.39) and >AlOH + Ox(2-) + H(+) = >AlOx(-) + H2O (log K = 10.39). The monodentate complex >AlOxH dominated adsorption below pH 4, and the bidentate complex >AlOx(-) was predominant at higher pH values. Both of the proposed inner-sphere oxalate species are qualitatively consistent with previously published diffuse reflectance FTIR spectroscopic results for oxalate on montmorillonite edge surface (Chem. Geol. 2014, 363, 283-292). Atomistic computational studies have been performed to understand the interactions at the molecular level between adsorbates and mineral surface, showing the atomic structures and IR frequency shifts of the adsorption complexes of oxalate with the edge surface of a periodic montmorillonite model.

The covalence and infrared spectra of cationic hydrogen bonds and dihydrogen bonds

A theoretical study of hydrogen bonds and dihydrogen bonds formed by ethyl cation, hydrocarbons and magnesium hydride is presented with calculations performed at the BHandHLYP/6-31G(d,p) level of theory. The structural results and IR analyses demonstrated great insights, mainly the strengthening and weakness of the CC bond of the ethyl cation and π or pseudo-π bonds, respectively. The interaction strength was measured through the supermolecule as well as by means of additional approaches. The QTAIM calculations were applied to characterize not only the intermolecular interactions but specifically the covalent character in the H + ⋯ π, H + ⋯ pseudo-π and H + ⋯ H contacts. The NBO calculations were useful to interpret the polarization on the CC bond and whether this effect is related with the bond length reduction as well as increase of charge density and frequency shifts.

Molecular structure, vibrational spectra, AIM, HOMO-LUMO, NBO, UV, first order hyperpolarizability, analysis of 3-thiophenecarboxylic acid monomer and dimer by Hartree-Fock and density functional theory

In this work, the molecular structure, harmonic vibrational frequencies, UV, NBO and AIM of 3-thiophenecarboxilic acid (abbreviated as 3-TCA) monomer and dimer has been investigated. The FT-IR and FT-Raman spectra were recorded. The ground-state molecular geometry and vibrational frequencies have been calculated by using the Hartree-Fock (HF) and density functional theory (DFT)/B3LYP methods and 6-311++G(d,p) as a basis set. The fundamental vibrations were assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with VEDA program. Comparison of the observed fundamental vibrational frequencies of 3-TCA with calculated results by HF and DFT methods indicates that B3LYP is better to HF method for molecular vibrational problems. The difference between the observed and scaled wavenumber values is very small. The theoretically predicted FT-IR and FT-Raman spectra of the title compound have been constructed. A study on the Mulliken atomic charges, the electronic properties were performed by time-dependent DFT (TD-DFT) approach, frontier molecular orbitals (HOMO-LUMO), molecular electrostatic potential (MEP) and thermodynamic properties have been performed. The electric dipole moment (μ) and the first hyperpolarizability (β) values of the investigated molecule have been also computed.

Experimental (FT-IR, NMR and UV) and theoretical (M06-2X and DFT) investigation, and frequency estimation analyses on (E)-3-(4-bromo-5-methylthiophen-2-yl)acrylonitrile

The spectroscopic properties of (E)-3-(4-bromo-5-methylthiophen-2-yl)acrylonitrile have been investigated by FT-IR, UV, (1)H and (13)C NMR techniques. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths and angles) have been calculated using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr) and DFT/M06-2X (the highly parameterized, empirical exchange correlation function) quantum chemical methods with 6-311++G(d,p) basis set by Gaussian 03 software, for the first time. The assignments of the vibrational frequencies have been carried out by potential energy distribution (PED) analysis by using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies were in good agreement with the corresponding experimental data, and with the results in the literature. (1)H and (13)C NMR chemical shifts were calculated by using the gauge-invariant atomic orbital (GIAO) method. The electronic properties, such as excitation energies, oscillator strength wavelengths were performed by B3LYP methods. In addition, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energies and the other related molecular energy values have been calculated and depicted.

Vibrational frequency analysis, FT-IR, DFT and M06-2X studies on tert-Butyl N-(thiophen-2yl)carbamate

In this study, the experimental and theoretical vibrational frequencies of a newly synthesized tert-Butyl N-(thiophen-2yl)carbamate have been investigated. The experimental FT-IR (4000-400 cm(-1)) spectrum of the molecule in the solid phase have been recorded. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths and bond angles) have been calculated by using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr) and DFT/M06-2X (the highly parametrized, empirical exchange correlation function) quantum chemical methods with the 6-311++G(d,p) basis set by Gaussian 09W software, for the first time. The vibrational frequencies have been assigned using potential energy distribution (PED) analysis by using VEDA 4 software. The computational optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data, and with related literature results. In addition, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energies and the other related molecular energy values have been calculated and are depicted.

Molecular structure, spectroscopic characterization (FT-IR, FT-Raman, UV and NMR), HOMO and LUMO analysis of 3-ethynylthiophene with DFT quantum chemical calculations

In this work, FT-IR, FT-Raman, UV and NMR spectra of 3-ethynylthiophene (3-ETP, C6H4S) were carried out by using density functional theory DFT/B3LYP method with the 6-311++G(d,p), 6-311+G(d,p), 6-311G(d,p), 6-31++G(d,p), 6-31+G(d,p), 6-31G(d,p) basis sets. FT-IR and FT-Raman spectra were recorded in the regions of 3500-400cm(-1) and 3500-50cm(-1), respectively. The geometrical parameters, energies and wavenumbers were obtained and the complete assignments of fundamental vibrations were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. The (1)H, (13)C and HMQC ((1)H-(13)C correlation) NMR spectra in chloroform (CDCl3) were recorded and calculated. The UV spectrum of investigated compound were recorded in the region of 200-400nm in ethanol solution. The electronic properties, such as excitation energies, absorption wavelengths, HOMO and LUMO energies were performed by DFT/B3LYP approach and the results were compared with experimental observations. The thermodynamic properties such zero-point vibrational energy, thermal energy, specific heat capacity, rotational constants, entropy, and dipole moment of the studied compound were calculated. As a result, the calculated results were compared with the observed data and found to be in good agreement.