Quantum Mechanical Force Field Research Articles

FTIR, FTRaman, UV–Visible and NMR spectroscopic studies on 3,3′,4,4′-tetrachloroazoxybenzene, an azoxybenzene derivative with toxic effects

We have synthesized 3,3′,4,4′ Tetrachloroazoxybenzene (TCAOB) and, later, characterized it by using infrared, Raman, 1H, 13C NMR and UV–visible spectroscopies. The structural, topological and vibrational properties of four Cis and three Trans isomers were theoretically predicted by using the hybrid B3LYP together with the 6-31G* and 6-311++G** basis sets. The 69 normal modes of vibration for all TCAOB isomers were assigned by using the scaled quantum mechanical force field (SQMFF) procedure and their experimental vibrational spectra and normal internal coordinates. The high stabilities of all Cis and Trans isomers are supported by the π→π*, n→σ*, n→π* and π*→π* electronic transitions calculated by NBO studies while the AIM analyses reveal for the Trans forms the existence of intra-molecular CH⋯O hydrogen bonds, as suggested by the broad IR band observed in the higher wavenumbers region. The low gap energy for the Trans I isomer supports their higher reactivity probably due to the repulsion of the more electronegative Cl and O atoms as a consequence of their proximities. In addition, the force constants for all Cis and Trans isomers were calculated by using both levels of theory. Here, the comparisons of the predicted IR, Raman, NMR and ultraviolet–visible spectra with the corresponding experimental ones demonstrate good concordances. The existence of the NO groups in all TCAOB isomers support the differences in their properties, as compared with those reported for TCAB.

Synthesis, X-ray Single Crystal Structure, Molecular Docking and DFT Computations on N-[(1E)-1-(2H-1,3-Benzodioxol-5-yl)-3-(1H-imidazol-1-yl)propylidene]-hydroxylamine: A New Potential Antifungal Agent Precursor.

Mycoses are serious health problem, especially in immunocompromised individuals. A new imidazole-bearing compound containing an oxime functionality was synthesized and characterized with different spectroscopic techniques to be used for the preparation of new antifungal agents. The stereochemistry of the oxime double bond was unequivocally determined via the single crystal X-ray technique. The title compound 4, C13H13N3O3·C3H8O, crystallizes in the monoclinic space group P21with a = 9.0963(3) Å, b = 14.7244(6) Å, c = 10.7035(4) Å, β = 94.298 (3)°, V = 1429.57(9) Å3, Z = 2. The molecules were packed in the crystal structure by eight intermolecular hydrogen bond interactions. A comprehensive spectral analysis of the title molecule 4 has been performed based on the scaled quantum mechanical (SQM) force field obtained by density-functional theory (DFT) calculations. A molecular docking study illustrated the binding mode of the title compound 4 into its target protein. The preliminary antifungal activity of the title compound 4 was determined using a broth microdilution assay.

Adsorption of Sulfonamides on Phyllosilicate Surfaces by Molecular Modeling Calculations

Sulfamides belong to a great group of antibiotics used for decades for human therapeutics and farm livestock. This intensive use has generated an important environmental risk due to the presence of these compounds in wastewaters and soils close to worldwide farm industries. The molecular structure and physicochemical properties of these molecules are interesting for evaluating the molecular interactions with surfaces of clay minerals. These interactions are important to know the mobility of these compounds through soils and to design new nanomaterials for drug delivery. The molecular structure and conformational analysis of the sulfonamides, sulfamethoxypyridazine and sulfamethoxydiazine, as models of sulfonamides, have been studied with quantum mechanical calculations and force fields based on empirical interatomic potentials calculations. The adsorption of these drugs on a phyllosilicate surface of (001) plane has been investigated, finding that it is an exothermic process for both sulfonamides.

Spectroscopic and theoretical studies of 2-acetylbenzo[b]selenophen-3(2H)-one

In the present study, the FT-IR spectrum of 2-acetylbenzo[b]selenophen-3(2H)-one (2ACSeP, C10H8O2Se) has been recorded in the range of 4000–400 cm−1. The molecular structure of 2ACSeP in the ground state has been investigated by the density functional method (B3PW91) with 6-31G(d,p), 6-311G(d,p), 6-311G(2df,p) and 6-311G(3df,3pd) basis sets. From the potential energy surface calculation, there are two conformers, s-cis and s-trans for this molecule. The computational results diagnose the most stable conformer of 2ACSeP as the s-trans form. Making use of the recorded data, the complete vibrational assignments are made and analysis of the observed fundamental bands of molecule is carried out. The complete assignments are performed on the basis of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMF). The molecular stability and bond strength were investigated by applying the natural bond orbital analysis (NBO) and natural localized molecular orbital (NLMO) analysis. The electronic properties, such as excitation energies, absorption wavelength, HOMO and LUMO energies were performed by the time dependent DFT (TD-DFT) approach. The 1H and 13C nuclear magnetic resonance chemical shifts of the molecule were calculated using the gauge-including atomic orbital (GIAO) method and compared with experimental results.

A Fundamental Study of Nano Electrodeposition Using a Combined Molecular Dynamics and Quantum Mechanical Electron Force Field Approach

Nano electrochemical additive manufacturing (Nano ECAM) is an emerging technology that combines the trends of miniaturization and additive manufacturing to fabricate complex 3D parts at the nano scale. A combined molecular dynamics and quantum mechanical electron force field approach is used in this work to study the electrochemical and physical input parameter effects on output deposition behavior to obtain fundamental understanding of Nano ECAM process. It was found that electron tunneling behavior occurs below a threshold interelectrode gap (IEG), which is not solvable by reducing the current. This tunneling would mean the electrons were not available to cause the electrolyte ions to deposit onto the substrate. Additionally, if the IEG was too high and the current was too low, the input electrons and cations from the electrolyte would combine and remain in a constant position near but not adsorbed to the surface. Furthermore, the effects of varying Watt's bath concentration were studied. It was found that there was an ideal concentration to perform Nano ECAM at, with values above and below causing deposition to occur less quickly and less efficiently. Finally, the work reported in this paper provides a very valuable computational framework for predicting the ECAM process results for subsequent experimental verification.

Structural properties and FTIR-Raman spectra of the anti-hypertensive clonidine hydrochloride agent and their dimeric species

The structural and vibrational properties of the α-adrenergic agonist clonidine hydrochloride agent and their anionic and dimeric species were studied combining the experimental FT-IR and Raman spectra in solid phase with ab-initio calculations based on the density functional theory (DFT). All the calculations were performed by using the hybrid B3LYP with the 6-31G* and 6-311++G** basis sets. The structural properties for those species were studied employing the Natural Bond Orbital (NBO), Atoms in Molecules theory (AIM) and frontier orbitals calculations. The complete assignments of the FTIR and Raman spectra were performed combining the DFT calculations with the Pulay's Scaled Quantum Mechanics Force Field (SQMFF) methodology. Very good concordances between the theoretical and experimental spectra were found. In addition, the force constants for those three species were computed and compared with the values reported for similar antihypertensive agents. The ionic nature of the H→Cl bond and the high value of the LP(1)N4 → LP*(1)H18 charge transfer could explain the high reactivity of clonidine hydrochloride in relation to other antihypertensive agent and the strong shifthing of the band assigned to the NH stretching mode linked to the HCl bond toward lower wavenumbers.

Theoretical and experimental study of a new thiosulfonate derivative: Methyl trifluoromethanethiosulfonate, CF3SO2SCH3. Conformational transferability in CX3SO2S-R compounds

Methyl trifluoromethanethiosulfonate, CF3SO2SCH3, was synthesized and characterized by 13C NMR, 19F NMR, and vibrational spectroscopy. This structural study was supported by MP2 and DFT (B3LYP and MPW1PW91) calculations, which revealed a strong dependence of the theoretical structure on the polarization of the basis set. Theoretical data indicate that only one conformer, gauche, is predicted by rotating around the S–S bond. This conformational preference was studied using the total energy scheme and natural bond orbital partition scheme. These results evidence that electron delocalization and especially LP S→σ∗ C(1)-S interactions play an interesting role in the reactivity-structure connection of oxoesters and thioesters.Gas and liquid infrared and liquid Raman spectra were recorded and assigned. The experimental vibrational data along with theoretical force constants (B3LYP) were used to define a scaled quantum mechanical force field, which enabled the reproduction of the measured frequencies with a final root-mean-square deviation of 8.06cm−1.

The effects of conformation and zwitterionic tautomerism on the structural and vibrational spectral data of anserine

In this study, the stable conformers of neutral anserine were searched by molecular dynamics simulations and energy minimization calculations using the MM2 force field. Thermochemical calculations at B3LYP/6-31G(d) level of theory followed these preliminary calculations. The results confirmed that neutral anserine has quite a flexible structure and many stable gauche and trans conformers at room temperature. Nevertheless, two are considerably more favourable in energy than the others and expected to dominate the gas-phase and matrix IR spectra of the molecule. The corresponding structural and vibrational spectral data for these two conformers of neutral anserine, whose relative stabilities were also examined by high-accuracy energy calculations carried out using G3MP2B3 method, and for the most stable conformer of anserine in zwitterion form were calculated at B3LYP/6-311++G(d,p) level of theory. The calculated harmonic force constants were refined using the Scaled Quantum Mechanical Force Field (SQM-FF) method and then used to produce the refined wavenumbers, potential energy distributions (PEDs) and IR and Raman intensities. These refined data together with the scaled harmonic wavenumbers obtained using another method, Dual Scale factors (DS), enabled us to correctly analyse the observed IR and Raman spectra of anserine and revealed the effects of conformation and zwitterionic tautomerism on its structural and vibrational spectral data.

Synthesis, characterization, computational studies, antimicrobial activities and carbonic anhydrase inhibitor effects of 2-hydroxy acetophenone-N-methyl p-toluenesulfonylhydrazone and its Co(II), Pd(II), Pt(II) complexes

2-Hydroxyacetophenone-N-methyl p-toluenesulfonylhydrazone (afptsmh) derived from p-toluenesulfonicacid-1-methylhydrazide (ptsmh) and its Co(II), Pd(II), Pt(II) complexes were synthesized for the first time. Synthesized compounds were characterized by spectroscopic methods (FT-IR, 1H13C NMR, LC-MS, UV–vis), magnetic susceptibility and conductivity measurements. 1H and 13C shielding tensors for crystal structure of ligand were calculated with GIAO/DFT/B3LYP/6-311++G(d,p) methods in CDCl3. The vibrational band assignments were performed at B3LYP/6-311++G(d,p) theory level combined with scaled quantum mechanics force field (SQMFF) methodology. The antibacterial activities of synthesized compounds were studied against some Gram positive and Gram negative bacteria by using microdilution and disc diffusion methods. In vitro enzyme inhibitory effects of the compounds were measured by UV–vis spectrophotometer. The enzyme activities against human carbonic anhydrase II (hCA II) were evaluated as IC50 (the half maximal inhibitory concentration) values. It was found that afptsmh and its metal complexes have inhibitory effects on hCA II isoenzyme. General esterase activities were determined using alpha and beta naphtyl acetate substrates (α- and β-NAs) of Drosophila melanogaster (D. melanogaster). Activity results show that afptsmh does not strongly affect the bacteria strains and also shows poor inhibitory activity against hCAII isoenzyme whereas all complexes posses higher biological activities.

РАСЧЕТ МАСШТАБИРУЮЩИХ МНОЖИТЕЛЕЙ ДЛЯ КВАНТОВО-МЕХАНИЧЕСКИХ СИЛОВЫХ ПОЛЕЙ

РАСЧЕТ МАСШТАБИРУЮЩИХ МНОЖИТЕЛЕЙ ДЛЯ КВАНТОВО-МЕХАНИЧЕСКИХ СИЛОВЫХ ПОЛЕЙ

An experimental and theoretical vibrational study of 3,3,6,6-tetramethyl-1,2,4,5-tetrathiane

3,3,6,6-tetrametyl-1,2,4,5-tetrathiane, [(CH3)2CS2]2, was prepared and the corresponding infrared and Raman spectra were measured. The observed bands were assigned to the different normal modes of vibration after a DFT calculation of the molecular vibrational properties. The experimental vibrational data and the corresponding assignments were subsequently used as a basis for the definition of a scaled quantum mechanics (SQM) force field for the studied molecule. A comparison of force constants and geometrical parameters was made with related molecules.

Raman and SERS study of N-acetyl-5-methoxytryptamine, melatonin—The influence of the different molecular fragments on the SERS effect

In this work a detailed experimental Raman and SERS study on melatonin is reported. Additional density functional theory (DFT) with the hybrid exchange-correlation functional B3LYP, in combination with the 6-311++G(d,p) basis set have been performed. Scaled quantum mechanical force field (SQM FF) method for the prediction of the vibrational spectra is used to determine the geometrical, energetic and vibrational characteristics of the molecule. The DFT-computed structural parameters and harmonic vibrational wavenumbers reproduce the experimental data very well and help to characterize the vibrational behaviour of the adsorbed species. The assignment of the normal modes obtained by calculations was supported by previous vibrational studies on the distinct functional groups present in melatonin. The SERS study was carried out with particular emphasis on the interaction and adsorption of the different parts of the molecule to the gold colloidal surface. Furthermore, the adsorption behavior of melatonin on colloidal Au surface is deduced from the SERS selection rules and analysis of the calculated molecular electrostatic potential (MEP).

Synthesis, crystal structure, vibrational spectral analysis and Z-scan studies of a new organic crystal N,N′dimethylurea ninhydrin: A scaled quantum mechanical force field study

A new organic material, N,N′dimethylurea ninhydrin (3a,8a-dihydroxy-1,3-dimethyl-1,3,3a,8a-tetrahydroindeno[2,1-d]imidazole-2,8-dione) (NDUN) was synthesized. Structural details were obtained from single crystal X-ray diffraction (XRD) data. A detailed interpretation of the vibrational spectra is carried out with the aid of normal coordinate analysis following the scaled quantum mechanical force field methodology. TG/DTA and 1H NMR studies were carried out. Linear optical properties were studied from UV–Vis spectra. From the open aperture Z-scan data, it is found that the molecule shows third order nonlinear optical behaviour due to two photon absorption (2PA) mechanism.

Synthesis, molecular structure, FT-IR, FT-Raman and XRD spectroscopic investigations of (E)-1-(5-((4-bromophenyl)diazenyl)-2- hydroxyphenyl)ethanone: A comparative DFT study

The (E)-2-acethyl-4-(4-bromophenyldiazenyl) phenol compound was synthesized and analysed by elemental analysis, single-crystal X-ray diffraction (XRD), FT-IR and FT-Raman spectroscopies. Furthermore, vibrational spectra of this compound have been assigned by using scaled quantum mechanical force field approximation from density functional method (B3LYP) with 6-31G(d) basis set. A well-agreement has been attained between the calculated and observed spectra. Moreover, NBO analysis indicates there are strong conjugate interactions inside the molecule. Apart from this, the single-crystal structure from X-ray study has showed that this compound has a strong intramolecular O–H … O hydrogen bond and π−π stacking.

Vibrational and structural study of onopordopicrin based on the FTIR spectrum and DFT calculations

In the present work, the structural and vibrational properties of the sesquiterpene lactone onopordopicrin (OP) were studied by using infrared spectroscopy and density functional theory (DFT) calculations together with the 6-31G∗ basis set. The harmonic vibrational wavenumbers for the optimized geometry were calculated at the same level of theory. The complete assignment of the observed bands in the infrared spectrum was performed by combining the DFT calculations with Pulay’s scaled quantum mechanical force field (SQMFF) methodology. The comparison between the theoretical and experimental infrared spectrum demonstrated good agreement. Then, the results were used to predict the Raman spectrum. Additionally, the structural properties of OP, such as atomic charges, bond orders, molecular electrostatic potentials, characteristics of electronic delocalization and topological properties of the electronic charge density were evaluated by natural bond orbital (NBO), atoms in molecules (AIM) and frontier orbitals studies. The calculated energy band gap and the chemical potential (μ), electronegativity (χ), global hardness (η), global softness (S) and global electrophilicity index (ω) descriptors predicted for OP low reactivity, higher stability and lower electrophilicity index as compared with the sesquiterpene lactone cnicin containing similar rings.

Molecular Spectroscopic Characterization and Electronic Structure Analysis of N- benzylaniline- A DFT Approach

The FT-IR and FT-Raman spectra of N-benzylaniline[NBZA] have been analysed in the region 4000-450cm-1 and 4000-50cm-1respectively. The geometrical structure, harmonic vibrational frequency, infrared intensity, Raman activities and bonding features of the title compound were carried out by DFT method with B3LYP/6-311++G(d, p) basis set. The complete vibrational frequency assignments were made by normal co-ordinate analysis following the scaled quantum mechanical force field methodology (SQM). The charge transfer and hyperconjugative interactions have been analysed using natural bond orbital (NBO) and HOMO-LUMO analysis. The reactivity sites are identified by mapping the electron density into electrostatic potential surface (MESP). The thermodynamic properties of the title compound at the different temperatures have been calculated. The mulliken charges, the values of electric dipole moment (µ) of the molecule were computed using DFT calculations and the results are interpreted. The UV absorption spectrum of the title compound has been described at the experimental level.

A vibrational spectroscopy study on anserine and its aqueous solutions

In this study based on vibrational spectroscopic measurements and Density Functional Theory (DFT), we aimed for a reliable interpretation of the IR and Raman spectra recorded for anserine in the solid phase and water (H2O) and heavy water (D2O) solutions. Initial DFT calculations at the B3LYP/6-31G(d) searched possible conformers of the anserine zwitterion using a systematic conformational search. The corresponding equilibrium geometrical parameters and vibrational spectral data were determined for each of the stable conformers (in water) by the geometry optimization and hessian calculations performed at the same level of theory using the polarized continuum model (PCM). The same calculations were repeated to determine the most energetically preferred dimer structure for the molecule and the associated geometry, force field and vibrational spectral data. The harmonic force constants obtained from these calculations were scaled by the Scaled Quantum Mechanical Force Field (SQM) method and then used in the calculation of the refined wavenumbers, potential energy distributions, IR and Raman intensities. These refined theoretical data, which confirm the zwitterion structure for anserine in the solid phase or aqueous solvents, revealed the remarkable effects of intermolecular hydrogen bonding on the structural properties and observed IR and Raman spectra of this molecule.

Synthesis, characterization, antibacterial activity and quantum chemical studies of N’-Acetyl propane sulfonic acid hydrazide

A new N’-Acetyl propane sulfonic acid hydrazide, C3H7SO2NHNHCOCH3 (Apsh, an sulfon amide compound) has been synthesized for the first time. The structure of Apsh was investigated using elemental analysis, spectral (IR, 1H/13C NMR) measurements. In addition, molecular structure of the Apsh was determined by single crystal X-ray diffraction technique and found that the compound crystallizes in monoclinic, space group P 21/c. 1H and 13C shielding tensors for crystal structure were calculated with GIAO/DFT/B3LYP/6-311++G(d,p) methods in CDCl3. The structure of Apsh is optimized using Density Functional Theory (DFT) method. The vibrational band assignments were performed at B3LYP/6-311++G(d,p) theory level combined with scaled quantum mechanics force field (SQMFF) methodology. The theoretical IR frequencies are found to be in good agreement with the experimental IR frequencies. Nonlinear optical (NLO) behaviour of Apsh is also examined by the theoretically predicted values of dipole moment (μ), polarizability (α0) and first hyperpolarizability (βtot). The antibacterial activities of synthesized compound were studied against Gram positive bacteria: Staphylococcus aureus ATCC 25923, Enterococcus faecalis ATCC 23212, Staphylococcus epidermidis ATCC 34384, Gram negative bacteria: Eschericha coli ATCC 25922, Pseudomonas aeruginosa ATCC 27853, Klebsiella pneumoniae ATCC 70063 by using microdilution method (as MICs) and disc diffusion method.

A vibrational spectroscopy study on 3-aminophenylacetic acid by DFT calculations

In this study, in which the group vibrations of 3-aminophenylacetic acid were investigated by electronic structure calculations based on Density Functional Theory (DFT), the possible stable conformers of the molecule were searched through a relaxed “potential energy surface scan” carried out at B3LYP/6-31G(d) level of theory. The corresponding equilibrium geometrical and vibrational spectral data for each of the determined stable conformers and for their possible dimer structures were obtained through “geometry optimisation” and “frequency” calculations carried out at B3LYP/6-31G(d) and B3LYP/6-311G++(d,p) levels of theory. The obtained results confirmed that anharmonic wavenumbers calculated at B3LYP/6-311G++(d,p) level generally quite well agree with the experimental wavenumbers, however, harmonic wavenumbers calculated at both levels of theory need an efficient refinement for a satisfactory agreement with experiment. In particular, the harmonic wavenumbers, IR and Raman intensities refined within Scaled Quantum Mechanical Force Field (SQM FF) methodology constituted the primary data set in the interpretation of the experimental FT-IR, FT-Raman and dispersive Raman spectra of 3-aminophenylacetic acid. By the help of these refined spectral data, the effects of conformation and intermolecular hydrogen bonding on the fundamental bands observed in the experimental spectra could be correctly predicted.

An investigations on the molecular structure, FT-IR, FT-Raman and NMR spectra of 1-(p-tolylsulfonyl) pyrrole by theoretical and experimental approach

Fourier-Transform-Infrared, Fourier-Transform-Raman and Nuclear Magnetic Rezonans spectra of 1-(p-tolylsulfonyl) pyrrole molecule have been recorded. In the powder form, vibrational spectra of 1-(p-tolylsulfonyl) pyrrol molecule were investigated in the region 4000–400cm−1 and 3500–50cm−1, respectively. The conformational analysis, geometrical structure, molecular electrostatic potential map, HOMO–LUMO and vibrational spectroscopic properties of the isolated 1-(p-tolylsulfonyl) pyrrole molecule have also been carried out at the Molecular Mechanic and Density Functional Theory approaches. Density Functional Theory results have been associated with Scaled Quantum Mechanics Force Field for fitting between the theoretical and the experimental frequencies.