Ground State Vibrational Frequencies Research Articles

Experimental and theoretical insights into structural features of methyl (E)-3-(3,4,5-trimethoxybenzylidene)dithiocarbazate with molecular docking and ADMET studies

A new Schiff base, methyl (E)-3-(3,4,5-trimethoxybenzylidene)dithiocarbazte (MTD), was successfully synthesized from a condensation reaction of methyldithiocarbazate with 3,4,5-trimethoxybenzaldehyde. The structure of MTD was confirmed by single-crystal X-ray, NMR, FTIR, TGA, UV-Vis and mass spectroscopy techniques. The Hirshfeld surface analysis of the MTD crystal structure showed dominant H⋅⋅⋅H contacts in the molecular system. Bond lengths and bond angles of the theoretical MTD structure optimized by density functional theory (DFT) using B3LYP label with 6-31G+(d,p) basis set showed excellent agreement with those of the crystal structure. The IR spectra calculated from ground-state vibrational frequency analysis and the UV-Vis spectra from time-dependent density functional theory correlate well with their respective experimental spectra. The results of frontier molecular orbitals (FMO), density of states and global descriptors such as chemical hardness, chemical potential, electrophilic index and chemical softness derived from FMOs with MTD optimized structure revealed that MTD is soft, polarizable, reactive and prone to intramolecular charge transfer. Close observation of frontier molecular orbital map indicated the N, S, O heteroatoms, phenyl ring and p‑methoxy group in negative potential regions while the rest of the molecule was in positive regions. Natural bond orbital analyses concluded that MTD is 98.085% Lewis structure. The molecular docking score result of MTD and Streptococcus pneumoniae protein (PDB code: 3OBH), which is very close to that of standard drugs (trimethoprim and sulfamethoxazole), suggests a potential drug candidature of MTD. The absorption, distribution, metabolism, excretion and toxicity (ADMET) study predicted the good drug-like character of MTD.

Molecular simulation, vibrational spectroscopy and global reactivity descriptors of pseudoephedrine molecule in different phases and states

The ground state molecular energy, vibrational frequencies and HOMO-LUMO analysis of the title compound have been calculated with density functional theory in the B3LYP/6-311 + G (d,p) basis set using Gaussian 09 W software. The FT-IR spectrum of pseudoephedrine has been computed in the gas phase and in the presence of solvent water both in neutral and anionic structures. The TED assignments of the vibrational spectra have been assigned in the selected intense region. On isotopic substitution of carbon atoms, the shifting of frequencies is distinctly observed. The reported values and HOMO-LUMO mappings reveal the possibility of different charge transfers occurring within the molecule. A MEP map is depicted and the Mulliken atomic charge is also calculated. The UV–Vis spectra have been illustrated and explained from the frontier molecular orbitals using a TD-DFT approach.

Dinuclear Phenoxo-Bridged Nickel(II) and Copper(II) Complexes of Phenolate-Based Tripodal Ligand: Theoretical and Experimental Insights

Three dinuclear complexes of composition [NiII 2(L)2][ClO4]2 and [CuII 2(L)2(OClO3)2] . 3H2O have been synthesized using a new tripodal ligand [(2-pyridyl)methyl](2-benzyl)-aminomethyl}-phenol (HL)], in its deprotonated form, providing a N2O donor set. Crystallographic analyses reveal that [CuII 2(L)2(OClO3)2] . 3H2O has a diphenoxo-bridged structure. In [CuII 2(L)2(OClO3)2] . 3H2O, each metal center is MIIN2O3-coordinated with a square-pyramidal environment for each copper(II) center. In this work, the molecular structure, harmonic vibrational frequencies and UV-Vis of [NiII 2(L)2]2+ and [CuII 2(L)2]2+ has been explored. With the help of density functional theory (DFT)/B3LYP techniques and LANL2DZ as a basis set, the ground-state molecule shape and vibrational frequencies were computed. The basic vibrations were allocated using the VEDA program to compute the potential energy distribution (PED) of the vibrational modes. The band gap energies of the title complexes ([NiII 2(L)2]2+ and [CuII 2(L)2]2+) are 3.21 eV and 1.59 eV, respectively, according to HOMO-LUMO energies. The maximal absorption wavelength and band gap energy of the title complexes were calculated theoretically using the UV absorption spectra. MEP analysis identifies electrophilic and nucleophilic sites. Hirshfeld surface analysis was used to characterize the 3D intermolecular interactions in ([NiII 2(L)2]2+ and [CuII 2(L)2]2+) of the crystal surface, whereas fingerprint plots were used to explain the 2D interactions. The biological activity of the complexes was investigated using molecular docking.

Asymmetrical Gaussian Potential Effects on Strongly Coupled Magnetopolaron Properties in Triangular Confinement Potential Quantum Wells

In this research, the existence of an asymmetrical Gaussian confinement potential (AGCP) along the quantum well (QW) growth direction and of a parabolic potential perpendicular to the polar coordinate direction were considered. The magnetic field and temperature properties of the longitudinal optical (LO)-phonon mean number, ground-state energy (GSE), ground-state binding energy (GSBE) and vibrational frequency (VF) of strongly coupled magnetopolarons in triangular confinement potential QWs (TCPQWs) were investigated according to the quantum statistical theory as well as the linear combination operator and unitary transformation methods. We obtained analytical expressions for the GSE, GSBE, VF and LO-phonon mean number as functions of the applied magnetic field, temperature, AGCP barrier height, AGCP range, polar coordinate system’s polar angle and polar coordinate system’s confinement strength. It was demonstrated by the calculated numerical results that the GSE, GSBE, VF and LO-phonon mean number varied with the related physical quantities. The obtained theoretical results are expected to provide a reference for future research on polarons.

Communication: Electronic transition of the l-C6 + cation at 417 nm.

A new electronic transition is reported for the linear C6 + cation with an origin at 416.8nm. This spectrum can be compared to the matrix isolation spectra at lower energies reported previously by Fulara et al. [J. Chem. Phys. 123, 044305 (2005)], which assigned linear and cyclic isomers, and to the gas phase spectrum reported previously by Campbell and Dunk [Rev. Sci. Instrum. 90, 103101 (2019)], which detected the same cyclic-isomer spectrum reported by Fulara. Comparisons to electronically excited states and vibrations predicted by various forms of theory allow assignment of the spectrum to a new electronic state of linear C6 +. The spectrum consists of a strong origin band, two vibronic progression members at higher energy and four hot bands at lower energies. The hot bands provide the first gas phase information on ground state vibrational frequencies. The vibrational and electronic structure of C6 + provide a severe challenge to computational chemistry.

Spectroscopic Investigation, DFT Calculations, anti-Inflammatory Activity and Molecular Dynamic Simulation Study on Fagaramide Alkaloid

Fagaramide (FA) alkaloid was investigated experimentally using FT-IR, FT-Raman and NMR (1H and 13C) spectra, also theoretically studied using density functional theory (DFT) calculations. To obtain the ground state geometry and vibrational frequencies of FA molecule, DFT calculations were performed at the B3LYP/6-31++G(d,p) level. The potential energy distribution (PED) analysis of the title molecule was obtained with the help of normal co-ordinate analysis (NCA) and these assignments were compared with the experimental FT-IR and FT-Raman spectrum. The natural bond orbital (NBO), reduced density gradient (RDG) and Hirshfeld surface analysis were applied to evaluate the relative strength of hydrogen bond interaction and to represent their effect on the stabilization of molecular arrangements. Electron localization function (ELF) and localized orbital locator (LOL) maps were generated to show electron delocalization in the molecule. The reactivity of the molecule was studied by the investigation of frontier molecular orbital analysis, density of states (DOS), molecular electrostatic potential (MEP) and chemical reactivity descriptors. Furthermore, through molecular docking, the anti-inflammatory activity of FA was studied and discussed. A molecular dynamic simulation (MDS) was employed to explore biomolecular stability.

Temperature effect of strong-coupling polaron in RbCl quantum wells with double asymmetric confined potentials

In this study, the ground state properties of strong-coupling polaron in RbCl quantum wells (QWs) by using double asymmetric confined potential were theoretically investigated based on effective mass approximation. Ground state binding energy (GSBE), ground state energy (GSE), vibrational frequency (VF), and mean LO phonon number (MLOPN) were obtained as functions of asymmetric confinement potential parameters in QWs by using the unitary transformation method and linear combination operator. GSBE, GSE, VF and MLOPN were found to be increasing functions of asymmetric semi-exponential confinement potential (ASECP) parameter [Formula: see text] and decreasing functions of parameter [Formula: see text]. GSE was rapidly increased with the increase of confinement strength. GSBE, GSE, VF and MLOPN increase as the increasing (decreasing) of anisotropic parabolic confinement potential strength (confinement length). In addition, the temperature effect was evaluated by using quantum statistical theory. With the increase of temperature, GSE and GSBE decreased while VF and MNLOP increased.

Electronically Excited Complex Formation in Magnesium Cluster-Halogen Atom Reactions.

A near ultraviolet transition of Mg2F has been observed in emission from the reaction between magnesium clusters, most likely Mg3, and fluorine atoms. Because there is little evidence for upper-state internal excitation, the spectrum is assigned assuming that the upper state is quenched to its lowest vibrational levels. Two of possibly three ground-state vibrational frequencies, υ1 = 516 ± 10 cm-1 and υ2 = 104 ± 10 cm-1, have been established. Dispersed laser-induced fluorescence studies extrapolating on the observed chemiluminescence indicate an excited-state symmetric stretch frequency of order 370 ± 30 cm-1. Electronic structure calculations at the CCSD(T)/CBS level predict that the ground state of Mg2F has C2v symmetry and can be described as an Mg2+F- ion pair with two Mg-F bonds. Like the MgF A-X transition that is largely a transition between Mg orbitals, the observed transition in Mg2F is largely between orbitals on the magnesium dimer ion. The asymmetric C∞v Mg2+F- complex is also a minimum and is predicted to be 6.7 kcal/mol higher in energy. Calculated structures for the Mg2Cl isomers are also presented and used to further interpret the experimental results for the reaction of Mg clusters with Cl atoms. In contrast to Mg2F, the ground state of Mg2Cl is a linear C∞v MgMgCl structure with the C2v and D∞h isomers of the MgClMg structure slightly higher in energy.

Structural, spectroscopic and electron collisional studies of isoxazole (C3H3NO)

• Comprehensive structural, spectroscopic and electron collision data of Isoxazole. • DFT calculations of ground state geometry and vibrational frequencies. • Comparison with earlier data; confirmation/revision of vibronic assignments. • Vertical excitation energies for singlet and triplet states using TDDFT. • Low energy electron scattering data for Isoxazole from 0.1-20 eV. The structural, spectroscopic, and electron collision data of Isoxazole (C 3 H 3 NO) were subjected to extensive computational studies. Spectroscopic calculations were performed on ground and excited states using the density functional theory (DFT) and the time dependent density functional theory (TDDFT) respectively. Ground state geometry and vibrational frequencies agree well with earlier works and lead to re-assignment of a few vibrational bands. Theoretically predicted singlet and triplet excitation energies are in good agreement with earlier experimental data, while predicted oscillator strengths of singlet states correlate well with the observed relative spectral intensities. The electron collision data for isoxazole molecule were calculated using Quantemol-N, which employs the UK Molecular R-matrix codes. These calculations were performed for the total elastic cross-sections along with their symmetrical components, differential and momentum transfer cross-sections, inelastic scattering cross-sections comprising of discrete electronic excitation, ionization and dissociative electron attachment processes. We employed the two most popular theoretical approaches to calculate the electron impact ionization cross-sections viz. Complex scattering potential-ionization contribution (CSP-ic) and the Binary encounter Bethe (BEB) model. The rate coefficients for elastic and inelastic processes were estimated over a wide electron temperature range. In addition to scattering calculations, the other motivation was to obtain resonances which are signatures of many significant low energy phenomena. The first two peak correspond to π* shape resonances which are observed at 2.1 eV and 4.69 eV and are in accordance with the earlier reported data. The third peak is observed at 10.96 eV which may be attributed to the σ* shape resonance.

Comparative experimental and theoretical study on the molecular structure and spectroscopic properties of sideroxol isolated from Sideritis stricta and its electronic properties

Sideroxol, a kaurene diterpene, was obtained from the acetone extract of Sideritis stricta plant. The ground-state molecular geometry, vibrational frequencies, and NMR chemical shifts were also investigated by using various density functional theories and Pople basis sets. The computed geometries are in good conformity with the experimental data. The comparison between theory and experiments indicates that B3LYP and M06 methods with the 6-31G(d) basis set are able to provide satisfactory results for predicting vibrational and NMR properties. There seems to be no significant effect of addition of diffuse and polarization functions in the basis set used herein.

Ab initio spectroscopy of the aluminum methylene (AlCH2) free radical.

Extensive ab initio investigations of the ground and electronic excited states of the AlCH2 free radical have been carried out in order to predict the spectroscopic properties of this, as yet, undetected species. Difficulties with erratic predictions of the ground state vibrational frequencies, both in the literature and in the present work, have been traced to serious broken-symmetry instabilities in the unrestricted Hartree-Fock orbitals at the ground state equilibrium geometry. The use of restricted open-shell Hartree-Fock or complete active space self consistent field orbitals avoids these problems and leads to consistent and realistic sets of vibrational frequencies for the ground state. Using the internally contracted multireference configuration interaction method with aug-cc-pV(T+d)Z basis sets, we have calculated the geometries, energies, dipole moments, and vibrational frequencies of eight electronic states of AlCH2 and AlCD2. In addition, we have generated Franck-Condon simulations of the expected vibronic structure of the Ã-X̃, B̃-X̃, C̃-X̃, and C̃-Ã band systems, which will be useful in searches for the electronic spectra of the radical. We have also simulated the expected rotational structure of the 0-0 absorption bands of these transitions at modest resolution under supersonic expansion cooled conditions. Our conclusion is that if AlCH2 can be generated in sufficient concentrations in the gas phase, it is most likely detectable through the B̃2A2-X̃2B1 or C̃2A1-X̃2B1 electronic transitions at 515 nm and 372 nm, respectively. Both band systems have vibrational and rotational signatures, even at modest resolution, that are diagnostic of the aluminum methylene free radical.

Calculation of vibrationally resolved absorption and fluorescence spectra of the rylenes.

A generating function method was used to simulate the vibrationally resolved absorption and emission spectra of perylene, terrylene and quaterrylene. This method operates on the basis of adiabatic excitation energies and electronic ground and excited state vibrational frequencies. These parameters were calculated using density functional theory with the PBE0 functional for perylene and terrylene and with the BH-LYP functional for quaterrylene. The vertical excitation energies of the lower excited states were calculated using functionals with differing amounts of Hartree-Fock exchange. The optimal functional for each molecule was chosen by comparing these energies to literature excitation energies. Using this technique the calculated absorption spectra and the calculated emission spectrum of perylene were found to be in excellent agreement with the literature experimental spectra after introducing a shift and a scaling factor. The most prominent bands of the absorption spectra were assigned to their respective vibronic transitions.

Extended first-principles thermochemistry for the oxidation of titanium tetrachloride

A detailed first-principles investigation of the gas-phase precursor chemistry of titanium tetrachloride (TiCl4) in an O2 environment is used to identify the thermodynamically most stable oxidation products. Candidate species are systematically proposed based on twelve manually defined base moieties in combination with possible functional groups attached to each moiety. The ground state geometry and vibrational frequencies for each candidate species are calculated using density functional theory at the B97-1/6-311+G(d,p) level of theory. A set of 2,328 unique candidate species are found to be physically reasonable. Their thermochemical data are calculated by applying statistical thermodynamics. Standard enthalpies of formation are estimated, if unknown, by using a set of error-cancelling balanced reactions. An equilibrium composition analysis of a mixture of TiCl4/O2 (50 mol%) at 3 bar is performed to identify the thermodynamically stable products. At low temperatures, below approximately 700 K, trimer species are dominant. This is followed by a mid-temperature range of 700 to 1975 K where Ti2OCl6 is the most abundant species, before its thermodynamic stability decreases. Between 1200 and 1825 K TiCl4 is the most stable monomer. At temperatures above 1975 K TiOCl2 becomes the dominant species. This species has been measured experimentally. A structural analysis is used to suggest further potentially stable higher polymers and defines a starting point to investigate the mechanisms leading to the formation of titanium dioxide (TiO2) particles.

Experimental and computational VUV photoabsorption study of dimethyl carbonate: A green solvent

VUV photoabsorption spectrum of dimethyl carbonate in the energy region 7–11 eV and its complete spectral analysis with the aid of quantum chemical calculations is reported for the first time. The spectrum recorded using synchrotron radiation comprises of weak bands overlapping a broad intense continuum. With a view to interpret possible vibronic structure, gas phase infrared spectrum in the region 500–4000 cm−1 is revisited. Density functional theory (DFT) and time dependent DFT (TDDFT) methodologies are used to obtain ground state geometry, vibrational frequencies and vertical excitation energies of dimethyl carbonate. The intense broad features in the spectrum could be attributed to valence transitions. Based on quantum defect calculations, energy ordering and symmetry, weak bands are designated as ns, np and nd type Rydberg transitions converging to the first five ionization potentials. The highest occupied molecular orbital is nonbonding in nature and largely localized on the oxygen atom of carbonyl group and quantum defect values obtained are consistent with excitation from oxygen lone pair. Excellent correlation is obtained between theoretically predicted (CAM-B3LYP levels of theory) and experimentally observed excited state energies. Potential energy curves of ground and first few excited states generated with a view to provide additional insights into their nature and further describe the observed spectra. The present study provides a comprehensive experimental and computation analysis of the VUV photoabsorption spectroscopy of dimethyl carbonate.

Theoretical Assessment of Excited State Gradients and Resonance Raman Intensities for the Azobenzene Molecule.

The ground state geometries and vibrational frequencies as well as the excitation energies and excited state gradients of the S1(nπ*) and S2(ππ*) states of trans- and cis-azobenzene are investigated by several DFT methods, namely B3LYP, PBE, M06-2X, CAM-B3LYP, and ωB97X. Excited state properties and in particular gradients are also assessed using the wave function based methods EOM-CCSD and RASPT2/RASSCF. Comparison with experimental data shows that the B3LYP functional gives the most accurate results for the ground state geometry and vibrational frequencies. The analysis of the vertical excitation energies reveals that the RASPT2 approach provides the most accurate excitation energies with deviations of the order of 0.1 eV. Among the TDDFT methods, the CAM-B3LYP functional shows the best performance on the excitation energies. By assessing the excited state gradients with respect to the reference RASPT2 data, the most accurate gradients are obtained with B3LYP, whereas other functionals as well as the EOM-CCSD and RASSCF calculations give less consistent results. Overall, despite the tendency of B3LYP to underestimate the excitation energies, this functional provides the most balanced description of both ground and excited state properties for both isomers of azobenzene in the Franck-Condon region.

Spectroscopic (FT-IR, FT-Raman, UV, NMR, NLO) investigation and molecular docking study of 1-(4-Methylbenzyl) piperazine

The title compound, 1-(4-Methylbenzyl) piperazine, was analyzed by recording FT-IR (4000-400 cm−1) and FT-Raman (4000-100 cm−1) spectra in solid phase, 1H and 13C NMR in CDCl3 (deuterated chloroform) and UV spectrum (200–400 nm) in solid phase and in ethanol solution. The different conformers of the compound and their minimum energies were studied by potential energy surface scan, using semi-empirical method PM6. Density functional theory (DFT) calculation with 6–311++G (d, p) basis set along with B3LYP and B3PW91 functionals have been used to compute ground state molecular geometries and vibrational frequencies. The assignments of the vibrational spectra have carried out with the help of Potential Energy distribution (PED) analysis. Factor group analysis has also been tabulated. Charge distribution, Frontier Molecular Orbitals, UV–Vis spectra, Molecular Electrostatic Potential (MEP) maps, Non-linear optical (NLO) property and thermodynamic properties of the title compound at different temperatures, were determined using B3LYP functional along with 6–311++G (d, p) basis set. The theoretical 1H and 13C NMR chemical shifts were computed using B3LYP functional with 6–311++G (2d, p) basis sets. Natural Bond orbital analysis were computed and possible transitions were correlated with the electronic transitions. The title compound not only exhibits appreciable dipole moment and hyper polarizability (indicating good NLO properties) but also forms a stable complex with Bacillus cereus, (2HUC), with binding affinity −6.7 kcal/mol through molecular docking, suggesting that, it might exhibit inhibitory activity against Bacillus cereus.

A theoretical study of the structures and electronic transitions of small silicon nitride clusters (SinNm, n + m ⩽ 4)

A quantum mechanical study of small silicon nitride clusters (SinNm, n+m⩽4) was performed for both the ground and excited electronic states. The diatomic SiN as well as the tri-atomic SiN2 and Si2N clusters were chosen as our benchmark systems for an extensive investigation of the various methods, functionals and basis sets. Among the methods investigated for the ground-state geometry optimization and vibrational frequency calculations, density functional theory (DFT) with the B3LYP functional was found to be the best performed method overall. For the basis set, 6-311G(d) is chosen for its nice balance between accuracy and efficiency in time. At the B3LYP/6-311G(d) level of theory, the most stable isomers of SiN2, Si2N, SiN3, Si3N and Si2N2, were determined to be the triplet (3Σ-) asymmetric linear isomer (SiNN), the doublet (2Πg) symmetric linear isomer (SiNSi), the doublet (2A′) nonlinear isomer (SiNNN), the doublet (2B1) Y-type isomer, and the singlet (1Σg+) symmetric linear isomer (SiNNSi), respectively. Analysis of the relative energies of various stable isomers shows that NN bonding is the most favored one and SiSi bonding is least favored. Due to its good performance in predicting the electronic transitions from the X2Σ+ ground state of SiN to three low-lying excited states A2Π, B2Σ+, and D2Π, TDDFT/B3LYP/6-311G(d) was chosen over EOMCCSD/6-311G(d) for the excited state calculations. The first ten electronic transitions for the most stable isomers of all SinNm (n+m⩽4) clusters were calculated.

First-Principles Thermochemistry for the Thermal Decomposition of Titanium Tetraisopropoxide.

The thermal decomposition of titanium tetraisopropoxide (TTIP) is investigated using quantum chemistry, statistical thermodynamics, and equilibrium composition analysis. A set of 981 Ti-containing candidate species are proposed systematically on the basis of the thermal breakage of bonds within a TTIP molecule. The ground state geometry, vibrational frequencies and hindrance potentials are calculated for each species at the B97-1/6-311+G(d,p) level of theory. Thermochemical data are computed by applying statistical thermodynamics and, if unknown, the standard enthalpy of formation is estimated using balanced reactions. Equilibrium composition calculations are performed under typical combustion conditions for premixed flames. The thermodynamically stable decomposition products for different fuel mixtures are identified. A strong positive correlation is found between the mole fractions of Ti species containing carbon and the TTIP precursor concentration.

Synthesis, computational and spectroscopic analysis on (E)-(4-(2-(benzo[d]thiazol-2-yl)hydrazono)-3-methyl-2,6-diphenylpiperidine-1-yl)(phenyl)methanone using DFT approach

(E)-(4-(2-(benzo[d]thiazol-2-yl)hydrazono)-3-methyl-2,6-diphenylpiperidin-1-yl)(phenyl)methanone [EPHDPM] and its derivatives were synthesized and characterized by FT-IR, 1H NMR, 13C NMR and elemental analysis. The target compound [EPHDPM] was computed using density functional theory (DFT) method. The ground-state molecular geometry and vibrational frequencies were calculated by using B3LYP/6-31G (d,p) level of theory. The experimentally observed FT-IR and FT-Raman bands were assigned to different normal modes of the molecule. The stability and charge delocalization of the molecule were also studied by natural bond orbital (NBO) analysis. The HOMO–LUMO energies describe the charge transfer takes place within the molecule. Molecular electrostatic potential has been analyzed. The reported EPHDPM molecule used as a potential NLO material since it has high μβ0 value. Thermodynamic parameter like entropy and enthalpy are calculated and these values are increased with increasing the temperature due to the enhancement of vibrational intensities.

Formation and spectroscopy of dicyanotriacetylene (NC₈N) in solid Kr.

Thermally induced creation of dicyanotriacetylene (NC8N) was observed in solid krypton. Samples were obtained by cryogenic trapping of gaseous cyanoacetylene/Kr mixtures subjected to electric discharges. Strong a (3)Σ(+)(u) → X (1)Σ(+)(g) phosphorescence of NC8N is reported here for the first time; its vibronic structure permitted the measurement of several ground-state vibrational frequencies. Other chemical species, mostly smaller than the precursor molecule, have also been formed, among them the dicarbon molecule (C2), and these may serve as indispensable building blocks in the NC8N synthesis. Processes leading to the elongation of cyanoacetylenic chains are of potential importance for the chemistry of icy grains present in the interstellar gas clouds.