Molecular structure,vibrational spectra and first-order hyperpolarisability analysis of 2-amino-6-nitrobenzothiazole by DFT method

Vibrational analysis of 2-amino-6-nitrobenzothiazole (2A6NBT) molecule has been carried out at room temperature using FT-IR and FT-Raman spectroscopic techniques. The equilibrium geometry, bonding features and harmonic vibrational frequencies have been investigated with the help of the density functional theory DFT method. The non-linear optical (NLO) behaviour of the examined molecule has been studied followed by the determination of the electric dipole moment μ, the polarisability α and hyperpolarisability β using HF/6-31G(d,p) method. Stability of the molecule arising from hyperconjugative interactions and charge delocalisation have been analysed using the natural bond orbital analysis. The results show that charge in electron density in the σ^* and π^* antibonding orbitals and second-order delocalisation energies (E²) confirms the occurrence of intramolecular charge transfer within the molecule. The assignments of the vibrational spectra have been carried out with the help of normal coordinate analysis following the scaled quantum mechanical force field methodology. The energy and oscillator strength calculated by time-dependent density functional theory complements with the experimental findings. The simulated spectra satisfactorily coincide with the experimental spectra.     

Density functional theory and ab initio studies of vibrational spectra of 2-bis (2-chloroethyl) aminoperhydro-1,3,2-oxazaphosphorinane-2-oxide

The Fourier transform Raman (FTR) and Fourier transform infrared (FTIR) spectra of 2-bis (2-chloroethyl) aminoperhydro-1,3,2-oxazaphosphorinane-2-oxide were recorded in the regions 4000–100 cm^? 1 and 4000–400 cm¹, respectively, in the solid phase. Molecular electronic energy, geometrical structure, harmonic vibrational spectra, infrared intensities and Raman scattering activities, highest occupied molecular orbital, lowest unoccupied molecular orbital energy, energy gaps and thermodynamical properties such as zero-point vibrational energies, rotational constants, entropies and dipole moment were computed at the Hartree–Fock/6-31G(d,p) and three parameter hybrid functional Lee–Yang–Parr/6-31G(d,p) levels of theory. The vibrational studies were interpreted in terms of potential energy distribution. The results were compared with experimental values with the help of scaling procedures. The observed wave number in FTIR and FTR spectra was analysed and assigned to different normal modes of the molecule. Most of the modes have wave numbers in the expected range and are in good agreement with computed values.     

Quantitative structure activity relationships of some pyridine derivatives as corrosion inhibitors of steel in acidic medium

Quantum chemical calculations using the density functional theory (B3LYP/6-31G* DFT) and semi-empirical AM1 methods were performed on ten pyridine derivatives used as corrosion inhibitors for mild steel in acidic medium to determine the relationship between molecular structure and their inhibition efficiencies. Quantum chemical parameters such as total negative charge (TNC) on the molecule, energy of highest occupied molecular orbital (E _HOMO), energy of lowest unoccupied molecular orbital (E _LUMO) and dipole moment (μ) as well as linear solvation energy terms, molecular volume (Vi) and dipolar-polarization (π*) were correlated to corrosion inhibition efficiency of ten pyridine derivatives. A possible correlation between corrosion inhibition efficiencies and structural properties was searched to reduce the number of compounds to be selected for testing from a library of compounds. It was found that theoretical data support the experimental results. The results were used to predict the corrosion inhibition of 24 related pyridine derivatives.     

Structural analysis,spectroscopic characterization and molecular docking studies of the cyclic heptapeptide

The theoretically possible stable conformer of the cyclic heptapeptide, that has significant anti-metastatic activity, was examined by conformational analysis followed by DFT calculations. Experimental infrared and Raman spectroscopy, together with theoretical DFT (6-31G (d,p) basis set)-based quantum chemical calculations, have been used to understand the structural and spectral characteristics of cyclo(Gly-Arg-Gly-Asp-Ser-Pro-Ala) {cyclo(GRGDSPA)}. A complete analysis of the vibrational spectrum has been reported on the basis of potential energy distribution (PED%) data of the vibrational modes. Finally, the calculation results were applied to simulate infrared and Raman spectra of the title compound. The simulated spectra satisfactorily coincide with the experimental spectra. In addition, molecular electrostatic potential and frontier molecular orbital analysis were investigated using theoretical calculations. The stability of the molecule, arising from hyperconjugative interaction and charge delocalization, has been analyzed using natural bond orbital analysis and a high E(2) value reveals the presence of strong interaction between donors and acceptors. Molecular docking studies with fibronectin were performed on cyclo(GRGDSPA) in order to understand its inhibitory nature. The results indicate that the docked ligand {cyclo(GRGDSPA)} forms a stable complex with human fibronectin and gives a binding affinity value of ?7.7 kcal/mol, which points out that cyclo(GRGDSPA) might exhibit inhibitory activity against the attachment of melanoma cells to human fibronectin.     

Molecular structure,vibrational spectra and HOMO,LUMO analysis of 4-piperidone by density functional theory and ab initio Hartree–Fock calculations

Vibrational frequencies and geometrical parameters of 4-piperidone (4-PID) in the ground state have been calculated by using the Hartree–Fock (HF) and density functional methods (B3LYP) with 6-311++G(d,p) and 6-311+G(3df,2p) basis sets. These methods are proposed as a tool to be applied in the structural characterisation of 4-PID (C₅H₉NO). The title molecule has C _s point group symmetry, thus providing useful support in the interpretation of experimental IR and Raman data. The DFT-B3LYP/6-311+G(3df,2p) calculations have been found more reliable than the ab initio HF/6-311++G(d,p) calculations for the vibrational study of 4-PID. The calculated highest occupied molecular orbital and lowest unoccupied molecular orbital energies show that charge transfer occurs within the molecule. The theoretical spectrograms for FT-IR and FT-Raman spectra of the title molecule have been constructed.     

Structural and vibrational spectroscopic elucidation of sulpiride in solid state

The study on the conformational and vibrational behaviors of sulpiride molecule which is known as a neuroleptic or antipsychotic drug that is widely used clinically in the treatment of schizophrenic or depressive disorders is an important scientific and practical task. In here, a careful enough study of monomer and dimeric forms of sulpiridine {5-(aminosulfonyl)-N-[(1-ethyl-2-pyrrolidinyl) ethyl]-2-methoxy-benzamide (C₁₅H₂₃N₃O₄S)} is undertaken by density functional theory (DFTB3LYP) method with the B3LYP/6-31G(d,p) basis set. The conformations of free molecule were searched by means of torsion potential energy surfaces scan studies through dihedral angles D₁ (8?N, 18C, 20C, 23?N), D₂ (18C, 20C, 23?N, 25C) and D₃ (28C, 30C, 41S, 44?N) in electronically ground state, employing 6-31G basic set. The final geometrical parameters for the obtained stable conformers were determined by means of geometry optimization, carried out at DFT/B3LYP/6-31G(d,p) theory level. Afterwards, the possible dimer forms of the molecule were formed and their energetically preferred conformations were investigated. Moreover, the effect of basis set superposition error on the structure and energy of the three energetically favourable sulpiride dimers has been determined. The optimized structural parameters of the most stable monomer and three low energy dimer forms were used in the vibrational wavenumber calculations. Raman and IR (4000–400?cm^?1) spectra of sulpiride have been recorded in the solid state. The assignment of the bands was performed based on the potential energy distribution data. The natural bond orbital analysis has been performed on both monomer and dimer geometries in order to elucidate delocalization of electron density within the molecule. The predicted frontier molecular orbital energies at DFT/B3LYP/6-31G(d,p) theory level show that charge transfer occurs within the molecule. The first-order hyperpolarizability (β₀) and related properties (μ and α) of the title molecule were also calculated.     

Probing the effect of electric field in 9,10-dimethoxy-2,6-bis(2-p-tolylethynyl)anthracene molecular nanowire using quantum chemical and charge density analysis

The effect of electric field (EF) in a newly designed molecular nanowire 9,10-dimethoxy-2,6-bis(2-p-tolylethynyl)anthracene has been analysed theoretically from the structural and electronic charge transport properties using quantum chemical and charge density calculations. The applied EF (0–0.36 VÅ^? 1) alters the molecular conformation, charge density distribution, electrostatic properties and the electronic energy levels of the molecule. Furthermore, the applied EF decreases the highest occupied molecular orbital–lowest unoccupied molecular orbital gap significantly from 1.775 to 0.258 eV and it also induces polarisation in the molecule, which leads to increase the dipole moment of the molecule. The electrostatic potential for various levels of applied EF reveals the charge-accumulated regions of the molecule. The I–V characteristics of the molecule have been studied against various applied fields using Landauer formalism.     

Density functional theory study on (LiNH<Subscript>2</Subscript>)<Subscript>n</Subscript> (<Emphasis Type="Italic">n</Emphasis> = 1–5) clusters

Geometrical structures and relative stabilities of (LiNH₂)_n (n = 1–5) clusters were studied using density functional theory (DFT) at the B3LYP/6-31G* and B3LYP/6-31++G* levels. The electronic structures, vibrational properties, N–H bond dissociation energies (BDE), thermodynamic properties, bond properties and ionization potentials were analyzed for the most stable isomers. The calculated results show that the Li–N and Li–Li bonds can be formed more easily than those of the Li–H or N–H bonds in the clusters, in which NH₂ is bound to the framework of Li atomic clusters with fused rings. The average binding energies for each LiNH₂ unit increase gradually from 142 kJ mol⁻¹ up to about 180 kJ mol⁻¹ with increasing n. Natural bond orbital (NBO) analysis suggests that the bonds between Li and NH₂ are of strong ionicity. Three-center–two-electron Li–N–Li bonding exists in the (LiNH₂)₂ dimer. The N–H BDE values indicate that the change in N–H BDE values from the monomer a1 to the singlet-state clusters is small. The N–H bonds in singlet state clusters are stable, while the N–H bonds in triplet clusters dissociate easily. A study of their thermodynamic properties suggests that monomer a1 forms clusters (b1, c1, d2 and e1) easily at low temperature, and clusters with fewer numbers of rings tend to transfer to ones with more rings at low temperature. E _g, E _HOMO and E _av decrease gradually, and become constant. Ring-like (LiNH₂)_3,4 clusters possess higher ionization energy (VIE) and E _g, but lower values of E _HOMO. Ring-like (LiNH₂)_3,4 clusters are more stable than other types. A comparison of structures and spectra between clusters and crystal showed that the NH₂ moiety in clusters has a structure and spectral features similar to those of the crystal.     

Effect of the Si,Al and B doping on the sensing behaviour of carbon nanotubes toward ethylene oxide: a computational study

ABSTRACT

Exo– and endo–adsorption of ethylene oxide (EO) on pristine (9,0) (zigzag) carbon nanotube (CNT) and its doped forms with silicon (Si–CNT), aluminum (Al–CNT) and boron (B–CNT) were investigated using density functional theory (DFT) at M06–2X/6–311++G** level. The natural bond orbital (NBO) and the quantum theory of atoms in molecules (QTAIM) analyses were also performed by using the same level of theory. The effect of the doping on sensing behaviour of the CNT toward EO molecule was investigated through intermolecular interactions studies by calculation of total and partial density of states (DOS, PDOS). The enhanced sensitivity of doped–CNTs towards EO molecule associated with adsorption energies (E_ads) and the changes in geometric and electronic structures was examined and the global chemical reactivity parameters were calculated and comprehensively analysed. The thermodynamic property changes were calculated and compared. The results indicated that the EO adsorption on the pristine and doped CNTs was an exothermic spontaneous process. Moreover, based on the calculated E_g change (ΔE_g) and E_ads values, Al–CNT with superior sensitivity for sensing of EO molecule, indicates promising perspectives for its use in fabrication of new EO gas–sensing devices.     

Anion–π interactions: CP-corrected vs. standard optimisation,AIM and NBO analyses

The anion–π interactions between Br^? , Cl^? , F^?  and H^?  anions and hexafluorobenzene (HFB), 1,2,4,5-tetracyanobenzene (TCB) and tetracyanopyrazine (TCP) have been studied by standard and counterpoise (CP) corrected methods at HF, B3LYP and MP2/6-31+ + G (d,p) levels of theory. The complexation energies were corrected for basis set superposition error (ΔE _BSSE) and zero point energy (ΔE _BSSE + ZPE). Also, the B3LYP results were corrected by single-point calculation at B3LYP/aug-cc-PVTZ level of theory. Although the CP-corrected method results in higher distances between anions and rings, the standard method gives lower complexation energies. TCP…X^?  series gives higher complexation energies in both CP-corrected and standard methods. Topological analysis of the charge density ρ(r) has been performed by the means of atoms in molecules method on the wave functions obtained at MP2/6-31+ + G (d,p) level of theory. The number and the nature of critical points depend on aromatic ring and anion. Natural bond orbital analysis indicates that n_X → π*_CC and n_X → π*_CN interactions are the most important interactions for TCB (and HFB)…X^?  and TCP…X^?  complexes, respectively.     

Regulation of arachidonate metabolism via lipoxygenase and cyclo-oxygenase by 12-HPETE, the product of human platelet lipoxygenase.

Circular dichroism and resonance Raman spectra of the cluster anion: [Cu(II)₆Cu(I)₈(D-Penicillamine)₁₂Cl]^5? enable the assignment of the S(mercaptide)→Cu(II) charge transfer transition to a band lying at 18250 cm^?1. The resonance Raman spectra compare with that of copper-diethyldithiocarbamate obtained previously. The implications of both series of data upon the resonance Raman spectra of blue copper proteins and the assignment of the CuS(cys) stretching mode are pointed out.     

Charge and energy spectra of fast multicharged ions in a laser plasma

In measuring the charge and energy spectra of the ions of a single-element laser plasma, in addition to thermal ions, fast multicharged ions are recorded that are accelerated by the electric field of laser radiation in the region of the critical plasma density. The charge and energy spectra of Co ions with the charge numbers z=1–3 are measured at laser intensities of q=5×10¹¹–10¹² W/cm². The energy spectra of these ions are broad and are located on the high-energy side (z _max=3, E>5.0 keV) with respect to the thermal ions (z _max=9, E<4.0 keV). The increase in q to 10¹⁴ W/cm² results in an increase in the charge number of both thermal and fast ions.     

Electronic structure simulations of 2,6-dimethyl-2,5-heptadien-4-one by FTIR,FT-Raman,NMR, UV–vis,NBO and density functional theory

Density functional theory (DFT) (B3LYP and B3PW91) calculations have been carried out for 2,6-dimethyl-2,5-heptadien-4-one (DMHD4O) using 6–311++ G** basis set. Complete vibrational assignment and analysis of the fundamental modes of the compound were carried out from the FTIR and FT-Raman spectral data. The theoretical electronic absorption has been calculated by using time-dependent DFT (TD-DFT) methods and compared with the experimental spectra. The theoretically computed Frontier energy gaps and TD-DFT calculations are in good agreement with the experimental UV–vis spectral absorption. The chemical hardness measured from the Frontier molecular orbital energies of DMHD4O is 0.0693 eV. Electronic stability of the compound arising from hyperconjugative interactions and charge delocalisation were also investigated based on the natural bond orbital (NBO) analysis. Effective stabilisation energy E ⁽²⁾ associated with the interactions of the π and the lone pair of electrons was determined by the NBO analysis. ¹³C and ¹H NMR chemical shifts of the compound have been calculated by means of Gauge-Invariant Atomic Orbital using B3LYP/6–311++ G** method. The partial ionic character of the carbonyl group due to resonance render a partially positive charge to the carbonyl carbon, and thus C4 chemical shift lie in the very downfield 191.6 ppm. Comparison between the experimental and the theoretical results indicates that B3LYP method is able to provide satisfactory results for predicting vibrational, electronic and NMR properties.     

Theoretical description of hydrogen bonding in oxalic acid dimer and trimer based on the combined extended-transition-state energy decomposition analysis and natural orbitals for chemical valence (ETS-NOCV)

In the present study we have analyzed hydrogen bonding in dimer and trimer of oxalic acid, based on a recently proposed charge and energy decomposition scheme (ETS-NOCV). In the case of a dimer, two conformations, α and β, were considered. The deformation density contributions originating from NOCV’s revealed that the formation of hydrogen bonding is associated with the electronic charge deformation in both the σ—(Δρ_σ) and π-networks (Δρ_π). It was demonstrated that σ-donation is realized by electron transfer from the lone pair of oxygen on one monomer into the empty r_{H - O}^* \rho_{H - O}^* orbital of the second oxalic acid fragment. In addition, a covalent contribution is observed by the density transfer from hydrogen of H-O group in one oxalic acid monomer to the oxygen atom of the second fragment. The resonance assisted component (Δρ_π), is based on the transfer of electron density from the π—orbital localized on the oxygen of OH on one oxalic acid monomer to the oxygen atom of the other fragment. ETS-NOCV allowed to conclude that the σ(O---HO) component is roughly eight times as important as π (RAHB) contribution in terms of energetic estimation. The electrostatic factor (ΔE_elstat) is equally as important as orbital interaction term (ΔE_orb). Finally, comparing β-dimer of oxalic acid with trimer we found practically no difference concerning each of the O---HO bonds, neither qualitative nor quantitative.     

Coherent phenomena of charge separation in reaction centers of LL131H and LL131H/LM160H/FM197H mutants of <Emphasis Type="Italic">Rhodobacter sphaeroides</Emphasis>

Primary stage of charge separation and transfer of charges was studied in reaction centers (RCs) of point mutants LL131H and LL131H/LM160H/FM197H of the purple bacterium Rhodobacter sphaeroides by differential absorption spectroscopy with temporal resolution of 18 fsec at 90 K. Difference absorption spectra measured at 0–4 psec delays after excitation of dimer P at 870 nm with 30 fsec step were obtained in the spectral range of 935–1060 nm. It was found that a decay of P* due to charge separation is considerably slower in the mutant RCs in comparison with native RCs of Rba. sphaeroides. Coherent oscillations were found in the kinetics of stimulated emission of the P* state at 940 nm. Fourier analysis of the oscillations revealed a set of characteristic bands in the frequency range of 20–500 cm⁻¹. The most intense band has the frequency of −30 cm⁻¹ in RCs of mutant LL131H and in native RCs and the frequency of ∼100 cm⁻¹ in RCs of the triple mutant. It was found that an absorption band of bacteriochlorophyll anion B_A⁻ which is registered in the difference absorption spectra of native RCs at 1020 nm is absent in the analogous spectra of the mutants. The results are analyzed in terms of the participation of the B_A molecule in the primary electron transfer in the presence of a nuclear wave packet moving along the inharmonic surface of P* potential energy.     

Molecular modelling and vibrational investigations of ammonium-based ionic liquid (CLTOAB)

CLTOAB is an ammonium-based ionic liquid composed of ε-Caprolactam (CL) C₆H₁₁NO and tetraoctylammonium bromide (TOAB) (C₃₂H₆₈BrN). In this study, experimental IR and Raman spectra of CLTOAB ionic liquid together with the computational results of the compound have been reported. The optimized geometry, vibrational frequencies, IR intensities and Raman activities of the CLTOAB were calculated using the wb97xd and B3LYP density functional methods combined with the 6-31G(d,p) basis set using Gaussian 03 program. The complete assignment of the bands was performed based on the potential energy distributions (PED%). The HOMO and LUMO analysis is used to determine the charge transfer within the molecule. The Gauge-including atomic orbital ¹H-NMR and ¹³C-NMR chemical shifts calculations were carried out and compared with the experimental data. Furthermore to evaluate interaction between CLTOAB and DNA, molecular docking study was carried out.

Communicated by Ramaswamy H. Sarma     

Spectroscopic Studies on Nicotine and Nornicotine in the UV Region

The UV absorption and electronic circular dichroism (ECD) spectra of (R)‐ and (S)‐nicotine and (S)‐nornicotine in aqueous solution were measured to a significantly lower wavelength range than previously reported, allowing the identification of four previously unobserved electronic transitions. The ECD spectra of the two enantiomers of nicotine were equal in magnitude and opposite in sign, while the UV absorption spectra were coincidental. In line with previous observations, (S)‐nicotine exhibited a negative cotton effect centered on 263 nm with vibronic structure (π–π₁* transition) and a broad, positive ECD signal at around 240 nm associated with the n–π₁* transition. As expected this band disappeared when the pyridyl aromatic moiety was protonated. Four further electronic transitions are reported between 215 and 180 nm; it is proposed the negative maxima around 206 nm is either an n–σ* transition or a charge transfer band resulting from the movement of charge from the pyrrolidyl N lone pair to the pyridyl π* orbital. The pyridyl π–π₂* transition may be contained within the negative ECD signal envelope at around 200 nm. Another negative maximum at 188 nm is thought to be the pyridyl π–π₃* transition, while the lowest wavelength end‐absorption and positive ECD may be associated with the π–π₄* transition. The UV absorption spectra of (S)‐nornicotine was similar to that of (S)‐nicotine in the range 280–220 nm and acidification of the aqueous solution enhanced the absorption. The ECD signals of (S)‐nornicotine were considerably less intense compared to (S)‐nicotine and declined further on acidification; in the far UV region the ECD spectra diverge considerably. Chirality 25:288–293, 2013. © 2013 Wiley Periodicals, Inc.     

Density functional theory study of the potassium complexation of an unsymmetrical 1,3-alternate calix[4]-crown-5-N-azacrown-5 bearing two different crown rings

Theoretical studies of an unsymmetrical calix[4]-crown-5-N-azacrown-5 (1) in a fixed 1,3-alternate conformation and the complexes 1·K⁺(a), 1·K⁺(b), 1·K⁺(c) and 1·K⁺K⁺ were performed using density functional theory (DFT) at the B3LYP/6-31G* level. The fully optimized geometric structures of the free macroligand and its 1:1 and 1:2 complexes, as obtained from DFT calculations, were used to perform natural bond orbital (NBO) analysis. The two main types of driving force metal–ligand and cation–π interactions were investigated. NBO analysis indicated that the stabilization interaction energies (E ₂) for O…K⁺ and N…K⁺ are larger than the other intermolecular interactions in each complex. The significant increase in electron density in the RY* or LP* orbitals of K⁺ results in strong host–guest interactions. In addition, the intermolecular interaction thermal energies (ΔE, ΔH, ΔG) were calculated by frequency analysis at the B3LYP/6-31G* level. For all structures, the most pronounced changes in the geometric parameters upon interaction are observed in the calix[4]arene molecule. The results indicate that both the intermolecular electrostatic interactions and the cation–π interactions between the metal ion and π orbitals of the two pairs that face the inverted benzene rings play a significant role.     

Raman,FT-IR spectroscopic analysis and first-order hyperpolarisability of 3-benzoyl-5-chlorouracil by first principles

3-Benzoyl-5-chlorouracil (3B5CU), a biologically active synthetic molecule, has been analysed at DFT/6-311+ + G(d,p) level and reported for the first time as a potential candidate for nonlinear optical (NLO) applications. The optimised skeleton of 3B5CU molecule is non-planar. The frontier orbital energy gap, dipole moment, polarisability and first static hyperpolarisability have been calculated. The first static hyperpolarisability is found to be almost 15 times higher than that of urea. The high value of first static hyperpolarisability (2.930 × 10^? 30 e.s.u.) due to the intra-molecular charge transfer in 3B5CU has been discussed using first principles. A complete vibrational analysis of the molecule has been performed by combining the experimental Raman, FT-IR spectral data and the quantum chemical calculations. In general, a good agreement of calculated modes with the experimental ones has been obtained. The strong vibrational modes contributing towards NLO activity, involving the whole charge transfer path, have been identified and analysed.