Structural and vibrational characterization of di-hydrated hydrochloride tacrine combining DFT with SQMFF approach.

This research is a continuation of previously reported article on anhydrous freebase, cationic and hydrochloride tacrine. Here, structures and properties of di-hydrated species of cholinesterase inhibitor tacrine have been studied in gas phase and aqueous solution by using B3LYP/6-311G* and wB97XD/6-311G* levels of theory. Both methods show strong changes in the positions of two water molecules and similar solvation energies (-192.52 kJ/mol with the B3LYP method and -191.95 kJ/mol with the other one). The B3LYP method predicts low gap values for the anhydrous (2.4572 eV) and di-hydrated (3.2708 eV) species of tacrine in gas phase than the wB97XD/6-311G* method (7.2300 eV). Hence, higher reactivities are expected for the di-hydrated species in both media. Atoms in molecules (AIM) calculations support the lower stability of di-hydrated species in solution in agreement with its higher reactivity in this medium. Complete assignments of 104 vibration modes expected for di-hydrated hydrochloride by using the scaled mechanical force field (SQMFF) methodology have been reported. Both methods predict different assignments and scaled force constants presenting higher values those calculated with the wB97XD/6-311G* method. The predicted IR, Raman and 1H NMR spectra with both methods show good correlations with the corresponding experimental ones, however, better concordances between the 13C NMR and UV spectra are observed with the wB97XD/6-311G* method.

Structural, harmonic force field and vibrational studies of cholinesterase inhibitor tacrine used for treatment of Alzheimer's disease.

Different structures of free base (FB), two cationic forms (CA) and three hydrochloride forms (HCl) of cholinesterase inhibitor tacrine used for treatment of Alzheimer 's disease was evaluated using hybrid B3LYP calculations in order to perform their complete vibrational assignments using the scaled harmonic force fields. Structures of anhydrous form of tacrine have been optimized in gas phase and in aqueous solution. The structure of form III HCl is in agreement with the experimental determined by X-ray diffraction while the predicted IR, Raman, 1H- 13C NMR and UV spectra show good correlations with the corresponding experimental ones. Energy values show that the three forms of HCl can exist in both media because these energetic values decrease from 35.15 kJ/mol in gas phase to 5.51 kJ/mol in solution. For the most stable species of tacrine, the following stability order using natural bond orbital (NBO) studies was found: form I HCl > form III HCl > form I CA > FB. CA presents the higher solvation energy value, as reported for hydrochloride species of alkaloids and antihypertensive agents. The structural parameters of form III of HCl present better concordance and corresponds to that experimental observed in the solid phase. Higher topological properties of form III together with the strong N2-H26⋯Cl31 interaction could justify the presence of this form in the solid phase and in solution and the higher stabilities in both media. The gap values support the higher reactivity of form III while FB is the less reactive species in both media. Complete vibrational assignments for FB, CA and HCl species together with the corresponding scaled force constants are reported.

A combined study on structures and vibrational spectra of the antiviral rimantadine using SQMFF and DFT calculations.

In this research, a combined study on structures and vibrational spectra of antiviral rimantadine have been performed using hybrid B3LYP/6-311++G∗∗ calculations and the scaled quantum force field (SQMFF) procedure. Harmonic force fields and scaled force constants of Free Base (FB), Cationic (CA) and Hydrochloride (HCl) species derived from the antiviral rimantadine have been calculated in gas phase and in aqueous solution using normal internal coordinates and scaling factors. Good correlations were acquired comparing the theoretical IR, Raman, 1H- 13C-NMR and UV spectra of three species with the analogous experimental ones, suggesting probably, the presence of all them in both phases. The main force constants of three species have evidenced lower values than the corresponding to antiviral amantadine. The ionic character of N1-H33⋯Cl36 bond of HCl species in aqueous solution evidence positive Mulliken charge on N1 atom indicating that this species is as CA one. Rimantadine presents higher solvation energies in water than other antiviral species, such as chloroquin, niclosamide, cidofovir and brincidofovir. The FB and HCl species of rimantadine are slightly less reactive than the corresponding to amantadine while the opposite is observed for the CA species. The predicted ECD spectra for the FB and CA species show positive Cotton effect different from the negative observed for the HCl one. These different behaviours of three species of rimantadine could probably explain the differences observed in the intensities of bands predicted in the electronic spectra of these species.

Crystal structure, Hirshfeld surfaces and DFT computation of NLO active (2E)-2-(ethoxycarbonyl)-3-[(1-methoxy-1-oxo-3-phenylpropan-2-yl)amino] prop-2-enoic acid.

Nonlinear optical (NLO) activity of the compound (2E)-2-(ethoxycarbonyl)-3-[(1-methoxy-1-oxo-3-phenylpropan-2-yl)amino] prop-2-enoic acid is investigated experimentally and theoretically using X-ray crystallography and quantum chemical calculations. The NLO activity is confirmed by both powder Second Harmonic Generation (SHG) experiment and first hyper polarizability calculation. The title compound displays 8 fold excess of SHG activity when compared with the standard compound KDP. The gas phase geometry optimization and vibrational frequencies calculations are performed using density functional theory (DFT) incorporated in B3LYP with 6-311G++(d,p) basis set. The title compound crystallizes in non-centrosymmetric space group P21. Moreover, the crystal structure is primarily stabilized through intramolecular N-H···O and O-H···O hydrogen bonds and intermolecular C-H···O and C-H···π interactions. These intermolecular interactions are analyzed and quantified using Hirshfeld surface analysis and PIXEL method. The detailed vibrational assignments are performed on the basis of the potential energy distributions (PED) of the vibrational modes.

QM/MM methodology, docking and spectroscopic (FT-IR/FT-Raman, NMR, UV) and Fukui function analysis on adrenergic agonist.

The Fourier transform infrared, FT-Raman, UV and NMR spectra of Ternelin have been recorded and analyzed. Harmonic vibrational frequencies have been investigated with the help of HF with 6-31G (d,p) and B3LYP with 6-31G (d,p) and LANL2DZ basis sets. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by GIAO method. The polarizability (α) and the first hyperpolarizability (ß) values of the investigated molecule have been computed using DFT quantum mechanical calculations. Stability of the molecule arising from hyper conjugative interactions, and charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The electron density-based local reactivity descriptors such as Fukui functions were calculated to explain the chemical selectivity or reactivity site in Ternelin. Finally the calculated results were compared to simulated infrared and Raman spectra of the title compound which show good agreement with observed spectra. Molecular docking studies have been carried out in the active site of Ternelin and reactivity with ONIOM was also investigated.

Molecular docking, spectroscopic studies and quantum calculations on nootropic drug.

A systematic vibrational spectroscopic assignment and analysis of piracetam [(2-oxo-1-pyrrolidineacetamide)] have been carried out using FT-IR and FT-Raman spectral data. The vibrational analysis was aided by an electronic structure calculation based on the hybrid density functional method B3LYP using a 6-311G++(d,p) basis set. Molecular equilibrium geometries, electronic energies, IR and Raman intensities, and harmonic vibrational frequencies have been computed. The assignments are based on the experimental IR and Raman spectra, and a complete assignment of the observed spectra has been proposed. The UV-visible spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies and the maximum absorption wavelengths λmax were determined by the time-dependent DFT (TD-DFT) method. The geometrical parameters, vibrational frequencies and absorption wavelengths were compared with the experimental data. The complete vibrational assignments are performed on the basis of the potential energy distributions (PED) of the vibrational modes in terms of natural internal coordinates. The simulated FT-IR, FT-Raman, and UV spectra of the title compound have been constructed. Molecular docking studies have been carried out in the active site of piracetam by using Argus Lab. In addition, the potential energy surface, HOMO and LUMO energies, first-order hyperpolarizability and the molecular electrostatic potential have been computed.

An experimental and theoretical study of the vibrational spectra and structure of Isosorbide dinitrate.

The present work aims at exploring the vibrational spectra of Isosorbide dinitrate and its chemical activity in a five membered ring system. The FT-IR and FT-Raman spectral studies of the Isosorbide dinitrate (ISDN) were carried out. The equilibrium geometry, various bonding features and harmonic vibrational frequencies of ISDN have been calculated using B3LYP density functional theory (DFT) with 6-31G(d,p) as basis set. The calculated HOMO and LUMO energies and density of states (DOS) show the chemical activity of the molecule. Good correlations between the experimental (1)H and (13)C NMR chemical shifts in methanol-d and calculated GIAO shielding tensors were found. The potential energy surface was studied using the DFT method.

Quantum mechanical, spectroscopic studies (FT-IR, FT-Raman, NMR, UV) and normal coordinates analysis on 3-([2-(diaminomethyleneamino) thiazol-4-yl] methylthio)-N'-sulfamoylpropanimidamide.

Famotidine (3-([2-(diaminomethyleneamino) thiazol-4-yl] methylthio)-N'-sulfamoylpropanimidamide) is a histamine H2-receptor antagonist that inhibits stomach acid production, and it is commonly used in the treatment of peptic ulcer disease (PUD) and gastroesophageal reflux disease (GERD/GORD). Quantum chemical calculations of the equilibrium geometry of famotidine in the ground state were carried out using density functional theory (DFT/B3LYP) with the 6-311G(d,p) basis set. In addition, harmonic vibrational frequencies, infrared intensities and Raman activities were calculated at the same level of theory. A detailed interpretation of the infrared and Raman spectrum of the drug is also reported. Theoretical simulations of the FT-IR, and FT-Raman spectra of the title compound have been calculated. Good correlations between the experimental (1)H and (13)C NMR chemical shifts and calculated GIAO shielding tensors were found. The results of the energy and oscillator strength calculations by time-dependent density functional theory (TD-DFT) supplement the experimental findings. Total and partial density of state (TDOS and PDOS) and also overlap population density of state (COOP or OPDOS) diagrams analysis were presented. The dipole moment, linear polarizability and first order hyperpolarizability values were also computed. The linear polarizability and first order hyperpolarizabilities of the studied molecule indicate that the compound is a good candidate for nonlinear optical materials.

Molecular structural, non-linear optical, second order perturbation and Fukui studies of Indole-3-Aldehyde using density functional calculations.

Indole-3-Aldehyde is a new organic non-linear material having good second harmonic generation. The optimized molecular geometry, harmonic vibrational frequencies, infrared intensities of Indole-3-Aldehyde (I3A, C9H7NO) in the ground state were carried out by using density functional theory (B3LYP) method with 6-31G(d,p) basis set. A detailed interpretation of the infrared spectrum of Indole-3-Aldehyde is reported. The vibrational frequencies are calculated and compared with experimental FT-IR spectra. The theoretical spectrograms of FT-IR of the title compound have been constructed in addition, theoretical information like ONIOM, potential energy surface, NBO, and Fukui function are also calculated. Unambiguous vibrational assignment of all the fundamentals was made using the potential energy distribution.

Vibrational analyses of 1,3-dibenzoyl-4,5-dihydro-1H-imidazole-2-thione and 1,3-dibenzoyl tetrahydropyrimidine-2(1H)-thione by normal coordinate treatment.

Vibrational analyses of 1,3-dibenzoyl-4,5-dihydro-1H-imidazole-2-thione and 1,3-dibenzoyl tetrahydropyrimidine-2(1H)-thione were carried out using normal coordinate analysis. FT-IR spectra were recorded in the region 4000-400 cm(-1). The harmonic vibrational frequencies, molecular geometry and atomic charges have been computed, and NBO analysis has been carried out with the help of B3LYP density functional theory (DFT). The computed geometrical bond lengths and bond angles agree well with the crystallographic data. Atomic charges based on Mulliken population analysis, natural population analysis, Hirshfeld-I analysis and CHelpG analysis were calculated using the basis sets of 6-31G(*) and 6-31G(**). Stabilities of the two molecules were analyzed by means of natural bond orbital (NBO) analysis and delocalized π-π(*) interactions.

Testing a new analytical approach for determination of vibrational transition moment directions in low symmetry planar molecules: 1-D- and 2-D-naphthalene.

A new analytical approach for improving the precision in determination of vibrational transition moment directions of low symmetry molecules (lacking orthogonal axes) is discussed in this paper. The target molecules are partially uniaxially oriented in nematic liquid crystalline solvent and are studied by IR absorption spectroscopy using polarized light. The fundamental problem addressed is that IR linear dichroism measurements of low symmetry molecules alone cannot provide sufficient information on molecular orientation and transition moment directions. It is shown that computational prediction of these quantities can supply relevant complementary data, helping to reveal the hidden information content and achieve a more meaningful and more precise interpretation of the measured dichroic ratios. The combined experimental and theoretical/computational method proposed by us recently for determination of the average orientation of molecules with C(s) symmetry has now been replaced by a more precise analytical approach. The new method introduced and discussed in full detail here uses a mathematically evaluated angle between two vibrational transition moment vectors as a reference. The discussion also deals with error analysis and estimation of uncertainties of the orientational parameters. The proposed procedure has been tested in an analysis of the infrared linear dichroism (IR-LD) spectra of 1-D- and 2-D-naphthalene complemented with DFT calculations using the scaled quantum mechanical force field (SQM FF) method.

Vibrational spectra of silatranes and germatranes XM(OCH2CH2)3N (X=F,Cl,H; M=Si,Ge). The problem of the theoretical prediction of condensed phase spectra.

The structures of silatranes and germatranes XM(OCH(2)CH(2))(3)N (X=F,Cl,H; M=Si,Ge) were optimized and their vibrational spectra were calculated at the B3LYP/aug-cc-pVDZ level of theory. Theoretical frequencies of vibrations perpendicular to the C(3) axis (E type) are in good agreement with experimental values, while the axial vibrations (MX and M...N stretchings) demonstrate a significant discrepancy with experimental spectra recorded for the crystalline state. This discrepancy stems from the well-known difference in the MX and M...N bond lengths in gas and solid state. The force constant scaling procedure was used to compensate for this difference. As a result a set of scaling factors was refined for 1-Cl-germatrane (the unique atrane for which the distinction between A and E modes was experimentally established). This set was transferred to the theoretical force fields of other atranes, which provided a fair reproduction of their experimental frequencies. The analysis of the normal modes allowed us to assign the ν M...N mode to bands in the 180-270 cm(-1) frequency range, although large contributions of these coordinates are in two other modes in the 450-500 cm(-1) and 600-800 cm(-1) frequency ranges. The frequencies of degenerate vibrations (with vectors perpendicular to the C(3) axis) do not depend substantially on the axial atom (X and M) substitution, while those of A-type in the 200-700 cm(-1) frequency range vary significantly.

Ab initio/DFT electronic structure calculations, spectroscopic studies and normal coordinate analysis of 2-chloro-5-bromopyridine.

FT-IR (4000-400 cm(-1)) and FT-Raman (3500-50 cm(-1)) spectral measurements of solid sample of 2-chloro-5-bromopyridine have been done. Ab initio and DFT calculations have been performed giving energies, optimized structures, harmonic vibrational frequencies, depolarization ratios, IR intensities, Raman activities and atomic displacements. Furthermore, force field calculations have been performed by normal coordinate analysis. A complete assignment of the observed spectra, based on spectral correlations, electronic structure calculations and normal coordinate analysis, has been proposed. The results of the calculations have been used to simulate IR and Raman spectra for the molecule that showed good agreement with the observed spectra. The SQM method, which implies multiple scaling of the DFT force fields, has been shown superior to the uniform scaling approach. The energy and oscillator strength calculated by Time-dependent DFT results are in good agreement with the experimental results.

Vibrational spectra, ab initio/DFT electronic structure calculations, and normal coordinate analysis of 2-bromo-5-fluorobenzaldehyde.

FT-IR (4000-400 cm(-1)) and FT-Raman (3500-50 cm(-1)) spectral measurements of solid samples of 2-bromo-5-fluorobenzaldehyde (BFB) have been done. Ab initio (RHF/6-311G*) and DFT (B3LY/6-311G* and B3PW91/6-311G*) calculations have been performed giving energies, optimized structures, harmonic vibrational frequencies, depolarization ratios, infrared intensities, Raman activities and atomic displacements. Furthermore force field calculations have been performed by normal coordinate analysis. Force field calculations showed that several normal modes are mixed in terms of the internal coordinates. A complete assignment of the observed spectra, based on spectral correlations, electronic structure and normal coordinate analysis, has been proposed. Optimization leads to C(S) symmetry with O-trans and O-cis isomers, with respect to aldehydic oxygen and bromine, with O-trans-isomer as the low energy stable form. The energy difference between the two isomers is 2.95084 kcal/mol. The results of the calculations have been used to simulate IR and Raman spectra for BFB that showed excellent agreement with the observed spectra. The SQM method, which implies multiple scaling of the ab initio and DFT force fields has been shown superior to the uniform scaling approach.

Rearrangements of [C(6)H(7)Si](+) cations. A radiochemical and quantum chemical study.

Nucleogenic cations were formed by beta-decay of phenylsilane tritiated at ortho- and para-positions of the benzene ring as well as at the silyl group and the products of their reactions with methyl tert-butyl ether were analyzed by radiochromatography. We found that the o-silatolyl cation was isomerized into the silabenzyl cation while the p-silatolyl cation was not. Furthermore, the silabenzyl cation was not converted into other isomers. The potential energy surface of the C(6)H(7)Si(+) system was constructed by B3LYP and MP2 methods using an aug-cc-pVDZ basis set. Theory predicts the low barrier for o-silatolyl-silabenzyl isomerization but high barriers for hydride shifts in the ring from para to meta- to ortho-isomers. It seems that nascent nucleogenic ions have enough internal energy to overcome the ortho-to-benzyl barrier but not enough to cross over the hydride-shift barriers. Theory also confirms that the isomerization of the silabenzyl cation to the [C(6)H(6).SiH](+) complex takes place in one step with a 62 kcal mol(-1) barrier, whereas that to either the global minimum [C(6)H(7).Si](+) or the silatropylium ion involves multisteps with 69-80 kcal/mol barriers. In addition, we find that the barrier of interconversion between the [C(6)H(6).SiH](+) complex and one of the low-lying [C(6)H(7).Si](+) complexes is only 29 kcal/mol.

Density functional theory study of vibrational spectra and assignment of fundamental vibrational modes of 1-methyl-4-piperidone.

The FT-IR and FT-Raman spectra of 1-methyl-4-piperidone was recorded and the observed bands were interpreted with the aid of normal coordinate analysis following a full structure optimization and force field calculation based on the density functional theory (DFT) using the standard B3LYP/6-311G** method and basis set combinations. A very good agreement obtained between the simulated and experimental spectra was established and unambiguous vibrational assignments of various modes were proposed based on the results of potential energy distribution (PED) calculations.

Scaled quantum chemical calculations and FTIR, FT-Raman spectral analysis of 3,4-diamino benzophenone.

The vibrational spectra of 3,4-diamino benzophenone (DABP) have been computed using B3LYP methodology and 6-31G* and 6-31G** basis sets. The solid phase FTIR and FT-Raman spectra were recorded in the region 4000-400 cm-1 and 3500-100 cm-1, respectively. A close agreement was achieved between the observed and calculated frequencies by employing normal coordinate calculations. The observed and simulated spectra were found to be well comparable.

Applicability of the SQM force field method to the vibrational spectra of sodium acetate.

The applicability of the scaled quantum mechanical force field (SQM FF) method to the prediction of the vibrational spectra of a charged molecule has been studied by the example of the acetate ion (CH3CO2-) in sodium acetate for which an efficient empirical valence force field (SVFF) based on observed IR spectra of six isotopomers of sodium acetate is available in the literature. Standard SQM FF calculations done on a free acetate ion at the B3LYP/6-31G level failed to give an acceptable estimation of even the most characteristic features of the observed spectra, which can be exemplified by the gross overestimation of the frequency separation of the nu(a)CO2- and nu(s)CO2- vibrations. In search for a better description, SQM calculations were done for three simple structural models of sodium acetate, testing different QM methods. The results indicate that in addition to taking into account the dielectric field effect of the surrounding medium, incorporation of a Na+ counterion is necessary to achieve a realistic simulation of the IR and Raman spectra. Satisfactory results were obtained with a bidentate Na-acetate complex by the SQM method coupled with a continuum model at the B3LYP/6-31+G level, whereas the use of the Onsager-type spherical cavity model and the polarizable continuum model (PCM) were found preferable over SCI-PCM.

Hydrogen bonding and molecular vibrations of 3,5-diamino-1,2,4-triazole.

This work deals with the analysis of hydrogen bonding and the vibrational spectroscopy of 3,5-diamino-1,2,4-triazole by means of quantum chemical calculations. The mid and far FTIR and FT-Raman spectra were measured in the condensed state. The fundamental vibrational frequencies were calculated under different possible symmetries by applying the density functional theory with the B3LYP functional and the 6-31G* basis set. The results of the calculations obtained under C(2) symmetry produces the global minimum on the potential energy surface. The vibrational spectra were interpreted with the aid of normal coordinate analysis based on scaled density functional force field. The infrared and Raman spectra were also predicted from the calculated intensities.

Analysis of vibrational spectra of some new E- and Z-4-arylidene-3-isochromanones; Part 2. Isomers and conformers of the 2'-pyrrolyl and 2'-nitrophenyl derivatives.

The infrared and Raman spectra of resolved E and Z isomers of some 4-arylidene-3-isochromanone derivatives were analyzed with the aim of pointing out the differences in vibrational behavior of their coexisting stable conformers. Quantum mechanical (QM) density functional (DFT/B3LYP/6-31*) and normal coordinate calculations were carried out to establish the equilibrium structures and to facilitate the interpretation of the vibrational spectra of the 2'-pyrrolyl and 2'-nitrophenyl derivatives. The frequencies and intensities calculated according to the scaled quantum mechanical (SQM) force field method were used to simulate the IR and Raman spectra and compare them to the measured ones. The results demonstrate that the adopted methodology is capable of treating these fairly large polycyclic molecules. The resulting spectral simulations and detailed vibrational description can be highly useful in clarifying spectral differences brought about by cis-trans isomerism and indicating the extent of spectral changes due to further conformational changes of the aryl substituent attached to the olefinic C=C bond.