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 thorn thorn G** calculations and the scaled quantum force field (SQMFF) proced-ure. 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 center dot center dot center dot 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, niclo-samide, 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 in-tensities of bands predicted in the electronic spectra of these species.Peer reviewe

Qualitative and quantitative approach towards the molecular understanding of structural, vibrational and optical features of urea ninhydrin monohydrate

In this study, single crystals of urea ninhydrin monohydrate (UNMH) have been grown by slow evaporation method. The grown crystals were characterized by FT-IR, FT-Raman and UV-Vis-NIR spectroscopies. The Kurtz and Perry powder method was employed to confirm the near-zero SHG efficiency of the as-grown centrosymmetric UNMH crystal. The third order nonlinearity of the crystal has been studied by the open aperture Z-scan method. The nonlinear absorption coefficient is calculated and the potentiality of UNMH in optical limiting applications is identified. The molecular geometry and the origin of optical non-linearity at the molecular level have been investigated by the density functional theory. The normal coordinate analysis was carried out to assign the molecular vibrational modes. Vibrational spectral studies confirms the presence of weak O-H ... O and moderate O-H ... O type hydrogen bonds in the molecule as well as O-H ... O, N-H ... O and blue-shifted C-H ... O type H-bonds in the crystal. The intramolecular charge transfer interactions and the electronic absorption mechanisms have been discussed. The static and the dynamic values of hyperpolarizabilities for UNMH were estimated theoretically by DFT methods. (C) 2017 Elsevier B.V. All rights reserved.Peer reviewe

Vibrational and electronic properties of 4 '-halomethyl-2-biphenylcarbonitrile compounds

In this paper we studied the structural, vibrational and electronic properties of the 4'-bromomethyl-2-biphenylcarbonitrile (BMBP) 4'-chloromethyl-2-biphenylcarbonitrile (CMBP) and 4'-fluoromethyl-2-biphenylcarbonitrile (FMBP) compounds using experimental and theoretical methods. The FT-IR and FT-Raman spectra of BMBP in solid phase were recorded in the region 4000-400 cm(-1) and 4000 -50 cm(-1), respectively. The UV absorption spectrum of BMBP was recorded in dichloromethane and methanol solvents in the range 180-400 nm. The theoretical spectral properties of title compounds were simulated using density functional theory (DFT) and time dependent DFT methods. Scaling of the vibrational frequencies was carried out with the MOLVIB program using multiple scaling factors and assignment to each vibrational frequency was consigned on the basis of potential energy distribution (PED). The electronic spectrum of BMBP in two different solvents (methanol and dichloromethane), calculated at the CAM-B3LYP/6-31G(d,p) level compares well with the experimental data and validates the current method for predicting the absorption spectrum of CMBP and FMBP. Furthermore, the electronic, nonlinear optical and thermodynamics properties of the three compounds were discussed in detailed. (C) 2017 Elsevier B.V. All rights reserved.Peer reviewe

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-l-oxo-3phenylpropan-2-yl)amino] prop-2-enoic add 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 center dot center dot center dot O and O-H center dot center dot center dot O hydrogen bonds and intermolecular C-H center dot center dot center dot O and C-H center dot center dot center dot pi 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. (C) 2015 Elsevier B.V. All rights reserved.Peer reviewe

Irreducibla spinorrymder

H. Weyl describes in his book “Gruppentheorie und Quantenmechanik” how the multidimensional representations of the unimodular unitary group in two dimensions can be constructed using polynomials in two complex variables. This “spinor method” was further developed by B. L. van der Waerden 1932 and was later frequently used by H.A. Kramers. In 1962 V. Bargmann showed that these polynomials generate a finite-dimensional subspace of a Hilbert space, which is constructed from analytical functions in two variables. However, using the spinor algebra of P. Kustaanheimo one can restrict the treatment to finite dimensional spinor spaces, and the existence of a Hilbert space need not be presumed. In the previously used spinor methods the spinor components were utilized, while the main point in this description lies on the spinor basis. In chapter I it is shown, how one in this way can construct symmetrical spinor spaces and the corresponding unitary representations. In addition, spinor polynomials with the same transformation properties as the basis spinors are constructed. They are analogous with the spin generating operators that formed the basis for J. Schwinger’s representation of the rotation group in 1952. In chapter II the Clebsch-Gordan series, which describes the complete reduction of two symmetric spinor spaces in irreducible subspaces, will be derived, and in the final chapter irreducible spinor operators are constructed using the spin generation operators.I sin bok "Gruppentheorie und Quantenmechanik" (1928) beskrev H. Weyl hur de flerdimensionella representationerna av den unimodulära unitära gruppen i två dimensioner kan erhållas utgående från polynom i två komplexa variabler. Denna "spinormetod" vidareutvecklades av B. L. van der Waerden 1932 och användes senare flitigt av H. A. Kramers. 1962 visade V. Bargmann att dessa polynom genererar en ändligt dimensionell subrymd av en Hilbert-rymd, som uppbyggs av analytiska funktioner i två variabler. Om man begagnar sig av P. Kustaanheimos spinoralgebra kan man emellertid inskränka sig till ändligt dimensionella spinorrymder och behöver icke a priori förutsätta existensen av en Hilbert-rymd. I de tidigare använda spinormetoderna utnyttjade man i själva verket spinorkomponenterna, medan tyngdpunkten i denna framställning vilar på spinorbasen. I kapitel I visas hur man på detta sätt kan konstruera symmetriska spinorrymder och de motsvarande unitära representationerna. Dessutom konstrueras spinorpolynom som har samma transformationsegenskaper som basspinorerna och är analoga med de spinalstringsoperatorer som utgjorde grunden för J. Schwingers framställning av rotationsgruppen år 1952. I kapitel II härledes Clebsch-Gordanserien, som uttrycker den fullständiga reduktionen av produkten av två symmetriska spinorrymder i irreducibla subrymder, och i det avslutande kapitlet konstrueras irreducibla spinoroperatorer på basis av spinalstringsoperatorerna

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 pi-pi* interactions.Ondokuz Mayıs Üniversitesi- PYO.FEN.1904.10.03

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

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.Peer reviewe