Ibrahim A. Shaaban

Synthesis, antimicrobial activity, structural and spectral characterization and DFT calculations of Co(II), Ni(II), Cu(II) and Pd(II) complexes of 4-amino-5-pyrimidinecarbonitrile

Co(II), Ni(II), Cu(II) and Pd(II) complexes of 4-amino-5-pyrimidinecarbonitrile (APC) have been synthesized and characterized using elemental analysis, magnetic susceptibility, mass spectrometry, infrared (4000-200 cm(-1)), UV-Visible (200-1100 nm), (1)H NMR and ESR spectroscopy as well as TGA analysis. The molar conductance measurements in DMSO imply non-electrolytic complexes, formulated as [M(APC)2Cl2] where M=Co(II), Ni(II), Cu(II) and Pd(II). The infrared spectra of Co(II), Ni(II) and Cu(II) complexes indicate a bidentate type of bonding for APC through the exocyclic amino and adjacent pyrimidine nitrogen as donors whereas APC coordinated to Pd(II) ion as a monodentated ligand via a pyrimidine nitrogen donor. The magnetic measurements and the electronic absorption spectra support distorted octahedral geometries for Co(II), Ni(II) and Cu(II) complexes however a square planar complex was favored for the Pd(II) complex (C2h skeleton symmetry). In addition, we carried out B3LYP and ω-B97XD geometry optimization at 6-31G(d) basis set except for Pd(II) where we implemented LanL2DZ/6-31G(d) combined basis set. The computational results favor all trans geometrical isomers where amino N, pyrimidine N and Cl are trans to each other (structure 1). Finally, APC and its divalent metal ion complexes were screened for their antibacterial activity, and the synthesized complexes were found to be more potent antimicrobial agents than APC against one or more microbial species.

Raman, infrared and NMR spectral analysis, normal coordinate analysis and theoretical calculations of 5-(methylthio)-1,3,4-thiadiazole-2(3H)-thione and its thiol tautomer.

Raman (3400-100 cm(-1)) and infrared (4000-200 cm(-1)) spectra of 5-(methylthio)-1,3,4-thiadiazole-2(3H)-thione (C3H4N2S3; MTT) were measured in the solid state, and the (1)H/(13)C NMR spectra were obtained in DMSO-d6. Initially, twelve structures were proposed as a result of thiol-thione tautomerism and the internal rotation about the C-S bonds. The energies and vibrational frequencies of the optimized structures were calculated using the 6-31G(d) basis set with the methods of MP2 and DFT/B3LYP with Gaussian 98 quantum calculations. Additionally, (1)H/(13)C NMR chemical shifts were predicted for the thiol (structure 5) and thione (structure 9) tautomers by means of B3LYP/6-311+G(d,p) calculations utilizing the GIAO approximation and the PCM solvation model. After complete relaxation of twelve candidate isomers, the thione tautomer (structure 9) was favored owing to its low energy and its predicted real spectral frequencies. These results agree with the recorded infrared and Raman results, in addition to the observed/calculated (1)H and (13)C NMR spectra. Aided by normal coordinate analysis and potential energy distributions (PEDs), complete vibrational assignments have been proposed for all observed fundamentals for the thione tautomer. With the aid of MP2/6-31G(d) potential surface scans, CH3, CH3S, and SH barriers to internal rotations were estimated with the optimized structural parameters from the MP2 method with the 6-31G(d) basis set. The results are discussed herein and compared with similar model compounds whenever appropriate.

Infrared and NMR spectra, tautomerism, vibrational assignment, normal coordinate analysis, and quantum mechanical calculations of 4-amino-5-pyrimidinecarbonitrile.

The infrared (4000-200 cm(-1)) spectrum for 4-amino-5-pyrimidinecarbonitrile (APC, C5H4N4) was acquired in the solid phase. In addition, the (1)H and (13)C NMR spectra of APC were obtained in DMSO-d6 along with its mass spectrum. Initially, six isomers were hypothesized and then investigated by means of DFT/B3LYP and MP2(full) quantum mechanical calculations using a 6-31G(d) basis set. Moreover, the (1)H and (13)C NMR chemical shifts were predicted using a GIAO approximation at the 6-311+G(d,p) basis set and the B3LYP method with (and without) solvent effects using PCM method. The correlation coefficients showed good agreement between the experimental/theoretical chemical shift values of amino tautomers (1 and 2) rather than the eliminated imino tautomers (3-6), in agreement with the current quantum mechanical calculations. Structures 3-6 are less stable than the amino tautomers (1 and 2) by about 5206-8673 cm(-1) (62.3-103.7 kJ/mol). The MP2(full)/6-31G(d) computational results favor the amino structure 1 with a pyramidal NH2 moiety and calculated real vibrational frequencies, however; structure 2 is considered a transition state owing to the calculated imaginary frequency. It is worth mentioning that, the calculated structural parameters suggest a strong conjugation between the amino nitrogen and pyrimidine ring. Aided by frequency calculations, normal coordinate analysis, force constants and potential energy distributions (PEDs), a complete vibrational assignment for the observed bands is proposed herein. Finally, NH2 internal rotation barriers for the stable non-planar isomer (1) were carried out using MP2(full)/6-31G(d) optimized structural parameters. Our results are discussed herein and compared to structural parameters for similar molecules whenever appropriate.

Analysis of UV and vibrational spectra (FT-IR and FT-Raman) of hexachlorocyclotriphosphazene based on normal coordinate analysis, MP2 and DFT calculations

The Raman (1400-100 cm(-1)) and infrared (4000-400 cm(-1)) of solid hexachlorocyclotriphosphazene, P(3)N(3)Cl(6) (HCCTP) were recorded. The conformational energies were calculated using MP2 and DFT (B3LYP and B3PW91) methods utilizing a variety of basis sets up to 6-311+G(d). On the basis of D(3h) symmetry, the simulated vibrational spectra of P(3)N(3)Cl(6) from MP2 and DFT methods were in excellent agreement with those obtained experimentally. Additionally, Frontier Molecular Orbitals and electronic transitions were predicted using steady state and time dependent DFT(B3LYP)/PCM calculations respectively, each employing the 6-311+G(d,p) optimized structural parameters. The predicted wavelengths were in excellent agreement with experimental values when CH(2)Cl(2) was used as solvent. The (14)N and (31)P chemical shifts were predicted with B3LYP/6-311+G(2d,p) calculations using the GIAO technique with solvent effect modeled using the PCM method. The computed structural parameters of the planar P(3)N(3)Cl(6) (D(3h)) agree well with experimental values from both X-ray and electron diffraction data with slight distortions observed due to lattice defects in the solid phase. The experimental/computational results favor a slightly distorted D(3h) symmetry for the title compound in the gas and solid phases and in solution (τPNPN and τNPNP ranged from 0.018° to 0.90°). Aided by normal coordinate analysis, and the simulated vibrational spectra utilizing MP2, B3LYP and B3PW91 methods at 6-31G(d) basis set, revised and complete vibrational assignments for all fundamentals are provided herein.

Infrared, 1H and 13C NMR spectra, structural charcterization and DFT calculations of novel adenine-cyclodiphosp(V)azane derivatives

Adenine tetrachlorocyclodiphospha(V)zane derivatives (III(a-c)) were prepared by the reaction of hexachlorocyclodiphospha(V)zane derivatives (I(a-c)) and adenine (II) as precursors. The synthesized compounds and their structures (III(a-c)) were firmly characterized (based on the presence of an inversion center) using FT-IR (4000-200 cm(-1)), UV-vis. (190-800 nm), (1)H, (13)C NMR and Mass spectral measurements in addition to C, H, N, P elemental analysis. The compounds (III(a-c)) were found to be a 1:2 molar ratio of (I(a-c)) and adenine (II) adducts, respectively. Confident and complete vibrational assignments are proposed for nearly all fundamental vibrations, along with detailed interpretation for all observed signals in both (1)H and (13)C NMR spectra of the investigated phospha(V)zanes (III(a-c)). In addition, unconstrained geometry optimization of III(a-c) were carried out by means of DFT-B3LYP/3-21G(d) calculations to provide new insight into the structural parameters and molecular geometries of compounds III(a-c). The results are reported herein and compared with similar molecules whenever appropriate.

Raman and DRIFT spectra, vibrational assignments and quantum mechanical calculations of centrosymmetric meso-2,3-Dimercaptosuccinic acid

The Raman spectrum (3700-100cm-1) of meso-2,3-Dimercaptosuccinic acid (meso-DMSA; C4H6O4S2) was recorded in the solid phase using 514.5 and 785nm excitation lines. Whereas, the DRIFT spectrum (4000-400cm-1) of the sample powdered in KBr was obtained. Moreover, DFT-B3LYP/6-31G(d) geometry optimization and frequency calculations were carried out for centrosymmetric trans (Ci), gauche (C1; G+/G-) and eclipsed (Cs; Ef and C1; E+/E-) rotational isomers in favor of a trans conformation, the least energy with real frequencies. However, other conformers were found at either local minima or local maxima as a result of the rotation of carboxyl, hydroxyl and thiol groups according to a potential energy surface scan. Moreover, an imaginary wavenumber was predicted; therefore, they are considered transition states. On the other hand, the mass spectrum of the sample dissolved in an acetonitrile/methanol mixture reveal 4-6% dimer through intermolecular hydrogen bonding interactions via the dicarboxylic groups. Therefore, we have modeled the complex structure obeying Ci restricted symmetry for an isolated dimer unit using DFT-B3LYP/6-31G(d) and for two molecules per unit cell in the solid phase implementing DFT-PBE functional. Thus, the meso-DMSA forms long strands in which individual molecules are bonded together at each termini through hydrogen bonding. Aided by normal coordinate analysis, complete vibrational assignments were provided herein which support Ci configuration of meso-DMSA in the solid state which found consistent with the observed broadening, composite, split bands, and the mutual exclusion rule.

Synthesis, characterization, computational studies and biological activities of Co(II), Ni(II) and Cu(II) complexes of 2-amino-1,3,4-thiadiazole derivatives

Abstract Co(II), Ni(II), and Cu(II) complexes of 2-Amino-5-ethyl-1,3,4-thiadiazole (AET) and 2-Amino-5-(ethylthio)-1,3,4-thiadiazole (AEST) have been synthesized and characterized based on elemental analysis, magnetic susceptibility, infrared (4000–400 cm−1), mass spectrometry (ESI and MALDI), UV–Vis (200–1100 nm) and thermal analysis (TGA/DTA). Molar conductance measurements proved that [M(L)2(H2O)2]Cl2·H2O are electrolytic complexes where M represents Co, Ni, and Cu divalent metal ions. The geometrical isomerism of [M(L)2(H2O)2]2+ ions were investigated by DFT-B3LYP calculations incorporated in Gaussian09 package; it favored the all trans isomers due to having the lowest energy points on the potential energy surface. The outcome of DFT-B3LYP quantum mechanical calculations using 6-31G(d) basis set favor six-coordinate sites via a bidentate ligand through exo amino and adjacent endo thiadiazole nitrogen (N3) donors. These results were consistent with magnetic measurements combined with infrared and UV–Vis spectral interpretations. The predicted metal–ligand binding energies from B3LYP/6-31G(d) calculations follow the trend Cu2+>Ni2+>Co2+, in agreement with the Irving–Williams series. Both AET and AEST ligands and the synthesized complexes were screened for their antibacterial activity and the outcome was high antimicrobial activity of the complexes compared to the free ligands against one or more microbial species and in some cases (copper complexes) higher activity than standard drugs. Graphical Abstract

Computational (DFT and MP2) and spectral interpretations, normal coordinate analysis, force constants and barriers to internal rotations of Trimethylacetonitrile

The Raman (3500cm−1−100cm−1) and IR spectra (4000cm−1−400cm−1) of liquid trimethylacetonitrile (C5H9N, TMA) have been obtained. In addition, the 1H and 13C NMR spectra of TMA were obtained in DMSO-d6 and CDCl3. The staggered conformer (C3v) was favored using MP2 and DFT(B3LYP/ωB97XD) quantum mechanical calculations utilizing a 6-311+G(d,p) basis set. High energy difference estimates of 4534cm−1−5338cm−1 (12.96kcal/mol−15.26kcal/mol) were predicted, along with three imaginary torsion frequencies for the eclipsed conformer, therefore considered a transition state. The 1H and 13C NMR chemical shifts were predicted with B3LYP and ωB97XD methods using the GIAO approximation and 6-311+G(d,p) basis set. B3LYP frequencies calculation is favored herein owing to the relatively good compilation with the experimental measurements. The computed structural parameters are well correlated to those reported from electron diffraction and microwave studies. Moreover, the 13C−1H coupling constant was estimated and found consistent with that observed for the sample dissolved in DMSO-d6/CDCl3 solvents. Using the observed methyl torsion at 266cm−1 in gas phase and the kinetic parameter F number, a potential function (V3) of 1578±30cm−1(4.51±.09kcal/mol) was obtained, this barrier to internal rotation is well correlated to 1527cm−1 (4.37kcal/mol) predicted from MP2/6-311+G(d,p) potential surface scan. Aided by the predicted wavenumbers and their IR intensity/Raman activity, the observed IR/Raman bands were intensively discussed and therefore assigned to their corresponding fundamentals, in agreement with novel normal coordinate analysis and potential energy distributions (PEDs).