Molecular structure and vibrational spectra of 3 (or 4 or 6)‐methyl‐5‐nitro‐2‐pyridinethiones: FT‐IR,FT‐Raman and DFT quantum chemical calculations

IR and Raman spectra (RS) of polycrystalline 3‐(or 4 or 6)‐methyl‐5‐nitro‐2‐pyridinethione have been measured and analyzed by means of density functional theory (DFT) quantum chemical calculations. The B3LYP/6‐311G(2d,2p) approach has been applied for both the thiol and thione tautomers due to the possibility of the formation of these two thiole forms. Molecular structures of these compounds have been optimized starting from different molecular geometries of the thiol group and thione group. Two conformations of the 2‐mercaptopyridine, trans and cis, have been taken into account. It was shown that the studied compounds appear in the solid state in the thione form. The effect of the hydrogen‐bond formation in the studied compounds has been considered. Copyright © 2008 John Wiley & Sons, Ltd.     

Tautomeric populations of the charged species of 1,12‐diamino‐3,6,9‐triazadodecane (SpmTrien) studied with computer simulations and cluster expansions

Correct net charge and protonation pattern in the polyamine backbone is one of the major factors that define the interactions of this class of compounds. 1,12‐diamino‐3,6,9‐triazadodecane (SpmTrien) is a isosteric charge deficient analogue of naturally occurring spermine (Spm) with different biological features. The tautomeric populations of each SpmTrien charge state were estimated with computer simulations, molecular dynamics (MD) and quantum mechanical calculations, and cluster expansions separately. In the computer simulations, tautomeric populations of each charge state were obtained by constrained least‐squares fitting the theoretically calculated (GIAO B3LYP/6‐311 + G**) ¹⁵ N NMR chemical shieldings of SpmTrien tautomers to the experimentally measured chemical shifts. Theoretical chemical shieldings were calculated for water complexes of SpmTrien obtained from MD simulations in explicit water. Both methods gave highly similar realistic results. SpmTrien has many major populations of tautomers at biologically relevant charge states of three (+3) and four (+4) thus enabling a large variety of structures for specific ionic interactions. Copyright © 2013 John Wiley & Sons, Ltd.     

Prototropy and π‐electron delocalization for purine and its radical ions – DFT studies

Complete tautomeric equilibria and π‐electron delocalization were studied at the B3LYP/6‐311+G** level for neutral purine ( P ) and its charged radicals ( P ^+? and P ^??). All possible nine tautomers (four NH and five CH forms) and all possible 36 tautomeric equilibria (six NⁱH → N^kH, twenty NH → CH, and ten CⁱH → C^kH conversions) were considered. The greatest variations of the tautomeric equilibrium constants (as pK_T) were observed for the NH → CH conversions when proceeding from neutral to reduced purine ( P + e → P ^??). These variations completely change the tautomeric preferences. One‐electron oxidation ( P ? e → P ^+?) has considerably smaller effect on the pK_T values and does not change the tautomeric preferences. π‐Electron delocalization depends on the position of the moving proton and on the type of the electron transfer. For individual tautomers, some linear relations between the relative stabilities and the HOMA (harmonic oscillator model of aromaticity) indices occur for neutral and oxidized purine. For reduced purine, a scatter plot is found. Copyright © 2010 John Wiley & Sons, Ltd.     

Structural,vibrational spectra and normal coordinate analysis for two tautomers of 4(5)‐(2′‐furyl)‐imidazole

We have synthesized both the 4 and 5 tautomeric forms of 4(5)‐(2′‐furyl)‐imidazole (1) and investigated their molecular vibrations by infrared and Raman spectroscopies as well as by calculation based on the density functional theory (DFT) approach. Examination of the temperature dependence of IR intensity revealed the band characteristics of the 4 and 5 tautomers of (1). Comparison of experimental and calculated chemical shifts in nuclear magnetic resonance (NMR) spectroscopy was made in order to identify the two tautomeric forms. The assignment of vibrational normal modes was performed, and the force field obtained reproduced the experimental vibrational wavenumbers with a root mean‐square deviation (RMSD) value of ca. 13 cm⁻¹ for both tautomers. The natural bond orbital (NBO) study reveals the characteristics of the electronic delocalization of the two tautomeric structures. Copyright © 2009 John Wiley & Sons, Ltd.     

A theoretical density functional study of association of Zn2+ with oxazolidine and its thio derivatives in the gas phase

We have performed density functional theory (DFT) calculations in order to study the gas‐phase interaction of oxo‐ and thio‐oxazolidine derivatives with Zn²⁺. The calculations were performed at B3LYP/6‐311+(2df,2p) level of theory. It has been found, in all cases, that the direct association of Zn²⁺ with the carbonyl and thiocarbonyl groups takes place at the heteroatom attached to position 2 irrespective of its nature. This preference has been attributed to the resonance effects caused by the nearest heteroatoms (oxygen and nitrogen). The most stable complexes correspond to structures with Zn²⁺ bridging between the heteroatom at position 2 or 4 of the 4‐ or 2‐enol (or the 4‐ or 2‐enethiol) tautomer and the dehydrogenated ring nitrogen atom, N3. Zn²⁺ association has a clear catalytic effect on the tautomerization processes which connect the oxo–thione forms with the enol–enethiol tautomers. Hence, although the enol–enethiol tautomers of oxazolidine and its thio derivatives should not be observed in the gas phase, the corresponding Zn²⁺ complexes are the most stable species and should be accessible, because the tautomerization barriers are smaller than the Zn²⁺ binding energies. Copyright © 2010 John Wiley & Sons, Ltd.     

Infrared Spectra of Metal (II) Complexes of 1, 3, 4-Thiadiazole-2, 5-Dithiol, 5-Amino-L, 2, 4-Dithiazol-3-Thione and Their Acetyl Derivatives

An infrared spectral interpretation of the structure of fifteen solid complexes formed by Co(II), Cu(II), Cd(II), Hg(II), Pb(II) and Zn(II) with ligands 1, 3, 4-thiadiazole-2, 5-dithiol (bismuthiol), 5-amino-l, 2, 4-dithiazolin-3-thione (xanthane) and the 2-acetyl-l, 3, 4-thiadiazol-5-thione and 5-acetylamide-l, 2, 4-dithiazol-3-t)thione derivatives is performed. The coexistence of different tautomers of bismuthiol and xanthane in the solid state is proposed. The bismuthiol-metal complexes display a unique and similar polymeric structure involving one tautomer. The xanthane-metal complexation stabilizes the 1, 1-dithiolate-type polymeric species; complexation with Cd, Co and Hg metal ions also stabilizes polymers involving the perthiocyanic teutomer.     

Computational Studies on the Ground State Tautomer,Hydrogen Conformations and Vibrational Spectroscopic Analysis of Antitumor Agents:3-Deazauracil and 6-Azauracil

The ground state hydrogen conformations and vibrational analysis of 3-deazauracil (3DAU) and 6-azauracil (6AU) tautomers (4-enol and 2,4-diol forms) have been calculated using ab initio Hartree-Fock (HF) and density functional theory (B3LYP) methods with 6-311++G(d,p) basis set level. The calculations have shown that the most probably preferential tautomer of 3DAU and 6AU are the 4-enol form, which gives best fit to the corresponding experimental data. The ground state conformer of the 2,4-diol form has two O-H bonds which are oriented externally and internally (to the N-H bond). The vibrational analyses of the ground state conformer of each tautomeric form of 3DAU and 6AU were done and their optimized geometry parameters (bond lengths and bond angles) were given. Furthermore, from the correlations values it was concluded that the B3LYP method is superior to the HF method for both the vibrational frequencies and the geometric parameters.     

Experimental and theoretical push‐pull Chemo‐ and regioselectivity in 1,3‐Dipolar cycloaddition reactions: the case of benzotriazepin‐5‐one with mesitylnitrile oxide

A novel heterocyclic compound 3‐mesityl‐5‐methyl‐4,5,11,11a‐tetrahydro‐6H‐[1,2,4]oxadiazolo [5,4‐b][1,3,4]benzotriazépin‐6‐one 4 has been synthesised by a 1,3 dipolar cycloaddition (13DC) reaction of 1,3,4‐benzotriazepin‐5‐one 1 with mesitylnitrile oxide 3 . The reaction, beside its synthetic interest, has shown to be completely chemo‐ and regioselective. The structure of the compound was determined by X‐ray crystallography and analysed by spectral methods (NMR and mass spectrometry). The molecular mechanism for the reaction has been studied using quantum mechanical calculations at the B3LYP/6‐31G* theory level. Two mechanisms are possible for the formation of the cycloadduct 4 . The first one involves a 13DC reaction between 1 , as dipolarophile and 3 , as dipole. Analysis of the results indicates that it takes place along asynchronous concerted bond‐formation process with a very low polar character. The regioselectivity obtained from the calculations are in complete agreement with the unique formation of the cycloadduct 4 . The second mechanism is initiated by the nucleophilic attack of the N3 nitrogen of the tautomer form of 2 , to the C5 carbon of the nitrile oxide 3 to yield an amidoxime. However, the large energy involved in this addition prevents this mechanism. The large energy difference between the tautomers 1 and 2 , makes that only the C?N site of benzotriazepin‐5‐one 1 could act as a dipolarophile site. This fact makes the 13DC reaction to be chemoselective. The analysis of global electrophilicity of the reagents allows explaining the low polar character of these 13DC reactions. Copyright © 2007 John Wiley & Sons, Ltd.     

FT‐Raman,FT‐IR spectra and DFT calculations on monomeric and dimeric structures of 5‐fluoro‐ and 5‐chloro‐salicylic acid

The experimental and theoretical study on the structures and vibrations of 5‐fluoro‐salicylic acid and 5‐chloro‐salicylic acid (5‐FSA and 5‐ClSA, C₇H₅FO₃ and C₇H₅ClO₃) is presented. The Fourier transform infrared spectra (4000–400 cm⁻¹) and the Fourier transform Raman spectra (4000–50 cm⁻¹) of the title molecules in the solid phase were recorded. The molecular structures, vibrational wavenumbers, infrared intensities, Raman intensities and Raman scattering activities were calculated for a pair of molecules linked by the intermolecular O H···O hydrogen bond. The geometrical parameters and energies of 5‐FSA and 5ClSA were obtained for all eight conformers/isomers from density functional theory (DFT) (B3LYP) with 6‐311++G(d,p) basis set calculations. The computational results identified the most stable conformer of 5‐FSA and 5‐ClSA as the C1 form. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. The spectroscopic and theoretical results were compared with the corresponding properties for 5‐FSA and 5‐ClSA monomers and dimer of C1 conformer. The optimized bond lengths, bond angles and calculated wavenumbers showed the best agreement with the experimental results. Copyright © 2010 John Wiley & Sons, Ltd.     

Formation of pyrazol‐1,3,4‐thiadiazoles through 1,3‐dipolar cycloadditions of 3‐thioxo‐[1,2,4]‐triazepin‐5‐one with nitrilimines: an experimental and computational study

In this work the experimental results and the computational study of the title compounds and some ancillary compounds are reported. Two bicyclic pyrazol‐1,3,4‐thiadiazole derivatives were synthezised by reaction between 6‐dimethylaminomethylene‐3‐thioxo‐[1,2,4]‐triazepin‐5‐one 1 and several nitrilimines 2a–f to give corresponding spirocycloadducts 3a–f , which undergo a rapid rearrangement leading to the new bicyclic compounds, 4a–f and 5a–f . These obtained bicyclic products were characterized by ¹H and ¹³C NMR spectroscopy and finally by X‐ray crystallography. Theoretical calculations have been carried out using DFT methods to rationalize the formation of the two new bicyclic compounds. Two reaction types are involved in the formation of the compounds 4a–f and 5a–f . The first one is a 1,3‐dipolar cycloaddition (13DC) reaction between 1 acting as dipolarophile and 2a–f as dipoles. The results indicate that the cycloaddition between 1 and 2g , as model of 2a–c , takes place via a high asynchronous bond‐formation process. The regioselectivity obtained from the calculations is in complete agreement with the formation of the unique spirocycloadducts 3a–f . The second reaction leading to the formation of the final products is a domino process that is initiated by the quick and irreversible cleavage in a catalytic acid environment of triazepenic ring. Copyright © 2008 John Wiley & Sons, Ltd.     

1,1,1‐Trichloro‐3‐(1‐phenethylamino‐ethylidene)‐ pentane‐2,4‐dione—synthesis,spectroscopic, theoretical and structural elucidation

1,1,1‐Trichloro‐3‐(1‐phenethylamino‐ethylidene)‐pentane‐2,4‐dione is spectroscopically and structurally elucidated by means of linear‐polarized IR spectroscopy (IR‐LD) of oriented solids as a colloidal suspension in nematic liquid crystal. Structural information and IR‐spectroscopic assignment are supported by quantum chemical calculations at MP2 and B3LYP level of theory and 6‐311++G** basis set. The geometry is characterized with an inramolecular hydrogen bond of NH^…O?C with length of 2.526 Å and a NHO angle of 140.5(1)°. The NH? C(CH₃)C?C? C?O(CH₃) fragment is nearly flat with a maximal deviation of total planarity of 10.4°. Copyright © 2007 John Wiley & Sons, Ltd.     

5‐Phenyl‐1,3,4‐oxadiazole‐2‐thiol/polyamide‐montmorillonite microbicides nanocomposites as drug delivery system

The preparation and structural characterization of polymeric microbicides consisting of 5‐phenyl‐1,3,4‐oxadiazole‐2‐thiol covalently bound to polyamide based on diethyl‐2,3‐dihydroxysuccinate and polyoxypropylenetriamine Jeffamine (T₄₀₃) are described. Two different mole ratios of 5‐phenyl‐1,3,4‐oxadiazole‐2‐thiol was reacted with chloroacetylated diethyl‐2,3‐dihydroxysuccinate followed by polycondensation with Jeffamine (T₄₀₃). The nanocomposites were prepared by modification of microbicide polyamides to yield polymers with phosphonium salt or amine hydrochloride salt followed by ion exchange process between the phosphonium salt or amine hydrochloride of the polyamides and the intermellar sodium cation of the clay mineral montmorillonite. The monomers were characterized by mass spectrum, proton nuclear magnetic resonance. The polymers showed good or moderate antimicrobial activities. Nanocomposites were characterized by Fourier transformed infrared spectroscopy, X‐ray diffraction, thermal gravimetric analysis, and transmission electron microscope. The swelling behavior and release of 5‐phenyl‐1,3,4‐oxadiazole‐2‐thiol in different pH values (2.3, 5.8, and 7.4) were studied. A slow release, ranging from 12% to 28% after 50 hours was recorded from nanocomposites. However, the release profile reached almost 70% from polyamides. The antimicrobial activity of the polyamides was studied against gram‐negative bacteria, gram‐positive bacteria, yeast, and the filamentous fungi by well diffusion method. The polyamides showed better antimicrobial activities than 5‐phenyl‐1,3,4‐oxadiazole‐2‐thiol.     

DFT study on abstraction reaction mechanism of oh radical with 2‐methoxyphenol

Reaction mechanism of 2‐methoxyphenol (2MP) (guaiacol) with OH radical has been performed using density functional theory methods BH&HLYP and MPW1K method with 6‐311++G(d,p) basis set. Single‐point energy calculations were done using CCSD(T)/6‐311++G(d,p). The theoretical results reveal that the hydrogen abstraction from methoxy group is found to be the dominant reaction channel with an energy barrier of 9.31 kcal/mol. Also, time‐dependent density functional theory calculations have been performed using BH&HLYP/6‐311++G(d,p) level of theory, and the results reveal that the reactions occur in ground state than the excited state. The results of reaction force profile indicate that structural rearrangements are most influential with high percentage than the relaxation process. The calculated theoretical rate constants (12.19 × 10^?11 cm³ molecule^?1 s^?1) are in good agreement with the experimental rate constant. The atmospheric lifetime of 2‐methoxyphenol with respect to OH radicals is 2.27 hours, which implies that OH radical plays an important role in the degradation of 2MP. The Wiberg bond index of the abstraction reaction reveals that the bond order is concerted, partially synchronic. The reactant‐like transition state satisfies Hammond postulate, which eventually results in an exothermic reaction, and the product‐like transition state reveals in endothermic nature.     

FT-IR,FT-Raman spectra and quantum mechanical study of piperidine-3-carboxylic acid and its tautomers,isomers

The mid-IR, far-IR, and Raman spectra of piperidine-3-carboxylic acid were measured and interpreted with support of the MP2 and B3LYP/6-311++G(d, p) calculated harmonic vibrational spectra. 10 stable piperidine-3-carboxylic acid tautomers/isomers were found after B3LYP, calculations. The experimental absorption bands of carboxylate (COO^?) group show that the free piperidine-3-carboxylic acid molecule exists in zwitterionic form and the most stable tautomer (NAT-1) can be stabilized by an intramolecular N-H...O hydrogen bond. All vibrational frequencies of NAT-1 assigned in detail with the help of total energy distribution (TED). The experimental vibrational wave numbers were compared with the calculated data.     

Gas-phase quasi-degeneracy of zwitterionic and canonical tautomers of glycine and proline induced by the presence of the MAlF4 (M = Li,Na, K) salts

The ionic MAlF₄ salts (M = Li, Na, K) are postulated to act as effective stabilising agents with respect to glycine and proline zwitterionic tautomers. On the basis of ab-initio MP2/6-311++G(d,p) theoretical calculations, it is demonstrated that strong electrostatic interactions between the polar MAlF₄ moiety and either Gly and Pro zwitterion should allow to suppress the intra-molecular proton transfer in the amino acid and thus render the zwitterion tautomer stable in the gas phase. Among the systems proposed, the K⁺AlF₄^– turned out to be the most efficient stabilising compound as its presence is expected to lead to the energetic quasi-degeneracy of the canonical and zwitterionic tautomers of glycine and proline.     

Structural and vibrational study of 2‐(2′‐ furyl)‐4,5‐1H‐dihydroimidazole

In this study 2‐(2′‐furyl)‐4,5‐1H‐dihydroimidazole (1) was prepared and then characterized by infrared, Raman, and multidimensional nuclear magnetic resonance (NMR) spectroscopies. The crystal and molecular structures of 1 were determined by X‐ray diffraction methods. The density functional theory (DFT) and second‐order Møller–Plesset theory (MP2) with Pople's basis set show that there are two conformers for the title molecule that have been theoretically determined in the gas phase, and that only one of them, conformer I, is present in the solid phase. NMR spectra observed for 1 were successfully compared with the calculated chemical shifts at the B3LYP/6‐311++G** level theorized for this conformer. The harmonic vibrational frequencies for the optimized geometry of the latter conformer were calculated at the B3LYP/6‐311++G** level in the approximation of the isolated molecule. For a complete assignment of the IR and Raman spectra in the solid phase of 1 , DFT calculations were combined with Pulay´s scaled quantum mechanics force field (SQMFF) methodology to fit the theoretical frequency values to the experimental ones. Copyright © 2009 John Wiley & Sons, Ltd.     

Double proton transfer in crystals of 1,3,4,6,7,8‐hexahydro‐2H‐pyrimido[1,2‐a] pyrimidine (hppH): 13C and 15N CPMAS NMR study of (hppH)2

In this paper, we report an example of intermolecular solid‐state proton transfer in the bicyclic guanidine, hppH. A combination of X‐ray crystallography, CPMAS NMR (¹³C and ¹⁵N) and theoretical calculations allows us to determine that a double proton transfer takes place in the (hppH)₂ dimer with an activation energy of about 50 kJ mol^?1. According to the B3LYP/6‐311++G(d,p) calculations, the double proton transfer occurs non‐symmetrically through a zwitterion. Copyright © 2009 John Wiley & Sons, Ltd.     

Mass spectrometric and ab initio study of the interaction between 9-methylguanine and amino acid amide group

The temperature dependent field ionization mass spectrometry method combined with ab initio calculations was used to determine the interaction energies and the structures of 9-methylguanine-acrylamide dimers. Acrylamide mimics the side chain amide group of the natural amino acids asparagine and glutamine. The experimental enthalpy of the dimer formation derived from the van't Hoff plot is ?59.5 ± 3.8 kJ mol^?1. The value is higher than interaction energies between acrylamide and other nucleic acid bases which were determined to be ?57.0 for 1-methylcytosine, ?52.0 for 9-methyladenine, and ?40.6 kJ mol^?1 for 1-methyl-uracil. In total, eight hydrogen bonded dimers formed by the three lowest energy 9-methylguanine tautomers and acrylamide were found in the quantum chemical calculations performed at the DFT/B3LYP/6-31++G?? and MP2/6-31++G?? levels of theory. The relative stability and the interaction energies of the dimers were calculated accounting for the basis set superposition error and the zero-point vibrational energy correction. The lowest energy dimer found in the calculations is formed by acrylamide (Ac) with the keto tautomer of 9-methylguanine (Gk). It is stabilized by two intermolecular H bonds, C6=O(Gk) · · · H—N(Ac) and Nl—H(Gk) · · ·O(Ac), and it is more stable than the second lowest energy dimer by ≈ 25 kJ mol^?1. The calculated interaction energies of the lowest energy 9-methylguanine-acrylamide dimer are ?65.0 kJ mol^?1 and ?67.7 kJ mol^?1 at the MP2 and DFT levels of theory, respectively. The experimental enthalpy of the dimer formation is in good agreement with both the calculated interaction energies of the GkAc dimer and much higher than the interaction energies calculated for all other 9-methylguanine-acrylamide dimers. This proved that only one dimer was present in the experimental samples. To verify whether acrylamide is a good model of the amino acid-amide group, we performed direct calculations of the 9-methylguanine-glutamine dimers at the same levels of theory as used for the complexes involving acrylamide. The interaction energies found for the lowest energy 9-methylguanine-glutamine dimer are ?65.1 kJ mon^?1 (MP2/6-31++G??) and ?66.2 kJ mol^?1 (DFT/B3LYP/6-31++G??) and these values are very close (within 0.5 kJ mol^?1) to the interaction energies obtained for the 9-methylguanine-acrylamide dimers.     

Tautomerism,dynamic properties and level crossing in 2‐(pyridin‐2‐yl) furan‐3‐ol by density functional theory and natural bond orbital analysis

2‐(Pyridin‐2‐yl)furan‐3‐ol (PYFO, T1) and (2E)‐2‐(pyridin‐2(1H)‐ylidene)furan‐3(2H)‐one (PYFO, T2) were considered to study their tautomerism interconversions, relative rotations of rings, OH bond rotations, and possibility of crossing between those energy surfaces using density functional theory methods at the Becke, three‐parameter, Lee–Yang–Parr/6‐311++G** level of theory. The optimized structures of both tautomers and the transition state of tautomerism are completely planar. A study of tautomerism in PYFO shows that T1 tautomer is about 24.38 kJ/mol more stable than T2. The rate constants of tautomerism interconversion for converting T1 to T2 is 1.98 × 10⁸ M^–1 s^–1 and for converting T2 to T1 is 3.70 × 10¹² M^–1 s^–1 at room temperature that show the possibility of this tautomerism with high rate at ambient temperature. Rotation of OH bond in T1 shows two minimum (at 0° (global minimum) and 180° (local minimum)) and a transition state at 110° (and 265°) with 47.10 kJ/mol barrier energy. Relative rotation of rings shows global minimum at 0° for both tautomers and local minimum at 154° and 206° for T1 and 180° for T2. The barrier energy for ring rotation of T1 was observed at 90° and 270° with 63.69 kJ/mol height and for T2 was observed at 120 with 170.86 kJ/mol height. Interestingly, the energy levels of ring rotations for T1 and T2 are the same and crossing between them was observed. Therefore, although these two potentials do not have the same symmetries, because of the crossing between their energy level, crossing is not avoided. Copyright © 2011 John Wiley & Sons, Ltd.