Experimental (FTIR and FT-Raman) and ab initio and DFT study of vibrational frequencies of 5-amino-2-nitrobenzoic acid

The FTIR and FT-Raman spectra of 5-amino-2-nitrobenzoic acid (ANB) have been recorded in the region 400-4000cm(-1). The observed frequencies were assigned to different modes of vibrations on the basis of fundamental, combination and overtones. The geometry has been optimized with complete relaxation on the potential energy surface at HF, MP2 and B3LYP level of theories using 6-311++G(d,p) basis set and compared with the crystal data. The possible hydrogen bond interaction has been estimated taking a model compound. Further harmonic vibrational frequency calculations have been carried out at HF and B3LYP levels and the scaled values were in good agreement with majority of the experimental observations. The theoretically constructed spectra coincide satisfactorily with those of experimental spectra.     

Solid state characterization of an antioxidant alkaloid boldine using vibrational spectroscopy and quantum chemical calculations

Boldo (Peumus boldus Mol.), a Chilean tree traditionally employed in folk medicine and recognized as a herbal remedy in a number of pharmacopoeias, mainly for the treatment of liver ailment, has recently been the subject of increasing attention. Boldine, in particular, the major and most characteristic alkaloid constituent of this plant species, now emerges as its most interesting active principle from the pharmacological viewpoint.In the present work the structural and spectral characteristics of boldine have been studied by methods of infrared, Raman spectroscopy and quantum chemistry. Electrostatic potential surface, optimized geometry, harmonic vibrational frequencies, infrared intensities and activities of Raman scattering were calculated by ab initio Hartree-Fock (HF) and density functional theory (DFT) employing B3LYP with complete relaxation in the potential energy surface using 6-311G(d,p) basis set. A complete vibrational assignment is provided for the observed Raman and infrared spectra of boldine molecule.     

The stereoselective addition of titanium(IV) enolates of 1,3-oxazolidin-2-one and 1,3-thiazolidine-2-thione to cyclic N-acyliminium ion. The total synthesis of (+)-isoretronecanol

(+)-Isoretronecanol (1) has been prepared in four steps and 36% overall yield via the diastereoselective addition of the titanium(IV) enolate derived from N-4-chlorobutyryl-1,3-thiazolidine-2-thione (3) to N-Boc-2-methoxypyrrolidine (5), which afforded 2-substituted pyrrolidine 7 in 84% yield (8:1 diastereoisomeric ratio), followed by reductive recovery of the chiral auxiliary and cyclization.     

Structural, vibrational and ab initio studies of L-histidine oxalate

Single crystals of L-histidine oxalate were obtained by slow evaporation of an aqueous solution at room temperature. The grown crystals have been subjected to X-ray diffraction (XRD), Infrared, and Raman spectroscopy. The title compound crystallises in the non-centrosymmetric space group P2(1)2(1)2(1,) the crystal cohesion is achieved by relatively strong hydrogen bonds, so that the NH3 groups show significant distortion with respect to the tetrahedral symmetry. Raman and infrared spectra of the title compound were recorded in the frequency range 300-3200 and 400-4000 cm-1, respectively. To obtain a reliable assignment of the observed spectral lines, we have calculated the geometry and the frequencies of the vibrational modes of histidine cation and the oxalate anion using the semi empirical PM3 method.     

2-Trif luoromethyl-4H-thiochromen-4-one and 2-trif luoromethyl-4H-thiochromene-4-thione: Synthesis and reactivities

2-Trifluoromethyl-4H-thiochromene-4-thione obtained from 2-trifluoromethyl-4H-thiochromen-4-one and P₂S₅ reacts with aromatic amines, hydrazine hydrate, phenylhydrazine, and hydroxylamine at the C(4) atom of the chromene ring to give the corresponding anils, azine, hydrazones, and oxime of thiochromone. 2-Trifluoromethyl-4H-thiochromen-4-one is oxidized by hydrogen peroxide in AcOH into 4-oxo-2-trifluoromethyl-4H-thiochromene 1,1-dioxide and reduced by NaBH₄ to 2-trifluoromethyl-4H-thiochromen-4-ol or cis-2-(trifluoromethyl)thiochroman-4-ol. When treated with hydrazine hydrate, thiochromen-4-one gives 3(5)-(2-mercaptophenyl)-5(3)-trifluoromethylpyrazole. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 504–509, March, 2006.     

Ab initio, density functional theory and structural studies of 4-amino-2-methylquinoline

The Fourier transform infrared (FTIR) and FT-Raman spectra of 4-amino-2-methylquinoline (AMQ) have been recorded in the range 4000–400 and 4000–100 cm⁻¹, respectively. The experimental vibrational frequency was compared with the wavenumbers obtained theoretically by ab initio HF and DFT–B3LYP gradient calculations employing the standard 6-31G** and high level 6-311++G** basis sets for optimised geometry of the compound. The complete vibrational assignment and analysis of the fundamental modes of the compounds were carried out using the experimental FTIR and FT-Raman data, and quantum mechanical studies. The geometry and normal modes of vibration obtained from the HF and DFT methods are in good agreement with the experimental data. The potential energy distribution of the fundamental modes was calculated with ab initio force fields utilising Wilson's FG matrix method. The NH-π interactions and the influence of amino and methyl groups on the skeletal modes are investigated.     

Theoretical and experimental study of molecular structure and vibrational spectra of <Emphasis Type="Italic">N</Emphasis>-(2-pyridylmethyl)-2-pyrazinecarboxamide

N-(2-Pyridylmethyl)-2-pyrazinecarboxamide was prepared and its crystal structure was investigated by X-ray analysis. The compound crystallizes in the triclinic space group \(P{\bar 1}\) with a = 4.262(3), b = 12.117(9), c = 20.840(18) Å, α = 91.802(6), β = 89.834(7), γ = 91.845(6)°, V = 1075.2(16) ų, Z = 4, and D = 1.323?Mg/m³. The structure was solved by direct method and refined to R = 0.0699 and wR ₂ = 0.1268 by full matrix anisotropic least-squares method. Using the Hartree-Fock and density functional method (B3LYP) with 6-31G(d) basis set, the molecular geometry and vibrational frequencies of the title compound has been investigated and compared with experimental ones from experimental studies. The optimized bond lengths obtained by RHF method and bond angles obtained by B3LYP method show better agreement with the experimental values. The vibrations computed of the title compound by the RHF and DFT methods are in good agreement with the observed IR spectra data.     

The molecular structure and vibrational spectra of 2-chloro-N-(diethylcarbamothioyl)benzamide by Hartree-Fock and density functional methods

2-Chloro-N-(diethylcarbamothioyl)benzamide (C(12)H(15)ClN(2)OS) has been synthesized and characterized by elemental analysis and IR spectroscopy. The crystal and molecular structure of the title compound has been determined from single crystal X-ray diffraction data. It crystallizes in the orthorhombic space group Pbca, Z=8 with a=9.581(3)A, b=9.992(3)A, c=26.640(8)A, V=2550.5(13)A(3) and D(calc)=1.410 Mg/m(3). The molecular geometry and vibrational frequencies of 2-chloro-N-(diethylcarbamothioyl)benzamide in the ground state have been calculated using the Hartree-Fock and density functional using Becke's three-parameter hybrid method with the Lee, Yang and Parr correlation functional (B3LYP) methods with 3-21G and 6-31G(d) basis sets. The calculated geometric parameters were compared to the corresponding X-ray structure of the title compound. The raw B3LYP frequencies approximate the experimental data much better than the results of Hartree-Fock. The scaled B3LYP/6-31G(d) results were more reliable than those obtained using the B3LYP/3-21G method with the mean absolute deviation about 13.7 cm(-1). On the basis of the comparison between calculated and experimental results, assignments of fundamental vibrational modes were examined.     

The molecular structure and vibrational spectra of 3-acetyl-4-[N-(2'-aminopyridinyl)-3-amino]-3-buten-2-one by Hartree-Fock and density functional theory calculations

The molecular structure and vibrational spectra of 3-acetyl-4-[N-(2'-aminopyridinyl)-3-amino]-3-buten-2-one (C(11)H(13)N(3)O(2)) in the ground state have been investigated by Hartree-Fock and density functional method (B3LYP and BLYP) with 6-31G(d) basis set. The optimized geometric bond lengths and bond angles obtained by using HF and DFT show the best agreement with the experimental data. Comparison of the observed fundamental vibrational frequencies of title compound and calculated results by HF and DFT methods indicate that B3LYP is superior to the scaled HF approach for molecular problems.     

Hydration of l-tyrosine in aqueous medium. An experimental and theoretical study by mixed quantum mechanical/molecular mechanics methods

Quantum mechanical/molecular mechanics (QM/MM) calculations were carried out in order to study the theoretical structures of l-tyrosine in both gas phase and in aqueous solution and observe the changes that occur on the structural and vibrational properties in two phases. Therefore, the molecule was characterized by infrared and Raman spectroscopy in solid phase and aqueous solution. Optimized geometries and relative stabilities for the zwitterion l-tyrosine derivatives have been calculated taking into account the solvent effects by using the self-consistent reaction field (SCRF) theory. For a complete assignment of the IR and Raman spectra of l-tyrosine in solid and aqueous solution phases, density functional theory (DFT) calculations were combined with Pulay's scaled quantum mechanical force field (SQMFF) methodology in order to fit the theoretical wavenumber values to the experimental ones. A good agreement between theoretical and available experimental results is found.     

Infrared and Raman spectra, conformational stability and vibrational assignment of 1-chloro-1-silacyclopentane

Infrared and Raman spectra (3500-60 cm⁻¹) of gas and/or liquid and solid 1-chloro-1-silacyclopentane (c-C₄H₈SiClH) have been recorded and the vibrational data indicate the presence of a single conformer with no symmetry which is consistent with the twisted form. Ab initio calculations with a variety of basis sets up to MP2(full)/aug-cc-pVTZ predict the envelope-axial and envelope-equatorial conformers are saddle points with nearly the same energies but much lower in energy than the planar conformer. Density functional theory calculations by the B3LYP method predicts slightly lower energies for the two envelope forms and considerably lower for the planar form. By utilizing the MP2(full)/6-31G(d) calculations the force constants, frequencies, infrared intensities, band contours, Raman activities, and depolarization values have been obtained to support the vibrational assignment. Estimated r₀ structural parameters have been obtained from adjusted MP2(full)/6-311 + G(d, p) calculations. These experimental and theoretical results are compared to the corresponding quantities of some other five-membered rings.     

Spectroscopic and structural elucidation of L-tyrosine-containing dipeptides valyl-tyrosine and tyrosyl-alanine: solid-state IR-LD spectroscopy, quantum chemical calculations and vibrational analysis

L-Tyrosine-containing dipeptides valyl-tyrosine (H-Val-Tyr-OH) and tyrosyl-alanine (H-Tyr-Ala-OH) are characterized structurally by means of quantum chemical ab initio calculations and solid-state linear-dichroic infrared (IR-LD) spectroscopy. The IR-characteristic bands are assigned by application of reducing-difference procedure for polarized IR-spectra interpretation. Infrared data obtained are supported as well by the made vibrational analysis. The structures of both peptides are predicted on the basis of conformational analysis and structural information, obtained by the shown IR-spectroscopic tool.     

Combined application of 2D NMR correlation methods and ab initio chemical shift calculations to the structure determination of new heterocyclic compounds

The combined use of 2D NMR correlation methods and ab initio chemical shift calculations is efficient and, in some cases, virtually the only way to determine the structures of new organic compounds. This approach enabled us to establish the structure of the major unusual product of the three-component reaction of imidazo[1,5-a]quinoxalin-4-one, bis(2-chloroethyl)amine hydrochloride, and potassium carbonate in DMF. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2172–2179, December, 2006. Dedicated to Professor A. V. Il’yasov on the occasion of his 70th birthday.     

Molecular Structure of an Isocytosine Analog: Combined X-ray Structural and Computational Study of 2-Diethylamino-6-methyl-5-n-propyl-4(3H)-pyrimidinone

The structure of 2-diethylamino-6-methyl-5-n-propyl-4(3H)-pyrimidinone has been studied by X-ray crystallography and quantum-chemical calculations. X-ray analysis established that 2-diethylamino-6-methyl-5-n-propyl-4(3H)-pyrimidinone exists exclusively as the lactam tautomer protonated at the N3 ring nitrogen in the solid state. Crystals of 2-diethylamino-6-methyl-5-n-propyl-4(3H)-pyrimidinone are monoclinic (space group P2₁/n); the unit-cell dimensions are: a = 11.0460(8) Å, b = 5.0064(4) Å, c = 22.8358(17) Å, = = 90°, = 90.521(1)°. In the crystal, molecules of 2-diethylamino-6-methyl-5-n-propyl-4(3H)-pyrimidinone are assembled in planar centrosymmetric dimers by strong resonance-assisted N—H···O intermolecular hydrogen bonds from the NH group of one molecule to the C=O of the adjacent molecule (N—H···O distance 2.804 Å). Bond distances and angles are generally similar to those reported for the corresponding tautomer of isocytosine and derivatives. Quantum-chemical calculations on 2-diethylamino-6-methyl-5-n-propyl-4(3H)-pyrimidinone are also reported in order to estimate the relative energies of the possible tautomeric forms; ab initio and DFT results predict the coexistence of the N3 and AH tautomers in the gas phase. There is excellent correspondence between the crystal and the HF/6-311G** or B3LYP/6-31G* calculated structures of the N3 lactam form; the largest deviations between the experimental and computed structures are mostly the effects of strong intermolecular H bonds in the crystal.     

Reaction of 6-methoxybenzo[b]furan-3(2H)-one and benzo[b]thiophen-3(2H)-one with 2-aryl-1,1-dicyanoethylenes as a convenient synthetic route to substituted 2-amino-4-aryl-1,3-dicyano-7-methoxydibenzo[b,d]furans and 2-amino-4-aryl-3-cyano-4H-benzothieno[3,2-b]pyrans

The reactions of 6-methoxybenzo[b]furan-3(2H)-one with 2-aryl-1,1-dicyanoethylenes and malononitrile or with aromatic aldehyde and two moles of malononitrile afford 2-amino-4-aryl-1,3-dicyano-7-methoxydibenzo[b,d]furans. The reactions of benzo[b]thiophen-3(2H)-one with 2-aryl-1,1-dicyanoethylenes or with aromatic aldehyde and one mole of malononitrile produce 2-amino-4-aryl-3-cyano-4H-benzothieno[3,2-b]pyrans.     

An Ab Initio Molecular Orbital Theory and Density Functional Theory (DFT) Study of Conformers and Rotamers of 4-Substituted (Methyl, Hydroxymethyl, Methanoyl, Ethanoyl, Cyano, Fluoro, Chloro, Bromo, Acetoxy) Tetrahydro-2H-thiopyran-1,1-dioxides

The structures and energies of axial and equatorial conformers and rotamers of 4-substituted tetrahydro-2H-thiopyran-1,1-dioxides (tetrahydrothiopyran-1,1-dioxides, thiacyclohexane-1,1-dioxides, thiane-1,1-dioxides, and 1,1-dioxothianes; CH₃, CH₂OH, CHO, COCH₃, CN, F, Cl, Br, and OCOCH₃) were calculated using the hybrid density functionals B3LYP, B3P86, and B3PW91, as well as MP2 and the 6-31G(d), 6-31G(2d), 6-31G(3d), 6-31G(d,p), and 6-31+G(d) basis sets. MP2/6-31+G(d)/ /HF/6-31+G(d) [–G° = 1.73 kcal/mol], B3P86/6-31G(d) [–G° = 1.75 kcal/mol], and B3PW91/6-31G(d) [–G° = 1.85 kcal/mol] gave conformational free energy (G°) values at 180 K for 4-methyltetrahydro-2H-thiopyran-1,1-dioxide which were similar to the reported experimental values for methylcyclohexane (–G° = 1.80 kcal/mol), 4-methyltetrahydro-2H-thiopyran (–G° = 1.80 kcal/mol), and other 4-methyl-substituted heterocycles. All levels of theory showed that the conformational preferences of the 4-methanoyl (4-formyl), 4-ethanoyl (4-acetyl), and 4-cyano substituents were small. The HF calculations gave conformational free energy (G°) values for 4-chlorotetrahydro-2H-thiopyran-1,1dioxide which were closer to the experimental value than the MP2 and density functional methods. The best agreement with available experimental data for 4-bromotetrahydro-2H-thiopyran-1,1-dioxide was obtained from the HF/6-31G(2d), HF/6-31G(3d), and B3LYP/6-31G(2d) calculations, and, for 4-acetoxytetrahydro-2H-thiopyran-1,1-dioxide, from the HF/6–31G(3d) calculations. The conformational free energies (G°) and relative energies (E) of the conformers and rotamers have been compared with the correspondingly substituted cyclohexanes and tetrahydro-2H-thiopyrans and are discussed in terms of dipole–dipole (electrostatic) interactions and repulsive nonbonded interactions (steric) in the most stable axial and equatorial conformers. The axial S=O bond lengths are shorter than the equatorial S=O bond lengths and the C2–C3 bond lengths in the substituents with carbon-bonded to the ring are shorter than the C3–C4 and C4–C-5 bond lengths. In contrast, the C2–C3 bond lengths in the 4-halogen and 4-acetoxy substituents are longer than the C3–C4 and C4–C-5 bond lengths.     

Theoretical studies of atmospheric molecules: SCF and correlated energy levels for the NO2, NO 2 + and NO 2 − systems

SCF and MC-SCF/CI calculations were carried out on the low-lying electronic states of NO₂, NO ₂ ⁺ and NO ₂ ^– , using a double-zeta quality basis set of contracted Gaussian functions. The calculations were performed primarily at the equilibrium geometry (R _NO = 2.25 a_o, _ONO=134 °) of theX ² A ₁ state of NO₂. SCF calculations on NO ₂ ⁺ in a linear conformation were also performed. Results are presented and compared with experiment and other calculations.Research supported in part by Air Force Delivery Orders F33615-72-M-5015 and MIPR889474-00117 and Air Force Office of Scientific Research and in part by the United States Energy Research and Development Administration.     

Zinc(II) Hydration in Aqueous Solution: A Raman Spectroscopic Investigation and An ab initio Molecular Orbital Study of Zinc(II) Water Clusters

Raman spectra of aqueous Zn(II)–perchlorate solutions were measured over broad concentration (0.50–3.54 mol-L^–1) and temperature (25–120°C) ranges. The weak polarized band at 390 cm^–1 and two depolarized modes at 270 and 214 cm^–1 have been assigned to ₁(a _1g), ₂(e _g), and ₅(f _2g) of the zinc–hexaaqua ion. The infrared-active mode at 365 cm^–1 has been assigned to ₃(f _1u). The vibrational analysis of the species [Zn(OH₂) ₂ ⁺ ] was done on the basis of O _h symmetry (OH₂ as point mass). The polarized mode ₁(a _1g)-ZnO₆ has been followed over the full temperature range and band parameters (band maximum, full width at half height, and intensity) have been examined. The position of the ₁(a _1g)-ZnO₆ mode shifts only about 4 cm^–1 to lower frequencies and broadens by about 32 cm^–1 for a 95°C temperature increase. The Raman spectroscopic data suggest that the hexaaqua–Zn(II) ion is thermodynamically stable in perchlorate solution over the temperature and concentration range measured. These findings are in contrast to ZnSO₄ solutions, recently measured by one of us, where sulfate replaces a water molecule of the first hydration sphere. Ab initio geometry optimizations and frequency calculations of [Zn(OH₂) ₂ ⁺ ] were carried out at the Hartree–Fock and second-order Møller–Plesset levels of theory, using various basis sets up to 6-31 + G*. The global minimum structure of the hexaaqua–Zn(II) species corresponds with symmetry T _h. The unscaled vibrational frequencies of the [Zn(OH₂) ₂ ⁺ ] are reported. The unscaled vibrational frequencies of the ZnO₆, unit are lower than the experimental frequencies (ca. 15%), but scaling the frequencies reproduces the measured frequencies. The theoretical binding enthalpy for [Zn(OH₂) ₂ ⁺ ] was calculated and accounts for ca. 66% of the experimental single-ion hydration enthalpy for Zn(II).Ab initio geometry optimizations and frequency calculations are also reported for a [Zn(OH₂) ₂ ¹⁸ ] (Zn[6 + 12]) cluster with 6 water molecules in the first sphere and 12 in the second sphere. The global minimum corresponds with T symmetry. Calculated frequencies of the zinc [6 + 12] cluster correspond well with the observed frequencies in solution. The ₁-ZnO₆ (unscaled) mode occurs at 388 cm^–1 almost in perfect correspondence to the experimental value. The theoretical binding enthalpy for [Zn(OH₂) ₂ ¹⁸ ] was calculated and is very close to the experimental single ion-hydration enthalpy for Zn(II). The water molecules of the first sphere form strong hydrogen bonds with water molecules in the second hydration shell because of the strong polarizing effect of the Zn(II) ion. The importance of the second hydration sphere is discussed.