Experimental and theoretical investigation of the electronic structure of 5-fluorouracil compounds

We present a comparison between experimental and theoretical X-ray absorption spectroscopy (XAS) and X-ray emission spectroscopy (XES) of 5-fluorouracil compounds, with an emphasis on the effects of the inclusion of nickel in the structure. By focusing on the 1s thresholds of carbon, nitrogen, oxygen, and fluorine it was possible to provide a complete picture of the occupied and unoccupied partial density of states of the 5-fluorouracil systems. Spectra calculated using density functional theory are compared to experimental results. Most experimental results agree well with our theoretical calculations for the XAS and XES of the compounds. All spectral features are assigned. Our results reveal that the nickel in the compound is coordinated with the nitrogen sites of the 5-fluorouracil ligands.     

Ab initio and density functional computations of the vibrational spectrum, molecular geometry and some molecular properties of the antidepressant drug sertraline (Zoloft) hydrochloride

Sertraline hydrochloride is a highly potent and selective inhibitor of serotonin (5HT). It is a basic compound of pharmaceutical application for antidepressant treatment (brand name: Zoloft). Ab initio and density functional computations of the vibrational (IR) spectrum, the molecular geometry, the atomic charges and polarizabilities were carried out. The infrared spectrum of sertraline is recorded in the solid state. The observed IR wave numbers were analysed in light of the computed vibrational spectrum. On the basis of the comparison between calculated and experimental results and the comparison with related molecules, assignments of fundamental vibrational modes are examined. The X-ray geometry and experimental frequencies are compared with the results of our theoretical calculations.     

Electronic structure of the nucleobases

We present a comparison between experimental and calculated soft X-ray spectra of DNA's nucleobases, adenine (A), guanine (G), cytosine (C), and thymine (T) using X-ray absorption spectroscopy (XAS) and soft X-ray emission spectroscopy (XES). Spectra of the 1s thresholds of carbon, nitrogen, and oxygen give a complete picture of the occupied and unoccupied partial density of states of the nucleobases. A combination of both Hartree-Fock and density functional theory calculations are used in the comparison to experimental results. Most experimental results agree well with our theoretical calculations for the XAS and XES of all bases. All spectral features are assigned. A comparison of the experimental highest occupied molecular orbital-lowest unoccupied molecular orbital energy gaps is made to the diverse values predicted in the literature.     

The most stable tautomer of 3-amino-1,2,4-triazin-5-one and its structural geometry

With the purpose of finding predominant tautomer among five possible isomers of 3-amino-1,2,4-triazin-5-one and to refine some unreasonable structural parameters previously reported from X-ray diffraction measurements, a series of ab initio calculations were carried out. In agreement with previous results, our calculations show that 3-amino-1,2,4-triazin-5(2H)-one tautomer is the most stable one. Concerning the predominant tautomer, comparisons were made between structural parameters calculated and those obtained by X-ray crystallographic analysis. The structural geometry of the main skeleton of the molecule calculated by the B3LYP/6-311++G** density functional method are generally in good agreement with the experimental values, and those predicted by Pauling's method. Bond distance values calculated are in excellent agreement with the conventionally accepted bond lengths in similar molecules. All bond distances, bond angles, dihedral angles, dipole moments and rotational constants are presented.     

Formation of the background component of the analytical signal in the long-wavelength region of X-ray fluorescence spectrum

Components of X-ray background in the long-wavelength spectral region of a crystal diffraction X-ray fluorescence spectrometer were calculated. The calculations took into account the bremsstrahlung radiation of free electrons, diffuse scattering and fluorescence of the crystal analyzer, and high-order reflections of the scattered radiation of the fluorescent sample by the crystal analyzer. The results of calculations were compared with the intensities of background samples measured in the region of the NaK _α fluorescence line on an SRM-25 wave X-ray spectrometer. The experimental background intensities (response function) well correlate with those found by the regression equation with calculated factors. The importance of particular processes in the formation of X-ray background was assessed.     

DFT computations,vibrational spectra,monomer, dimer,NBO and NMR analyses of antifungal agent: 3,5-Dibromosalicylic acid

The experimental and theoretical study on the structures and vibrations of 3,5-dibromosalicylic acid (DBSA) are presented. The FT-IR and FT-Raman of the title compound have been recorded. The molecular structures, vibrational wavenumbers, infrared intensities, Raman activities were calculated. The energies of DBSA are obtained for all the eight conformers from density functional theory with 6-311++G(d,p) basis set calculations. From the computational results, C1 or C5 forms are identified as the most stable conformers of DBSA. The spectroscopic and theoretical results are compared with the corresponding properties for DBSA monomer and dimer of C1 (or C5) conformer. Intermolecular hydrogen bonds are discussed in dimer structure of the molecule. NBO analysis is useful to understand the intramolecular hyperconjugative interaction between lone pair O9 and C7O8. The calculated HOMO–LUMO energies reveal charge transfer occurs within the molecule. The polarizability, first hyperpolarizability, anisotropy polarizability invariant has been computed using quantum chemical calculations. The isotopic chemical shift computed by ¹H and ¹³C nuclear magnetic resonance (NMR) chemical shifts of the DBSA molecule, calculated using the gauge invariant atomic orbital (GIAO) method, also shows good agreement with experimental observations.     

FT-IR,XPS, and DFT Study of Adsorption Mechanism of Sodium Acetohydroxamate onto Goethite or Hematite

The adsorption of sodium acetohydroxamate on the goethite or hematite surface was investi-gated by Fourier transform infrared spectroscopy (FT-IR), X-ray photoemission spectroscopy and periodic plane-wave density functional theory (DFT) calculations. The core-level shifts and charge transfers of the adsorbed surface iron sites calculated by DFT with periodic in-terfacial structures were confronted to the X-ray photoemission experiments. FT-IR results reveal that the interfacial structure of sodium acetohydroxamate adsorbed on the goethite or hematite surface may be assigned to a ve-membered ring complex. In agreement with the adsorption energies determined by the DFT calculations, a ve-membered ring complex is formed via bonding of one surface iron atom of goethite (101) or (100) to both oxygen atoms of hydroxamate group, and these two oxygen atoms of the hydroxamate group correspond-ingly attach to two neighboring iron atoms of the goethite surface. But a ve-membered ring complex between two oxygen atoms of the hydroxamate group and one surface iron atom of hematite (001) is formed without any extra attachments. The calculated core-level shifts of Fe2p for the interfacial structures are correspondingly in good agreement with the experimental observed one, which con rmed the reliability of the calculated results.     

Synthesis, molecular structure and vibrational spectra of a dimeric complex formed by cobalt and glycine

The structure of [Co(gly)(2)(OH)(2)].1.5(H(2)O) was solved by X-ray diffraction. It crystallizes in the space group P-1, with two independent dimmers in the unit cell. The results for the calculated vibrational spectra are in good agreement with the experimental one. The infrared spectrum and ab initio calculations are consistent with the crystallographic results.     

Theoretical and experimental study of the structure and vibration spectra of 4,4′-carbonyl-di-morpholine

4,4′-Carbonyl-di-morpholine was synthesized and characterized by X-ray diffraction, the FTIR and NMR spectra. The extended MO calculations using density functional theory (DFT) and self-consistent field molecular orbital Hartree-Fock theory were carried out. The results of the calculations were compared with experimental data. The experimental and calculated results were supported each other. The performance of a hybrid B3LYP density functional was compared with the ab initio restricted Hartree-Fock method. With the basis sets of the 6-311G** quality, the DFT calculated bond lengths, dipole moments and harmonic vibrations were predicted in a very good agreement with available experimental data.     

新型π-扩展TTF衍生物的合成、晶体结构及量子化学计算

以对苯二胺为起始原料合成了2个新型的π-扩展四硫富瓦烯(TTF)衍生物,即N,N’-2(4,5-二苄硫基-1,3-二硫杂环戊烯-2-叶立德)-苯-1,4-二胺(5a)和N,N’-2(4,5-二甲酯基-1,3-二硫杂环戊烯-2-叶立德)-苯-1,4-二胺(5b),并利用氢核磁共振(1H NMR)、质谱(MS)、傅里叶变换红外光谱(FTIR)和单晶X射线衍射(XRD)等方法对化合物结构进行了表征.晶体结构分析结果表明,化合物5a和5b分属三斜晶系、P1空间群和单斜晶系、P21/n空间群.化合物5a和5b均为非平面结构分子,分子中对苯二亚胺平面和1,3-二硫杂环平面形成的二面角分别为87.61°(5a)和43.77°(5b).运用Gaussian 09程序,采用密度泛函理论(DFT)方法在B3LYP/6-31+G(d,p)水平上进行了量子化学计算,对化合物的前线分子轨道、静电势和电子吸收光谱进行了讨论,计算结果与实验值基本一致.     

Synthesis, characterization, crystal structure and DFT studies on 1-acetyl-3-(2,4-dichloro-5-fluoro-phenyl)-5-phenyl-pyrazoline

The title compound, 1-acetyl-3-(2,4-dichloro-5-fluoro-phenyl)-5-phenyl-pyrazoline, has been synthesized and characterized by elemental analysis, IR, UV-vis and X-ray single crystal diffraction. Density functional (DFT) calculations have been carried out for the title compound by using B3LYP method at 6-31G* basis set. The calculated results show that the predicted geometry can well reproduce the structural parameters. Predicted vibrational frequencies have been assigned and compared with experimental IR spectra and they are supported each other. The theoretical electronic absorption spectra have been calculated by using TD-DFT method. Molecular orbital coefficients analyses suggest that the above electronic transitions are mainly assigned to n-->pi* and pi-->pi* electronic transitions. On the basis of vibrational analyses, the thermodynamic properties of the title compound at different temperatures have been calculated, revealing the correlations between C(p,m)(0),S(m)(0),H(m)(0) and temperatures.     

Theoretical Aspects of the Acetonitrile Oxide Cycloaddition to tert-Butyl-, Trimethylsilyl-, and Trimethylgermyl-substituted Thiophene 1,1-Dioxides

The results of X-ray diffraction studies on molecular packing of tert-butyl-, trimethylsilyl-, and trimethylgermylthiophene 1,1-dioxides have been reviewed and analyzed. We also interpret their experimental and calculated UV spectra. Using quantum chemical calculations, we have studied the theoretical aspects of the acetonitrile oxide dipolar [2+3] cycloaddition to 2,5- and 2,4-disubstituted sulfones. The reasons for the regiospecificity of cycloaddition and desilylation have been explained.     

Microwave spectrum, rotational parameters, and DFT geometry calculations for trans- and cis-isomers of 2,5-dimethyl-1,3-dioxane

The microwave spectrum of 2,5-dimethyl-1,3-dioxane is studied. The spectrum is identified to have the a and c type rotational transitions of the trans- and cis-isomers of the molecule. The experimental frequencies of the transitions are used to calculate the rotational constants and the quartic centrifugal distortion constants of the isomers. The dipole moments are determined. Quantum chemical calculations are performed by the B3PW91/aug-cc-pVDZ density functional method. The calculated results are compared with the experimental data. The equilibrium geometries of 1,3-dioxane and 2-methyl-, 5-methyl-, and 2,5-dimethyl-1,3-dioxanes are compared. It is found that the alkyl substitution leads to a change in the ring geometry     

X-ray spectra and features of the electron energy structure of TaC, TaN, HfC, TaC0.5N0.5, and Hf0.5Ta0.5C

The electron energy structure of titanium and hafnium carbide, titanium and solid solutions of TaC_0.5N_0.5 and Hf_0.5Ta_0.5C nitride is investigated experimentally (by X-ray and X-ray photoelectron spectroscopy) and theoretically (based on the quantum mechanical calculations in a full multiple scattering approximation, by the program FEFF8 with a self-consistent semirelativistic potential). A good accordance between the calculated curves of the densities of electronic states and the corresponding experimental curves is obtained. The chemical bond features in the investigated compounds and solutions are revealed.     

Experimental (13C NMR, 1H NMR, FT-IR, single-crystal X-ray diffraction) and DFT studies on 3,4-bis(isoproylamino)cyclobut-3-ene-1,2-dione

In this work, 3,4-bis(isoproylamino)cyclobut-3-ene-1,2-dione C(10)H(16)N(2)O(2) (I), was synthesized and characterized by (13)C NMR, (1)H NMR, FT-IR, UV-vis spectroscopy and single-crystal X-ray diffraction. DFT method with 6-31G(d,p) basis set has been used to calculate the optimized geometrical parameters, atomic charges, vibrational frequencies and chemical shift values. The calculated vibrational frequencies and chemical shift values are compared with experimental FT-IR and NMR spectra. The results of the calculation shows good agreement between experimental and calculated values of the compound I. The existence of N-H?O type intermolecular ve C-H?O type intramolecular hydrogen bonds can be deduced from differences between experimental and calculated results of FT-IR and NMR. In addition, the molecular electrostatic potential map and frontier molecular orbitals and electronic absorption spectra were performed at B3LYP/6-31G(d,p) level of theory. HOMO-LUMO electronic transition of 4.90 eV are derived from the contribution of the bands π→π* and n→π* The spectral results obtained from FT-IR, NMR and X-ray of I revealed that the compound I is in predominantly enamine tautomeric form, which was supported by DFT calculations.     

Theoretical and Experimental Study on 3-Phenyl-5-Phenylazo-3H-[1,3,4] Thiadiazole-2-Thione

3-Phenyl-5-phenylazo-3H-[1,3,4] thiadiazole-2-thione has been synthesized and characterized by X-ray diffraction and FTIR spectra. An extended MO calculation using density functional theory (DFT) at B3LYP/6-31g* level has been carried out. The results of the calculations were compared with experimental data and they are found to support each other. The thermodynamic properties of the title compound at different temperatures also have been calculated on the basis of vibration analyses.     

Theoretical 13C chemical shift, 14N, and 2H quadrupole coupling- constant studies of hydrogen bonding in L-alanylglycine dipeptide

(13)C chemical shieldings and (14)N and (2)H electric field gradient (EFG) tensors of L-alanylglycine (L-alagly) dipeptide were calculated at RHF/6-31 + + G** and B3LYP/6-31 + + G** levels of theory respectively. For these calculations a crystal structure of this dipeptide obtained from X-ray crystallography was used. Atomic coordinates of different clusters containing several L-alagly molecules were used as input files for calculations. These clusters consist of central and surrounding L-alagly molecules, the latter forming short, strong, hydrogen bonds with the central molecule. Since the calculations did not converge for these clusters, the surrounding L-alagly molecules were replaced by glycine molecules. In order to improve the accuracy of calculated chemical shifts and nuclear quadrupole coupling constants (NQCCs), different geometry-optimization strategies were applied for hydrogen nuclei. Agreement between calculated and experimental data confirms that our optimized coordinates for hydrogen nuclei are more accurate than those obtained by X-ray diffraction.     

Inelastic X-ray scattering and vibrational effects at the K-edges of gaseous N2, N2O, and CO2

We report non-resonant inelastic X-ray scattering experiments of several gaseous samples in the inner-shell excitation energy range. The experimental near-edge spectra from all the K-edges of N(2), N(2)O, and CO(2) including the momentum transfer dependence are presented. The results are analyzed using density functional theory calculations that accurately reproduce the experimental spectral features. We observe vibrational effects in the measured spectrum and in the calculations the atomic motion is modeled using the Franck-Condon approximation and the linear coupling model. Our findings show that vibrational effects cannot be neglected in the analysis of high resolution inelastic X-ray scattering spectroscopy. The results also support the validity of the transition potential approximation for calculating core excited state potential energy surfaces.     

Determining the absolute configuration of (+)-mefloquine HCl, the side-effect-reducing enantiomer of the antimalaria drug Lariam

Even though the important antimalaria drug rac-erythro-mefloquine HCl has been on the market as Lariam for decades, the absolute configurations of its enantiomers have not been determined conclusively. This is needed, since the (-) enantiomer is believed to cause adverse side effects in malaria treatment resulting from binding to the adenosine receptor in the human brain. Since there are conflicting assignments based on enantioselective synthesis and anomalous X-ray diffraction, we determined the absolute configuration using a combination of NMR, optical rotatory dispersion (ORD), and circular dichroism (CD) spectroscopy together with density functional theory calculations. First, structural models of erythro-mefloquine HCl compatible with NMR-derived (3)J(HH) scalar couplings, (15)N chemical shifts, rotational Overhauser effects, and residual dipolar couplings were constructed. Second, we calculated ORD and CD spectra of the structural models and compared the calculated data with the experimental values. The experimental results for (-)-erythro-mefloquine HCl matched our calculated chiroptical data for the 11R,12S model. Accordingly, we conclude that the assignment of 11R,12S to (-)-erythro-mefloquine HCl is correct.     

NMR spectra of free-base porphine, porphyrazine, phthalocyanine and naphthalocyanine as well as their metal complexes: density functional calculations

Nuclear magnetic shielding tensors of porphine have been calculated at density functional B3LYP and PBE level using the gauge independent atomic orbital (GIAO) method. The geometries used were optimized using the 6-31G(d) basis set and the NMR calculations were performed using 6-31G(d) and 6-311G(d,p) basis sets, respectively. The calculated NMR shielding tensors and chemical shifts of porphine are compared with previous calculations as well as experimental data and satisfying results are obtained. Further NMR calculations are extended to metal-free and metallo-porphyrazine, -phthalocyanine, and -naphthalocyanine for the first time and the results are compared with experimental data available. The chemical shifts of the atoms in these compounds are assigned according to the experimental data available.