The SPASIBA force field for chondroitin sulfate: vibrational analysis of D-glucuronic and N-acetyl-D-galactosamine 4-sulfate sodium salts

Normal-mode analyses were carried out on the two components of the chondroitin 4-sulfate linear glycosaminoglycan, a copolymer implying alternate D-glucuronate beta-(1-->3) and N-acetyl-D-galactosamine 4-sulfate beta-(1-->4) (hereafter named D-galactosamine 4-sulfate) residues. Scaled quantum mechanical calculations (SQM) using the density functional theory approach at different levels of theory (B3LYP/6-31G** and B3LYP/6-31++G**) were performed to obtain correct vibrational assignments. The SPASIBA empirical force field parameters were then obtained from both theoretical predictions and observed IR and Raman data. It is shown that calculations including diffuse functions at the B3LP/6-31++G** level and the introduction of the Na+ counterion are necessary to give correct assignments of the CO2- symmetric (nu(s)) and antisymmetric (nu(a)) stretching modes for the glucuronic carboxylate residue.     

5水合甘氨酸复合体的结构和性能的理论研究

为了探讨“几个水分子导致甘氨酸两性离子复合体与其中性分子复合体等能”, 采用mp2/6-31＋＋g**//b3lyp/6- 31＋＋g**方法研究了甘氨酸水化的微观机理, 发现答案是5个水分子, 并证实了实验结果. 最稳定的5水合甘氨酸两性离子复合体具有双链结构, 与最稳定的5水合甘氨酸中性分子复合体能量接近(仅相差2.26 kJ/mol), 能够共存; 中性复合体和两性复合体之间可以通过直接质子迁移和桥助质子迁移等两种途径相互转化, 双链结构的甘氨酸复合体中质子迁移的能垒较低甚至无垒, 能够自发进行.     

Infrared and ab initio studies of conducting molecules: 2,5-diamino-3,6-dichloro-1,4-benzoquinone

2,5-Diamino-3,6-dichloro-1,4-benzoquinone has been synthesized by modifying the procedure reported in literature. Its IR spectrum has been recorded in the solid phase in the range 4000-400cm(-1). Ab initio calculations have been performed using Gaussian '03 program to compute optimized geometry, harmonic vibrational frequencies along with intensities in IR and Raman spectra and atomic charges at RHF/6-31+G*, B3LYP/6-31+G* and B3LYP/6-311++G** levels. To make vibrational analysis Gaussian View software was used. The optimized molecular structure is found to possess C2h point group symmetry. The observed IR frequencies have been assigned to different modes taking C2h molecular symmetry with the help of pictorial view of normal modes. From the magnitude of the observed frequencies corresponding to the NH2 stretching motions an indication of H-bonding is noticed. From geometrical parameters of the molecule it appears that two parallel sets of conjugated strands are formed in this molecule providing a route to conduct charges. The N-H bonds facing towards chlorine atoms are found to be shorter than those facing towards oxygen atoms indicating the presence of H-bonding between hydrogen atom of an NH2 group and carbonyl (quinoid) oxygen atom.     

Structure and vibrational assignment of the enol form of 1,1,1-trifluoro-2,4-pentanedione

Molecular structure of 1,1,1-trifluoro-pentane-2,4-dione, known as trifluoro-acetylacetone (TFAA), has been investigated by means of Density Functional Theory (DFT) calculations and the results were compared with those of acetylacetone (AA) and hexafluoro-acetylacetone (HFAA). The harmonic vibrational frequencies of both stable cis-enol forms were calculated at B3LYP level of theory using 6-31G** and 6-311++G** basis sets. We also calculated the anharmonic frequencies at B3LYP/6-31G** level of theory for both stable cis-enol isomers. The calculated frequencies, Raman and IR intensities, and depolarization ratios were compared with the experimental results. The energy difference between the two stable cis-enol forms, calculated at B3LYP/6-311++G**, is only 5.89 kJ/mol. The observed vibrational frequencies and Raman and IR intensities are in excellent agreement with the corresponding values calculated for the most stable conformation, 2TFAA. According to the theoretical calculations, the hydrogen bond strength for the most stable conformer is 57 kJ/mol, about 9.5kJ/mol less than that of AA and about 14.5 kJ/mol more than that of HFAA. These hydrogen bond strengths are consistent with the frequency shifts for OH/OD stretching and OH/OD out-of-plane bending modes upon substitution of CH(3) groups with CF(3) groups. By comparing the vibrational spectra of both theoretical and experimental data, it was concluded that 2TFAA is the dominant isomer.     

Neutron scattering, infra red, Raman spectroscopy and ab initio study of L-threonine.

Inelastic incoherent neutron scattering spectra (IINS) were obtained for normal and deuterated L-threonine. Raman and infrared spectra were also recorded. Geometries were optimized for the zwitterion form using ab initio Hartree-Fock (HF) levels with 6-31G*, 6-311G*, 6-311G** and 6-311 + + G** basis sets. Force fields and normal modes were calculated and used as basis for an assignment of the spectral features.     

Theoretical study of light-metal tetrahydroborates

Ab initio calculations of the structural, energetic, vibrational, and magnetic characteristics of the lowest-lying structures for isolated molecules and ions of light-metal tetrahydroborates (Li, Na, Be, Mg, and Al) have been performed by the perturbation theory (MP2), quadratic configuration interaction (QCISD(T)), coupled cluster (CCSD(T)), and density functional theory (B3LYP) methods using the 6-31G*, 6-31G**, 6-311+G**, and 6-311++G** basis sets. The trends in the behavior of the structural parameters, the energies of different decomposition pathways, barriers to internal rotation of BH₄ groups, normal mode frequencies, magnetic shielding constants, and spin density distribution (in radicals) have been analyzed in various related series of these compounds. The results obtained by ab initio methods and at the DFT level are compared. The economical approximation B3LYP/6-311++G**//B3LYP/6-311+G** adequately reproduces the results obtained at the higher level of theory CCSD(T)/6-311++G*s*//MP2/6-31G* even though it requires considerably shorter CPU times and smaller amounts of memory.     

苯并咪唑羧酸及其碱土金属配合物电子光谱性质的含时密度泛函及其概念密度泛函研究

用密度泛函理论(DFT)以及B3 LYlP泛函在6-311++G**水平上,对苯并咪唑羧酸(L)及其3种碱土金属配合物ML(M=Mg,Ca,Ba)的基态(S0)结构进行优化,用含时密度泛函理论(TD-DFT)在6-311++G**水平下计算其吸收光谱.用单激发组态相互作用(CIS)法在HF/6-31+G*上优化其最低激发单重态(S1)的几何结构,用ID-DFT B3IYP/6-311++G**计算其发射光谱.结果表明,配体L与M(Ⅱ)结合成ML后,随原子序数的增大(Mg相似文献   

Raman spectroscopic study of the tellurite minerals: rajite and denningite

Tellurites may be subdivided according to formula and structure. There are five groups based upon the formulae (a) A(XO3), (b) A(XO3).xH2O, (c) A2(XO3)3.xH2O, (d) A2(X2O5) and (e) A(X3O8). Raman spectroscopy has been used to study rajite and denningite, examples of group (d). Minerals of the tellurite group are porous zeolite-like materials. Raman bands for rajite observed at 740, and 676 and 667 cm(-1) are attributed to the nu1 (Te2O5)(2-) symmetric stretching mode and the nu3 (TeO3)(2-) antisymmetric stretching modes, respectively. A second rajite mineral sample provided a more complex Raman spectrum with Raman bands at 754 and 731 cm(-1) assigned to the nu1 (Te2O5)(2-) symmetric stretching modes and two bands at 652 and 603 cm(-1) are accounted for by the nu3 (Te2O5)(2-) antisymmetric stretching mode. The Raman spectrum of dennigite displays an intense band at 734 cm(-1) attributed to the nu1 (Te2O5)(2-) symmetric stretching mode with a second Raman band at 674 cm(-1) assigned to the nu3 (Te2O5)(2-) antisymmetric stretching mode. Raman bands for rajite, observed at (346, 370) and 438 cm(-1) are assigned to the (Te2O5)(2-)nu2 (A1) bending mode and nu4 (E) bending modes.     

Fourier transform Raman and DFT study of three annulated oligothiophenes with different molecular shapes.

Herein, we study the conjugation properties of three different thienoacenes, each of which has three or four fused thiophene rings, by means of Fourier transform Raman spectroscopy. The B3LYP/6-31G** vibrational analysis of all of the collected spectroscopic data evidences that the selective enhancement of a limited number of Raman scatterings is related to the occurrence in the three thienoacenes of a vibronic coupling between the lowest unoccupied frontier molecular orbital (LUMO) and some Raman-active skeletal nu(C==C) stretching modes of 1600-1300 cm(-1).     

Vibrational anharmonicity and harmonic force fields for dichloromethane from quantum-chemical calculations

Anharmonic and related constants have been calculated for CH2Cl2, CD2Cl2, and CHDCl2 by using the program Gaussian03 and B3LYP and MP2 models. Bases used were 6-311++G** and cc-pVTZ. The size of grid used in the B3LYP/6-311++G** model had a noticeable effect on resulting data. Features of the MP2/6-311++G** calculations suggested a deleterious effect of the absence of f functions in this basis set. The need for the replacement of second-order terms in the perturbation theory formulas for the vibrational anharmonic constants x ij in the presence of Fermi resonance was explored, and minor resonances were found associated with the cubic constants varphi 122 and varphi 299 (d 0 isotopomer), phi122 and phi849 (d2), and phi278 (d1). Computed xij values for nuCH and nuCD motions agree quite well with earlier experimental data. Observed anharmonic frequencies, nu obsd, were corrected to "observed" harmonic frequencies, omega obsd, by using computed differences Delta = omegaQC-nuQC. These differences Delta are larger for the antisymmetric nuasCH2 mode than for symmetric nusCH2 motion. This fact made it necessary to use differing scale factors for the two kinds of CH stretching force constants in a subsequent scaling of the harmonic force field to nuobsd. Force field scaling was also carried out by refining to omega obsd. In both approaches, the B3LYP models required differing scale factors for symmetric and antisymmetric CCl stretching force constants, indicating a failure to compute an accurate C-Cl stretch-stretch interaction force constant. The MP2/cc-pVTZ force field was preferred. Both scaled and unscaled harmonic force fields were used to calculate centrifugal distortion constants (CDCs) and contributions to the vibrational dependence of the rotational constants (alphas). Variations in the CDCs can, in part, be explained by the magnitudes of the frequencies used in the scaling process.     

Adsorption of CF4 on the internal and external surfaces of opened single-walled carbon nanotubes: a vibrational spectroscopy study

Infrared spectroscopy has been used to make the first experimental discrimination between molecules bound by physisorption on the exterior surface of carbon single-walled nanotubes (SWNTs) and molecules bound in the interior. In addition, the selective displacement of the internally bound molecules has been observed as a second adsorbate is added. SWNTs were opened by oxidative treatment with O(3) at room temperature, followed by heating in a vacuum to 873 K. It was found that, at 133 K and 0.033 Torr, CF(4) adsorbs on closed SWNTs, exhibiting its nu(3) asymmetric stretching mode at 1267 cm(-1) (red shift relative to the gas phase, 15 cm(-1)). Adsorption on the nanotube exterior is accompanied by adsorption in the interior in the case of opened SWNTs. Internally bound CF(4) exhibits its nu(3) mode at 1247 cm(-1) (red shift relative to the gas phase, 35 cm(-1)). It was shown that, at 133 K, Xe preferentially displaces internally bound CF(4) species, and this counterintuitive observation was confirmed by molecular simulations. The confinement of CF(4) inside (10,10) single-walled carbon nanotubes does not result in the production of lattice modes that are observed in large 3D ensembles of CF(4).     

Theoretical study of “deep” fragmentation of hemin ion with successive loss of methyl and vinyl groups

The electronic and geometric structures, energy stability, normal mode frequencies, and spin density distribution have been calculated by the density functional theory B3LYP method with the Gen = 6-31+G*(Fe) + 6-31G(C,H,N,O), 6-31G*, and 6-311++G** basis sets for the deep fragmentation products of the free hemin ion with successive removal of methyl and vinyl groups in the electronic states with different multiplicities. The computation results are compared with the available experimental data and previous computation results for the fragmentation products of the isolated heme molecule and hemin ion with removal of carboxymethyl groups. The trends in the behavior of these properties are analyzed as a function of multiplicity, external charge, and the number of peripheral substituents at the porphyrin core.     

Theoretical study of light-metal tetrahydroaluminates

Ab initio calculations of the structural, energetic, vibrational, and magnetic characteristics of the lowest-lying structures for isolated molecules and ions of light-metal tetrahydroaluminates (Li, Na, Be, Mg, and Al) have been performed by the perturbation theory (MP2), quadratic configuration interaction (QCISD(T)), coupled cluster (CCSD(T)), and density functional theory (B3LYP) methods using the 6-31G*, 6-31G**, 6-311+G**, and 6-311++G** basis sets. The trends in the behavior of the molecular characteristics have been analyzed in various related series of these compounds. The results are compared with the data on analogous light-metal tetrahydroborates calculated at the same levels of theory. The differences in structure and stability between analogous hydroborate and alanate complexes are examined. The economical approximation B3LYP/6-311++G**//B3LYP/6-311+G** has been shown to adequately reproduce the results obtained at the higher level of theory CCSD(T)/6-311++G**//MP2/6-31G* even though it requires considerably shorter CPU times and smaller amounts of memory.     

Raman spectroscopic study of the tellurite minerals: carlfriesite and spiroffite

Raman spectroscopy has been used to study the tellurite minerals spiroffite and carlfriesite, which are minerals of formula type A(2)(X(3)O(8)) where A is Ca(2+) for the mineral carlfriesite and is Zn(2+) and Mn(2+) for the mineral spiroffite. Raman bands for spiroffite observed at 721 and 743 cm(-1), and 650 cm(-1) are attributed to the nu(1) (Te(3)O(8))(2-) symmetric stretching mode and the nu(3) (Te(3)O(8))(2-) antisymmetric stretching modes, respectively. A second spiroffite mineral sample provided a Raman spectrum with bands at 727 cm(-1) assigned to the nu(1) (Te(3)O(8))(2-) symmetric stretching modes and the band at 640cm(-1) accounted for by the nu(3) (Te(3)O(8))(2-) antisymmetric stretching mode. The Raman spectrum of carlfriesite showed an intense band at 721 cm(-1). Raman bands for spiroffite, observed at (346, 394) and 466 cm(-1) are assigned to the (Te(3)O(8))(2-)nu(2) (A(1)) bending mode and nu(4) (E) bending modes. The Raman spectroscopy of the minerals carlfriesite and spiroffite are difficult because of the presence of impurities and other diagenetically related tellurite minerals.     

Substituent effects on benzdiyne: a density functional theory study

Density functional theory (DFT) studies were performed to investigate the effect of substituents on the properties of benzdiyne derivatives. Twelve substituted benzdiynes-C(6)X(2), where X = F, Cl, Br, Me, CF(3), CN, OH, NO(2), NH(2), OMe, NMe(2), and Ph-were considered along with the unsubstituted 1,4-benzdiyne. The structures, vibrational frequencies, and IR intensities of these benzdiynes were studied with a popular three-parameter hybrid density functional (B3LYP) combined with the split-valence 6-31G(d) basis set and Dunning's correlation-consistent polarized triple-zeta (cc-pVTZ) basis set. The relative stabilities of the substituted benzdiynes were studied with the help of reaction energies of isodesmic reactions, which showed that the electron-withdrawing groups destabilized the benzdiynes more than they did the corresponding benzenes, whereas the electron-donating groups stabilized the benzdiynes more than they did their benzene counterparts. Correlation analyses revealed that field/inductive effects played a more important role than did resonance effects. The changes in atomic charges and spin populations due to the substituents were also studied. The asymmetric nu(Ctbd1;C) stretching modes obtained were close to the 1500-cm(-)(1) mark. Reinvestigation of the experimental results supported these results; a weak IR band at 1486 cm(-)(1) was assigned to this asymmetric stretching mode in C(6)(CF(3))(2) F. Some other benzdiynes also had large IR intensity values for their asymmetric nu(Ctbd1;C) vibrational modes due to the coupling with other vibrational modes. Heats of formation for the substituted benzdiynes were obtained from the reaction energies calculated at the B3LYP/cc-pVTZ level of theory.     

An ab initio study of intermolecular interactions of nitromethane dimer and nitromethane trimer

Different geometries of nitromethane dimer and nitromethane trimer have been fully optimized employing the density functional theory B3LYP method and the 6-31++G** basis set. Three-body interaction energy has been obtained with the ab initio supermolecular approach at the levels of MP2/6-31++G**//B3LYP/6-31++G** and MP2/aug-cc-pVDZ//B3LYP/6-31++G**. The internal rotation of methyl group induced by intermolecular interaction has been observed theoretically. For the optimized structures of nitromethane dimer, the strength of C--H...O--N H-bond ranges from -9.0 to -12.4 kJ mol(-1) at the MP2/aug-cc-pVDZ//B3LYP/6-31++G** level, and the B3LYP method underestimates the interaction strength compared with the MP2 method, while MP2/6-31++G**//B3LYP/6-31++G** calculated DeltaE(C) is within 2.5 kJ mol(-1) of the corresponding value at the MP4(SDTQ)/6-31G**//B3LYP/6-31++G** level. The analytic atom-atom intermolecular potential has been successfully regressed by using the MP2/6-31++G**//B3LYP/6-31++G** calculated interaction energies of nitromethane dimer. For the optimized structures of nitromethane trimer the three-body interaction energies occupy small percentage of corresponding total binding energies, but become important for the compressed nitromethane explosive. In addition, it has been discovered that the three-body interaction energy in the cyclic nitromethane trimer is more and more negative as intermolecular distances decrease from 2.2 to 1.7 A.     

Spectroscopic characterization of chromite from the Moa-Baracoa Ophiolitic Massif, Cuba

The Cuban chromites with a spinel structure, FeCr2O4 have been studied using optical absorption and EPR spectroscopy. The spectral features in the electronic spectra are used to map the octahedral and tetrahedral co-ordinated cations. Bands due Cr3+ and Fe3+ ions could be distinguished from UV-vis spectrum. Chromite spectrum shows two spin allowed bands at 17,390 and 23,810 cm(-1) due to Cr3+ in octahedral field and they are assigned to 4A2g(F) --> 4T2g(F) and 4A2g(F) --> 4T1g(F) transitions. This is in conformity with the broad resonance of Cr3+ observed from EPR spectrum at g = 1.903 and a weak signal at g = 3.861 confirms Fe3+ impurity in the mineral. Bands of Fe3+ ion in the optical spectrum at 13,700, 18,870 and 28,570 cm(-1) are attributed to 6A1g(S) --> 4T1g(G), 6A1g(S) --> 4T2g(G) and 6A1g(S) --> 4T2g(P) transitions, respectively. Near-IR reflectance spectroscopy has been used effectively to show intense absorption bands caused by electronic spin allowed d-d transitions of Fe2+ in tetrahedral symmetry, in the region 5000-4000 cm(-1). The high frequency region (7500-6500 cm(-1)) is attributed to the overtones of hydroxyl stretching modes. Correlation between Raman spectral features and mineral chemistry are used to interpret the Raman data. The Raman spectrum of chromite shows three bands in the CrO stretching region at 730, 560 and 445 cm(-1). The most intense peak at 730 cm(-1) is identified as symmetric stretching vibrational mode, A1g(nu1) and the other two minor peaks at 560 and 445 cm(-1) are assigned to F2g(nu4) and E(g)(nu2) modes, respectively. Cation substitution in chromite results various changes both in Raman and IR spectra. In the low-wavenumber region of Raman spectrum a significant band at 250 cm(-1) with a component at 218 cm(-1) is attributed F2g(nu3) mode. The minor peaks at 195, 175, 160 cm(-1) might be due to E(g) and F2g symmetries. Broadening of the peak of A1g mode and shifting of the peak to higher wavenumber observed as a result of increasing the proportion of Al3+O6. The presence of water in the mineral shows bands in the IR spectrum at 3550, 3425, 3295, 1630 and 1455 cm(-1). The vibrational spectrum of chromite gives raise to four frequencies at 985, 770, 710 and 650 cm(-1). The first two frequencies nu1 and nu2 are related to the lattice vibrations of octahedral groups. Due to the influence of tetrahedral bivalent cation, vibrational interactions occur between nu3 and nu4 and hence the low frequency bands, nu3 and nu4 correspond to complex vibrations involving both octahedral and tetrahedral cations simultaneously. Cr3+ in Cuban natural chromites has highest CFSE (20,868 cm(-1)) when compared to other oxide minerals.     

Density functional efficiency in the calculations of vibrational frequencies and molecular structures of β-diketones

Density functional theory (DFT) levels are employed to calculate the vibrational frequencies and geometrical data of β-diketones. We evaluate the relative performance of the different levels by comparing theoretical results to experimental values. The applied DFT levels in this work are B3LYP, BLYP, B3P86, B3PW91, BPW91, G96LYP, BP86, and G96PW91 with the standard 6-31G, 6-31G*, 6-31G**, 6-31+G**, 6-31++G**, 6-311G**, 6-311++G** basis sets. The best results are obtained at the B3LYP, B3PW91, and B3P86 levels.     

Structural and conformational properties of 1,1,1-trifluoro-2-propanol investigated by microwave spectroscopy and quantum chemical calculations

The microwave spectrum of 1,1,1-trifluoro-2-propanol, CF(3)CH(OH)CH(3), and one deuterated species, CF(3)CH(OD)CH(3), have been investigated in the 20.0-62.0 GHz spectral region at about -50 degrees C. The rotational spectrum of one of the three possible rotameric forms was assigned. This conformer is stabilized by an intramolecular hydrogen bond formed between the hydrogen atom of the hydroxyl group and the nearest fluorine atoms. The hydrogen bond is weak and assumed to be mainly a result of attraction between the O-H and the C-F bond dipoles, which are nearly antiparallel. The identified rotamer is at least 3 kJ/mol more stable than any other rotameric form. Two vibrationally excited states belonging to two different normal modes were assigned for this conformer, and their frequencies were determined by relative intensity measurements. The microwave work has been assisted by quantum chemical computations at the MP2/cc-pVTZ and B3LYP/6-311++G** levels of theory, as well as by the infrared spectrum of the O-H stretching vibration.     

The vibrational group frequency of the N-O* stretching band of nitroxide stable free radicals

The group frequency of the N-O radical stretching vibration has received scant attention in the literature. The few existing treatments of the vibrational spectroscopy of nitroxides are incomplete at best and potentially misleading to workers in the field. To close this gap in the available knowledge, the existing literature on the vibrational spectra of nitroxide stable free radicals is critically reviewed with particular reference to the wavenumber position of the N-O stretching vibration, nu(N-O). Poor evidentiary bases for the assignment nu(N-O) were found in many instances. Ab initio Density Field Theory calculations using a model chemistry of UB3LYP at the 6-311++G(d,p) level were performed to obtain a theoretical band position of nu(N-O) for comparison with the published data. Large discrepancies between the theoretical and experimental values were found for the radical 3-carbamoyl-2,2,5,5-tetramethyl-3-pyrrolin-1-yloxyl, which currently sets the lower limit of the accepted wavenumber range of nu(N-O), as well as for the nitronyl and iminyl nitroxides. The wavenumber position of nu(N-O) was found to occur in the range 1450-1420cm(-1) for 5-membered cyclic nitroxides and 1395-1340cm(-1) for 6-membered cyclic and acyclic nitroxides. In nitronyl nitroxides, the symmetric stretching vibration occurs in the region 1470cm(-1), but coupling to other modes makes specific band assignments problematic for the nitronyl nitroxide group.