Evaluation of the efficiency of the concurrent use of IR and mass spectrometry databases for structure elucidation

The applicability of structural analogy to structure elucidation of organic compounds by searching two molecular spectroscopy databases (DBs) is examined. Using structural analogy is based on the representation of DB structures as sets of structural fragments. Of primary concern are the structural fragments that are represented in the search results of both infrared (IR) and mass spectroscopy (MS) DBs. The statistically justified estimates of the efficiency of the combined search depending on the spectral similarity are given.     

The Crystal Structures of Peroxonium Hexafluoroantimonate H3O2SbF6 and Bis(dihydrogenperoxo)hydrogen Hexafluoroantimonate H5O4SbF6

Protonated hydrogen peroxide is produced from the reaction of antimony pentafluoride with bis(trimethylsilyl)peroxide in the presence of hydrogen fluoride. Depending on the stoichiometry of the reaction mixture, the compounds H₃O₂SbF₆ and H₅O₄SbF₆ are formed, which are stable up to room temperature and have been characterized by X-ray crystallography. The structure of the H₃O₂⁺ ion is shown on the right.     

Elucidating ‘undecipherable’ chemical structures using computer‐assisted structure elucidation approaches

Structure elucidation using 2D NMR data and application of traditional methods of structure elucidation are known to fail for certain problems. In this work, it is shown that computer‐assisted structure elucidation methods are capable of solving such problems. We conclude that it is now impossible to evaluate the capabilities of novel NMR experimental techniques in isolation from expert systems developed for processing fuzzy, incomplete and contradictory information obtained from 2D NMR spectra. Copyright © 2012 John Wiley & Sons, Ltd.     

Probing Protonation Sites of Isolated Flavins Using IR Spectroscopy: From Lumichrome to the Cofactor Flavin Mononucleotide

Infrared spectra of the isolated protonated flavin molecules lumichrome, lumiflavin, riboflavin (vitamin B₂), and the biologically important cofactor flavin mononucleotide are measured in the fingerprint region (600–1850 cm^?1) by means of IR multiple‐photon dissociation (IRMPD) spectroscopy. Using density functional theory calculations, the geometries, relative energies, and linear IR absorption spectra of several low‐energy isomers are calculated. Comparison of the calculated IR spectra with the measured IRMPD spectra reveals that the N10 substituent on the isoalloxazine ring influences the protonation site of the flavin. Lumichrome, with a hydrogen substituent, is only stable as the N1‐protonated tautomer and protonates at N5 of the pyrazine ring. The presence of the ribityl unit in riboflavin leads to protonation at N1 of the pyrimidinedione moiety, and methyl substitution in lumiflavin stabilizes the tautomer that is protonated at O2. In contrast, flavin mononucleotide exists as both the O2‐ and N1‐protonated tautomers. The frequencies and relative intensities of the two C?O stretch vibrations in protonated flavins serve as reliable indicators for their protonation site.     

IR Spectrum and Structure of Protonated Monosilanol: Dative Bonding between Water and the Silylium Ion

We report the spectroscopic characterization of protonated monosilanol (SiH₃OH₂⁺) isolated in the gas phase, thus providing the first experimental determination of the structure and bonding of a member of the elusive silanol family. The SiH₃OH₂⁺ ion is generated in a silane/water plasma expansion, and its structure is derived from the IR photodissociation (IRPD) spectrum of its Ar cluster measured in a tandem mass spectrometer. The chemical bonding in SiH₃OH₂⁺ is analyzed by density functional theory (DFT) calculations, providing detailed insight into the nature of the dative H₃Si⁺‐OH₂ bond. Comparison with protonated methanol illustrates the differences in bonding between carbon and silicon, which are mainly related to their different electronegativity and the different energy of the vacant valence p_z orbital of SiH₃⁺ and CH₃⁺.     

Vibrational spectral fingerprinting for chemical recognition of biominerals

Pathologies associated with calcified tissue, such as osteoporosis, demand in vivo and/or in situ spectroscopic analysis to assess the role of chemical substitutions in the inorganic component. High energy X-ray or NMR spectroscopies are impractical or damaging in biomedical conditions. Low energy spectroscopies, such as IR and Raman techniques, are often the best alternative. In apatite biominerals, the vibrational signatures of the phosphate group are generally used as fingerprint of the materials although they provide only limited information. Here, we have used first principles calculations to unravel the complexity of the complete vibrational spectra of apatites. We determined the spectroscopic features of all the phonon modes of fluoroapatite, hydroxy-apatite, and carbonated fluoroapatite beyond the analysis of the phosphate groups, focusing on the effect of local corrections induced by the crystalline environment and the specific mineral composition. This provides a clear and unique reference to discriminate structural and chemical variations in biominerals, opening the way to a widespread application of non-invasive spectroscopies for in vivo diagnostics, and biomedical analysis.     

Acidity of heteropoly acids with various structures and compositions studied by IR spectroscopy of the pyridinium salts

The acidity on the proton affinity scale was determined by IR spectroscopy of the pyridinium salts for nineteen heteropoly acids of nine structural types (including two with the previously unknown structure) and one isopoly acid. All heteropoly acids exhibited a high acidity at the level of CF₃SO₃H and HClO₄. H₃PW₁₂O₄₀ was the strongest acid.     

IR Expert: A New Type of IR Spectroscopy Information System for Solving Spectrum-Structure Problems

This paper discusses the possibilities which the new information system IR EXPERT offers to chemists and spectroscopists. Examples of spectrum-structure problems solved by using the system are discussed — namely, generation of structural hypotheses based on the IR spectrum of the compound, verification of these hypotheses, and construction of empirical models of IR spectra based on the structure of the compound.     

Application of quantitative IR spectral analysis of bacterial cells to acetone-butanol-ethanol fermentation monitoring

Clostridium acetobutylicum ATCC 824 was grown under three different acetone-butanol-ethanol (ABE) fermentation conditions: (1) strictly anaerobic conditions with vegetative inoculum; (2) semi-anaerobic conditions with vegetative inoculum; and (3) strictly anaerobic conditions with spore inoculum. Semi-anaerobic fermentation with vegetative inoculum and strictly anaerobic fermentation with spore inoculum produced solvents at high level. Strictly anaerobic fermentation with vegetative inoculum showed an “acid crash”, i.e. produced mainly acids and did not switch to predominant solvent production. The content of carbohydrates, nucleic acids, proteins and lipids in Clostridium cells during the fermentation were evaluated from the mid-IR spectra. The content of nucleic acids decreased with process time, and the lipid content increased, corresponding to ceasing growth and formation of the toxic fermentation products. It was shown that the physiological states of either solvent production or acid crash are reflected in the microbial biomass composition, which can be assessed by IR spectroscopy.     

The crystal structures at 80 K and IR spectra of the complex of 4-methylpyridine with pentachlorophenol and its deuterated analogue

The crystal structures of the complex of 4-methylpyridine with pentachlorophenol (MP-PCP) and its deuterated analogue (MP-PCP-d) were determined at 80 K by X-ray diffraction. The MP-PCP complex crystallizes in the space group P with a = 7.267(7), b = 8.966(9), c = 13.110(14)Å, = 99.70(8), β = 118.16(9), γ = 103.38(8)° and Z = 2 and the MP-PCP-d complex in the monoclinic Cc space group with a = 3.826(2), b = 27.54(2), c = 13.209(12)Å, β = 101.38(9)° and Z = 4. The O… H … N bridge bond distance of 2.515(4) Å is significantly shorter than that determined at room temperature (2.552(4) Å) and the O---D … N bond length of 2.628(6) Å is only slightly shorter than at room temperature (2.638(3) Å). The temperature dependence of the IR spectra confirms the symmetrization of the OHN hydrogen bond.     

The crystal structures at 80 K and IR spectra of the complex of 4-methylpyridine with pentachlorophenol and its deuterated analogue

The crystal structures of the complex of 4-methylpyridine with pentachlorophenol (MP---PCP) and its deuterated analogue (MP---PCP-d) were determined at 80 K by X-ray diffraction. The MP---PCP complex crystallizes in the space group with a = 7.267(7), b = 8.966(9), c = 13.110(14) Å, = 99.70(8), β = 118.16(9), γ = 103.38(8)° and Z = 2 and the MP---PCP-d complex in the monoclinic Cc space group with a = 3.826(2), b = 27.54(2), c = 13.209(12) Å, β = 101.38(9)° and Z = 4. The O…H…N bridge bond distance of 2.515(4) Å is significantly shorter than that determined at room temperature (2.552(4) Å) and the O---D…N bond length of 2.628(6) Å is only slightly shorter than at room temperature (2.638(3) Å). The temperature dependence of the IR spectra confirms the symmetrization of the OHN hydrogen bond.     

Gas‐Phase Peptide Structures Unraveled by Far‐IR Spectroscopy: Combining IR‐UV Ion‐Dip Experiments with Born–Oppenheimer Molecular Dynamics Simulations

Vibrational spectroscopy provides an important probe of the three‐dimensional structures of peptides. With increasing size, these IR spectra become very complex and to extract structural information, comparison with theoretical spectra is essential. Harmonic DFT calculations have become a common workhorse for predicting vibrational frequencies of small neutral and ionized gaseous peptides. ¹ Although the far‐IR region (<500 cm^?1) may contain a wealth of structural information, as recognized in condensed phase studies, ² DFT often performs poorly in predicting the far‐IR spectra of peptides. Here, Born–Oppenheimer molecular dynamics (BOMD) is applied to predict the far‐IR signatures of two γ‐turn peptides. Combining experiments and simulations, far‐IR spectra can provide structural information on gas‐phase peptides superior to that extracted from mid‐IR and amide A features.     

人工合成化合物S-A的核磁共振研究

利用核磁共振技术对人工合成化合物S-A的溶液行为进行了研究, 确定该化合物在氯仿溶剂中存在分子内氢键过程, 而该交换过程对核磁共振结果的影响异常明显. 针对以上现象, 通过外加试剂和改变温度的手段对样品体系或测试环境进行了调制, 提高了核磁共振谱图的信号质量和“可读性”.