Molecular structure of the trans and cis isomers of metal-free phthalocyanine studied by gas-phase electron diffraction and high-level quantum chemical calculations: NH tautomerization and calculated vibrational frequencies

The molecular structure of the trans isomer of metal-free phthalocyanine (H2Pc) is determined using the gas electron diffraction (GED) method and high-level quantum chemical calculations. B3LYP calculations employing the basis sets 6-31G**, 6-311++G**, and cc-pVTZ give two tautomeric isomers for the inner H atoms, a trans isomer having D2h symmetry and a cis isomer having C2v symmetry. The trans isomer is calculated to be 41.6 (B3LYP/6-311++G**, zero-point corrected) and 37.3 kJ/mol (B3LYP/cc-pVTZ, not zero-point corrected) more stable than the cis isomer. However, Hartree-Fock (HF) calculations using different basis sets predict that cis is preferred and that trans does not exist as a stable form of the molecule. The equilibrium composition in the gas phase at 471 degrees C (the temperature of the GED experiment) calculated at the B3LYP/6-311++G** level is 99.8% trans and 0.2% cis. This is in very good agreement with the GED data, which indicate that the mole fraction of the cis isomer is close to zero. The transition states for two mechanisms of the NH tautomerization have been characterized. A concerted mechanism where the two H atoms move simultaneously yields a transition state of D2h symmetry and an energy barrier of 95.8 kJ/mol. A two-step mechanism where a trans isomer is converted to a cis isomer, which is converted into another trans isomer, proceeds via two transition states of C(s) symmetry and an energy barrier of 64.2 kJ/mol according to the B3LYP/6-311++G** calculation. The molecular geometry determined from GED is in very good agreement with the geometry obtained from the quantum chemical calculations. Vibrational frequencies, IR, and Raman intensities have been calculated using B3LYP/6-311++G**. These calculations indicate that the molecule is rather flexible with six vibrational frequencies in the range of 20-84 cm(-1) for the trans isomer. The cis isomer might be detected by infrared matrix spectroscopy since the N-H stretching frequencies are very different for the two isomers.     

Why is the antipodal effect in closo-1-SB9H9 so large? A possible explanation based on the geometry from the concerted use of gas electron diffraction and computational methods

The molecular structure of 1-thia-closo-decaborane(9), 1-SB(9)H(9), has been determined by the concerted use of gas electron diffraction and quantum-chemical calculations. Assuming C(4v) symmetry, the cage structure was distorted from a symmetrically bicapped square antiprism (D(4d) symmetry) mainly through substantial expansion of the tetragonal belt of boron atoms adjacent to sulfur. The S-B and (B-B)(mean) distances are well determined with r(h1) = 193.86(14) and 182.14(8) pm, respectively. Geometrical parameters calculated using the MP2(full)/6-311++G** method and at levels reported earlier [MP2(full)/6-311G**, B3LYP/6-311G** and B3LYP/cc-pVQZ], as well as calculated vibrational amplitudes and (11)B NMR chemical shifts, are in good agreement with the experimental findings. In particular, the so-called antipodal chemical shift of apical B(10) (71.8 ppm) is reproduced well by the GIAO-MP2 calculations and its large magnitude is schematically accounted for, as is the analogous antipodal chemical shift of B(12) in the twelve-vertex closo-1-SB(11)H(11).     

Efficient separation of oxidized cello-oligosaccharides generated by cellulose degrading lytic polysaccharide monooxygenases

We present an evaluation of HPLC-based analytical tools for the simultaneous analysis of native and oxidized cello-oligosaccharides, which are products of enzymatic cellulose degradation. Whereas cello-oligosaccharides arise from cellulose depolymerization by glycoside hydrolases, oxidized cello-oligosaccharides are produced by cellobiose dehydrogenase and the recently identified copper dependent lytic polysaccharide monooxygenases (LPMOs) currently classified as CBM33 and GH61. The latter enzymes are wide-spread and expected to play crucial roles in further development of efficient enzyme technology for biomass conversion. Three HPLC approaches with well documented performance in the field of oligosaccharide analysis have been investigated: high-performance anion-exchange chromatography (HPAEC), hydrophilic interaction chromatography (HILIC) and porous graphitized carbon liquid chromatography (PGC-LC). HPAEC with pulsed amperometric detection (PAD) was superior for analysis of oxidized oligosaccharides, combining the best separation with superior sensitivity for oligosaccharide species with a degree of polymerization (DP) ranging from 1 to 10. Furthermore, the HPAEC method can be optimized for operation in a high-throughput manner (run time 10 min). Both PGC-LC and HILIC allow reasonable run times (41 and 25 min, respectively), with acceptable separation, but suffer from poor sensitivity compared to HPAEC-PAD. On the other hand, PGC-LC and HILIC benefit from being fully compatible with online mass spectrometry. Using an LC–MS setup, these methods will deliver much better sensitivity than what can be obtained with conventional detectors such as ultraviolet-, charged aerosol-, or evaporative light scattering and may reach sensitivities similar to or even better than what is obtained in HPAEC-PAD. Pure oxidized cello-oligosaccharide standards, ranging from DP2 to DP5, were obtained by semi-preparative PGC and characterized by MS and NMR analysis.     

Extension of least squares spectral resolution algorithm to high-resolution lipidomics data

Lipidomics, which focuses on the global study of molecular lipids in biological systems, has been driven tremendously by technical advances in mass spectrometry (MS) instrumentation, particularly high-resolution MS. This requires powerful computational tools that handle the high-throughput lipidomics data analysis. To address this issue, a novel computational tool has been developed for the analysis of high-resolution MS data, including the data pretreatment, visualization, automated identification, deconvolution and quantification of lipid species. The algorithm features the customized generation of a lipid compound library and mass spectral library, which covers the major lipid classes such as glycerolipids, glycerophospholipids and sphingolipids. Next, the algorithm performs least squares resolution of spectra and chromatograms based on the theoretical isotope distribution of molecular ions, which enables automated identification and quantification of molecular lipid species. Currently, this methodology supports analysis of both high and low resolution MS as well as liquid chromatography-MS (LC-MS) lipidomics data. The flexibility of the methodology allows it to be expanded to support more lipid classes and more data interpretation functions, making it a promising tool in lipidomic data analysis.     

Hexaene derivatives of nystatin produced as a result of an induced rearrangement within the nysC polyketide synthase gene in S. noursei ATCC 11455

Genetic manipulation of the polyketide synthase (PKS) gene nysC involved in the biosynthesis of the tetraene antifungal antibiotic nystatin yielded a recombinant strain producing hexaene nystatin derivatives. Analysis of one such compound, S48HX, by LC-MS/MS suggested that it comprises a 36-membered macrolactone ring completely decorated by the post-PKS modification enzymes. Further characterization by bioassay has shown that S48HX exhibits antifungal activity. Genetic analysis of the hexaene-producing mutant revealed an in-frame deletion within the nysC gene via recombination between two homologous ketoreductase domain-encoding sequences. Apparently, this event resulted in the elimination of one complete module from NysC PKS, subsequently leading to the production of the nystatin derivative with a contracted macrolactone ring. These results represent the first example of manipulation of a PKS gene for the biosynthesis of a polyene antibiotic.     

Theoretical study of geometry and nucleophilicity of the exocyclic methylene in five-membered ring cyclic ketene acetals,neutral and protonated,containing pnictogen and chalcogen heteroatoms

A series of neutral and protonated five-membered ring cyclic ketene acetals have been examined computationally for any trends in nucleophilicity in the exocyclic methylene and for their ground state geometries. A total of 58 different species were examined, 29 neutral molecules and the corresponding 29 protonated species. The heteroatoms that were used in the heterocyclic ring were a combination of nitrogen, phosphorus, and arsenic from the pnictogen family and oxygen, sulfur, and selenium from the chalcogen family. All geometries were initially optimized at using density functional theory and all stationary points were confirmed to be either minima or transition states through vibrational analysis. All the geometries were consequentially optimized using Møller–Plesset second order perturbation theory with a polarized triple zeta basis set. The main focus of the study was the nucleophilicity of the exocyclic methylene carbon atom and its dependence on heteroatom substitution. As probes for nucleophilicity, the proton affinities of the neutral species, the bond lengths of the exocyclic double bond, and atomic charges were used. The study also resulted in some interesting molecular geometries.     

Identification of fatty acids in gas chromatography by application of different temperature and pressure programs on a single capillary column

A method for the identification of fatty acid methyl esters (FAME) based on the analysis of shifts in equivalent chain lengths (ECL) is described. The method is based on two-dimensional retention data achieved on one capillary column. Various temperature and pressure programs are applied on the same cyanopropyl column and the shifts in the ECL values are analysed by multivariate methods. The chain length, number of double bonds, and the double bond positions can be determined with high accuracy. The same procedure is suitable for determination of the number of trans and cis double bonds in trans fatty acids, and for detection of artefacts in fatty acid methyl ester chromatograms.     

Validation of a one-step extraction/methylation method for determination of fatty acids and cholesterol in marine tissues

A simple and fast direct extraction/methylation with methanolic hydrogen chloride was validated for determination of fatty acids (FA) in marine tissues. Three parameters: reaction time, temperature and presence of non-polar solvent, were studied by an experimental 2(3) full factorial design. The method was validated for five different types of samples; cod liver (high lipid content >60%, mainly triacylglycerol), cod muscle (low lipid content, approximately 1%, mainly phospholipids), cod plasma (lipid content, approximately 2%, mainly lipoprotein complex, high water amount), cod testis (lipid content approximately 3%, high levels of cholesterol), and herring muscle (lipid content approximately 7%). The one-step procedure for extraction/methylation of wet tissues was compared with the traditional procedure of extraction of the lipids by the Folch method (chloroform/methanol, 2:1, v/v), followed by methylation. The two methods gave similar FA profiles. The one-step extraction/methylation procedure gave a higher recovery of the total FA than the traditional procedure. Problems with carry-over peaks of cholesterol from previous samples were avoided by application of extra long GC temperature programs. The cholesterol decomposed to some degree under the preceding methanolysis step, giving several peaks in the chromatograms. The decomposition peaks were identified by mass spectrometry as cholestdienes originating from dehydration of cholesterol, a metylether of cholesterol and a cholesteryl chloride. These cholesterol artefacts can be used for quantitative determination of cholesterol in the samples. Standard samples of cholesterol were determined with high accuracy, (R(2)>0.99), and cholesterol in cod plasma was compared with good agreement (R(2)=0.97) to an enzymatic method.     

Molecular structure of phthalocyaninatotin(II) studied by gas-phase electron diffraction and high-level quantum chemical calculations

The molecular structure of phthalocyaninatotin(II), Sn(II)Pc, is determined by density functional theory (DFT/B3LYP) calculations using various basis sets and gas-phase electron diffraction (GED). The quantum chemical calculations show that Sn(II)Pc has C4V symmetry, and this symmetry is consistent with the structure obtained by GED at 427 degrees C. GED locates the Sn atom at h(Sn) ) 112.8(48) pm above the plane defined by the four isoindole N atoms, and a N-Sn bond length of 226.0(10) pm is obtained. Calculation at the B3LYP/ccpVTZ/cc-pVTZ-PP(Sn) level of theory gives h(Sn) ) 114.2 pm and a N-Sn bond length of 229.4 pm. The phthalocyanine (Pc) macrocycle has a slightly nonplanar structure. Generally, the GED results are in good agreement with the X-ray structures and with the computed structure; however, the comparability between these three methods has been questioned. The N-Sn bond lengths determined by GED and X-ray are significantly shorter than those from the B3LYP predictions. Similar trends have been found for C-Sn bonds for conjugated organometallic tin compounds. Computed vibrational frequencies give five low frequencies in the range of 18-54 cm-1, which indicates a flexible molecule.     

Computational and Variable‐Temperature Infrared Spectroscopic Studies on Carbon Monoxide Adsorption on Zeolite Ca‐A

Bridged Ca ²⁺ ???CO???Ca ²⁺ complexes are formed on dual‐cation sites, constituted by a pair of nearby Ca²⁺ cations, when CO is adsorbed on zeolite Ca‐A. Two types of such species can be formed, designated S2–S1 and S1–S1 (see picture). Ca²⁺???CO monocarbonyl species are also identified, and at a relatively high CO equilibrium pressure, dicarbonyl complexes can also form.