Systematic evaluation of the conformational properties of aliphatic omega-hydroxy acids

A systematic conformational study of omega-hydroxy acids, HO-(CH(2))(n)()-COOH with n ranging from 2 to 5, has been performed using quantum mechanical calculations at the MP2 level. To distinguish between intrinsic and environmentally induced conformational preferences, calculations have been carried out in both gas phase and chloroform solution, a polarizable continuum solvation model being used to represent the latter. Results indicate a consistent conformational behavior, as reflects the feature that the lowest energy minimum for n = 2, 3, 4, and 5 corresponds to the g+g-t, g+g+g-t, g-g+g+g-t, and g+g-g+g+g-t conformations, respectively. Furthermore, the stability of the extended and semi-extended conformations increases systematically with the size of the central aliphatic segment. The relationship between the size of the aliphatic segment and the stability of folded conformations is analyzed and discussed.     

An open-source approach to automation in organic synthesis: The flow chemical formation of benzamides using an inline liquid-liquid extraction system and a homemade 3-axis autosampling/product-collection device

Several open-source hardware and software technologies (RAMPS, Python, PySerial, OpenCV) were used to control an automated flow chemical synthesis system. The system was used to effect the synthesis of a series of benzamides. An inexpensive Raspberry Pi single board computer provided an electronic interface between the control computer and the RAMPS motor driver boards.     

The K5 capsular polysaccharide of the bacterium Acinetobacter baumannii SDF with the same K unit containing Leg5Ac7Ac as the K7 capsular polysaccharide but a different linkage between the K units

Russian Chemical Bulletin - The K5 capsular polysaccharide (CPS) was isolated from the bacterium Acinetobacter baumannii (A. baumannii) SDF and studied by 1D and 2D 1H and 13C NMR spectroscopy...     

Triple Quadrupole Versus High Resolution Quadrupole-Time-of-Flight Mass Spectrometry for Quantitative LC-MS/MS Analysis of 25-Hydroxyvitamin D in Human Serum

We describe a systematic comparison of high and low resolution LC-MS/MS assays for quantification of 25-hydroxyvitamin D₃ in human serum. Identical sample preparation, chromatography separations, electrospray ionization sources, precursor ion selection, and ion activation were used; the two assays differed only in the implemented final mass analyzer stage; viz. high resolution quadrupole-quadrupole-time-of-flight (QqTOF) versus low resolution triple quadrupole instruments. The results were assessed against measured concentration levels from a routine clinical chemiluminescence immunoassay. Isobaric interferences prevented the simple use of TOF-MS spectra for extraction of accurate masses and necessitated the application of collision-induced dissociation on the QqTOF platform. The two mass spectrometry assays provided very similar analytical figures of merit, reflecting the lack of relevant isobaric interferences in the MS/MS domain, and were successfully applied to determine the levels of 25-hydroxyvitamin D for patients with chronic liver disease.

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Asymmetric bioreduction of alkenes using ene-reductases YersER and KYE1 and effects of organic solvents

Asymmetric trans-bioreduction of activated alkenes by KYE1 from Kluyveromyces lactis and Yers-ER from Yersinia bercovieri, two ene-reductases from the Old Yellow Enzyme family, showed a broad substrate spectrum with a moderate to excellent degree of stereoselectivity. Both substrate- and enzyme-based stereocontrols were observed to furnish opposite stereoisomeric products. The effects of organic solvents on enzyme activity and stereoselectivity were outlined in this study, where two-phase systems hexane and toluene are shown to sustain bioreduction efficiency even at high organic solvent content.     

Sesquiterpenoids—27: X-ray crystallographic analysis of istanbulin-B,A 1-oxo-eremophilenolide

The stereochemistry of istanbulin-B has been defined by X-ray crystal-structure analysis. Rings A and B are transfused, with the Me groups at C(4) and C(5) cis. The α,β-unsaturated,γ -lactone ring is essentially planar. Crystals of istanbulin-B are orthorhombic, space group P2₁2₁,2₁, with a = 6.729(2), b = 13.447(3), c = 14.721(3)Â,and Z = 4. The crystal structure was determined by direct phasing and the atomic parameters were subsequently adjusted by least-squares calculations that converged at R 38% over 1179 diffractometer |F_a| values     

Effect of additives on the stereochemical integrity and reactivity of alpha-alkoxycarbonyl alkenylcopper intermediates. Optimal conditions for the synthesis of isomerically pure tetrasubstituted alkenes

A systematic study on the effect of additives on the isomerizability of 1-alkoxycarbonyl alkenylcopper(I) intermediates revealed that the lithium chelator 12-crown-4 is significantly more efficient than HMPA at retarding isomerization. On the other hand, 12-crown-4 alone is unable to promote effective coupling with alkyl halides. The combination of 12-crown-4 and a reduced amount of HMPA, however, led to an improved procedure for the preparation of useful, isomerically pure tetrasubstituted alkenes such as allylation reagents and skipped dienes.     

The reaction of indolizines with tetracyanoethylene

Tetracyanoethylene (TCNE) reacts with indolizines ( 1a-c ) to give mixtures of 1- and 3-sub-stituted tricyanovinylindolizines, respectively. The isomers are identified by nmr spectroscopy. The occurrence of intramolecular charge-transfer bands in the visible spectra is discussed.     

Optimal population analysis

An easy method of approximating the electron density of a molecule by expressing it as a sum of squares of atomic orbitals is described. The coefficients are determined by minimizing the error in the electric field. The optimal population analysis is an integration of this optimized density over the orbitals belonging to one atom. The Mulliken population analysis can be interpreted as the integral of a Mulliken density that is a similar expression with fixed coefficients. The two densities are compared in détail using calculations on the water molecule and, more briefly, HF, LiH, BH, and C₂H₄. The error in the densities is identified and examined. The optimal population analysis is strongly recommended as a practical improvement to the Mulliken populations.     

Modeling the active sites in metalloenzymes. 3. Density functional calculations on models for [Fe]-hydrogenase: structures and vibrational frequencies of the observed redox forms and the reaction mechanism at the Diiron Active Center.

Optimized structures for the redox species of the diiron active site in [Fe]-hydrogenase as observed by FTIR and for species in the catalytic cycle for the reversible H(2) oxidation have been determined by density-functional calculations on the active site model, [(L)(CO)(CN)Fe(mu-PDT)(mu-CO)Fe(CO)(CN)(L')](q)(L = H(2)O, CO, H(2), H(-); PDT = SCH(2)CH(2)CH(2)S, L' = CH(3)S(-), CH(3)SH; q = 0, 1-, 2-, 3-). Analytical DFT frequencies on model complexes (mu-PDT)Fe(2)(CO)(6) and [(mu-PDT)Fe(2)(CO)(4)(CN)(2)](2)(-) are used to calibrate the calculated CN(-) and CO frequencies against the measured FTIR bands in these model compounds. By comparing the predicted CN(-) and CO frequencies from DFT frequency calculations on the active site model with the observed bands of D. vulgaris [Fe]-hydrogenase under various conditions, the oxidation states and structures for the diiron active site are proposed. The fully oxidized, EPR-silent form is an Fe(II)-Fe(II) species. Coordination of H(2)O to the empty site in the enzyme's diiron active center results in an oxidized inactive form (H(2)O)Fe(II)-Fe(II). The calculations show that reduction of this inactive form releases the H(2)O to provide an open coordination site for H(2). The partially oxidized active state, which has an S = (1)/(2) EPR signal, is an Fe(I)-Fe(II) species. Fe(I)-Fe(I) species with and without bridging CO account for the fully reduced, EPR-silent state. For this fully reduced state, the species without the bridging CO is slightly more stable than the structure with the bridging CO. The correlation coefficient between the predicted CN(-) and CO frequencies for the proposed model species and the measured CN(-) and CO frequencies in the enzyme is 0.964. The proposed species are also consistent with the EPR, ENDOR, and M?ssbauer spectroscopies for the enzyme states. Our results preclude the presence of Fe(III)-Fe(II) or Fe(III)-Fe(III) states among those observed by FTIR. A proposed reaction mechanism (catalytic cycle) based on the DFT calculations shows that heterolytic cleavage of H(2) can occur from (eta(2)-H(2))Fe(II)-Fe(II) via a proton transfer to "spectator" ligands. Proton transfer to a CN(-) ligand is thermodynamically favored but kinetically unfavorable over proton transfer to the bridging S of the PDT. Proton migration from a metal hydride to a base (S, CN, or basic protein site) results in a two-electron reduction at the metals and explains in part the active site's dimetal requirement and ligand framework which supports low-oxidation-state metals. The calculations also suggest that species with a protonated Fe-Fe bond could be involved if the protein could accommodate such species.