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Carbonyl Oxygen (carbonyl + oxygen)
Terms modified by Carbonyl Oxygen Selected AbstractsExpression and characterization of active site mutants of hevamine, a chitinase from the rubber tree Hevea brasiliensisFEBS JOURNAL, Issue 3 2002Evert Bokma Hevamine is a chitinase from the rubber tree Hevea brasiliensis. Its active site contains Asp125, Glu127, and Tyr183, which interact with the ,1 sugar residue of the substrate. To investigate their role in catalysis, we have successfully expressed wild-type enzyme and mutants of these residues as inclusion bodies in Escherichia coli. After refolding and purification they were characterized by both structural and enzyme kinetic studies. Mutation of Tyr183 to phenylalanine produced an enzyme with a lower kcat and a slightly higher Km than the wild-type enzyme. Mutating Asp125 and Glu127 to alanine gave mutants with ,,2% residual activity. In contrast, the Asp125Asn mutant retained substantial activity, with an approximately twofold lower kcat and an approximately twofold higher Km than the wild-type enzyme. More interestingly, it showed activity to higher pH values than the other variants. The X-ray structure of the Asp125Ala/Glu127Ala double mutant soaked with chitotetraose shows that, compared with wild-type hevamine, the carbonyl oxygen atom of the N -acetyl group of the ,1 sugar residue has rotated away from the C1 atom of that residue. The combined structural and kinetic data show that Asp125,and Tyr183 contribute to catalysis by positioning the,carbonyl oxygen of the N -acetyl group near to the C1 atom. This allows the stabilization of a positively charged transient intermediate, in agreement with a previous proposal that the enzyme makes use of substrate-assisted catalysis. [source] First-principle studies of intermolecular and intramolecular catalysis of protonated cocaineJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2005Chang-Guo Zhan Abstract We have performed a series of first-principles electronic structure calculations to examine the reaction pathways and the corresponding free energy barriers for the ester hydrolysis of protonated cocaine in its chair and boat conformations. The calculated free energy barriers for the benzoyl ester hydrolysis of protonated chair cocaine are close to the corresponding barriers calculated for the benzoyl ester hydrolysis of neutral cocaine. However, the free energy barrier calculated for the methyl ester hydrolysis of protonated cocaine in its chair conformation is significantly lower than for the methyl ester hydrolysis of neutral cocaine and for the dominant pathway of the benzoyl ester hydrolysis of protonated cocaine. The significant decrease of the free energy barrier, ,4 kcal/mol, is attributed to the intramolecular acid catalysis of the methyl ester hydrolysis of protonated cocaine, because the transition state structure is stabilized by the strong hydrogen bond between the carbonyl oxygen of the methyl ester moiety and the protonated tropane N. The relative magnitudes of the free energy barriers calculated for different pathways of the ester hydrolysis of protonated chair cocaine are consistent with the experimental kinetic data for cocaine hydrolysis under physiologic conditions. Similar intramolecular acid catalysis also occurs for the benzoyl ester hydrolysis of (protonated) boat cocaine in the physiologic condition, although the contribution of the intramolecular hydrogen bonding to transition state stabilization is negligible. Nonetheless, the predictability of the intramolecular hydrogen bonding could be useful in generating antibody-based catalysts that recruit cocaine to the boat conformation and an analog that elicited antibodies to approximate the protonated tropane N and the benzoyl O more closely than the natural boat conformer might increase the contribution from hydrogen bonding. Such a stable analog of the transition state for intramolecular catalysis of cocaine benzoyl-ester hydrolysis was synthesized and used to successfully elicit a number of anticocaine catalytic antibodies. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 980,986, 2005 [source] Transferable intermolecular potentials for carboxylic acids and their phase behaviorAICHE JOURNAL, Issue 2 2010Amir Vahid Abstract Transferable step potentials are characterized for 39 carboxylic acids. The reference potential is treated with discontinuous molecular dynamics, including detailed molecular structure. Thermodynamic perturbation theory is used to interpret the simulation results and to provide an efficient basis for molecular modeling and characterization of the attractive forces. Four steps are used for representation of the attractive forces with only the first and last steps varied independently. The two middle steps are interpolated such that each site type is characterized by three parameters: the diameter, ,, the depth of the inner well, ,1, and the depth of the outer well, ,4. The depths of the attractive wells are optimized to fit experimental vapor pressure and liquid density data. Generally, the vapor pressure is correlated to an overall 43% average absolute deviation (% AAD) and the liquid density to 5% AAD. The deviations tend to be largest for the higher molecular weight acids. These deviations are larger than the errors previously encountered in characterizing organic compounds, but carboxylic acids present exceptional challenges owing to their peculiar dimerization behavior. Simultaneous correlation of vapor pressure, vapor compressibility factor, and phase equilibria of water + carboxylic acids place several constraints on the nature of the potential model, with the parameters of the present model representing a reasonable tradeoff. In other words, our model represents minimal deviations for vapor pressure, vapor compressibility factor, and phase equilibria of all acids simultaneously while varying the parameters ,, ,1, ,4, ,CC(dimerizing site bonding energy), ,AD(acceptor-donor bonding energy), and KHB(hydrogen bonding volume) for the acid O and OH site types. The present model is characterized by one acceptor and one dimerizing site on the carbonyl oxygen and one acceptor and one donor site on the hydroxyl oxygen. The acceptor and donor are capable of interacting with water while the dimerizing site is not. With this model, the saturated vapor compressibility factor of acids with seven or fewer carbons is near 0.5 while higher carbon ratios lead to a compressibility factor approaching 1.0. To compensate for the high vapor pressure deviations of the transferable potential model, a correction is introduced to customize the molecule-molecule self interaction energy. This adaptation results in deviations of 3.1% for vapor pressure of the pure acid database. To validate the behavior of the model for carboxylic acids in mixtures, 33 binary solutions were considered. Acids in this database ranged from formic to hexadecanoic. The average absolute deviation in bubble pressure for aqueous acid systems is 4.4%, 10.5% for acid + acid systems, and 4.7% for acid + n-alkane systems without a customized interaction correction. When applying the correction, deviations were 2.4% for aqueous systems, 2% for acid systems, and 2.8% for acid + n-alkane systems. © 2009 American Institute of Chemical Engineers AIChE J, 2010 [source] Interaction of cysteine with Cu2+ and group IIb (Zn2+, Cd2+, Hg2+) metal cations: a theoretical studyJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 3 2005M. Belcastro Abstract The structure and energetics of complexes obtained upon interaction between cysteine and Zn2+, Cd2+, Hg2+ and Cu2+ cations were studied using quantum chemical density functional theory calculations with the 6,311++G** orbital basis set and relativistic pseudopotentials for the cations. Different coordination sites for metal ions on several cysteine conformers were considered. In their lowest energy complexes with the amino acid, the Zn2+ and Cd2+ cations appear to be three-coordinated to carbonyl oxygen, nitrogen and sulfur atoms, whereas the Cu2+ and Hg2+ ions are coordinated to both the carbonyl oxygen and sulfur atoms of one of the zwitterion forms of the amino acid. Bonds of metal cations with the coordination sites are mainly ionic except those established with sulfur, which show a small covalent character that become most significant when Cu2+ and Hg2+ are involved. The order of metal ion affinity proposed is Cu > Zn > Hg > Cd. Copyright © 2005 John Wiley & Sons, Ltd. [source] A remarkable difference in the deprotonation steps of the Friedel,Crafts acylation and alkylation reactionsJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 11 2009Shinichi Yamabe Abstract Friedel,Crafts acylation and alkylation reactions were investigated using density functional theory calculations. The reaction systems studied were (benzene,+,acetyl chloride,+,Al2Cl6 (or AlCl3)) and (benzene,+,2-chloropropane,+,Al2Cl6). In the acylation reaction, the acylium ion intermediate is reached either via a MeC(Cl)OAl2Cl6 complex or via direct Cl transfer: MeC(O)ClAl2Cl6,,,MeCO,+Al2Cl. The ion adds to benzene electrophilically to form a Wheland intermediate containing a strong CHCl hydrogen bond, which leads to deprotonation and the subsequent formation of acetophenone. The resulting HClAl2Cl6 fragment is subjected to a nucleophilic attack by the carbonyl oxygen of the acetophenone, and recovery of the Al2Cl6 bridge is unlikely. Attack of the Al2Cl6 moiety by MeC(Cl)O gives the complex MeC(Cl)O,AlCl3, whose reactivity toward acylation is similar to that of the MeC(Cl)O,Al2Cl6 complex. In the alkylation reaction, deprotonation does not take place, but rather a [1,2] H-shift from the Wheland intermediate. The resulting , -protonated cumene undergoes deprotonation, with subsequent recovery of the Al2Cl6 bridge. In addition, the Al2Cl6 -catalyzed isomerization of the n -propyl to the isopropyl cation was found to be a dyotropic shift. Copyright © 2009 John Wiley & Sons, Ltd. [source] Acid-catalyzed hydrolysis of bridged bi- and tricyclic compounds.JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 9 20023-acetylnortricyclanes, Kinetics, XXXIX, mechanisms of the hydration reactions of 1- Abstract The disappearance of 1- and 3-acetylnortricyclanes (1-Ac and 2-Ac) in aqueous perchloric acid was followed by capillary gas chromatography at different temperatures and acid concentrations. 1-Ac is much less reactive than 2-Ac. The activation parameters, solvent deuterium isotope effects and parameters of excess acidity equations were measured and the products studied. 1-Acetylnortricyclane is hydrated according to the A -2 mechanism, i.e. the carbonyl oxygen is protonated in the fast pre-equilibrium and one water molecule attacks at the rate-limiting stage the partially open cyclopropane ring, producing 6-acetyl-2-norborneols. 3-Acetylnortricyclane is hydrated according to the AdE2 mechanism, i.e. the cyclopropane ring is slowly protonated and opened, with subsequent fast attack of water producing 3-, 5- and 7-acetyl-2-norborneols. Copyright © 2002 John Wiley & Sons, Ltd. [source] Extended application of a chiral stationary phase based on (+)-(18-crown-6)-2,3,11,12-tetracarboxylic acid to the resolution of N -(substituted benzoyl)-,-amino acid amidesJOURNAL OF SEPARATION SCIENCE, JSS, Issue 10 2006Guanghui Tan Abstract A chiral stationary phase (CSP 1) based on (+)-(18-crown-6)-2,3,11,12-tetracarboxylic acid was applied to the resolution of N -(substituted benzoyl)-,-amino acid amides and esters. N -(Substituted benzoyl)-,-amino acid amides were well resolved using a mixture of acetic acid-triethylamine-acetonitrile (0.01 : 0.05 : 100, v/v/v) as an optimum mobile phase while N -(substituted benzoyl)-,-amino acid esters were not resolved at all. In contrast, both N -(substituted benzoyl)-,-amino acid amides and esters were not resolved at all or resolved very poorly on another CSP (CSP 2), which lacks the two N,H hydrogens of the amide tethers of CSP 1. Among the substituents on the benzoyl group of analytes, the nitro group was the best for good resolution of analytes on CSP 1. From these results, the two N,H hydrogens of the amide tethers of CSP 1, the carbonyl oxygen of the amide group of analytes, and the nitro group on the benzoyl group of analytes were concluded to play significant roles in chiral recognition. In addition, various N -(3,5-dinitrobenzoyl)leucine amides with different lengths of N -alkylamide chains were resolved on CSP 1 and N -(3,5-dinitrobenzoyl)leucine N -propylamide was found to show the best chiral recognition in terms of the separation (, = 1.30) and the resolution factor (RS = 3.17). [source] Removal of N -methylpyrrolidone hydrogen-bonded to polyaniline free-standing films by protonation,deprotonation cycles or thermal heatingPOLYMER INTERNATIONAL, Issue 11 2001Eduardo A Ponzio Abstract Free-standing films of polyaniline (PANI), in an emeraldine base state, prepared by evaporation of polymer solutions in N -methylpyrrolidone (NMP) retain solvent even under dynamic vacuum drying as indicated by transmission Fourier transform infrared (FTIR) spectroscopy, where a band at 1670,cm,1 is clearly observed. Upon protonation,deprotonation cycles in aqueous media the weight of the dry base film decreases indicating gradual loss of NMP. Transmission FTIR spectra shows also the washing out of NMP with a clear decrease in intensity of the hydrogen-bonded >CO stretching band (1670,cm,1) of NMP. During this process the bands between 3500 and 3200,cm,1, assigned to >NH stretching in the PANI backbone, change intensity suggesting that intermolecular hydrogen-bonded >NH, with carbonyl oxygen of NMP, is replaced by free >NH. This is clear evidence of specific interaction of NMP with the emeraldine base. A similar loss of NMP is observed during heating but evidence of polymer degradation is also present. A mechanism is proposed to account for the loss of hydrogen-bonding ability upon protonation which requires delocalization of the radical cations in the protonated films. © 2001 Society of Chemical Industry [source] Alkali Metal Complexes of the Dipeptides PheAla and AlaPhe: IRMPD Spectroscopy,CHEMPHYSCHEM, Issue 4 2008Nick C. Polfer, Prof. Abstract Complexes of PheAla and AlaPhe with alkali metal ions Na+ and K+ are generated by electrospray ionization, isolated in the Fourier-transform ion cyclotron resonance (FT,ICR) ion trapping mass spectrometer, and investigated by infrared multiple-photon dissociation (IRMPD) using light from the FELIX free electron laser over the mid-infrared range from 500 to 1900 cm,1. Insight into structural features of the complexes is gained by comparing the obtained spectra with predicted spectra and relative free energies obtained from DFT calculations for candidate conformers. Combining spectroscopic and energetic results establishes that the metal ion is always chelated by the amide carbonyl oxygen, whilst the C-terminal hydroxyl does not complex the metal ion and is in the endo conformation. It is also likely that the aromatic ring of Phe always chelates the metal ion in a cation-, binding configuration. Along with the amide CO and ring chelation sites, a third Lewis-basic group almost certainly chelates the metal ion, giving a threefold chelation geometry. This third site may be either the C-terminal carbonyl oxygen, or the N-terminal amino nitrogen. From the spectroscopic and computational evidence, a slight preference is given to the carbonyl group, in an ROaOt chelation pattern, but coordination by the amino group is almost equally likely (particularly for K+PheAla) in an ROaNt chelation pattern, and either of these conformations, or a mixture of them, would be consistent with the present evidence. (R represents the , ring site, Oa the amide oxygen, Ot the terminal carbonyl oxygen, and Nt the terminal nitrogen.) The spectroscopic findings are in better agreement with the MPW1PW91 DFT functional calculations of the thermochemistry compared with the B3LYP functional, which seems to underestimate the importance of the cation,, interaction. [source] Exploring the primary electron acceptor (QA)-site of the bacterial reaction center from Rhodobacter sphaeroidesFEBS JOURNAL, Issue 4 2002Binding mode of vitamin K derivatives The functional replacement of the primary ubiquinone (QA) in the photosynthetic reaction center (RC) from Rhodobacter sphaeroides with synthetic vitamin K derivatives has provided a powerful tool to investigate the electron transfer mechanism. To investigate the binding mode of these quinones to the QA binding site we have determined the binding free energy and charge recombination rate from QA, to D+ (kAD) of 29 different 1,4-naphthoquinone derivatives with systematically altered structures. The most striking result was that none of the eight tested compounds carrying methyl groups in both positions 5 and 8 of the aromatic ring exhibited functional binding. To understand the binding properties of these quinones on a molecular level, the structures of the reaction center-naphthoquinone complexes were predicted with ligand docking calculations. All protein,ligand structures show hydrogen bonds between the carbonyl oxygens of the quinone and AlaM260 and HisM219 as found for the native ubiquinone-10 in the X-ray structure. The center-to-center distance between the naphthoquinones at QA and the native ubiquinone-10 at QB (the secondary electron acceptor) is essentially the same, compared to the native structure. A detailed analysis of the docking calculations reveals that 5,8-disubstitution prohibits binding due to steric clashes of the 5-methyl group with the backbone atoms of AlaM260 and AlaM249. The experimentally determined binding free energies were reproduced with an rmsd of ,,4 kJ·mol,1 in most cases providing a valuable tool for the design of new artificial electron acceptors and inhibitors. [source] Theoretical study of the substituent effect on the intramolecular hydrogen bonds in di(4-hydroxycoumarin) derivativesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 6 2006Tzvetan Mihaylov Abstract Geometry optimization of ortho -, meta -, and para -pyridyl-substituted di(4-hydroxycoumarin) [di(4-HC)] was performed with the density functional theory (DFT) [B3LYP/6-31G(d)] method. Two asymmetrical intramolecular OH,O hydrogen bonds (HBs) stabilized the structures. The calculated single HB energies varied from ,62.56 to ,47.53 kJ mol,1 and pointed to a relative strong hydrogen bond in the systems studied. The 2- and 6-pyridyl substituents produced the largest geometrical changes in di(4-hydroxycoumarin) fragment. The highest total HB energy was found for 2-pyridyl-substituted and the lowest one for 6-pyridyl-substituted di(4-hydroxycoumarin). The HB energy variations were confirmed with rotational barrier method calculations. Both steric and electrostatic factors were found to be responsible for the HB asymmetry in the compounds studied. According to the molecular electrostatic potential (MEP) calculations the most preferred reactive site for electrophilic attack of pyridyl-substituted di(4-hydroxycoumarin)s are the pyridine nitrogen and the carbonyl oxygens, followed by the hydroxyl oxygens. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source] Calix[4] crowns with Methoxynaphthoylmethyl Pendant GroupsCHINESE JOURNAL OF CHEMISTRY, Issue 11 2003Chuan-Min Jin Abstract The novel calix [4] crowns with two pendant groups were prepared by the alkylation of calix [4] crowns with 6-methoxy-2-bromoacetylnaphthalene. 1H NMR titration and picrate extraction experiments indicated that they exhibit higher complexing efficiency than their parent compounds and possess obvious selectivity for Na+ or K+, respectively, and that the cation is encapsulated inside the preorganized ionophoric cavity defined by carbonyl oxygens, the crown ether and the phenoxy oxygens. From UV and fluorescent spectra it is revealed that calix [4]-crown-4 3a with 6-methoxy-2-naphthoylmethyl pedant groups exhibits remarkable cation-induced photophysical effects and it could be utilized as a selective fluorescent sensor for Ca2+. [source] | ||||||||||