José Walkimar de M. Carneiro

Bio: José Walkimar de M. Carneiro is an academic researcher from Federal Fluminense University. The author has contributed to research in topics: Density functional theory & Adsorption. The author has an hindex of 20, co-authored 124 publications receiving 1693 citations. Previous affiliations of José Walkimar de M. Carneiro include AREA Science Park & University of Erlangen-Nuremberg.

Unified mechanistic concept of electrophilic aromatic nitration: convergence of computational results and experimental data.

Abstract: The mechanism of electrophilic aromatic nitration was revisited. Based on the available experimental data and new high-level quantum chemical calculations, a modification of the previous reaction mechanism is proposed involving three separate intermediates on the potential energy diagram of the reaction. The first, originally considered an unoriented π-complex or electron donor acceptor complex (EDA), involves high electrostatic and charge-transfer interactions between the nitronium ion and the π-aromatics. It explains the observed low substrate selectivity in nitration with nitronium salts while maintaining high positional selectivity, as well as observed oxygen transfer reactions in the gas phase. The subsequent second intermediate originally considered an oriented “π-complex” is now best represented by an intimate radical cation−molecule pair, C6H6+•/NO2, that is, a SET complex, indicative of single-electron transfer from the aromatic π-system to NO2+. Subsequently, it collapses to afford the final σ-c...

The tert-butyl cation (C4H9+) potential energy surface

Abstract: The CH 49 * potential energy surface (PES) is investigated using level ab initio molecular orbital theory. All structures were fully optimized at Hartree-Fock (HF) and correlated levels (HF/6-31G * , MP2(full)/6-31G * , and MP2-(full)/6-31G ** ) followed by single point energy calculations at MP4sdtq/6-31G ** //MP2(full)/6-31G ** . The C s 1, C 3h 2, and C 3v 3 forms of the tert-butyl cation were investigated

Adsorption of CO2 on amine-functionalised MCM-41: experimental and theoretical studies

Abstract: Adsorption of CO2 on MCM-41 functionalised with [3-(2-aminoethylamino)propyl]trimethoxysilane (MCM-41-N2), N1-(3-trimethoxysilylpropyl)diethylenetriamine (MCM-41-N3), 4-aminopyridine (MCM-41-aminopyridine), 4-(methylamino)pyridine (MCM-41-methylaminopyridine) and 1,5,7-triazabicyclo[4.4.0]dec-5-ene (MCM-41-guanidine) was investigated. The amine-functionalised materials were characterised by 29Si and 13C solid-state nuclear magnetic resonance, N2 adsorption/desorption isotherms, X-ray diffraction and transmission electron microscopy. CO2 adsorption at 1.0 bar and 30 °C showed that the amount of CO2 (nads/mmol g−1) adsorbed on MCM-41-N2 and MCM-41-N3 is approximately twice the amount adsorbed on MCM-41. For MCM-41-aminopyridine, MCM-41-methylaminopyridine and MCM-41-guanidine, the CO2 adsorption capacity was smaller than that of MCM-41 at the same conditions. The proton affinity (computed with wB97x-D/6-311++G(d,p)) of the secondary amino groups is higher than that of the primary amino groups; however, the relative stabilities of the primary and secondary carbamates are similar. The differential heat of adsorption decreases as the number of secondary amino groups increases.

Electrophilic aromatic nitration: understanding its mechanism and substituent effects.

Abstract: Theoretical calculations and gas-phase mass spectrometric studies were performed for the reaction of the naked (NO2+) and monosolvated (CH3NO2·NO2+) nitronium ion with several monosubstituted aromatic compounds. From these studies, we propose a general model for regioselectivity based on the single-electron transfer (SET) mechanism and an alternative mechanistic scheme for electrophilic aromatic nitration. This scheme considers the SET and the polar (Ingold−Hughes) mechanisms as extremes in a continuum pathway, the occurrence and extents of both mechanisms being governed mainly by the ability, or lack of ability, of the aromatic compound to transfer an electron to NO2+.

Methods in Enzymology.

Abstract: I read this book the same weekend that the Packers took on the Rams, and the experience of the latter event, obviously, colored my judgment. Although I abhor anything that smacks of being a handbook (like, \"How to Earn a Merit Badge in Neurosurgery\") because too many volumes in biomedical science already evince a boyscout-like approach, I must confess that parts of this volume are fast, scholarly, and significant, with certain reservations. I like parts of this well-illustrated book because Dr. Sj6strand, without so stating, develops certain subjects on technique in relation to the acquisition of judgment and sophistication. And this is important! So, given that the author (like all of us) is somewhat deficient in some areas, and biased in others, the book is still valuable if the uninitiated reader swallows it in a general fashion, realizing full well that what will be required from the reader is a modulation to fit his vision, propreception, adaptation and response, and the kind of problem he is undertaking. A major deficiency of this book is revealed by comparison of its use of physics and of chemistry to provide understanding and background for the application of high resolution electron microscopy to problems in biology. Since the volume is keyed to high resolution electron microscopy, which is a sophisticated form of structural analysis, but really morphology in a modern guise, the physical and mechanical background of The instrument and its ancillary tools are simply and well presented. The potential use of chemical or cytochemical information as it relates to biological fine structure , however, is quite deficient. I wonder when even sophisticated morphol-ogists will consider fixation a reaction and not a technique; only then will the fundamentals become self-evident and predictable and this sine qua flon will become less mystical. Staining reactions (the most inadequate chapter) ought to be something more than a technique to selectively enhance contrast of morphological elements; it ought to give the structural addresses of some of the chemical residents of cell components. Is it pertinent that auto-radiography gets singled out for more complete coverage than other significant aspects of cytochemistry by a high resolution microscopist, when it has a built-in minimal error of 1,000 A in standard practice? I don't mean to blind-side (in strict football terminology) Dr. Sj6strand's efforts for what is \"routinely used in our laboratory\"; what is done is usually well done. It's just that …

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

Abstract: : The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Review of biodiesel composition, properties, and specifications

Abstract: Biodiesel is a renewable transportation fuel consisting of fatty acid methyl esters (FAME), generally produced by transesterification of vegetable oils and animal fats. In this review, the fatty acid (FA) profiles of 12 common biodiesel feedstocks were summarized. Considerable compositional variability exists across the range of feedstocks. For example, coconut, palm and tallow contain high amounts of saturated FA; while corn, rapeseed, safflower, soy, and sunflower are dominated by unsaturated FA. Much less information is available regarding the FA profiles of algal lipids that could serve as biodiesel feedstocks. However, some algal species contain considerably higher levels of poly-unsaturated FA than is typically found in vegetable oils. Differences in chemical and physical properties among biodiesel fuels can be explained largely by the fuels’ FA profiles. Two features that are especially influential are the size distribution and the degree of unsaturation within the FA structures. For the 12 biodiesel types reviewed here, it was shown that several fuel properties – including viscosity, specific gravity, cetane number, iodine value, and low temperature performance metrics – are highly correlated with the average unsaturation of the FAME profiles. Due to opposing effects of certain FAME structural features, it is not possible to define a single composition that is optimum with respect to all important fuel properties. However, to ensure satisfactory in-use performance with respect to low temperature operability and oxidative stability, biodiesel should contain relatively low concentrations of both long-chain saturated FAME and poly-unsaturated FAME.

Geometric and Electronic Structure/Function Correlations in Non-Heme Iron Enzymes

Abstract: ion step follows the decarboxylation, which is consistent with the deuterium isotopic effects observed for thymine 7-hydroxylase which indicate that an irreversible step (or steps) occurs prior to the C-H bond breaking.395 It has also been shown for prolyl 4-hydroxylase that a substrate-derived radical is generated in the reaction, which is consistent with a rebound mechanism.437 It is important to point out that no oxygen intermediate (i.e., bridged superoxo or oxo-ferryl) has been observed for any R-KGdependent enzyme. This warrants future theoretical and experimental study. A detailed molecular mechanism has been proposed for IPNS based on spectroscopic and crystallographic studies.422 Resting IPNS/FeII is also 6C and thus relatively stable toward dioxygen. Substrate ACV binds directly to FeII IPNS through its thiolate group, providing an open coordination position at the FeII. O2 can then react to form an FeIII-superoxo intermediate. This intermediate is suggested422 to perform the first hydrogen-atom abstraction step and close the â-lactam ring, resulting in the formation of the first water molecule and generating an FeIVdO-II intermediate, which completes the second ringclosure process by hydrogen-atom abstraction forming a thiazolidine ring. Previously proposed mechanisms of ACCO involved direct binding of cosubstrate ascorbate to the iron before O2 as part of the oxygen activation process.438,439 The EPR and ESEEM studies of the NO complex of ACCO suggested a quite different molecular mechanism for ACCO.435 An FeIII-superoxo intermediate is proposed. Whether it is preceded by a 6C f 5C process with substrate binding is presently under study.440 This intermediate is thought to initiate a radical process by single hydrogen-atom abstraction or electron-coupled proton transfer (PT)ion or electron-coupled proton transfer (PT) from the bound amino group. The resulting substrate radical may undergo spontaneous conversion into products. The role of cosubstrate ascorbate is proposed to reduce the toxic peroxo byproduct to water. Alternatively, the two-electron reduction of FeIIIsuperoxo by the cosubstrate ascorbate could result in an FeIVdO-II intermediate which initiates the radical reaction.435 4. Rieske-Type Dioxygenases Biochemical Characterization. The Rieske ironsulfur center is a two iron-two sulfur cluster ([2Fe2S]) which has a 2His (on one iron), 2Cys (on the other iron) coordination environment, instead of the 4Cys present in plant ferredoxins. It plays a key role in the electron transport pathway in membranebound cytochrome complexes as well as in some dioxygenases.441 The latter are mainly comprised of two protein components: a reductase containing flavin and a ferredoxin [2Fe-2S], and a terminal oxygenase containing a Rieske [2Fe-2S] cluster and a non-heme iron active site.442 Except for the recently reported alkene monooxygenase that has a binuclear iron site in its terminal oxygenase,10 most of the Rieske-type oxygenases have a mononuclear iron site, which is believed to be the site of dioxygen activation and substrate oxygenation.442,443 The majority of the Rieske-type mononuclear non-heme oxygenases form a family of enzymes which are aromatic-ring-hydroxylating dioxygenases. These catalyze the regioand stereospecific cis-dihydroxylation of an aromatic ring using dioxygen and NAD(P)H (Table 1). Examples include benzene dioxygenase (BDO, EC 1.14.12.3),444 phthalate dioxygenase (PDO, EC 1.14.12.7),445 toluene dioxygenase (EC 1.14.12.11),446 and naphthalene 1,2-dioxygenase (NDO, EC 1.14.12.12),447 which initiate the aerobic degradation of aromatic compounds in the soil bacteria and are targets for bioengineering in bioremediation. This step is the first step in the pathway that ultimately leads to ring cleavage by the intraand extradiol dioxygenases (sections II.B.2 and II.C.1).443 Besides these bacterial dioxygenases, other Rieske-type mononuclear non-heme oxygenases include anthranilate 1,2-dioxygenase (EC 1.14.12.1),448 which deaminates and decarboxylates the substrate to produce catechol; chlorophenylacetate 3,4-dioxygenase (EC 1.14.2.13),449 which converts substrate to catechol with chloride elimination; and 4-methoxybenzoate O-demethylase (putidamonooxin),450 which catalyzes the conversion of 4-methoxybenzoic acid to 4-hydroxybenzoic acid and formaldehyde. The reductase component is usually a monomer (MW ) 12-15 kDa) and utilizes flavin to mediate ET from the two-electron donor NAD(P)H to the oneelectron acceptor [2Fe-2S] cluster and is specific to each terminal oxygenase; other electron donors do not support efficient oxygenation.442 The crystal structure of phthalate dioxygenase reductase is available.451 The terminal oxygenases are large protein aggregates (MW ) 150-200 kDa) containing either multiples of R subunits (BDO R2, PDO R4) or an equimolar combination of R and â subunits (toluene dioxygenase R2â2, NDO R3â3). The R subunits contain a Rieske [2Fe-2S] cluster and a catalytic non-heme FeII center. â subunits do not seem to be involved in the catalytic function (vide infra). Kinetics. Steady-state kinetic studies coupled with various rapid reaction studies of the partial reactions of PDO allowed Ballou et al. to propose a kinetic scheme (Scheme 15).443 On the basis of steady state 278 Chemical Reviews, 2000, Vol. 100, No. 1 Solomon et al.

Nitric oxide, oxidants, and protein tyrosine nitration

Abstract: The occurrence of protein tyrosine nitration under disease conditions is now firmly established and represents a shift from the signal transducing physiological actions of (.)NO to oxidative and potentially pathogenic pathways. Tyrosine nitration is mediated by reactive nitrogen species such as peroxynitrite anion (ONOO(-)) and nitrogen dioxide ((.)NO2), formed as secondary products of (.)NO metabolism in the presence of oxidants including superoxide radicals (O2(.-)), hydrogen peroxide (H2O2), and transition metal centers. The precise interplay between (.)NO and oxidants and the identification of the proximal intermediate(s) responsible for nitration in vivo have been under controversy. Despite the capacity of peroxynitrite to mediate tyrosine nitration in vitro, its role on nitration in vivo has been questioned, and alternative pathways, including the nitrite/H2O2/hemeperoxidase and transition metal-dependent mechanisms, have been proposed. A balanced analysis of existing evidence indicates that (i) different nitration pathways can contribute to tyrosine nitration in vivo, and (ii) most, if not all, nitration pathways involve free radical biochemistry with carbonate radicals (CO3(.-)) and/or oxo-metal complexes oxidizing tyrosine to tyrosyl radical followed by the diffusion-controlled reaction with (.)NO2 to yield 3-nitrotyrosine. Although protein tyrosine nitration is a low-yield process in vivo, 3-nitrotyrosine has been revealed as a relevant biomarker of (.)NO-dependent oxidative stress; additionally, site-specific nitration focused on particular protein tyrosines may result in modification of function and promote a biological effect. Tissue distribution and quantitation of protein 3-nitrotyrosine, recognition of the predominant nitration pathways and individual identification of nitrated proteins in disease states open new avenues for the understanding and treatment of human pathologies.