Relevant bibliographies by topics / Binding and catalysis

Academic literature on the topic 'Binding and catalysis'

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Published: 11 March 2023

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Journal articles on the topic "Binding and catalysis"

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Williams, Ian H. "Catalysis: transition-state molecular recognition?" Beilstein Journal of Organic Chemistry 6 (November 3, 2010): 1026–34. http://dx.doi.org/10.3762/bjoc.6.117.

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The key to understanding the fundamental processes of catalysis is the transition state (TS): indeed, catalysis is a transition-state molecular recognition event. Practical objectives, such as the design of TS analogues as potential drugs, or the design of synthetic catalysts (including catalytic antibodies), require prior knowledge of the TS structure to be mimicked. Examples, both old and new, of computational modelling studies are discussed, which illustrate this fundamental concept. It is shown that reactant binding is intrinsically inhibitory, and that attempts to design catalysts that focus simply upon attractive interactions in a binding site may fail. Free-energy changes along the reaction coordinate for SN2 methyl transfer catalysed by the enzyme catechol-O-methyl transferase are described and compared with those for a model reaction in water, as computed by hybrid quantum-mechanical/molecular-mechanical molecular dynamics simulations. The case is discussed of molecular recognition in a xylanase enzyme that stabilises its sugar substrate in a (normally unfavourable) boat conformation and in which a single-atom mutation affects the free-energy of activation dramatically.
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ABBADI, Amine, Monika BRUMMEL, Burkhardt S. SCHüTT, Mary B. SLABAUGH, Ricardo SCHUCH, and Friedrich SPENER. "Reaction mechanism of recombinant 3-oxoacyl-(acyl-carrier-protein) synthase III from Cuphea wrightii embryo, a fatty acid synthase type II condensing enzyme." Biochemical Journal 345, no. 1 (December 17, 1999): 153–60. http://dx.doi.org/10.1042/bj3450153.

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A unique feature of fatty acid synthase (FAS) type II of higher plants and bacteria is 3-oxoacyl-[acyl-carrier-protein (ACP)] synthase III (KAS III), which catalyses the committing condensing reaction. Working with KAS IIIs from Cuphea seeds we obtained kinetic evidence that KAS III catalysis follows a Ping-Pong mechanism and that these enzymes have substrate-binding sites for acetyl-CoA and malonyl-ACP. It was the aim of the present study to identify these binding sites and to elucidate the catalytic mechanism of recombinant Cuphea wrightii KAS III, which we expressed in Escherichia coli. We engineered mutants, which allowed us to dissect the condensing reaction into three stages, i.e. formation of acyl-enzyme, decarboxylation of malonyl-ACP, and final Claisen condensation. Incubation of recombinant enzyme with [1-14C]acetyl-CoA-labelled Cys111, and the replacement of this residue by Ala and Ser resulted in loss of overall condensing activity. The Cys111Ser mutant, however, still was able to bind acetyl-CoA and to catalyse subsequent binding and decarboxylation of malonyl-ACP to acetyl-ACP. We replaced His261 with Ala and Arg and found that the former lost activity, whereas the latter retained overall condensing activity, which indicated a general-base action of His261. Double mutants Cys111Ser/His261Ala and Cys111Ser/His261Arg were not able to catalyse overall condensation, but the double mutant containing Arg induced decarboxylation of [2-14C]malonyl-ACP, a reaction indicating the role of His261 in general-acid catalysis. Finally, alanine scanning revealed the involvement of Arg150 and Arg306 in KAS III catalysis. The results offer for the first time a detailed mechanism for a condensing reaction catalysed by a FAS type II condensing enzyme.
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Khan, Mohammad Niyaz, and Ibrahim Isah Fagge. "Kinetics and Mechanism of Cationic Micelle/Flexible Nanoparticle Catalysis: A Review." Progress in Reaction Kinetics and Mechanism 43, no. 1 (March 2018): 1–20. http://dx.doi.org/10.3184/146867818x15066862094905.

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The aqueous surfactant (Surf) solution at [Surf] > cmc (critical micelle concentration) contains flexible micelles/nanoparticles. These particles form a pseudophase of different shapes and sizes where the medium polarity decreases as the distance increases from the exterior region of the interface of the Surf/H2O particle towards its furthest interior region. Flexible nanoparticles (FNs) catalyse a variety of chemical and biochemical reactions. FN catalysis involves both positive catalysis ( i.e. rate increase) and negative catalysis ( i.e. rate decrease). This article describes the mechanistic details of these catalyses at the molecular level, which reveals the molecular origin of these catalyses. Effects of inert counterionic salts (MX) on the rates of bimolecular reactions (with one of the reactants as reactive counterion) in the presence of ionic FNs/micelles may result in either positive or negative catalysis. The kinetics of cationic FN (Surf/MX/H2O)-catalysed bimolecular reactions (with nonionic and anionic reactants) provide kinetic parameters which can be used to determine an ion exchange constant or the ratio of the binding constants of counterions.
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Pitson, Stuart M., Paul A. B. Moretti, Julia R. Zebol, Reza Zareie, Claudia K. Derian, Andrew L. Darrow, Jenson Qi, et al. "The Nucleotide-binding Site of Human Sphingosine Kinase 1." Journal of Biological Chemistry 277, no. 51 (October 18, 2002): 49545–53. http://dx.doi.org/10.1074/jbc.m206687200.

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Sphingosine kinase catalyzes the formation of sphingosine 1-phosphate, a lipid second messenger that has been implicated in a number of agonist-driven cellular responses including mitogenesis, anti-apoptosis, and expression of inflammatory molecules. Despite the importance of sphingosine kinase, very little is known regarding its structure or mechanism of catalysis. Moreover, sphingosine kinase does not contain recognizable catalytic or substrate-binding sites, based on sequence motifs found in other kinases. Here we have elucidated the nucleotide-binding site of human sphingosine kinase 1 (hSK1) through a combination of site-directed mutagenesis and affinity labeling with the ATP analogue, FSBA. We have shown that Gly82of hSK1 is involved in ATP binding since mutation of this residue to alanine resulted in an enzyme with an ∼45-fold higherKm(ATP). We have also shown that Lys103is important in catalysis since an alanine substitution of this residue ablates catalytic activity. Furthermore, we have shown that this residue is covalently modified by FSBA. Our data, combined with amino acid sequence comparison, suggest a motif of SGDGX17–21K is involved in nucleotide binding in the sphingosine kinases. This motif differs in primary sequence from all previously identified nucleotide-binding sites. It does, however, share some sequence and likely structural similarity with the highly conserved glycine-rich loop, which is known to be involved in anchoring and positioning the nucleotide in the catalytic site of many protein kinases.
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Breslow, Ronald. "Bifunctional binding and catalysis." Supramolecular Chemistry 1, no. 2 (February 1993): 111–18. http://dx.doi.org/10.1080/10610279308040656.

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Oliveira, Maria Teresa, and Ji-Woong Lee. "Asymmetric Cation-Binding Catalysis." ChemCatChem 9, no. 3 (January 12, 2017): 377–84. http://dx.doi.org/10.1002/cctc.201601441.

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MacMillan, Fraser, and Carola Hunte. "Quinone binding and catalysis." Biochimica et Biophysica Acta (BBA) - Bioenergetics 1797, no. 12 (December 2010): 1841. http://dx.doi.org/10.1016/j.bbabio.2010.10.021.

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Zapata-Pérez, Rubén, Fernando Gil-Ortiz, Ana Belén Martínez-Moñino, Antonio Ginés García-Saura, Jordi Juanhuix, and Álvaro Sánchez-Ferrer. "Structural and functional analysis of Oceanobacillus iheyensis macrodomain reveals a network of waters involved in substrate binding and catalysis." Open Biology 7, no. 4 (April 2017): 160327. http://dx.doi.org/10.1098/rsob.160327.

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Macrodomains are ubiquitous conserved domains that bind or transform ADP-ribose (ADPr) metabolites. In humans, they are involved in transcription, X-chromosome inactivation, neurodegeneration and modulating PARP1 signalling, making them potential targets for therapeutic agents. Unfortunately, some aspects related to the substrate binding and catalysis of MacroD-like macrodomains still remain unclear, since mutation of the proposed catalytic aspartate does not completely abolish enzyme activity. Here, we present a functional and structural characterization of a macrodomain from the extremely halotolerant and alkaliphilic bacterium Oceanobacillus iheyensis (OiMacroD), related to hMacroD1/hMacroD2, shedding light on substrate binding and catalysis. The crystal structures of D40A, N30A and G37V mutants, and those with MES, ADPr and ADP bound, allowed us to identify five fixed water molecules that play a significant role in substrate binding. Closure of the β6–α4 loop is revealed as essential not only for pyrophosphate recognition, but also for distal ribose orientation. In addition, a novel structural role for residue D40 is identified. Furthermore, it is revealed that OiMacroD not only catalyses the hydrolysis of O -acetyl-ADP-ribose but also reverses protein mono-ADP-ribosylation. Finally, mutant G37V supports the participation of a substrate-coordinated water molecule in catalysis that helps to select the proper substrate conformation.
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Bearne, Stephen L. "Asymmetry in catalysis: ‘unidirectional’ amino acid racemases." Biochemist 43, no. 1 (January 22, 2021): 28–34. http://dx.doi.org/10.1042/bio_2020_101.

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d-Amino acids play widespread structural, functional and regulatory roles in organisms. These d-amino acids often arise through the stereoinversion of the more plentiful l-amino acids catalysed by amino acid racemases and epimerases. Such enzymes are of interest since many are recognized targets for the development of drugs or may be employed industrially in biotransformation reactions. Despite their enzyme–substrate complexes being diastereomers, some racemases and epimerases exhibit a kinetic pseudo-symmetry, binding their enantiomeric or epimeric substrate pairs with roughly equal affinities and catalyzing their stereoinversion with similar turnover numbers. In other cases, this kinetic pseudo-symmetry is absent or may be ‘broken’ by substitution of a catalytic Cys by Ser at the active site of cofactor-independent racemases and epimerases, or by altering the Brønsted base of the catalytic dyad that facilitates deprotonation of the Cys residue. Moreover, a natural Thr-containing l-Asp/Glu racemase was discovered that catalyses ‘unidirectional’ substrate turnover, unlike the typical bidirectional racemases and epimerases. These observations suggest that bidirectional Cys–Cys racemases may be re-engineered into ‘unidirectional’ racemases through substitution of the thiol by a hydroxyl group. Catalysis by such ‘unidirectional’ racemase precursors could then be optimized further by site-directed mutagenesis and directed evolution to furnish useful enzymes for biotechnological applications.
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Pusuluk, Onur, Tristan Farrow, Cemsinan Deliduman, Keith Burnett, and Vlatko Vedral. "Proton tunnelling in hydrogen bonds and its implications in an induced-fit model of enzyme catalysis." Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 474, no. 2218 (October 2018): 20180037. http://dx.doi.org/10.1098/rspa.2018.0037.

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The role of proton tunnelling in biological catalysis is investigated here within the frameworks of quantum information theory and thermodynamics. We consider the quantum correlations generated through two hydrogen bonds between a substrate and a prototypical enzyme that first catalyses the tautomerization of the substrate to move on to a subsequent catalysis, and discuss how the enzyme can derive its catalytic potency from these correlations. In particular, we show that classical changes induced in the binding site of the enzyme spreads the quantum correlations among all of the four hydrogen-bonded atoms thanks to the directionality of hydrogen bonds. If the enzyme rapidly returns to its initial state after the binding stage, the substrate ends in a new transition state corresponding to a quantum superposition. Open quantum system dynamics can then naturally drive the reaction in the forward direction from the major tautomeric form to the minor tautomeric form without needing any additional catalytic activity. We find that in this scenario the enzyme lowers the activation energy so much that there is no energy barrier left in the tautomerization, even if the quantum correlations quickly decay.
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Dissertations / Theses on the topic "Binding and catalysis"

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DeChancie, Jason M. "Computational design of new enzyme catalysts and investigations of biological catalysis and binding." Diss., Restricted to subscribing institutions, 2008. http://proquest.umi.com/pqdweb?did=1619413221&sid=1&Fmt=2&clientId=1564&RQT=309&VName=PQD.

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Brackett, David Michael. "Ligand binding and catalysis in an RNA aptamer /." For electronic version search Digital dissertations database. Restricted to UC campuses. Access is free to UC campus dissertations, 2005. http://uclibs.org/PID/11984.

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Dervan, Joe Jude. "Substrate binding and catalysis by T5 5' nuclease." Thesis, University of Sheffield, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.392925.

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Yu, Junru. "Ligand Binding and Catalysis in Selected Sirtuin Isozymes." Diss., North Dakota State University, 2016. http://hdl.handle.net/10365/25733.

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Due to their intimate roles in survival, longevity as well as pathogenesis via “epigenetic” and “metabolic” regulatory mechanisms, sirtuins have gained considerable interest toward undertaking detailed biochemical/biophysical studies. The present study was designed to ascertain the mechanistic details of ligand binding and catalysis in selected sirtuin isozymes (viz., SIRT1 and SIRT5) from the point of view of designing isozyme selective inhibitors as potential therapeutics. By screening of the in-house synthesized compounds, two barbiturate derivatives were identified as the SIRT5 selective inhibitors. These, along with some of known inhibitors of SIRT1 and SIRT5, namely, MH5-75, nicotinamide, suramin were investigated by a combination of spectroscopic, kinetic, and thermodynamic techniques. The influence of the sirtuin inhibitors in modulating the structural features of the enzymes were ascertained by CD spectroscopic, lifetime fluorescence, and thermal denaturation studies using wild-type and selected site-specific mutant enzymes. The experimental data revealed that the substrate selectivity and inhibitory features in SIRT5 were manifested via the mutual cooperation between Y102 and R105 residues of the enzyme, and the overall catalytic feature of the enzyme was modulated by changes in the protein structure. Whereas the stoichiometry of SIRT1 to suramin remained invariant as 1:1, that of SIRT5 to suramin increased from 1:1 to 2:1 upon increase in the molar ratio of the enzyme to the ligand. A comparative account of the experimental data presented herein sheds light on the structural-functional differences between SIRT1 and SIRT5, leading to the design of isozyme selective inhibitors as therapeutic tools for the treatment of sirtuin associated diseases.
NIH (GM110367)
NSF (DMR1306154)
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Kelly, Bernard Thomas. "Development of In vitro selections for binding and catalysis." Thesis, University of Cambridge, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.621351.

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Zhang, Hu. "Engaging Chiral Cationic Intermediates by Anion-Binding in Asymmetric Catalysis." Thesis, Harvard University, 2016. http://nrs.harvard.edu/urn-3:HUL.InstRepos:26718738.

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Anion-binding catalysis by dual hydrogen-bond donors such as ureas and squaramides has been demonstrated as a powerful strategy for the development of highly enantioselective transformations involving prochiral cationic intermediates, such as iminium ions, oxocarbenium ions, carbenium ions, and episulfonium ions. The research described in this dissertation explores the ability of dual H-bond donor catalysts to engage chiral cationic intermediates and to induce enantioselectivity in transformations involving such intermediates. In Chapters 1, we provide an overview of the progress and challenges in the development of enantioselective halo- and seleno-functionalization reactions, which proceed via three-membered ring cationic halonium or seleniranium ions. In Chapter 2, we report a highly enantioselective selenocyclization reaction that is promoted by the combination of a chiral squaramide catalyst, a mineral acid, and an achiral Lewis base. Mechanistic studies reveal that the enantioselectivity originates from the dynamic kinetic resolution of seleniranium ions through anion-binding catalysis. Chapter 3 details our discovery of a squaramide-catalyzed enantioselective iodoisocyanation reaction, which represents a rare example in asymmetric intermolecular halofunctionalization of simple olefins. Kinetic studies reveal that [I(NCO)2]–1 anion is the counterion of iodonium intermediate and the dual H-bond donor catalyst aggregates in the resting state. Hammett analysis indicates that the degree of stabilization by catalyst to the iodonium intermediate accounts for both catalysis and enantioselectivity. The reactions developed in Chapter 2 and 3 have therefore extended anion-binding catalysis to reactions involving chiral and stereochemically labile halonium and seleniranium cations. Knowledge learned in these studies will provide valuable guidance to the development of asymmetric transformations involving other chiral cationic intermediates.
Chemistry and Chemical Biology
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Xu, Chongsong. "Development of functionalized spiroligomers for metal-binding and asymmetric catalysis." Diss., Temple University Libraries, 2019. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/595512.

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Chemistry
Ph.D.
This thesis describes the synthesis of functionalized spiroligomers and their applications in metal binding, metal-mediated catalysis, and organocatalysis. By synthesizing a family of functionalized bis-amino acids achieved from reductive alkylation, the Schafmeister group has developed access to highly functionalized and shape programmable structures named “spiroligomers.” The rigid backbones of spiroligomers are good at organizing the orientations of functional groups on their side chains. This property enables them as promising candidates for catalysts. Firstly we synthesized a few spiroligomer dimers presenting metal-binding groups such as terpys and bipys. With the right orientation of metal binding groups controlled by adjusting the stereocenter of the spiroligomer, macrocyclic “square” complexes with metals were obtained. The crystal structures of these intriguing complexes were solved. This work rendered the first structurally, spectroscopically and electronically characterized metal-spiroligomer complexes as well as the first crystal structure of spiroligomer. Secondly, the question of whether metal-binding spiroligomers are able to catalyze certain reactions became our major concern. We developed a binuclear copper catalyst that could accelerate a phosphate ester rearrangement, and that demonstrated that when the two copper binding terpyridine groups were best able to approach each other, they accelerated the rearrangement more than 1,000 times faster than the background reaction. Other molecules that did not properly organize the two copper atoms demonstrate considerably slower reaction rates. At last, catalysts based on spiroligomers without metals are also of interests. By displaying two hydrophobic groups in various directions on a monomeric spiroligomer (also can be regarded as a proline derivative), we observed variable activities and enantioselectivities in the catalysis of asymmetric Michael addition (up to 94% ee at -40 °C for one organocatalyst).
Temple University--Theses
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Keffer-Wilkes, Laura Carole. "Substrate binding and catalysis by the pseudouridine synthases RluA and TruB." Thesis, Lethbridge, Alta. : University of Lethbridge, Dept. of Chemistry and Biochemistry, c2012, 2012. http://hdl.handle.net/10133/3253.

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Pseudouridine is the most common RNA modification found in all forms of life. The exact role pseudouridines play in the cell is still relatively unknown. However, its extensive incorporation in functionally important areas of the ribosome and the fitness advantage provided to cells by pseudouridines implies that its presence is important for the cell. The enzymes responsible for this modification, pseudouridine synthases, vary greatly in substrate recognition mechanisms, but all enzymes supposedly share a universally conserved catalytic mechanism. Here, I analyze the kinetic mechanisms of pseudouridylation utilized by the exemplary pseudouridine synthase RluA in order to compare it with the previously determined rate of pseudouridylation of the pseudouridine synthase TruB. My results demonstrate that RluA has the same uniformly slow catalytic step as previously determined for TruB and TruA. This constitutes the first step towards identifying the catalytic mechanism of the pseudouridine synthase family. Additionally, it was my aim to identify the major determinants for RNA binding by pseudouridine synthases. By measuring the dissociation constants (KD) for substrate and product tRNA by nitrocellulose filtration assays, I showed that both tRNA species could bind with similar affinities. These binding studies also revealed that TruB’s interaction with the isolated T-arm is the major contact site contributing to the affinity of the enzyme to RNA. Finally, a new contact between tRNA and TruB’s PUA domain was identified which was not observed in the crystal structure. In summary, my results provide new insight into the common catalytic step of pseudouridine synthases and the specific interactions contributing to substrate binding by the enzyme TruB. These results will enable future studies on the kinetic mechanism of pseudouridine synthases, in particular the kinetics of substrate and product binding and release, as well as on the chemical mechanism of pseudouridine formation.
xi, 122 leaves : ill. (some col.) ; 29 cm
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Zhou, Min. "Understanding non-covalent interactions : cooperativity in ligand binding and enzyme catalysis." Thesis, University of Cambridge, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.615013.

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Kimani, Serah. "Catalysis, substrate binding and specificity in the amidase from Nesterenkonia species." Doctoral thesis, University of Cape Town, 2011. http://hdl.handle.net/11427/10837.

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To investigate the structural determinants of NitN specificity on short aliphatic amide substrates by analyzing binding and interactions of these molecules with the NitN binding pocket. To probe the catalytic role of the two active site glutamate residues (Glu61 and Glu139) using NitN as a model enzyme. To monitor the activity, interactions and reactivity of the WT NitN and the Glu61 and Glu139 NitN mutants with ACR.
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Books on the topic "Binding and catalysis"

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Kuby, Stephen Allen. Enzyme catalysis, kinetics, and substrate binding. Boca Raton: CRC Press, 1991.

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Huynh, My Ngan. Mutational analysis of residues involved in substrate binding and catalysis of E. coli argininosuccinate synthetase. Ottawa: National Library of Canada, 2003.

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Garcia-Mancheno, Olga. Anion-Binding Catalysis. Wiley & Sons, Limited, John, 2021.

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García Mancheño, Olga, ed. Anion‐Binding Catalysis. Wiley, 2021. http://dx.doi.org/10.1002/9783527830664.

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Garcia-Mancheno, Olga. Anion-Binding Catalysis. Wiley & Sons, Incorporated, John, 2021.

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Garcia-Mancheno, Olga. Anion-Binding Catalysis. Wiley & Sons, Incorporated, John, 2021.

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Garcia-Mancheno, Olga. Anion-Binding Catalysis. Wiley & Sons, Incorporated, John, 2021.

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Kuby, Stephen A. A Study of Enzymes: Volume I Enzyme Catalysis, Kinetics, and Substrate Binding. CRC Press, 2019. http://dx.doi.org/10.1201/9780429291579.

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Shroyer, Mary Jane N. Escherichia coli uracil-DNA glycosylase: DNA binding, catalysis, and mechanism of action. 1999.

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Shroyer, Mary Jane N. Escherichia coli uracil-DNA glycosylase: DNA binding, catalysis, and mechanism of action. 1999.

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Book chapters on the topic "Binding and catalysis"

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Breslow, Ronald. "Binding and Catalysis in Water." In Supramolecular Chemistry, 411–28. Dordrecht: Springer Netherlands, 1992. http://dx.doi.org/10.1007/978-94-011-2492-8_28.

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Henderson, Richard A. "Binding Substrates to Synthetic Fe-S-Based Clusters and the Possible Relevance to Nitrogenases." In Bioinspired Catalysis, 289–324. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2014. http://dx.doi.org/10.1002/9783527664160.ch11.

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Cornell, Candace N., and Matthew S. Sigman. "Molecular Oxygen Binding and Activation: Oxidation Catalysis." In Activation of Small Molecules, 159–86. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2006. http://dx.doi.org/10.1002/9783527609352.ch5.

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von König, Konstanze, and Ilme Schlichting. "Cytochromes P450 - Structural Basis for Binding and Catalysis." In The Ubiquitous Roles of Cytochrome P450 Proteins, 235–65. Chichester, UK: John Wiley & Sons, Ltd, 2007. http://dx.doi.org/10.1002/9780470028155.ch8.

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Jencks, William P. "Binding Energy, Specificity, and Enzymic Catalysis: The Circe Effect." In Advances in Enzymology - and Related Areas of Molecular Biology, 219–410. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2006. http://dx.doi.org/10.1002/9780470122884.ch4.

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Nigra, Michael M., and Alexander Katz. "Identification of Binding and Reactive Sites in Metal Cluster Catalysts: Homogeneous-Heterogeneous Bridges." In Bridging Heterogeneous and Homogeneous Catalysis, 325–50. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2014. http://dx.doi.org/10.1002/9783527675906.ch9.

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Schrank, Travis P., James O. Wrabl, and Vincent J. Hilser. "Conformational Heterogeneity Within the LID Domain Mediates Substrate Binding to Escherichia coli Adenylate Kinase: Function Follows Fluctuations." In Dynamics in Enzyme Catalysis, 95–121. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/128_2012_410.

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Cohn, Mildred. "Magnetic Resonance Studies of Specificity in Binding and Catalysis of Phosphotransferases." In Ciba Foundation Symposium 31 - Energy Transformation in Biological Systems, 87–104. Chichester, UK: John Wiley & Sons, Ltd., 2008. http://dx.doi.org/10.1002/9780470720134.ch6.

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Dunn, M. F., E. U. Woehl, D. Ferrari, O. Hur, U. Banik, L. H. Yang, and E. W. Miles. "Salt Bridging and Movalent Cation Binding Regulate Catalysis and Channeling in Tryptophan Synthase." In Biochemistry and Molecular Biology of Vitamin B6 and PQQ-dependent Proteins, 151–56. Basel: Birkhäuser Basel, 2000. http://dx.doi.org/10.1007/978-3-0348-8397-9_24.

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Zhang, Keya, Karan Bhuripanyo, Yiyang Wang, and Jun Yin. "Coupling Binding to Catalysis: Using Yeast Cell Surface Display to Select Enzymatic Activities." In Methods in Molecular Biology, 245–60. New York, NY: Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2748-7_14.

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Conference papers on the topic "Binding and catalysis"

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Morris, Benjamin L., Priyadarshan Damle, Zaid Nawaz, and Steven R. Grossman. "Abstract 2199: Evaluation of critical residues in the C-terminal binding protein (CtBP) dehydrogenase domain contributing to substrate binding, catalysis, and oncogenic activity." In Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.am2015-2199.

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Bottomley, D. J., G. Lüpke, and H. M. van Driel. "Second-harmonic probing of the Si(100) - SiO2 interface on flat and vicinal Si(100): interfacial structure and step binding sites." In Nonlinear Optics. Washington, D.C.: Optica Publishing Group, 1992. http://dx.doi.org/10.1364/nlo.1992.tha8.

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Of the various surfaces of crystalline silicon, Si (100) is industrially the most important and the formation of a stable oxide on this surface has allowed it to be used as the dominant material in modern semiconductor technology. Recently there has been a great deal of interest in steps on vicinal Si (100) since they are seen to play a central role in various chemical and physical processes including epitaxial growth, catalysis and oxide formation [1,2]. The study of stepped surfaces of Si (100) to date has been carried out primarily by conventional surface science techniques such as those based on electron diffraction or scanning tunneling microscopy, which normally require ultra high vacuum (UHV). However, over the last few years it has clearly been demonstrated that surface second harmonic generation (SHG) can be sensitive to the surface-vacuum interface as well as buried interfaces and can be used ”in situ” in various types of environments [3]. Our group and others have also shown that SHG can also be senstive to the presence of steps on oxidized or bare solid surface [4].
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Rabiet, M. J., B. C. Furie, and B. Furie. "MOLECULAR DEFECT IN PROTHROMBIN MADRID: SUBSTITUTION OF ARGININE 273 BY CYSTEINE PRECLUDES ACTIVATION." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643936.

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Prothrombin Madrid, a mutant prothrombin, was detected in a patient with a excessive bleeding history. The defect was characterized by a low coagulant activity contrasting with a normal level of prothrombin antigen in plasma. Activation of the purified protein was impaired by the absence of one of the two factor Xa catalyzed cleavages, generating meizothrombin which expressed a thrombin-like activity but was inactive on fibrinogen (Guillin et al., Ann. N.Y. Acad. Sci. 370:414, 1981). Prothrombin and prothrombin Madrid were isolated directly from plasma, with high yield, by immunoaffinity chromatography using conformation specific antibodies immobilized on Sepharose. After reduction and alkylation, purified proteins were hydrolyzed by trypsin. Resulting peptides were separated by reverse phase HPLC. Comparison of the two peptide maps showed that the prothrombin Madrid digest contained an additional peptide, identified by automated Edman degradation as residues 269 to 287 in prothrombin with the substitution of cysteine for arginine at position 273. Peptide 274—287, present in the prothrombin digest, was missing in the prothrombin Madrid digest. The mutation, precluding cleavage by factor Xa and normal generation of thrombin, is identical to the one described for prothrombin Barcelona. The two patients families are not related, raising the possibility that the gene coding for the cysteine 273 mutation in prothrombin is more common than anticipated. Of the seven mutants of vitamin E-dependant blood clotting proteins structurally characterized to date, three are functionally defective due to the presence of the propeptide on the mature amino-ternfinus (factor IX Cambridge, Oxford 3 and San Dimas) and three are due to an alteration that precludes zymogen activation (faotor TX Chapel Hill, prothrombin Barcelona and Madrid). This sample remains too small to anticipate the different classes of point mutations seen in the human population but functional abnormalities of protein processing, metal and lipid binding, zymogen activation, substrate recognition and enzyme catalysis will likely be important phenotypes. However genetic defects may be limited to a discrete group of point mutations that have significant functional implication for the proteins
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Menon, Shruti Mohandas, and Navid Goudarzi. "Exhaust Systems: CO2 Emission Reduction Using Zeolite Catalyst." In ASME 2017 11th International Conference on Energy Sustainability collocated with the ASME 2017 Power Conference Joint With ICOPE-17, the ASME 2017 15th International Conference on Fuel Cell Science, Engineering and Technology, and the ASME 2017 Nuclear Forum. American Society of Mechanical Engineers, 2017. http://dx.doi.org/10.1115/es2017-3389.

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Air pollution is a leading public health concern that needs to be tackled. About 30% of the total greenhouse gas emissions, such as CO, HC and NOx are due to automobiles. By 2030, the US Department of Transportation aims to reduce light duty vehicle emissions by 18%. This can be achieved by public policy approaches such as implementing emission control norms and performance improvements such as exhaust system design. In this work, the implementation of a pure Zeolite catalyst to reduce the exhaust CO2 emission of a SI engine is studied theoretically and experimentally. The complete exhaust system including the catalytic converter, muffler, and pipes is modeled in a 3D CAD modeling software, using the engine specifications. Current expensive precious metals in the catalytic converter are replaced with a binding agent along with Zeolite catalyst. The exhaust system is fabricated and the experimental tests are performed at the maximum engine RPM to obtain threshold emission reduction values. The results showed obtaining an emission reduction of CO2 at a lower cost. Furthermore, it is found that employing Zeolite sieves can further reduce the pollutant emission at a similar cost.
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Schorer, Anna E., and Kathleen V. Watson. "THE "LUPUS ANTICOAGULANT" INDUCES FUNCTIONAL CHANGES IN ENDOTHELIAL CELLS AND PLATELETS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643656.

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The presence of the "lupus anticoagulant" (LA) predicts a clinical syndrome of excessive arterial, venous and microvascu-lar thrombosis. LA is an antibody which reacts with negatively charged phospholipid (PL) species in vitro. Since PL is involved in many aspects of the regulation of thrombosis, we postulated that LA might modify one or more of the membrane-(PL-dependent reactions of platelets and endothelial cells (EC). Blood samples from 20 patients with a history of thrombosis were tested for the presence of LA (kaolin PTT) and titres determined. LA-positive (LA+) sera and plasma were compared to LA-negative (LA−) samples from normal donors (n=6) or patients who had lupus but no clinical thrombosis (n=4). These specimens were tested in a panel of assays. The thrombin-stimulated release of prostacyclin (PG12) from cultured human EC was markedly reduced (52%±12.5 s.e.) by preincubation of the EC with LA+ sera (30 minutes). Purified LA+ IgG from one patient reproduced this effect. Thrombin induction of EC synthesis of the procoagulant, tissue factor-which is dissociable from prostaglandin metabolism-was also inhibited by LA+ sera. Normal platelets incubated in LA+ plasma became refractory to thrombin (1 unit/ml) but retained their responsiveness to epinephrine and ADP. The reduced responsiveness to thrombin was not due to altered (specific or total) binding of thrombin. The cleavage of Factor X by Factor VII requires PL as a co-factor for the EC procoagulant, tissue factor (TF). Unlike the inhibitory effect of LA on thrombin activation of EC and platelets, this distinct membrane-(PL-) dependent function was variably enhanced by LA+ sera. Brief (20 min) exposure of EC to LA+ sera increased TF co-catalysis of Factor VII cleavage of Factor X (measured by chromogenic Xa substrate, S-2222) by up to 10 fold (p<0.05, unpaired t test). This effect was not the result of EC disruption or changes in whole-cell TF content. These data suggest multiple, complex and heterogenous effects of LA, including impaired production of PG12, impaired EC modulation, and heightened ability of endogenous EC tissue factor to initiate coagulation. These (and perhaps other) membrane-dependent effects may contribute to the tendency of LA+ patients to develop clots.
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Svensson, Birte, Haruhide Mori, Birte Kramhoft, Peter K. Nielsen, Birgit C. Bonsager, Morten T. Jensen, Kristian S. Bak-Jensen, et al. "PROTEIN ENGINEERING OF CATALYTIC, SUGAR BINDING, AND PROTEINACEOUS INHIBITOR BINDING REGIONS IN BARLEY ALPHA-AMYLASE." In XXIst International Carbohydrate Symposium 2002. TheScientificWorld Ltd, 2002. http://dx.doi.org/10.1100/tsw.2002.480.

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Niederst, P. N., M. Asbach, M. Ott, and R. E. Zimmermann. "IN VITRO REACTION MODELS OF THROMBIN AND ITS PHYSIOLOGICAL INHIBITOR ANTITHROMBIN III IN THE PRESENCE OF HEPARIN." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644356.

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Antithrombin III (AT III) neutralizes thrombin and other serine proteases of plasma coagulation system by forming a stable 1:1 covalent complex. The inhibition rates are greatly increased by the potent catalyst heparin. The catalytic mechanism of heparin was studied in the presence of dextran sulfate (DS), a thrombin-binding sulfated Polysaccharid. DS did not influence the reaction of AT III with heparin and the amidolytic activity of thrombin, but preincubation with thrombin could inhibit the catalytic activity of heparin in the reaction of thrombin with AT III. We conclude that the reaction of heparin with enzyme and inhibitor, thus forming a ternary complex, is necessary for its catalytic activity.It is known that heparin also converts AT III from an inhibitor to a substrate for thrombin in a dose dependent manner. By cleavage of the reaction site bound Arg(385)-Ser(386) an AT III-fragment (MG 50000 d) occurs, which has a decreased affinity to heparin and does not inhibit F I la. At physiological ionic strength we have only measured a small percentage of AT 111-proteolysis (4%, 1 U/ml Hep). The extent of AT III-fragment formation could be enhanced by lowering the ionic strength (max 44%, 1 U/ml Hep., 1=0,02).
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Belin, D., D. Baccino, A. Wohlwend, A. Estreicher, J. Hurate, and J.-D. Vassalli. "A CELLULAR RECEPTOR FOR UROKINASE-TYPE PLASMINOGEN ACTIVATOR." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642957.

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Recent cell biological and biochemical studies on the urokinase-type plasminogen activator (u-PA) have revealed an unsuspected property of this protein: it binds with high affinity and specificity to the plasma membrane of a number of cell types. Hence, while the interaction of tissue-type plasminogen activator (t-PA) with fibrin suggests a preferred role for this enzyme in the maintenance of fluidity of the extracellular milieu, the cellular binding of u-PA results in the focalisation of plasmin generation to the close environment of the cell surface; this appears as an optimal configuration if u-PA is to participate in the enzymatic events required for cell migration.The available information on the cellular binding of u-PA can be summarized as follows:1. Human monocytes-macrophages, monocyte-like cell lines, fibroblasts, and a variety of other cell lines all express u-PA binding sites. The number of u-PA binding sites on a given cell type may vary as a function of the functional state of the cells. In some cases all sites are occupied by “endogenous” u-PA.2. Binding does not require u-PA activity, and prou-PA binds with the same affinity as does the active enzyme.3. The Kd for u-PA binding is between 1 and 10×10-10 M. The binding site appears to be specific for u-PA.4. Binding requires the presence of the A chain of u-PA; the growth factor module of the A chain is involved in this interaction.5. Bound enzyme does not dissociate readily, nor is it rapidly endocytosed; most importantly, it retains catalytic activity.Studies in progress are aimed at further defining the u-PA determinants responsible for binding. In this context it is noteworthy that there is a tight species specificity of binding: human and murine u-PA, for instance, bind only to cells of the homologous species. Characterization of the u-PA binding site suggests that it is an integral membrane protein that includes at least one Mf 50.000 polypeptide chain.In addition to allowing for the peri-cellular focalisation of u-PA catalysed proteolysis, expression of the u-PA binding site provides a mecanism whereby one cell type can acquire membrane-bound u-PA activity following secretion of the (pro)enzyme by another cell population. A striking example of this is the binding of u-PA, synthesized by the epithelial layer of the male genital tract, to the head region of murine spermatozoa.
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Christensen, Ulla. "Kinetics of piasminogen-activation. Effects of ligands binding to the AH-site of plasminogen." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644420.

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Detailed kinetic studies of the urokinase catalysed conversion of Lys-77- and Val-440-plasminogens in the presence and absence of ligands binding to the AH-site of the plasminogens shows that the effects of such ligand-binding correspond with a model of the activation reaction in which the effective Km and kc decreases, but kc/Km increases when the ligands bind. Apparently plasminogen with a free AH-site is a less specific substrate for urokinase, than is plasminogen with an AH-site-bound ligand.The AH-site is a weak lysine binding site of plasminogen located in the mini plasminogen part (Val-440-Asn-790) of plasminogen and is suggested to participate in the binding of the plasminogens to undegraded fibrin.
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Cai, Xiaoyu, Marcio de Queiroz, Glen Meades, and Grover Waldrop. "Modeling the Negative Feedback Mechanism in the Enzyme Carboxyltransferase." In ASME 2011 Dynamic Systems and Control Conference and Bath/ASME Symposium on Fluid Power and Motion Control. ASMEDC, 2011. http://dx.doi.org/10.1115/dscc2011-6171.

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The enzyme acetyl-CoA carboxylase catalyzes the first committed step in fatty acid synthesis in all organisms. The E. coli form of the carboxyltransferase subunit was recently found to regulate its own activity and expression by binding its own mRNA. By binding acetyl-CoA or the mRNA encoding its own subunits, Carboxyltransferase is able to sense the metabolic state of the cell and attenuate its own translation and enzymatic activity using a negative feedback mechanism. In this paper, this network of interactions is modeled mathematically using mass action kinetics. Numerical simulations of the model show agreement with experimental results.
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Reports on the topic "Binding and catalysis"

1

Thayumanavan, Sankaran. Amphiphilic Nanocontainers for Binding and Catalysis. Fort Belvoir, VA: Defense Technical Information Center, December 2003. http://dx.doi.org/10.21236/ada424480.

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Timko, Michael P. Structural domains in NADPH: Protochlorophyllide oxidoreductases involved in catalysis and substrate binding. Final report. Office of Scientific and Technical Information (OSTI), September 1999. http://dx.doi.org/10.2172/766046.

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Porter, M. A., and F. C. Hartman. Thioredoxin binding site of phosphoribulokinase overlaps the catalytic site. [R]. Office of Scientific and Technical Information (OSTI), January 1986. http://dx.doi.org/10.2172/5463659.

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Klier, K., R. G. Herman, and S. Hou. Binding and catalytic reduction of NO by transition metal aluminosilicates. Office of Scientific and Technical Information (OSTI), December 1991. http://dx.doi.org/10.2172/6011458.

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Klier, K., R. G. Herman, and Shaolie Hou. Binding and catalytic reduction of NO by transition metal aluminosilicates. Office of Scientific and Technical Information (OSTI), September 1991. http://dx.doi.org/10.2172/5146760.

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Klier, K., R. G. Herman, and S. Hou. Binding and catalytic reduction of NO by transition metal aluminosilicates. Office of Scientific and Technical Information (OSTI), June 1992. http://dx.doi.org/10.2172/7033566.

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Klier, K., R. G. Herman, and S. Hou. Binding and catalytic reduction of NO by transition metal aluminosilicates. Office of Scientific and Technical Information (OSTI), September 1992. http://dx.doi.org/10.2172/7072865.

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Clare P. Grey. Joint NMR and Diffraction Studies of Catalyst Structure and Binding. Office of Scientific and Technical Information (OSTI), March 2012. http://dx.doi.org/10.2172/1037331.

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Negre, Christian Francisco Andres, and Ivana Gonzales. Investigation of Structure and Reactivity Relationship in M-N-C Type Catalysts using Density Functional Tight Binding. Office of Scientific and Technical Information (OSTI), March 2019. http://dx.doi.org/10.2172/1499319.

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Negre, Christian Francisco Andres, and Ivana Gonzales. Investigation of Structure and Reactivity Relationship in M-N-C Type Catalysts using Density Functional Tight Binding. Office of Scientific and Technical Information (OSTI), January 2018. http://dx.doi.org/10.2172/1417833.

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