Study of quinones reactions with wine nucleophiles by cyclic voltammetry.

PubMed

Oliveira, Carla M; Barros, António S; Ferreira, António C S; Silva, Artur M S

2016-11-15

Quinones are electrophilic species which can react with various nucleophiles, like wine antioxidants, such as sulfur dioxide or ascorbic acid, thiols, amino acids, and numerous polyphenols. These reactions are very important in wine aging because they mediate oxygen reactions during both production and bottle aging phases. In this work, the major challenge was to determine the interaction between ortho-quinones and wine nucleophiles (amino acids, thiols, and the antioxidants SO2 and ascorbic acid), by cyclic voltammetry. Wine-model solutions with gallic acid, caffeic acid, or (+)-catechin and nucleophilic compounds were used. To understand the effect of nucleophilic addition in wine, a white wine with the same added nucleophiles was also analysed. Cyclic voltammograms were taken with glassy carbon electrode or screen-printed carbon electrodes, respectively, for wine-model and white wines solutions, in the absence and in the presence of nucleophiles. A nucleophilic order profile related to the cathodic current intensity decrease was observed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Novel thiourea-amine bifunctional catalysts for asymmetric conjugate addition of ketones/aldehydes to nitroalkenes: rational structural combination for high catalytic efficiency.

PubMed

Chen, Jia-Rong; Cao, Yi-Ju; Zou, You-Quan; Tan, Fen; Fu, Liang; Zhu, Xiao-Yu; Xiao, Wen-Jing

2010-03-21

A series of thiourea-amine bifunctional catalysts have been developed by a rational combination of prolines with cinchona alkaloids, which are connected by a thiourea motif. The catalyst 3a, prepared from L-proline and cinchonidine, was found to be a highly efficient catalyst for the conjugate addition of ketones/aldehydes to a wide range of nitroalkenes (up to 98/2 dr and 96% ee). The privileged cinchonidine backbone and the thiourea motif are essential to the reaction activity and enantioselectivity.

Nucleophilic Aromatic Substitution.

ERIC Educational Resources Information Center

Avila, Walter B.; And Others

1990-01-01

Described is a microscale organic chemistry experiment which demonstrates one feasible route in preparing ortho-substituted benzoic acids and provides an example of nucleophilic aromatic substitution chemistry. Experimental procedures and instructor notes for this activity are provided. (CW)

A Safer, Discovery-Based Nucleophilic Substitution Experiment

ERIC Educational Resources Information Center

Horowitz, Gail

2009-01-01

A discovery-based nucleophilic substitution experiment is described in which students compare the reactivity of chloride and iodide ions in an S[subscript N]2 reaction. This experiment improves upon the well-known "Competing Nucleophiles" experiment in that it does not involve the generation of hydrogen halide gas. The experiment also introduces…

Amino acids as novel nucleophiles for silver nanoparticle-luminol chemiluminescence.

PubMed

Li, Na; Ni, Shubiao

2014-12-01

The use of noble metal nanoparticles (NPs) as reductants in chemiluminescence (CL) has been reported only rarely owing to their high oxidation potentials. Interestingly, nucleophiles could dramatically lower the oxidation potential of Ag NPs, such that in the presence of nucleophiles Ag NPS could be used as reductants to induce the CL emission of luminol, an important CL reagent widely used in forensic analysis for the detection of trace amounts of blood. Although nucleophiles are indispensible in Ag NP-luminol CL, only inorganic nucleophiles such as Cl(-), Br(-), I(-) and S2O3 (2-) have been shown to be efficient. The effects of organic nucleophiles on CL remain unexplored. In this study, 20 standard amino acids were evaluated as novel organic nucleophiles in Ag NP-luminol CL. Histidine, lysine and arginine could initiate CL emission; the others could not. It is proposed that the different behaviors of 20 standard amino acids in the CL reactions derive from the interface chemistry between Ag NPs and these amino acids. UV/vis absorption spectra were studied to validate the interface chemistry. In addition, imidazole and histidine were chosen as a model pair to compare the behavior of the monodentate nucleophile with that of the corresponding multidentate nucleophile in Ag NP-luminol CL. Copyright © 2014 John Wiley & Sons, Ltd.

Enantioselective Synthesis of 2-Amino-1,1-diarylalkanes Bearing a Carbocyclic Ring Substituted Indole through Asymmetric Catalytic Reaction of Hydroxyindoles with Nitroalkenes.

PubMed

Vila, Carlos; Rostoll-Berenguer, Jaume; Sánchez-García, Rubén; Blay, Gonzalo; Fernández, Isabel; Muñoz, M Carmen; Pedro, José R

2018-06-07

An asymmetric catalytic reaction of hydroxyindoles with nitroalkenes leading to the Friedel-Crafts alkylation in the carbocyclic ring of indole is presented. The method is based on the activating/directing effects of the hydroxy group situated in the carbocyclic ring of the indole providing nitroalkylated indoles functionalizated at the C-4, C-5, and C-7 positions with high yield, regio-, and enantioselectivity. The optically enriched nitroalkanes were transformed efficiently in optically enriched 2-amino-1,1-diarylalkanes bearing a carbocyclic ring substituted indole.

Detection of Electrophilic and Nucleophilic Chemical Agents

DOEpatents

McElhanon, James R.; Shepodd, Timothy J.

2008-11-11

A "real time" method for detecting electrophilic and nucleophilic species generally by employing tunable, precursor sensor materials that mimic the physiological interaction of these agents to form highly florescent berberine-type alkaloids that can be easily and rapidly detected. These novel precursor sensor materials can be tuned for reaction with both electrophilic (chemical species, toxins) and nucleophilic (proteins and other biological molecules) species.

An unprecedented chemospecific and stereoselective tandem nucleophilic addition/cycloaddition reaction of nucleophilic carbenes with ketenimines.

PubMed

Cheng, Ying; Ma, Yang-Guang; Wang, Xiao-Rong; Mo, Jun-Ming

2009-01-16

The first study of the reaction between nucleophilic carbenes and ketenimines is reported. The interaction of thiazole and benzothiazole carbenes with ketenimines proceeded in a chemospecific and stereoselective manner to produce thiazole- and benzothiazole-spiro-pyrrole derivatives generally in good yields. The reaction was proposed to proceed via a tandem nucleophilic addition of carbene to the C=N bond of ketenimine followed by a stepwise [3+2] cycloaddition of the 1,3-dipolar intermediate with the C=C bond of ketenimine. This reaction provides a powerful protocol for the construction of novel polyfunctional thiazole-spiro-pyrrole or benzothiazole-spiro-pyrrole compounds that are not readily accessible by other methods.

Driving force and nucleophilicity in SN2 displacements

PubMed Central

Streitwieser, Andrew

1985-01-01

The free energies of activation for reaction of six anionic nucleophiles with methyl iodide in dimethylformamide correlate linearly with the overall heats of reaction in the gas phase. The result indicates that nucleophilicity in this SN2 displacement reaction is dominated by electron affinity and bond-strength effects. PMID:16593634

Hydrolysis of Nerve Agents by Model Nucleophiles: A Computational Study

PubMed Central

Beck, Jeremy M.

2008-01-01

Density functional theory calculations were employed to study the reaction of five nerve agents with model nucleophiles, including EtX− and EtXH (X = O, S, Se) for serine, cysteine and selenocysteine, respectively. Calculations at the B3LYP/6-311++G(2d,p) level of theory predict an exothermic reaction between ethoxide and all of the nerve agents studied. As compared to EtO− as a nucleophile, these reactions become ~30 kcal/mol more endothermic for EtS−, and by ~40 kcal/mol for EtSe−. The equivalent reactions with the neutral nucleophiles (EtXH) were more endothermic. The effect of solvation on the reaction thermochemistry was determined using a polarizable continuum model simulating the dielectric constant of chloroform. While there was a large exothermic shift for reactions involving charged nucleophiles with solvation modeling, the corresponding shift was minimal for the reaction with neutral nucleophiles. PMID:18538754

Erosion of stereochemical control with increasing nucleophilicity: O-glycosylation at the diffusion limit.

PubMed

Beaver, Matthew G; Woerpel, K A

2010-02-19

Nucleophilic substitution reactions of 2-deoxyglycosyl donors indicated that the reactivity of the oxygen nucleophile has a significant impact on stereoselectivity. Employing ethanol as the nucleophile resulted in a 1:1 (alpha:beta) ratio of diastereomers under S(N)1-like reaction conditions. Stereoselective formation of the 2-deoxy-alpha-O-glycoside was only observed when weaker nucleophiles, such as trifluoroethanol, were employed. The lack of stereoselectivity observed in reactions of common oxygen nucleophiles can be attributed to reaction rates of the stereochemistry-determining step that approach the diffusion limit. In this scenario, both faces of the prochiral oxocarbenium ion are subject to nucleophilic addition to afford a statistical mixture of diastereomeric products. Control experiments confirmed that all nucleophilic substitution reactions were performed under kinetic control.

Lewis base activation of Lewis acids. Vinylogous aldol addition reactions of conjugated N,O-silyl ketene acetals to aldehydes.

PubMed

Denmark, Scott E; Heemstra, John R

2006-02-01

N,O-Silyl dienyl ketene acetals derived from unsaturated morpholine amides have been developed as highly useful reagents for vinylogous aldol addition reactions. In the presence of SiCl4 and the catalytic action of chiral phosphoramide (R,R)-3, N,O-silyl dienyl ketene acetal 8 undergoes high-yielding and highly site-selective addition to a wide variety of aldehydes with excellent enantioselectivity. Of particular note is the high yields and selectivities obtained from aliphatic aldehydes. Low catalyst loadings (2-5 mol %) can be employed. The morpholine amide serves as a useful precursor for further synthetic manipulation.

Nucleophile Promiscuity of Natural and Engineered Aldolases.

PubMed

Clapes, Pere; Hernández, Karel; Szekrenyi, Anna

2018-04-12

Asymmetric aldol addition reaction mediated by aldolases is recognized as a green and sustainable way for carbon-carbon bond formation. Research in this line has unveiled their unprecedented synthetic potentiality toward diverse new chemical structures, novel product families and even as a technology for industrial manufacturing processes. Despite that, aldolases have long been regarded as strictly selective catalysts, particularly for the nucleophilic substrate, limiting their broad applicability. In recent years, the advances in screening technologies and metagenomics uncovered novel C-C biocatalysts from superfamilies of widely known lyases. Moreover, protein engineering revealed the extraordinary malleability of different carboligases, offering a toolbox of biocatalysts active towards a large structural diversity of nucleophile substrates. In this paper, the nucleophile ambiguity of native and engineered aldolases is discussed with recent examples proving this novel concept. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Theoretical study on the reaction mechanisms of Michael chirality addition between propionaldehyde and nitroalkene catalyzed by an enantioselective catalyst.

PubMed

Zhou, Xinming; Li, Ling; Sun, Xuejun; Wang, Yajun; Du, Dongmei; Fu, Hui

2018-06-01

The asymmetric Michael addition between propionaldehyde and nitroalkene catalyzed by 8-(ethoxycarbonyl)-1,2,3,3a,8,8a-hexahydropyrrolo[2,3-b]indole-2-carboxylic acid has obtained relatively high yields and excellent enantioselectivities at room temperature. In this study, the molecular structures and optical activity of the most stable conformation I are optimized at B3LYP/6-311++ G(d,p) level. We find that levorotatory conformation I catalyzing the same Michael addition can produce laevo-product A and dextrorotatory conformation I' can obtain the dextral-product A'. These results have guiding significance for further studying on the new chemzymes and the mechanism of the obtained different chiral products. © 2018 Wiley Periodicals, Inc.

Nucleophilic Substitution Reactions Using Phosphine Nucleophiles: An Introduction to Phosphorus-31 NMR

ERIC Educational Resources Information Center

Sibbald, Paul A.

2015-01-01

Nuclear magnetic resonance (NMR) spectroscopy is commonly used in modern synthetic chemistry to monitor the conversion of reactants to products. Since instruction in the use of NMR spectroscopy typically does not occur until after the introduction of nucleophilic substitution reactions, organic chemistry students are not able to take advantage of…

Nucleophilic Aromatic Substitution Between Halogenated Benzene Dopants and Nucleophiles in Atmospheric Pressure Photoionization.

PubMed

Kauppila, Tiina J; Haack, Alexander; Kroll, Kai; Kersten, Hendrik; Benter, Thorsten

2016-03-01

In a preceding work with dopant assisted-atmospheric pressure photoionization (DA-APPI), an abundant ion at [M + 77](+) was observed in the spectra of pyridine and quinoline with chlorobenzene dopant. This contribution aims to reveal the identity and route of formation of this species, and to systematically investigate structurally related analytes and dopants. Compounds containing N-, O-, and S-lone pairs were investigated with APPI in the presence of fluoro-, chloro-, bromo-, and iodobenzene dopants. Computational calculations on a density functional theory (DFT) level were carried out to study the reaction mechanism for pyridine and the different halobenzenes. The experimental and computational results indicated that the [M + 77](+) ion was formed by nucleophilic aromatic ipso-substitution between the halobenzene radical cation and nucleophilic analytes. The reaction was most efficient for N-heteroaromatic compounds, and it was weakened by sterical effects and enhanced by resonance stabilization. The reaction was most efficient with chloro-, bromo-, and iodobenzenes, whereas with fluorobenzene the reaction was scarcely observed. The calculated Gibbs free energies for the reaction between pyridine and the halobenzenes were shown to increase in the order I < Br < Cl < F. The reaction was found endergonic for fluorobenzene due to the strong C-F bonding, and exergonic for the other halobenzenes. For fluoro- and chlorobenzenes the reaction was shown to proceed through an intermediate state corresponding to [M + dopant](+), which was highly stable for fluorobenzene. For the bulkier bromine and iodine, this intermediate did not exist, but the halogens were shown to detach already during the approach by the nucleophile.

Polyimidazoles Via Aromatic Nucleophilic Displacement

NASA Technical Reports Server (NTRS)

Connell, John W.; Hergenrother, Paul M.

1990-01-01

Experiments show variety of polyimidazoles prepared by aromatic nucleophilic displacement, from reactions of bisphenol imidazoles with activated difluoro compounds. Polyimidazoles have good mechanical properties making them suitable for use as films, moldings, and adhesives.

Detection of electrophilic and nucleophilic chemical agents

DOE Office of Scientific and Technical Information (OSTI.GOV)

McElhanon, James R.; Shepodd, Timothy J.

2014-08-12

A "real time" method for detecting chemical agents generally and particularly electrophilic and nucleophilic species by employing tunable, precursor sensor materials that mimic the physiological interaction of these agents to form highly florescent berberine-type alkaloids that can be easily and rapidly detected. These novel precursor sensor materials can be tuned for reaction with both electrophilic (chemical species, toxins) and nucleophilic (proteins and other biological molecules) species. By bonding or otherwise attaching these precursor molecules to a surface or substrate they can be used in numerous applications.

Pentamethylcyclopentadienyl-ruthenium catalysts for regio- and enantioselective allylation of nucleophiles.

PubMed

Bruneau, Christian; Renaud, Jean-Luc; Demerseman, Bernard

2006-07-05

Ruthenium(II) complexes containing the pentamethylcyclopentadienyl ligand efficiently perform the activation of allylic carbonates and halides to generate cationic and dicationic ruthenium(IV) complexes. This activation has been transferred as a key step to the catalytic allylation of nucleophiles. The structural and electronic properties of the allylic moieties lead to the regioselective formation of chiral products resulting from nucleophilic addition to their most substituted terminus. The catalytic activity of various Ru(Cp*) precatalysts in several allylic substitutions by C and O nucleophiles will be presented. The enantioselective version that has been demonstrated by using optically pure bisoxazoline ligands will also be discussed.

Nucleophile sensitivity of Drosophila TRPA1 underlies light-induced feeding deterrence

PubMed Central

Du, Eun Jo; Ahn, Tae Jung; Wen, Xianlan; Seo, Dae-Won; Na, Duk L; Kwon, Jae Young; Choi, Myunghwan; Kim, Hyung-Wook; Cho, Hana; Kang, KyeongJin

2016-01-01

Solar irradiation including ultraviolet (UV) light causes tissue damage by generating reactive free radicals that can be electrophilic or nucleophilic due to unpaired electrons. Little is known about how free radicals induced by natural sunlight are rapidly detected and avoided by animals. We discover that Drosophila Transient Receptor Potential Ankyrin 1 (TRPA1), previously known only as an electrophile receptor, sensitively detects photochemically active sunlight through nucleophile sensitivity. Rapid light-dependent feeding deterrence in Drosophila was mediated only by the TRPA1(A) isoform, despite the TRPA1(A) and TRPA1(B) isoforms having similar electrophile sensitivities. Such isoform dependence re-emerges in the detection of structurally varied nucleophilic compounds and nucleophilicity-accompanying hydrogen peroxide (H2O2). Furthermore, these isoform-dependent mechanisms require a common set of TRPA1(A)-specific residues dispensable for electrophile detection. Collectively, TRPA1(A) rapidly responds to natural sunlight intensities through its nucleophile sensitivity as a receptor of photochemically generated radicals, leading to an acute light-induced behavioral shift in Drosophila. DOI: http://dx.doi.org/10.7554/eLife.18425.001 PMID:27656903

Nucleophilic fluorination of aromatic compounds

DOEpatents

Satyamurthy, Nagichettiar; Barrio, Jorge R

2014-03-18

Iodylbenzene derivatives substituted with electron donating as well as electron withdrawing groups on the aromatic ring are used as precursors in aromatic nucleophilic substitution reactions. The iodyl group (IO.sub.2) is regiospecifically substituted by nucleophilic fluoride to provide the corresponding fluoroaryl derivatives. No-carrier-added [F-18]fluoride ion derived from anhydrous [F-18](F/Kryptofix, [F-18]CsF or a quaternary ammonium fluoride (e.g., Me.sub.4NF, Et.sub.4NF, n-Bu.sub.4NF, (PhCH.sub.2).sub.4NF) exclusively substitutes the iodyl moiety in these derivatives and provides high specific activity F-18 labeled fluoroaryl analogs. Iodyl derivatives of a benzothiazole analog and 6-iodyl-L-dopa derivatives have been synthesized as precursors and have been used in the preparation of no-carrier-added [F-18]fluorobenzothiazole as well as 6-[F-18]fluoro-L-dopa.

Pyrrolidinyl-camphor derivatives as a new class of organocatalyst for direct asymmetric Michael addition of aldehydes and ketones to beta-nitroalkenes.

PubMed

Ting, Ying-Fang; Chang, Chihliang; Reddy, Raju Jannapu; Magar, Dhananjay R; Chen, Kwunmin

2010-06-18

Practical and convenient synthetic routes have been developed for the synthesis of a new class of pyrrolidinyl-camphor derivatives (7 a-h). These novel compounds were screened as catalysts for the direct Michael addition of symmetrical alpha,alpha-disubstituted aldehydes to beta-nitroalkenes. When this asymmetric transformation was catalyzed by organocatalyst 7 f, the desired Michael adducts were obtained in high chemical yields, with high to excellent stereoselectivities (up to 98:2 diastereomeric ratio (d.r.) and 99 % enantiomeric excess (ee)). The scope of the catalytic system was expanded to encompass various aldehydes and ketones as the donor sources. The synthetic application was demonstrated by the synthesis of a tetrasubstituted-cyclohexane derivative from (S)-citronellal, with high stereoselectivity.

The Application of Vinylogous Iminium Salt Derivatives and Microwave Accelerated Vilsmeier-Haack Reactions to Efficient Relay Syntheses of the Polycitone and Storniamide Natural Products

PubMed Central

Gupton, John T.; Banner, Edith J.; Sartin, Melissa D.; Coppock, Matthew B.; Hempel, Jonathan E.; Kharlamova, Anastasia; Fisher, Daniel C.; Giglio, Ben C.; Smith, Kristin L.; Keough, Matt J.; Smith, Timothy M.; Kanters, Rene P.F.; Dominey, Raymond N.; Sikorski, James A.

2008-01-01

Studies directed at the synthesis of polycitone and storniamide natural products via vinylogous iminium salts and microwave accelerated Vilsmeier-Haack formylations are described. The successful strategy relies on the formation of a 2,4-disubstituted pyrrole or a 2,3,4-trisubstituted pyrrole from a vinamidinium salt or vinamidinium salt derivative followed by formylation at the 5-position of the pyrrole. Subsequent transformations of the selectively formylated pyrroles lead to efficient and regiocontrolled relay syntheses of the respective pyrrole containing natural products. PMID:18709182

Reference scales for the characterization of cationic electrophiles and neutral nucleophiles.

PubMed

Mayr, H; Bug, T; Gotta, M F; Hering, N; Irrgang, B; Janker, B; Kempf, B; Loos, R; Ofial, A R; Remennikov, G; Schimmel, H

2001-10-03

Twenty-three diarylcarbenium ions and 38 pi-systems (arenes, alkenes, allyl silanes and stannanes, silyl enol ethers, silyl ketene acetals, and enamines) have been defined as basis sets for establishing general reactivity scales for electrophiles and nucleophiles. The rate constants of 209 combinations of these benzhydrylium ions and pi-nucleophiles, 85 of which are first presented in this article, have been subjected to a correlation analysis to determine the electrophilicity parameters E and the nucleophilicity parameters N and s as defined by the equation log k(20 degrees C) = s(N + E) (Mayr, H.; Patz, M. Angew. Chem., Int. Ed. Engl. 1994, 33, 938-957). Though the reactivity scales thus obtained cover more than 16 orders of magnitude, the individual rate constants are reproduced with a standard deviation of a factor of 1.19 (Table 1). It is shown that the reactivity parameters thus derived from the reactions of diarylcarbenium ions with pi-nucleophiles (Figure 3) are also suitable for characterizing the nucleophilic reactivities of alkynes, metal-pi-complexes, and hydride donors (Table 2) and for characterizing the electrophilic reactivities of heterosubstituted and metal-coordinated carbenium ions (Table 3). The reactivity parameters in Figure 3 are, therefore, recommended for the characterization of any new electrophiles and nucleophiles in the reactivity range covered. The linear correlation between the electrophilicity parameters E of benzhydryl cations and the corresponding substituent constants sigma(+) provides Hammett sigma(+) constants for 10 substituents from -1.19 to -2.11, i.e., in a range with only very few previous entries.

Polyphenylquinoxalines Via Aromatic Nucleophilic Displacement

NASA Technical Reports Server (NTRS)

Hergenrother, Paul M.; Connell, John W.

1991-01-01

Process for synthesis of polyphenylquinoxalines (PPQ's) involves nucleophilic displacement reactions of di(hydroxyphenyl) quinoxaline monomers with activated aromatic dihalides. New process costs less than other processes for synthesis of PPQ's. Facilitates synthesis of PPQ's of new and varied molecular structures. Useful as adhesives, coatings, films, membranes, and matrices for composites.

Nucleophilic Addition of Reactive Dyes on Amidoximated Acrylic Fabrics

PubMed Central

El-Shishtawy, Reda M.; El-Zawahry, Manal M.; Abdelghaffar, Fatma; Ahmed, Nahed S. E.

2014-01-01

Seven reactive dyes judiciously selected based on chemical structures and fixation mechanisms were applied at 2% owf of shade on amidoximated acrylic fabrics. Amidoximated acrylic fabric has been obtained by a viable amidoximation process. The dyeability of these fabrics was evaluated with respect to the dye exhaustion, fixation, and colour strength under different conditions of temperature and dyeing time. Nucleophilic addition type reactive dyes show higher colour data compared to nucleophilic substitution ones. FTIR studies further implicate the binding of reactive dyes on these fabrics. A tentative mechanism is proposed to rationalize the high fixation yield obtained using nucleophilic addition type reactive dyes. Also, the levelling and fastness properties were evaluated for all dyes used. Excellent to good fastness and levelling properties were obtained for all samples irrespective of the dye used. The result of investigation offers a new method for a viable reactive dyeing of amidoximated acrylic fabrics. PMID:25258720

Experimental Determination of Activation Energy of Nucleophilic Aromatic Substitution on Porphyrins

ERIC Educational Resources Information Center

Rizvi, Waqar; Khwaja, Emaad; Siddiqui, Saim; Bhupathiraju, N. V. S. Dinesh K.; Drain, Charles Michael

2018-01-01

A physical organic chemistry experiment is described for second-year college students. Students performed nucleophilic aromatic substitution (NAS) reactions on 5,10,15,20-tetrakis(2,3,4,5,6-pentafluorophenyl)porphyrin (TPPF[subscript 20]) using three different nucleophiles. Substitution occurs preferentially at the 4-position ("para")…

Chemoselective reductive nucleophilic addition to tertiary amides, secondary amides, and N-methoxyamides.

PubMed

Nakajima, Minami; Oda, Yukiko; Wada, Takamasa; Minamikawa, Ryo; Shirokane, Kenji; Sato, Takaaki; Chida, Noritaka

2014-12-22

As the complexity of targeted molecules increases in modern organic synthesis, chemoselectivity is recognized as an important factor in the development of new methodologies. Chemoselective nucleophilic addition to amide carbonyl centers is a challenge because classical methods require harsh reaction conditions to overcome the poor electrophilicity of the amide carbonyl group. We have successfully developed a reductive nucleophilic addition of mild nucleophiles to tertiary amides, secondary amides, and N-methoxyamides that uses the Schwartz reagent [Cp2 ZrHCl]. The reaction took place in a highly chemoselective fashion in the presence of a variety of sensitive functional groups, such as methyl esters, which conventionally require protection prior to nucleophilic addition. The reaction will be applicable to the concise synthesis of complex natural alkaloids from readily available amide groups. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Polybenzimidazoles Via Aromatic Nucleophilic Displacement

NASA Technical Reports Server (NTRS)

Connell, John W.; Hergenrother, Paul M.; Smith, Joseph G.

1994-01-01

Soluble polybenzimidazoles (PBI's) synthesized by nucleophilic displacement reaction of di(hydroxyphenyl)-benzimidazole monomers with activated aromatic difluoride compounds in presence of anhydrous potassium carbonate. These polymers exhibit good thermal, thermo-oxidative, and chemical stability, and high mechanical properties. Using benzimidazole monomers, more economical, and new PBI's processed more easily than commercial PBI, without loss of desirable physical properties.

Chiral phosphines in nucleophilic organocatalysis

PubMed Central

Xiao, Yumei; Sun, Zhanhu

2014-01-01

Summary This review discusses the tertiary phosphines possessing various chiral skeletons that have been used in asymmetric nucleophilic organocatalytic reactions, including annulations of allenes, alkynes, and Morita–Baylis–Hillman (MBH) acetates, carbonates, and ketenes with activated alkenes and imines, allylic substitutions of MBH acetates and carbonates, Michael additions, γ-umpolung additions, and acylations of alcohols. PMID:25246969

Analysis of the Nucleophilic Solvation Effects in Isopropyl Chlorothioformate Solvolysis

PubMed Central

D’Souza, Malcolm J.; Mahon, Brian P.; Kevill, Dennis N.

2010-01-01

Correlation of the solvent effects through application of the extended Grunwald-Winstein equation to the solvolysis of isopropyl chlorothioformate results in a sensitivity value of 0.38 towards changes in solvent nucleophilicity (l) and a sensitivity value of 0.72 towards changes in solvent ionizing power (m). This tangible l value coupled with the negative entropies of activation observed indicates a favorable predisposition towards a modest rear-side nucleophilic solvation of a developing carbocation. Only in 100% ethanol was the bimolecular pathway dominant. These observations are very different from those obtained for the solvolysis of isopropyl chloroformate, where dual reaction channels were proposed, with the addition-elimination reaction favored in the more nucleophilic solvents and a unimolecular fragmentation-ionization mechanism favored in the highly ionizing solvents. PMID:20717524

Non-stabilized nucleophiles in Cu-catalysed dynamic kinetic asymmetric allylic alkylation

NASA Astrophysics Data System (ADS)

You, Hengzhi; Rideau, Emeline; Sidera, Mireia; Fletcher, Stephen P.

2015-01-01

The development of new reactions forming asymmetric carbon-carbon bonds has enabled chemists to synthesize a broad range of important carbon-containing molecules, including pharmaceutical agents, fragrances and polymers. Most strategies to obtain enantiomerically enriched molecules rely on either generating new stereogenic centres from prochiral substrates or resolving racemic mixtures of enantiomers. An alternative strategy--dynamic kinetic asymmetric transformation--involves the transformation of a racemic starting material into a single enantiomer product, with greater than 50 per cent maximum yield. The use of stabilized nucleophiles (pKa < 25, where Ka is the acid dissociation constant) in palladium-catalysed asymmetric allylic alkylation reactions has proved to be extremely versatile in these processes. Conversely, the use of non-stabilized nucleophiles in such reactions is difficult and remains a key challenge. Here we report a copper-catalysed dynamic kinetic asymmetric transformation using racemic substrates and alkyl nucleophiles. These nucleophiles have a pKa of >=50, more than 25 orders of magnitude more basic than the nucleophiles that are typically used in such transformations. Organometallic reagents are generated in situ from alkenes by hydrometallation and give highly enantioenriched products under mild reaction conditions. The method is used to synthesize natural products that possess activity against tuberculosis and leprosy, and an inhibitor of para-aminobenzoate biosynthesis. Mechanistic studies indicate that the reaction proceeds through a rapidly isomerizing intermediate. We anticipate that this approach will be a valuable complement to existing asymmetric catalytic methods.

Cation Radical Accelerated Nucleophilic Aromatic Substitution via Organic Photoredox Catalysis.

PubMed

Tay, Nicholas E S; Nicewicz, David A

2017-11-15

Nucleophilic aromatic substitution (S N Ar) is a direct method for arene functionalization; however, it can be hampered by low reactivity of arene substrates and their availability. Herein we describe a cation radical-accelerated nucleophilic aromatic substitution using methoxy- and benzyloxy-groups as nucleofuges. In particular, lignin-derived aromatics containing guaiacol and veratrole motifs were competent substrates for functionalization. We also demonstrate an example of site-selective substitutive oxygenation with trifluoroethanol to afford the desired trifluoromethylaryl ether.

Polyphenylquinoxalines via aromatic nucleophilic displacement

NASA Technical Reports Server (NTRS)

Hergenrother, Paul M. (Inventor); Connell, John W. (Inventor)

1990-01-01

Polyphenylquinoxalines are prepared by the nucleophilic displacement reaction of di(hydroxyphenyl)quinoxaline monomers with activated aromatic dihalides or dinitro compounds. The reactions are carried out in polar aprotic solvents using alkali metal bases at elevated temperatures under nitrogen. The di(hydroxyphenyl)quinoxaline monomers are prepared either by reacting stoichiometric quantities of aromatic bis(o-diamines) with a hydroxybenzil or by reacting o-phenylenediamine with a dihydroxybenzil or bis(hydroxyphenylglyoxylyl)benzene.

Polyphenylquinoxalines via aromatic nucleophilic displacement

NASA Technical Reports Server (NTRS)

Hergenrother, Paul M. (Inventor); Connell, John W. (Inventor)

1991-01-01

Polyphenylquinoxalines are prepared by the nucleophilic displacement reaction of di(hydroxyphenyl)quinoxaline monomers with activated aromatic dihalides or dinitro compounds. The reactions are carried out in polar aprotic solvents during alkali metal bases at elevated temperatures under nitrogen. The di(hydroxyphenyl)quinoxaline monomers are prepared either by reacting stoichiometric quantities of aromatic bis(o-diamines) with a hydroxybenzil or by reacting o-phenylenediamine with a dihydroxybenzil or bis(hydroxyphenylglyoxylyl)benzene.

Dehalogenation of arenes via SN2 reactions at bromine: competition with nucleophilic aromatic substitution.

PubMed

Gronert, Scott; Garver, John M; Nichols, Charles M; Worker, Benjamin B; Bierbaum, Veronica M

2014-11-21

The gas-phase reactions of carbon- and nitrogen-centered nucleophiles with polyfluorobromobenzenes were examined in a selected-ion flow tube (SIFT) and modeled computationally at the MP2/6-31+G(d,p)//MP2/6-31+G(d) level. In the gas-phase experiments, rate constants and branching ratios were determined. The carbon nucleophiles produce expected nucleophilic aromatic substitution (SNAr) and proton transfer products along with unexpected products that result from SN2 reactions at the bromine center (polyfluorophenide leaving group). With nitrogen nucleophiles, the SN2 at bromine channel is suppressed. In the SNAr channels, the "element effect" is observed, and fluoride loss competes with bromide loss. The computational modeling indicates that all the substitution barriers are well below the entrance channel and that entropy and dynamics effects control the product distributions.

Polybenzimidazole via aromatic nucleophilic displacement

NASA Technical Reports Server (NTRS)

Connell, John W. (Inventor); Hergenrother, Paul M. (Inventor); Smith, Joseph G. (Inventor)

1994-01-01

Di(hydroxyphenyl)benzimidazole monomers were prepared from phenyl-4-hydroxybenzoate and aromatic bis(o-diamine)s. These monomers were used in the synthesis of soluble polybenzimidazoles. The reaction involved the aromatic nucleophilic displacement of various di(hydroxyphenyl)benzimidazole monomers with activated aromatic dihalides or activated aromatic dinitro compounds in the presence of an alkali metal base. These polymers exhibited lower glass transition temperatures, improved solubility, and better compression moldability over their commercial counterparts.

Nucleotides as nucleophiles: Reactions of nucleotides with phosphoimidazolide activated guanosine

NASA Astrophysics Data System (ADS)

Kanavarioti, Anastassia; Rosenbach, Morgan T.; Brian Hurley, T.

1992-07-01

An earlier study of the reaction of phosphoimidazolide activated nucleosides (ImpN) in aqueous phosphate buffers indicated two modes of reaction of the phosphate monoanion and dianion. The first mode is catalysis of the hydrolysis of the P-N bond in ImpN's which leads to imidazole and nucleoside 5'-monophosphate. The second represents a nucleophilic substitution of the imidazole to yield the nucleoside 5'-diphosphate. This earlier study thus served as a model for the reaction of ImpN with nucleoside monophosphates (pN) because the latter can be regarded as phosphate derivatives. In the present study we investigated the reaction of guanosine 5'-phosphate-2-methylimidazolide, 2-MeImpG, in the presence of pN (N=guanosine, adenosine and uridine) in the range 6.9 ≤ pH ≤ 7.7. We observed that pN's do act as nucleophiles to form NppG, and as general base to enhance the hydrolysis of the P-N bond in 2-MeImpG, i.e. pN show the same behavior as inorganic phosphate. The kinetic analysis yields the following rate constants for the dianion pN2-:k {/n pN}=0.17±0.02 M-1 h-1 for nucleophilic attack andk {/h pN}=0.11±0.07 M-1 h-1 for general base catalysis of the hydrolysis. These rate constants which are independent of the nucleobase compare withk p 2=0.415 M-1 h-1 andk_h^{p^2 } =0.217 M-1 h-1 for the reactions of HPO{4/2-}. In addition, this study shows that under conditions where pN presumably form stacks, the reaction mechanism remains unchanged although in quantitative terms stacked pN are somewhat less reactive. Attack by the 2'-OH and 3'-OH groups of the ribose moiety in amounts ≥1% is not observed; this is attributed to the large difference in nucleophilicity in the neutral pH range between the phosphate group and the ribose hydroxyls. This nucleophilicity rank is not altered by stacking.

Synthesis, electronic structure and spectral fluorescent properties of vinylogous merocyanines derived from 1,3-dialkyl-benzimidazole and malononitrile

NASA Astrophysics Data System (ADS)

Kulinich, Andrii V.; Mikitenko, Elena K.; Ishchenko, Alexander A.

2017-01-01

A vinylogous series of merocyanines were synthesized with 1,3-dibutyl-benzimidazole and malononitrile residues as the donor and acceptor terminal groups. These dyes do not comprise carbonyl groups, which are prone to the strong specific solvation by polar solvents up to hydrogen bond formation, and nevertheless they possess distinct reversed solvatochromism, i.e. their molecules have very high dipolarity. At that, they are soluble in a wide range of solvents from n-hexane to ethanol and do not aggregate readily. They were studied thoroughly by UV/Vis, fluorescence, IR, and NMR spectroscopy methods. Their structure and spectral properties in the ground and excited fluorescent states were modelled at the DFT level both in vacuum and in solvents of various polarities by using the PCM solvent field simulation. The calculations were performed using several hybrid functionals (B3LYP, CAM-B3LYP, and wB97XD) and the split-valence 6-31G (d,p) basis set.

Hyperbranched Polycarbosilanes via Nucleophilic Substitution Reactions

NASA Astrophysics Data System (ADS)

Interrante, L.; Shen, Q.

Nucleophilic substitution reactions involving organomagnesium (Grignard) [1] and organolithium reagents have been used extensively for many years to form Si—C bonds (see Reaction Scheme 12.1). However, their use for the construction of hyperbranched polymers whose backbone contains, as a major structural component, silicon—carbon bonds, i.e., polycarbosilanes [2] is relatively more recent. (12.1) begin{array}{l} {{R}}_3 {{SiX + MR'}} to {{R}}_3 {{SiR' + MX}} \\ left({{{R,R' = alkyl}} {{or aryl;}} {{M = Mg(X),}} {{Li,}} {{Na}};{{X = halogen, OR''}}} right) \\ This chapter focuses on the application of such nucleophilic substitution reactions toward the synthesis of hyperbranched polycarbosilanes, with particular emphasis on those preparations that have resulted in relatively well characterized products. These syntheses are organized by the type of ABn monomer unit used (see Section 1.2), where A and B refer to the (C)X and (Si)Xn, respectively, functional ends of the monomer unit and where the nature of the coupling reaction leads to entirely or primarily Si—C bond formation. In most cases, these are “one-pot” reactions that employ monomers that bear halogen or alkoxy groups on the C and Si ends of the unit. Indeed, hyperbranched polycarbosilanes have been described, in general, as “obtained in one synthetic step via a random, one-pot polymerization of multifunctional monomers of AB n type” [2]. Treatment of the ABn monomer with either elemental Mg or an organolithium reagent, ideally (but not always) forms a complexed carbanion (the nucleophile) by reaction with the C-X end of the monomer unit, resulting in an intermediate of the type, (XxM)CSiXn, where M = Mg or Li, X = halogen or alkoxy, and x = 1 (Mg) or 0 (Li). Self-coupling of this reagent via reactions of the type shown in Reaction Scheme 12.1 leads to oligomeric and polymeric products that are connected primarily through Si—C bonds and yield an inorganic MXx by-product.

Advances in Nucleophilic Phosphine Catalysis of Alkenes, Allenes, Alkynes, and MBHADs

PubMed Central

Fan, Yi Chiao

2014-01-01

In nucleophilic phosphine catalysis, tertiary phosphines undergo conjugate additions to activated carbon–carbon multiple bonds to form β-phosphonium enolates, β-phosphonium dienolates, β-phosphonium enoates, and vinyl phosphonium ylides as intermediates. When these reactive zwitterionic species react with nucleophiles and electrophiles, they may generate carbo- and heterocycles with multifarious molecular architectures. This Article describes the reactivities of these phosphonium zwitterions, the applications of phosphine catalysis in the syntheses of biologically active compounds and natural products, and recent developments in the enantioselective phosphine catalysis. PMID:24196409

Nucleotides as nucleophiles: reactions of nucleotides with phosphoimidazolide activated guanosine

NASA Technical Reports Server (NTRS)

Kanavarioti, A.; Rosenbach, M. T.; Hurley, T. B.

1991-01-01

An earlier study of the reaction of phosphoimidazolide activated nucleosides (ImpN) in aqueous phosphate buffers indicated two modes of reaction of the phosphate monoanion and dianion. The first mode is catalysis of the hydrolysis of the P-N bond in ImpN's which leads to imidazole and nucleoside 5'-monophosphate. The second represents a nucleophilic substitution of the imidazole to yield the nucleoside 5'-diphosphate. This earlier study thus served as a model for the reaction of ImpN with nucleoside monophosphates (pN) because the latter can be regarded as phosphate derivatives. In the present study we investigated the reaction of guanosine 5'-phosphate-2-methylimidazolide, 2-MeImpG, in the presence of pN (N = guanosine, adenosine and uridine) in the range 6.9 less than or equal to pH less than or equal to 7.7. We observed that pN's do act as nucleophiles to form NppG, and as general base to enhance the hydrolysis of the P-N bond in 2-MeImpG, i.e. pN show the same behavior as inorganic phosphate. The kinetic analysis yields the following rate constants for the dianion pN2-: knpN = 0.17 +/- 0.02 M-1 h-1 for nucleophilic attack and khpN = 0.11 +/- 0.07 M-1 h-1 for general base catalysis of the hydrolysis. These rate constants which are independent of the nucleobase compare with kp.2 = 0.415 M-1 h-1 and khp2. = 0.217 M-1 h-1 for the reactions of HPO4(2-). In addition, this study shows that under conditions where pN presumably form stacks, the reaction mechanism remains unchanged although in quantitative terms stacked pN are somewhat less reactive. Attack by the 2'-OH and 3'-OH groups of the ribose moiety in amounts greater than or equal to 1% is not observed; this is attributed to the large difference in nucleophilicity in the neutral pH range between the phosphate group and the ribose hydroxyls. This nucleophilicity rank is not altered by stacking.

Palladium-catalyzed substitution of (coumarinyl)methyl acetates with C-, N-, and S-nucleophiles

PubMed Central

Chattopadhyay, Kalicharan; Fenster, Erik; Grenning, Alexander J

2012-01-01

Summary The palladium-catalyzed nucleophilic substitution of (coumarinyl)methyl acetates is described. The reaction proceeds though a palladium π-benzyl-like complex and allows for many different types of C-, N-, and S-nucleophiles to be regioselectively added to the biologically active coumarin motif. This new method was utilized to prepare a 128-membered library of aminated coumarins for biological screening. PMID:23019448

Oxidative trifluoromethylation and trifluoromethylthiolation reactions using (trifluoromethyl)trimethylsilane as a nucleophilic CF3 source.

PubMed

Chu, Lingling; Qing, Feng-Ling

2014-05-20

The trifluoromethyl group is widely prevalent in many pharmaceuticals and agrochemicals because its incorporation into drug candidates could enhance chemical and metabolic stability, improve lipophilicity and bioavailability, and increase the protein bind affinity. Consequently, extensive attention has been devoted toward the development of efficient and versatile methods for introducing the CF3 group into various organic molecules. Direct trifluoromethylation reaction has become one of the most efficient and important approaches for constructing carbon-CF3 bonds. Traditionally, the nucleophilic trifluoromethylation reaction involves an electrophile and the CF3 anion, while the electrophilic trifluoromethylation reaction involves a nucleophile and the CF3 cation. In 2010, we proposed the concept of oxidative trifluoromethylation: the reaction of nucleophilic substrates and nucleophilic trifluoromethylation reagents in the presence of oxidants. In this Account, we describe our recent studies of oxidative trifluoromethylation reactions of various nucleophiles with CF3SiMe3 in the presence of oxidants. We have focused most of our efforts on constructing carbon-CF3 bonds via direct trifluoromethylation of various C-H bonds. We have demonstrated copper-mediated or -catalyzed or metal-free oxidative C-H trifluoromethylation of terminal alkynes, tertiary amines, arenes and heteroarenes, and terminal alkenes. Besides various C-H bonds, aryl boronic acids proved to be viable nucleophilic coupling partners for copper-mediated or -catalyzed cross-coupling reactions with CF3SiMe3. To further expand the reaction scope, we also applied H-phosphonates to the oxidative trifluoromethylation system to construct P-CF3 bonds. Most recently, we developed silver-catalyzed hydrotrifluoromethylation of unactivated olefins. These studies explore boronic acids, C-H bonds, and P-H bonds as novel nucleophiles in transition-metal-mediated or -catalyzed cross-coupling reactions with CF3SiMe3

Electronic forces as descriptors of nucleophilic and electrophilic regioselectivity and stereoselectivity.

PubMed

Liu, Shubin; Rong, Chunying; Lu, Tian

2017-01-04

One of the main tasks of theoretical chemistry is to rationalize computational results with chemical insights. Key concepts of such nature include nucleophilicity, electrophilicity, regioselectivity, and stereoselectivity. While computational tools are available to predict barrier heights and other reactivity properties with acceptable accuracy, a conceptual framework to appreciate above quantities is still lacking. In this work, we introduce the electronic force as the fundamental driving force of chemical processes to understand and predict molecular reactivity. It has three components but only two are independent. These forces, electrostatic and steric, can be employed as reliable descriptors for nucleophilic and electrophilic regioselectivity and stereoselectivity. The advantages of using these forces to evaluate molecular reactivity are that electrophilic and nucleophilic attacks are featured by distinct characteristics in the electrostatic force and no knowledge of quantum effects included in the kinetic and exchange-correlation energies is required. Examples are provided to highlight the validity and general applicability of these reactivity descriptors. Possible applications in ambident reactivity, σ and π holes, frustrated Lewis pairs, and stereoselective reactions are also included in this work.

Nucleophile Assisting Leaving Groups: A Strategy for Aliphatic 18F-Fluorination

PubMed Central

Lu, Shuiyu; Lepore, Salvatore D.; Li, Song Ye; Mondal, Deboprosad; Cohn, Pamela C.; Bhunia, Anjan K.; Pike, Victor W.

2009-01-01

A series of arylsulfonate nucleophile assisting leaving groups (NALGs) were prepared in which the metal chelating unit is attached to the aryl ring via an ether linker. These NALGs exhibited significant rate enhancements in halogenation reactions using metal halides. Studies with a NALG containing a macrocyclic ether unit suggest that rate enhancements of these nucleophilic halogenation reactions are facilitated by stabilization of charge in the transition state rather than through strong pre-complexation with metal cation. In several cases, a primary substrate containing one of the new leaving groups rivaled or surpassed the reactivity of triflates when exposed to nucleophile but was otherwise highly stable and isolable. These and previously disclosed chelating leaving groups were used in 18F-fluorination reactions using no-carrier-added [18F]fluoride ion (t1/2 = 109.7 min, β+ = 97%) in CH3CN. Under microwave irradiation and without the assistance of a cryptand, such as K2.2.2, primary substrates with select NALGs led to a substantial improvement (2 to 3 fold) in radiofluorination yields over traditional leaving groups. PMID:19572583

Magnesium Induced Nucleophile Activation in the Guanylyltransferase mRNA Capping Enzyme

PubMed Central

Swift, Robert V.; Ong, Chau D.; Amaro, Rommie E.

2012-01-01

The messenger RNA guanylyltransferase, or mRNA capping enzyme, co-transcriptionally caps the 5′-end of nascent mRNA with GMP during the second in a set of three enzymatic reactions that result in the formation of an N7-methyl guanosine cap during mRNA maturation. The mRNA capping enzyme is characterized, in part, by a conserved lysine nucleophile that attacks the alpha-phosphorous atom of GTP, forming a lysine-GMP intermediate. Experiments have firmly established that magnesium is required for efficient intermediate formation, but have provided little insight into the requirement’s molecular origins. Using empirical and thermodynamic integration pKa estimates, along with conventional MD simulations, we show that magnesium binding likely activates the lysine nucleophile by increasing its acidity and by biasing the deprotonated nucleophile into conformations conducive to intermediate formation. These results provide additional functional understanding of an important enzyme in the mRNA transcript life cycle and allow functional analogies to be drawn that affect our understanding of the metal dependence of related superfamily members. PMID:23205906

Polyphenylquinoxalines via Aromatic Nucleophilic Displacement

NASA Technical Reports Server (NTRS)

Hergenrother, Paul M.; Connell, John W.

1988-01-01

Polyphenylquinoxalines are produced by an aromatic nucleophilic displacement reaction involving an activated aromatic dihalide with an appropriate quinoxaline monomer. Polyphenylquinoxalines are high temperature thermoplastics used as adhesives, coatings, films and composite matrices. The novelty of this invention is threefold: (1) some of the quinoxaline monomers are new compositions of matter; (2) the phenylquinoxaline polymers which are the end products of the invention are new compositions of matter; and (3) the method of forming the polymers is novel, replacing a more costly prior art process, which is also limited in the kinds of products prepared therefrom.

Nucleophilic substitution by grignard reagents on sulfur mustards.

PubMed

Converso, Antonella; Saaidi, Pierre-Loïc; Sharpless, K Barry; Finn, M G

2004-10-15

With proper activation of the leaving group, sulfur mustards react with Grignard reagents with neighboring group participation of the sulfur atom. 2,6-Dichloro-9-thiabicyclo[3.3.1]nonane is especially useful in this regard, providing clean reactivity with organomagnesium nucleophiles on a topologically constrained scaffold.

Allylic aminations with hindered secondary amine nucleophiles catalyzed by heterobimetallic Pd-Ti complexes.

PubMed

Walker, Whitney K; Anderson, Diana L; Stokes, Ryjul W; Smith, Stacey J; Michaelis, David J

2015-02-06

Phosphinoamide-scaffolded heterobimetallic palladium-titanium complexes are highly effective catalysts for allylic aminations of allylic chlorides with hindered secondary amine nucleophiles. Three titanium-containing ligands are shown to assemble active catalysts in situ and enable catalysis at room temperature. A variety of sterically bulky secondary amines are efficiently allylated in high yields with as little as 1 mol % palladium catalyst. Piperidine and pyrrolidine products are also efficiently generated via intramolecular aminations with hindered amine nucleophiles.

Functionalization of metallabenzenes through nucleophilic aromatic substitution of hydrogen.

PubMed

Clark, George R; Ferguson, Lauren A; McIntosh, Amy E; Söhnel, Tilo; Wright, L James

2010-09-29

The cationic metallabenzenes [Ir(C(5)H(4){SMe-1})(κ(2)-S(2)CNEt(2))(PPh(3))(2)]PF(6) (1) and [Os(C(5)H(4){SMe-1})(CO)(2)(PPh(3))(2)][CF(3)SO(3)] (2) undergo regioselective nucleophilic aromatic substitution of hydrogen at the metallabenzene ring position γ to the metal in a two-step process that first involves treatment with appropriate nucleophiles and then oxidation. Thus, reaction between compound 1 and NaBH(4), MeLi, or NaOEt gives the corresponding neutral iridacyclohexa-1,4-diene complexes Ir(C(5)H(3){SMe-1}{H-3}{Nu-3})(κ(2)-S(2)CNEt(2))(PPh(3))(2) (Nu = H (3), Me (4), OEt (5)). Similarly, reaction between 2 and NaBH(4) or MeLi gives the corresponding osmacyclohexa-1,4-diene complexes Os(C(5)H(3){SMe-1}{H-3}{Nu-3})(CO)(2)(PPh(3))(2) (Nu = H (8), Me (9)). The metallacyclohexa-1,4-diene rings in all these compounds are rearomatized on treatment with the oxidizing agent O(2), CuCl(2), or 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ). Accordingly, the cationic metallabenzene 1 or 2 is returned after reaction between 3 and DDQ/NEt(4)PF(6) or between 8 and DDQ/NaO(3)SCF(3), respectively. The substituted cationic iridabenzene [Ir(C(5)H(3){SMe-1}{Me-3})(κ(2)-S(2)CNEt(2))(PPh(3))(2)]PF(6) (6) or [Ir(C(5)H(4){SMe-1}{OEt-3})(κ(2)-S(2)CNEt(2))(PPh(3))(2)]PF(6) (7) is produced in a similar manner through reaction between 4 or 5, respectively, and DDQ/NEt(4)PF(6), and the substituted cationic osmabenzene [Os(C(5)H(3){SMe-1}{Me-3})(CO)(2)(PPh(3))(2)]Cl (10) is formed in good yield on treatment of 9 with CuCl(2). The starting cationic iridabenzene 1 is conveniently prepared by treatment of the neutral iridabenzene Ir(C(5)H(4){SMe-1})Cl(2)(PPh(3))(2) with NaS(2)CNEt(2) and NEt(4)PF(6), and the related starting cationic osmabenzene 2 is obtained by treatment of Os(C(5)H(4){S-1})(CO)(PPh(3))(2) with CF(3)SO(3)CH(3) and CO. The stepwise transformations of 1 into 6 or 7 as well as 2 into 10 provide the first examples in metallabenzene chemistry of regioselective

FACTORS AFFECTING THE ELECTROPHILICITY AND NUCLEOPHILICITY OF REAGENTS.

DTIC Science & Technology

The apparent simplicity of the reactions of Malachite Green cation (bis-(p-dimethylaminophenyl), phenylmethyl cation) with nucleophilic reagents...initiated to study the rates of the reactions of a series of Malachite Green cations with a number of nucleophilies in several dipolar aprotic solvents, and the same reactions in water for comparison. (Author)

Nucleophilic Substitution in Solution: Activation Strain Analysis of Weak and Strong Solvent Effects

PubMed Central

Hamlin, Trevor A.; van Beek, Bas; Wolters, Lando P.

2018-01-01

Abstract We have quantum chemically studied the effect of various polar and apolar solvents on the shape of the potential energy surface (PES) of a diverse collection of archetypal nucleophilic substitution reactions at carbon, silicon, phosphorus, and arsenic by using density functional theory at the OLYP/TZ2P level. In the gas phase, all our model SN2 reactions have single‐well PESs, except for the nucleophilic substitution reaction at carbon (SN2@C), which has a double‐well energy profile. The presence of the solvent can have a significant effect on the shape of the PES and, thus, on the nature of the SN2 process. Solvation energies, charges on the nucleophile or leaving group, and structural features are compared for the various SN2 reactions in a spectrum of solvents. We demonstrate how solvation can change the shape of the PES, depending not only on the polarity of the solvent, but also on how the charge is distributed over the interacting molecular moieties during different stages of the reaction. In the case of a nucleophilic substitution at three‐coordinate phosphorus, the reaction can be made to proceed through a single‐well [no transition state (TS)], bimodal barrier (two TSs), and then through a unimodal transition state (one TS) simply by increasing the polarity of the solvent. PMID:29457865

Nucleophilic Influences and Origin of the SN2 Allylic Effect.

PubMed

Galabov, Boris; Koleva, Gergana; Schaefer, Henry F; Allen, Wesley D

2018-05-27

The potential energy surfaces for the SN2 reactions of allyl and propyl chlorides with 21 anionic and neutral nucleophiles have been studied using ωB97X-D/6-311++G(3df,2pd) computations. The "allylic effect" on SN2 barriers is well manifested for all reactions and ranges between -0.2 and -4.5 kcal mol-1 in the gas phase. Strong correlations of the SN2 net activation barriers with cation affinities, proton affinities, and electrostatic potentials at nuclei (EPN) demonstrate the powerful influence of electrostatics on these reactions. For the reactions of anionic (but not neutral) nucleophiles with allyl chloride, some of the incoming negative charge (0.2% - 18%) migrates into the carbon chains, which may provide some secondary stabilization of the SN2 transition states. Activation strain analysis provides additional insight into the allylic effect by showing that the energy of geometric distortion for the reactants to reach the SN2 transition state (ΔEstrain) is smaller for each allylic reaction in comparison to its propyl analogue. In many cases the interaction energies (ΔEint) between the substrate and nucleophile in this analysis are more favorable for propyl chloride reactions, but this compensation does not overcome the predominant strain energy effect. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nucleophilic substitution reaction for post-functionalization of polyoxometalates

DOE PAGES

Yin, Panchao; Li, Qiang; Zhang, Jin; ...

2015-07-06

In this study, a hexamolybdate-based organic inorganic hybrid molecule containing a chloralkane fragment is synthesized and its Cl atom can be substituted by iodine and nitrate through nucleophilic substitution reactions in high yields, which provide a post-functionalization protocol to bring in various additional functional groups into polyoxometalate-based hybrid materials under mild conditions.

Chemically modified electrodes by nucleophilic substitution of chlorosilylated platinum oxide surfaces

NASA Astrophysics Data System (ADS)

Chen, Chun-Hsien; Hutchison, James H.; Postlethwaite, Timothy A.; Richardson, John N.; Murray, R. W.

1994-07-01

Chlorosilylated platinum oxide electrode surfaces can be generated by reaction of SiCl4 vapor with an electrochemically prepared monolayer of platinum oxide. A variety of nucleophilic agents (such as alcohols, amines, thiols, and Grignard reagents) can be used to displace chloride and thereby functionalize the metal surface. Electroactive surfaces prepared with ferrocene methanol as the nucleophile show that derivatization by small molecules can achieve coverages on the order of a full monolayer. Surfaces modified with long-chain alkyl groups efficiently block electrode reactions of redox probes dissolved in the contacting solution, but other electrochemical (double layer capacitance and surface coverage) and contact angle measurements suggest that these molecule films are not highly ordered, self-assembled monolayers.

Polybenzimidazoles Via Aromatic Nucleophilic Displacement

NASA Technical Reports Server (NTRS)

Connell, John W. (Inventor); Hergerrother, Paul M. (Inventor); Smith, Joseph G., Jr. (Inventor)

1997-01-01

Novel molecular weight controlled and endcapped polybenzimidazoles (PBI) are prepared by the aromatic nucleophilic displacement reaction of di(hydroxyphenylbenzimidazole) monomers with activated aromatic dihalides or activated aromatic dinitro compounds. The PBI are endcapped with mono(hydroxyphenyl)benzimidazoles. The polymerizations are carried out in polar aprotic solvents such as N-methyl-2-pyrrolidinone or N,N-dimethylacetamide using alkali metal bases such as potassium carbonate at elevated temperatures under nitrogen. Mono(hydroxyphenyl)benzimidazoles are synthesized by reacting phenyl-4-hydroxybenzoate with aromatic (o-diamine)s in diphenylsulfone. Molecular weight controlled and endcapped PBI of new chemical structures are prepared that exhibit a favorable combination of physical and mechanical properties.

Polybenzimidazoles via aromatic nucleophilic displacement

NASA Technical Reports Server (NTRS)

Connell, John W. (Inventor); Hergenrother, Paul M. (Inventor); Smith, Joseph G., Jr. (Inventor)

1995-01-01

Novel molecular weight controlled and endcapped polybenzimidazoles (PBI) are prepared by the aromatic nucleophilic displacement reaction of di(hydroxyphenyl benzimidazole) monomers with activated aromatic dihalides or activated aromatic dinitro compounds. The PBI are endcapped with mono(hydroxyphenyl) benzimidazoles. The polymerizations are carried out in polar aprotic solvents such as N-methyl-2-pyrrolidinone or N,N-dimethylacetamide using alkali metal bases such as potassium carbonate at elevated temperatures under nitrogen. Mono(hydroxyphenyl) benzimidazoles are synthesizedby reacting phenyl-4-hydroxybenzoate with aromatic (o-diamine)s in diphenylsulfone. Molecular weight controlled and endcapped PBI of new chemical structures are prepared that exhibit a favorable combination of physical and mechanical properties.

Breaking the Dogma of Aldolase Specificity: Simple Aliphatic Ketones and Aldehydes are Nucleophiles for Fructose-6-phosphate Aldolase.

PubMed

Roldán, Raquel; Sanchez-Moreno, Israel; Scheidt, Thomas; Hélaine, Virgil; Lemaire, Marielle; Parella, Teodor; Clapés, Pere; Fessner, Wolf-Dieter; Guérard-Hélaine, Christine

2017-04-11

d-Fructose-6-phosphate aldolase (FSA) was probed for extended nucleophile promiscuity by using a series of fluorogenic substrates to reveal retro-aldol activity. Four nucleophiles ethanal, propanone, butanone, and cyclopentanone were subsequently confirmed to be non-natural substrates in the synthesis direction using the wild-type enzyme and its D6H variant. This exceptional widening of the nucleophile substrate scope offers a rapid entry, in good yields and high stereoselectivity, to less oxygenated alkyl ketones and aldehydes, which was hitherto impossible. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Alternative Nucleophilic Substrates for the Endonuclease Activities of Human Immunodeficiency Virus Type 1 Integrase

PubMed Central

Ealy, Julie B.; Sudol, Malgorzata; Krzeminski, Jacek; Amin, Shantu; Katzman, Michael

2012-01-01

Retroviral integrase can use water or some small alcohols as the attacking nucleophile to nick DNA. To characterize the range of compounds that human immunodeficiency virus type 1 integrase can accommodate for its endonuclease activities, we tested 45 potential electron donors (having varied size and number or spacing of nucleophilic groups) as substrates during site-specific nicking at viral DNA ends and during nonspecific nicking reactions. We found that integrase used 22 of the 45 compounds to nick DNA, but not all active compounds were used for both activities. In particular, 13 compounds were used for site-specific and nonspecific nicking, 5 only for site-specific nicking, and 4 only for nonspecific nicking; 23 other compounds were not used for either activity. Thus, integrase can accommodate a large number of nucleophilic substrates but has selective requirements for its different activities, underscoring its dynamic properties and providing new information for modeling and understanding integrase. PMID:22910593

Nucleophilic ring opening reactions of aziridines.

PubMed

Akhtar, Rabia; Naqvi, Syed Ali Raza; Zahoor, Ameer Fawad; Saleem, Sameera

2018-05-04

Aziridine ring opening reactions have gained tremendous importance in the synthesis of nitrogen containing biologically active molecules. During recent years, a great effort has been put forward by scientists toward unique bond construction methodologies via ring opening of aziridines. In this regard, a wide range of chiral metal- and organo-catalyzed desymmetrization reactions of aziridines have been reported with carbon, sulfur, oxygen, nitrogen, halogen, and other nucleophiles. In this review, an outline of methodologies adopted by a number of scientists during 2013-2017 for aziridine ring opening reactions as well as their synthetic applications is described.

Benzimidazoles and benzoxazoles via the nucleophilic addition of anilines to nitroalkanes.

PubMed

Aksenov, Alexander V; Smirnov, Alexander N; Aksenov, Nicolai A; Bijieva, Asiyat S; Aksenova, Inna V; Rubin, Michael

2015-04-14

PPA-induced umpolung triggers efficient nucleophilic addition of unactivated anilines to nitroalkanes to produce N-hydroxyimidamides. The latter undergo sequential acid-promoted cyclocondensation with ortho-OH or ortho-NHR moieties to afford benzoxazoles and benzimidazoles, respectively.

Identification of the nucleophile catalytic residue of GH51 α-l-arabinofuranosidase from Pleurotus ostreatus

DOE PAGES

Amore, Antonella; Iadonisi, Alfonso; Vincent, Florence; ...

2015-12-21

In this paper, the recombinant α-l-arabinofuranosidase from the fungus Pleurotus ostreatus (rPoAbf) was subjected to site-directed mutagenesis in order to identify the catalytic nucleophile residue. Based on bioinformatics and homology modelling analyses, E449 was revealed to be the potential nucleophilic residue. Thus, the mutant E449G of PoAbf was recombinantly expressed in Pichia pastoris and its recombinant expression level and reactivity were investigated in comparison to the wild-type. The design of a suitable set of hydrolysis experiments in the presence or absence of alcoholic arabinosyl acceptors and/or formate salts allowed to unambiguously identify the residue E449 as the nucleophile residue involvedmore » in the retaining mechanism of this GH51 arabinofuranosidase. 1H NMR analysis was applied for the identification of the products and the assignement of their anomeric configuration.« less

Reactions of glycidyl derivatives with ambident nucleophiles; part 2: amino acid derivatives

PubMed Central

Dyker, Gerald; Thöne, Andreas; Henkel, Gerald

2007-01-01

A three-step procedure for the synthesis of multifunctionalized heterocycles from a pyroglutamic acid derivative, glycidyl components and anilines by nucleophilic substitution and cobalt catalysis is presented. PMID:17900352

Specific anion binding to sulfobetaine micelles and kinetics of nucleophilic reactions.

PubMed

Marte, Luisa; Beber, Rosane C; Farrukh, M Akhyar; Micke, Gustavo A; Costa, Ana C O; Gillitt, Nicholas D; Bunton, Clifford A; Di Profio, Pietro; Savelli, Gianfranco; Nome, Faruk

2007-08-23

With fully micellar bound substrates reactions of OH- with benzoic anhydride, Bz(2)O, and of Br- with methyl naphthalene-2-sulfonate, MeONs, in micellized sulfobetaines are strongly inhibited by NaClO4 which displaces the nucleophilic anions from the micellar pseudophases. Micellar incorporations of ClO4- and Br- are estimated with an ion-selective electrode and by electrophoresis, and partitioning of Br- between water and micelles is related to changes in NMR spectral (79)Br- line widths. Extents of inhibition by ClO4- of these nucleophilic reactions in the micellar pseudophase are related to quantitative displacement of the reactive anions from the micelles by ClO4-. The kinetic data are correlated with physical evidence on the strong interactions between sulfobetaines and ClO4-, which turn sulfobetaine micelles anionic and effectively provoke displacement of OH- and Br-.

Nucleophilically assisted and cationic ring-opening polymerization of tin-bridged [1]ferrocenophanes.

PubMed

Baumgartner, Thomas; Jäkle, Frieder; Rulkens, Ron; Zech, Gernot; Lough, Alan J; Manners, Ian

2002-08-28

To obtain mechanistic insight, detailed studies of the intriguing "spontaneous" ambient temperature ring-opening polymerization (ROP) of tin-bridged [1]ferrocenophanes Fe(eta-C(5)H(4))(2)SnR(2) 3a (R = t-Bu) and 3b (R = Mes) in solution have been performed. The investigations explored the influence of non-nucleophilic additives such as radicals and radical traps, neutral and anionic nucleophiles, Lewis acids, protic species, and other cationic electrophiles. Significantly, two novel methodologies and mechanisms for the ROP of strained [1]ferrocenophanes are proposed based on this study. First, as the addition of amine nucleophiles such as pyridine was found to strongly accelerate the polymerization rate in solution, a new nucleophilicallyassisted ROP methodology was proposed. This operates at ambient temperature in solution even in the presence of chlorosilanes but, unlike the anionic polymerization of ferrocenophanes, does not involve cyclopentadienyl anions. Second, the addition of small quantities of the electrophilic species H(+) and Bu(3)Sn(+) was found to lead to a cationic ROP process. These studies suggest that the "spontaneous" ROP of tin-bridged [1]ferrocenophanes may be a consequence of the presence of spurious, trace quantities of Lewis basic or acidic impurities. The new ROP mechanisms reported are likely to be of general significance for the ROP of other metallocenophanes (e.g., for thermal ROP in the melt) and for other metallacycles containing group 14 elements.

Propargylic activation across a heterobimetallic ir-sn catalyst: nucleophilic substitution and indene formation with propargylic alcohols.

PubMed

Chatterjee, Paresh Nath; Roy, Sujit

2010-07-02

A nucleophilic substitution of propargylic alcohols with carbon (arene, heteroarene, and allyltrimethylsilane), sulfur (thiol), oxygen (alcohol), and nitrogen (sulfonamide) nucleophiles has been demonstrated using a high-valent [Ir(COD)(SnCl(3))Cl(mu-Cl)](2) catalyst in 1,2-dichloroethane to afford the corresponding propargylic products in moderate to excellent yields. Alkyl or aryl substituted tertiary propargylic alcohols produce substituted indenes with bulky arenes via allenylic intermediate. An electrophilic mechanism is proposed from Hammett correlation.

Mechanism of alkoxy groups substitution by Grignard reagents on aromatic rings and experimental verification of theoretical predictions of anomalous reactions.

PubMed

Jiménez-Osés, Gonzalo; Brockway, Anthony J; Shaw, Jared T; Houk, K N

2013-05-01

The mechanism of direct displacement of alkoxy groups in vinylogous and aromatic esters by Grignard reagents, a reaction that is not observed with expectedly better tosyloxy leaving groups, is elucidated computationally. The mechanism of this reaction has been determined to proceed through the inner-sphere attack of nucleophilic alkyl groups from magnesium to the reacting carbons via a metalaoxetane transition state. The formation of a strong magnesium chelate with the reacting alkoxy and carbonyl groups dictates the observed reactivity and selectivity. The influence of ester, ketone, and aldehyde substituents was investigated. In some cases, the calculations predicted the formation of products different than those previously reported; these predictions were then verified experimentally. The importance of studying the actual system, and not simplified models as computational systems, is demonstrated.

Mechanism of Alkoxy Groups Substitution by Grignard Reagents on Aromatic Rings and Experimental Verification of Theoretical Predictions of Anomalous Reactions

PubMed Central

Jiménez-Osés, Gonzalo; Brockway, Anthony J.; Shaw, Jared T.; Houk, K. N.

2013-01-01

The mechanism of direct displacement of alkoxy groups in vinylogous and aromatic esters by Grignard reagents, a reaction that is not observed with expectedly better tosyloxy leaving groups, is elucidated computationally. The mechanism of this reaction has been determined to proceed through the inner-sphere attack of nucleophilic alkyl groups from magnesium to the reacting carbons via a metalaoxetane transition state. The formation of a strong magnesium chelate with the reacting alkoxy and carbonyl groups dictates the observed reactivity and selectivity. The influence of ester, ketone and aldehyde substituents was investigated. In some cases, the calculations predicted the formation of products different than those previously reported; these predictions were then verified experimentally. The importance of studying the actual system, and not simplified models as computational systems, is demonstrated. PMID:23601086

Old tricks, new dogs: organocatalytic dienamine activation of α,β-unsaturated aldehydes.

PubMed

Marcos, Vanesa; Alemán, José

2016-12-21

Chiral secondary amines are some of the most commonly used kinds of catalysts. They have become a reliable tool for the α- and β-activation of carbonyl compounds, via HOMO, SOMO or LUMO activation pathways. Recently, chemists have turned their attention to the development of novel organocatalytic strategies for remote functionalisation, targeting stereocentres even more distant from the catalyst-activation site, through dienamine, trienamine, and vinylogous iminium ion pathways (γ-, ε- and δ-positions, respectively). Here we outline and discuss the state-of-the-art in dienamine activation, classifying examples according to the different reactive activation pathways followed by the formed dienamine intermediate (1,3-, 1,5-, 2,5- and 4,5-functionalisation) and the reaction type developed, as determined by the structure and the nature of electrophiles and nucleophiles.

Old tricks, new dogs: organocatalytic dienamine activation of α,β-unsaturated aldehydes

PubMed Central

2016-01-01

Chiral secondary amines are some of the most commonly used kinds of catalysts. They have become a reliable tool for the α- and β-activation of carbonyl compounds, via HOMO, SOMO or LUMO activation pathways. Recently, chemists have turned their attention to the development of novel organocatalytic strategies for remote functionalisation, targeting stereocentres even more distant from the catalyst-activation site, through dienamine, trienamine, and vinylogous iminium ion pathways (γ-, ε- and δ-positions, respectively). Here we outline and discuss the state-of-the-art in dienamine activation, classifying examples according to the different reactive activation pathways followed by the formed dienamine intermediate (1,3-, 1,5-, 2,5- and 4,5-functionalisation) and the reaction type developed, as determined by the structure and the nature of electrophiles and nucleophiles. PMID:27805198

Easy access to nucleophilic boron through diborane to magnesium boryl metathesis

NASA Astrophysics Data System (ADS)

Pécharman, Anne-Frédérique; Colebatch, Annie L.; Hill, Michael S.; McMullin, Claire L.; Mahon, Mary F.; Weetman, Catherine

2017-04-01

Organoboranes are some of the most synthetically valuable and widely used intermediates in organic and pharmaceutical chemistry. Their synthesis, however, is limited by the behaviour of common boron starting materials as archetypal Lewis acids such that common routes to organoboranes rely on the reactivity of boron as an electrophile. While the realization of convenient sources of nucleophilic boryl anions would open up a wealth of opportunity for the development of new routes to organoboranes, the synthesis of current candidates is generally limited by a need for highly reducing reaction conditions. Here, we report a simple synthesis of a magnesium boryl through the heterolytic activation of the B-B bond of bis(pinacolato)diboron, which is achieved by treatment of an easily generated magnesium diboranate complex with 4-dimethylaminopyridine. The magnesium boryl is shown to act as an unambiguous nucleophile through its reactions with iodomethane, benzophenone and N,N'-di-isopropyl carbodiimide and by density functional theory.

Transition-state charge transfer reveals electrophilic, ambiphilic, and nucleophilic carbon-hydrogen bond activation.

PubMed

Ess, Daniel H; Nielsen, Robert J; Goddard, William A; Periana, Roy A

2009-08-26

Absolutely localized molecular orbital energy decomposition analysis of C-H activation transition states (TSs), including Pt, Au, Ir, Ru, W, Sc, and Re metal centers, shows an electrophilic, ambiphilic, and nucleophilic charge transfer (CT) continuum irrespective of the bonding paradigm (oxidative addition, sigma-bond metathesis, oxidative hydrogen migration, 1,2-substitution). Pt(II) insertion and Au(III) substitution TSs are highly electrophilic and dominated by C-H bond to metal/ligand orbital stabilization, while Ir-X and Ru-X (X = R, NH(2), OR, or BOR(2)) substitution TSs are ambiphilic in nature. In this ambiphilic activation regime, an increase in one direction of CT typically leads to a decrease in the reverse direction. Comparison of Tp(CO)Ru-OH and Tp(CO)Ru-NH(2) complexes showed no evidence for the classic d(pi)-p(pi) repulsion model. Complexes such as and Cp(CO)(2)W-B(OR)(2), (PNP)Ir(I), Cp(2)ScMe, and (acac-kappaO,kappaO)(2)Re(III)-OH were found to mediate nucleophilic C-H activation, where the CT is dominated by the metal/ligand orbital to C-H antibonding orbital interaction. This CT continuum ultimately affects the metal-alkyl intermediate polarization and possible functionalization reactions. This analysis will impact the design of new activation reactions and stimulate the discovery of more nucleophilic activation complexes.

Homologation chemistry with nucleophilic α-substituted organometallic reagents: chemocontrol, new concepts and (solved) challenges.

PubMed

Castoldi, Laura; Monticelli, Serena; Senatore, Raffaele; Ielo, Laura; Pace, Vittorio

2018-05-31

The transfer of a reactive nucleophilic CH2X unit into a preformed bond enables the introduction of a fragment featuring the exact and desired degree of functionalization through a single synthetic operation. The instability of metallated α-organometallic species often poses serious questions regarding the practicability of using this conceptually intuitive and simple approach for forming C-C or C-heteroatom bonds. A deep understanding of processes regulating the formation of these nucleophiles is a precious source of inspiration not only for successfully applying theoretically feasible transformations (i.e. determining how to employ a given reagent), but also for designing new reactions which ultimately lead to the introduction of molecular complexity via short experimental sequences.

Polyimidazoles via aromatic nucleophilic displacement

NASA Technical Reports Server (NTRS)

Connell, John W. (Inventor); Hergenrother, Paul M. (Inventor)

1992-01-01

Polyimidazoles (PI) are prepared by the aromatic nucleophilic displacement reaction of di(hydroxyphenyl) imidazole monomers with activated aromatic dihalides or activated aromatic dinitro compounds. The reactions are carried out in polar aprotic solvents such as N,N-dimethyl acetamide, sulfolane, N-methylpyrrolidinone, dimethylsulfoxide, or diphenylsulfone using alkali metal bases such as potassium carbonate at elevated temperatures under nitrogen. The di(hydroxyphenyl) imidazole monomers are prepared by reacting an aromatic aldehyde with a dimethoxybenzil or by reacting an aromatic dialdehyde with a methoxybenzil in the presence of ammonium acetate. The di(methoxyphenyl) imidazole is subsequently treated with aqueous hydrobromic acid to give the di(hydroxphenyl) imidazole monomer. This synthetic route has provided high molecular weight PI of new chemical structure, is economically and synthetically more favorable than other routes, and allows for facile chemical structure variation due to the availability of a large variety of activated aromatic dihalides and dinitro compounds.

Polyimidazoles via aromatic nucleophilic displacement

NASA Technical Reports Server (NTRS)

Hergenrother, Paul M. (Inventor); Connell, John W. (Inventor)

1991-01-01

Polyimidazoles (Pl) are prepared by the aromatic nucleophilic displacement reaction of di(hydroxyphenyl)imidazole monomers with activated aromatic dihalides or activated aromatic dinitro compounds. The reactions are carried out in polar aprotic solvents such as N,N-dimethylacetamide, sulfolane, N-methylpyrroldinone, dimethylsulfoxide, or diphenylsulfone using alkali metal bases such as potassium carbonate at elevated temperature under nitrogen. The di(hydroxyphenyl)imidazole monomers are prepared by reacting an aromatic aldehyde with a dimethoxybenzil or by reacting an aromatic dialdehyde with a methoxybenzil in the presence of ammonium acetate. The di(methoxyphenyl)imidazole is subsequently treated with aqueous hydrobromic acid to give the di(hydroxyphenyl)imidazole monomer. This synthetic route has provided high molecular weight Pl of new chemical structure, is economically and synthetically more favorable than other routes, and allows for facile chemical structure variation due to the availability of a large variety of activated aromatic dihalides and dinitro compounds.

One molecule of ionic liquid and tert-alcohol on a polystyrene-support as catalysts for efficient nucleophilic substitution including fluorination.

PubMed

Shinde, Sandip S; Patil, Sunil N

2014-12-07

The tert-alcohol and ionic liquid solvents in one molecule [mim-(t)OH][OMs] was immobilized on polystyrene and reported to be a highly efficient catalyst in aliphatic nucleophilic substitution using alkali metal salts. Herein, we investigated the catalytic activity of a new structurally modified polymer-supported tert-alcohol functionalized imidazolium salt catalyst in nucleophilic substitution of 2-(3-methanesulfonyloxypropyoxy)naphthalene as a model substrate with various metal nucleophiles. The tert-alcohol moiety of the ionic liquid with a hexyl chain distance from polystyrene had a better catalytic activity compared to the other resin which lacked an alkyl linker and tert-alcohol moiety. We found that the maximum [mim-(t)OH][OMs] loading had the best catalytic efficacy among the tested polystyrene-based ionic liquids (PSILs) in nucleophilic fluorination. The catalytic efficiency of the PS[him-(t)OH][OMs] as a phase transfer catalyst (PTC) was determined by carrying out various nucleophilic substitutions using the corresponding alkali metal salts from the third to sixth periodic in CH3CN or tert-BuOH media. The scope of this protocol with primary and secondary polar substrates containing many heteroatoms is also reported. This PS[him-(t)OH][OMs] catalyst not only enhances the reactivity of alkali metal salts and reduces the formation of by-products but also affords high yield with easy isolation.

Determination of acidity and nucleophilicity in thiols by reaction with monobromobimane and fluorescence detection.

PubMed

Sardi, Florencia; Manta, Bruno; Portillo-Ledesma, Stephanie; Knoops, Bernard; Comini, Marcelo A; Ferrer-Sueta, Gerardo

2013-04-01

A method based on the differential reactivity of thiol and thiolate with monobromobimane (mBBr) has been developed to measure nucleophilicity and acidity of protein and low-molecular-weight thiols. Nucleophilicity of the thiolate is measured as the pH-independent second-order rate constant of its reaction with mBBr. The ionization constants of the thiols are obtained through the pH dependence of either second-order rate constant or initial rate of reaction. For readily available thiols, the apparent second-order rate constant is measured at different pHs and then plotted and fitted to an appropriate pH function describing the observed number of ionization equilibria. For less available thiols, such as protein thiols, the initial rate of reaction is determined in a wide range of pHs and fitted to the appropriate pH function. The method presented here shows excellent sensitivity, allowing the use of nanomolar concentrations of reagents. The method is suitable for scaling and high-throughput screening. Example determinations of nucleophilicity and pK(a) are presented for captopril and cysteine as low-molecular-weight thiols and for human peroxiredoxin 5 and Trypanosoma brucei monothiol glutaredoxin 1 as protein thiols. Copyright © 2013 Elsevier Inc. All rights reserved.

Reactions of aromatic diazonium salts with unsaturated compounds in the presence of nucleophiles

NASA Astrophysics Data System (ADS)

Grishchuk, B. D.; Gorbovoi, P. M.; Ganushchak, N. I.; Dombrovskii, A. V.

1994-03-01

The review surveys the reactions of aromatic diazonium salts with diene and monounsaturated compounds in the presence of nucleophiles. Certain further reactions of the reaction products and their application are considered. The bibliography includes 63 references.

2-Oxo promoted hydrophosphonylation & aerobic intramolecular nucleophilic displacement reaction.

PubMed

Battula, Satyanarayana; Battini, Narsaiah; Singh, Deepika; Ahmed, Qazi Naveed

2015-08-28

Highly efficient catalyst free methods for the synthesis of α-hydroxy-β-oxophosphonates and α-oxoesters have been described. The existence of a 2-oxo group in α-oxoaldehydes is a key factor in promoting the reaction of the tervalent phosphite form towards 2-oxoaldehydes in the synthesis of α-hydroxy-β-oxophosphonates. The in situ activated α-C-H atom of α-hydroxy-β-oxophosphonates sustains aerobic intramolecular nucleophilic displacement in a curious way to produce α-oxoester.

Predicting Catalytic Proton Donors and Nucleophiles in Enzymes: How Adding Dynamics Helps Elucidate the Structure-Function Relationships.

PubMed

Huang, Yandong; Yue, Zhi; Tsai, Cheng-Chieh; Henderson, Jack A; Shen, Jana

2018-03-15

Despite the relevance of understanding structure-function relationships, robust prediction of proton donors and nucleophiles in enzyme active sites remains challenging. Here we tested three types of state-of-the-art computational methods to calculate the p K a 's of the buried and hydrogen bonded catalytic dyads in five enzymes. We asked the question what determines the p K a order, i.e., what makes a residue proton donor vs a nucleophile. The continuous constant pH molecular dynamics simulations captured the experimental p K a orders and revealed that the negative nucleophile is stabilized by increased hydrogen bonding and solvent exposure as compared to the proton donor. Surprisingly, this simple trend is not apparent from crystal structures and the static structure-based calculations. While the generality of the findings awaits further testing via a larger set of data, they underscore the role of dynamics in bridging enzyme structures and functions.

Inversion of Configuration at the Phosphorus Nucleophile in the Diastereoselective and Enantioselective Synthesis of P-Stereogenic syn-Phosphiranes from Chiral Epoxides.

PubMed

Muldoon, Jake A; Varga, Balázs R; Deegan, Meaghan M; Chapp, Timothy W; Eördögh, Ádám M; Hughes, Russell P; Glueck, David S; Moore, Curtis E; Rheingold, Arnold L

2018-04-23

Nucleophilic substitution results in inversion of configuration at the electrophilic carbon center (S N 2) or racemization (S N 1). The stereochemistry of the nucleophile is rarely considered, but phosphines, which have a high barrier to pyramidal inversion, attack electrophiles with retention of configuration at P. Surprisingly, cyclization of bifunctional secondary phosphine alkyl tosylates proceeded under mild conditions with inversion of configuration at the nucleophile to yield P-stereogenic syn-phosphiranes. DFT studies suggested that the novel stereochemistry results from acid-promoted tosylate dissociation to yield an intermediate phosphenium-bridged cation, which undergoes syn-selective cyclization. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

REVISITING CLASSICAL NUCLEOPHILIC SUBSTITUTIONS IN AQUEOUS MEDIUM: MICROWAVE-ASSISTED SYNTHESIS OF ALKYL AZIDES

EPA Science Inventory

An efficient and clean synthesis of alkyl azides using microwave (MW) radiation is described in aqueous medium by reacting alkyl halides or tosylates with alkali azides. This general and expeditious MW-enhanced approach to nucleophilic substitution reactions is applicable to the ...

Lewis base activation of Lewis acids: catalytic, enantioselective addition of silyl ketene acetals to aldehydes.

PubMed

Denmark, Scott E; Beutner, Gregory L; Wynn, Thomas; Eastgate, Martin D

2005-03-23

The concept of Lewis base activation of Lewis acids has been reduced to practice for catalysis of the aldol reaction of silyl ketene acetals and silyl dienol ethers with aldehydes. The weakly acidic species, silicon tetrachloride (SiCl4), can be activated by binding of a strongly Lewis basic chiral phosphoramide, leading to in situ formation of a chiral Lewis acid. This species has proven to be a competent catalyst for the aldol addition of acetate-, propanoate-, and isobutyrate-derived silyl ketene acetals to conjugated and nonconjugated aldehydes. Furthermore, vinylogous aldol reactions of silyl dienol ethers are also demonstrated. The high levels of regio-, anti diastereo-, and enantioselectivity observed in these reactions can be rationalized through consideration of an open transition structure where steric interactions between the silyl cation complex and the approaching nucleophile are dominant.

Copper-Catalyzed Electrophilic Amination of Organoaluminum Nucleophiles with O-Benzoyl Hydroxylamines.

PubMed

Zhou, Shuangliu; Yang, Zhiyong; Chen, Xu; Li, Yimei; Zhang, Lijun; Fang, Hong; Wang, Wei; Zhu, Xiancui; Wang, Shaowu

2015-06-19

A copper-catalyzed electrophilic amination of aryl and heteroaryl aluminums with N,N-dialkyl-O-benzoyl hydroxylamines that affords the corresponding anilines in good yields has been developed. The catalytic reaction proceeds very smoothly under mild conditions and exhibits good substrate scope. Moreover, the developed catalytic system is also well suited for heteroaryl aluminum nucleophiles, providing facile access to heteroaryl amines.

Theoretical Investigation of the Gas-Phase SN2 Reactions of Anionic and Neutral Nucleophiles with Chloramines.

PubMed

Liu, Jieqing; Dong, Meng; Zhang, Shuo; Liu, Yong Dong; Zhong, Rugang

2018-03-22

The S N 2 reactions at nitrogen center (S N 2@N) play a significant role in organic synthesis, carcinogenesis, and the formation of some environmentally toxic compounds. However, the S N 2@N reactions specifically for neutral compounds as nucleophiles are less known. In this work, reactions of dimethylamine (DMA) and F - with NH 2 Cl were investigated as model reactions to validate an accurate functional from 24 DFT functionals by comparing with the CCSD(T) reference data. M06-2X functional was found to perform best and applied to systematically explore the trends in reactivity for halides (F - and Cl - ) and simple amines toward the substrates NH 2 Cl and NHCl 2 (S N 2@N) as well as CH 3 Cl and CH 2 Cl 2 (S N 2@C). The computational results show that the backside inversion channel dominates most the S N 2@N reactions except for the case of F - + NHCl 2 , which reacts preferentially via proton transfer. The overall activation free energies (Δ G ‡ ) of the inversion channel for the S N 2 reactions of F - and Cl - with chloramines are negative, whereas those for amines as nucleophiles are around 30-44 kcal/mol. The S N 2@N reactions for all the nucleophiles investigated here are faster than the corresponding S N 2@C. Moreover, amines react faster when they have a higher extent of methyl substitution. Additionally, the energy gap between the HOMO of nucleophile and LUMO of substrate generally correlates well with Δ G ‡ of the corresponding S N 2 reactions, which is consistent with previous results.

A Substrate-Assisted Mechanism of Nucleophile Activation in a Ser-His-Asp Containing C-C Bond Hydrolase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ruzzini, Antonio C.; Bhowmik, Shiva; Ghosh, Subhangi

The meta-cleavage product (MCP) hydrolases utilize a Ser–His–Asp triad to hydrolyze a carbon–carbon bond. Hydrolysis of the MCP substrate has been proposed to proceed via an enol-to-keto tautomerization followed by a nucleophilic mechanism of catalysis. Ketonization involves an intermediate, ES red, which possesses a remarkable bathochromically shifted absorption spectrum. We investigated the catalytic mechanism of the MCP hydrolases using DxnB2 from Sphingomonas wittichii RW1. Pre-steady-state kinetic and LC ESI/MS evaluation of the DxnB2-mediated hydrolysis of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid to 2-hydroxy-2,4-pentadienoic acid and benzoate support a nucleophilic mechanism catalysis. In DxnB2, the rate of ES red decay and product formation showed amore » solvent kinetic isotope effect of 2.5, indicating that a proton transfer reaction, assigned here to substrate ketonization, limits the rate of acylation. For a series of substituted MCPs, this rate was linearly dependent on MCP pK a2 (β nuc ~ 1). Structural characterization of DxnB2 S105A:MCP complexes revealed that the catalytic histidine is displaced upon substrate-binding. The results provide evidence for enzyme-catalyzed ketonization in which the catalytic His–Asp pair does not play an essential role. The data further suggest that ES red represents a dianionic intermediate that acts as a general base to activate the serine nucleophile. This substrate-assisted mechanism of nucleophilic catalysis distinguishes MCP hydrolases from other serine hydrolases.« less

Poly(N-arylenbenzimidazoles) via aromatic nucleophilic displacement

NASA Technical Reports Server (NTRS)

Connell, John W. (Inventor); Hergenrother, Paul M. (Inventor); Smith, Joseph G., Jr. (Inventor)

1995-01-01

Novel poly(N-arylenebenzimidazole)s (PNABIs) are prepared by the aromatic nucleophilic displacement reaction of novel di(hydroxyphenyl-N-arylene benzimidazole) monomers with activated aromatic dihalides or activated aromatic dinitro compounds. The polymerizations are carried out in polar aprotic solvents such as N-methyl-2-pyrrolidinone or N,N-dimethylacetamide using alkali metal bases such as potassium carbonate at elevated temperatures under nitrogen. The di(hydroxyphenyl N-arylenebenzimidazole) monomers are synthesized by reacting phenyl 4-hydroxybenzoate with bis(2-aminoanilino) arylenes in diphenylsulfone. Moderate molecular weight PNABIs of new chemical structures were prepared that exhibit a favorable combination of physical and mechanical properties. The use of the novel di(hydroxyphenyl N-arylenebenzimidazole)s permits a more economical and easier way to prepare PNABIs than previous routes.

Nucleophilic reactivity of a series of peroxomanganese(III) complexes supported by tetradentate aminopyridyl ligands.

PubMed

Geiger, Robert A; Chattopadhyay, Swarup; Day, Victor W; Jackson, Timothy A

2011-02-28

Peroxomanganese(iii) adducts have been postulated as important intermediates in manganese-containing enzymes and small molecule oxidation catalysts. Synthetic peroxomanganese(iii) complexes are known to be nucleophilic and facilitate aldehyde deformylation, offering a convenient way to compare relative reactivities of complexes supported by different ligands. In this work, tetradentate dipyridyldiazacycloalkane ligands with systematically perturbed steric and electronic properties were used to generate a series of manganese(ii) and peroxomanganese(iii) complexes. X-Ray crystal structures of five manganese(ii) complexes all show the ligands bound to give trans complexes. Treatment of these Mn(II) precursors with H(2)O(2) and Et(3)N in MeCN at -40 °C results in the formation of peroxomanganese(iii) complexes that differ only in the identity of the pyridine ring substituent and/or the number of carbons in the diazacycloalkane backbone. To determine the effects of small ligand perturbations on the reactivity of the peroxo group, the more thermally stable peroxomanganese(iii) complexes were reacted with cyclohexanecarboxaldehyde. For these complexes, the rate of deformylation does not correlate with the expected nucleophilicity of the peroxomanganese(iii) unit, as the inclusion of methyl substituents on the pyridines affords slower deformylation rates. It is proposed that adding methyl-substituents to the pyridines, or increasing the number of carbons on the diazacycloalkane, sterically hinders nucleophilic attack of the peroxo ligand on the carbonyl carbon of the aldehyde.

Preparation of 6-substituted quinoxaline JSP-1 inhibitors by microwave accelerated nucleophilic substitution.

PubMed

Zhang, Li; Qiu, Beiying; Li, Xin; Wang, Xin; Li, Jingya; Zhang, Yongliang; Liu, Jian; Li, Jia; Shen, Jingkang

2006-12-21

A small library of 6-aminoquinoxalines has been prepared by nucleophilic substitution of 6-fluoroquinoxaline with amines and nitrogen-containing heterocycles under computer-controlled microwave irradiation. Some compounds were found to be potent inhibitors of JNK Stimulatory Phosphatase-1 (JSP-1) in an in vitro biological assay.

Structure-Based Insight into the Asymmetric Bioreduction of the C=C Double Bond of α,β-Unsaturated Nitroalkenes by Pentaerythritol Tetranitrate Reductase

PubMed Central

Toogood, Helen S.; Fryszkowska, Anna; Hare, Victoria; Fisher, Karl; Roujeinikova, Anna; Leys, David; Gardiner, John M.; Stephens, Gill M.; Scrutton, Nigel S.

2009-01-01

Biocatalytic reduction of α- or β-alkyl-β-arylnitroalkenes provides a convenient and efficient method to prepare chiral substituted nitroalkanes. Pentaerythritol tetranitrate reductase (PETN reductase) from Enterobacter cloacae st. PB2 catalyses the reduction of nitroolefins such as 1-nitrocyclohexene (1) with steady state and rapid reaction kinetics comparable to other old yellow enzyme homologues. Furthermore, it reduces 2-aryl-1-nitropropenes (4a-d) to their equivalent (S)-nitropropanes 9a-d. The enzyme shows a preference for the (Z)-isomer of substrates 4a-d, providing almost pure enantiomeric products 9a-d (ees up to > 99%) in quantitative yield, whereas the respective (E)-isomers are reduced with lower enantioselectivity (63-89% ee) and lower product yields. 1-Aryl-2-nitropropenes (5a, b) are also reduced efficiently, but the products (R)-10 have lower optical purities. The structure of the enzyme complex with 1-nitrocyclohexene (1) was determined by X-ray crystallography, revealing two substrate-binding modes, with only one compatible with hydride transfer. Models of nitropropenes 4 and 5 in the active site of PETN reductase predicted that the enantioselectivity of the reaction was dependent on the orientation of binding of the (E)- and (Z)-substrates. This work provides a structural basis for understanding the mechanism of asymmetric bioreduction of nitroalkenes by PETN reductase. PMID:20396603

Silyl Ketene Imines: Highly Versatile Nucleophiles for Catalytic, Asymmetric Synthesis

PubMed Central

Denmark, Scott E.; Wilson, Tyler W.

2012-01-01

This Minireview provides an overview on the development of silyl ketene imines and their recent applications in catalytic, enantioselective reactions. The unique structure of the ketene imine allows a diverse range of reactivity patterns and provides solutions to existing challenges in the enantioselective construction of quaternary stereogenic carbon centers and cross-benzoin adducts. A variety of reactions for which silyl ketene imines have been applied are presented with an overall goal of inspiring new uses for these underutilized nucleophiles. PMID:22968901

Revisiting the Dielectric Constant Effect on the Nucleophile and Leaving Group of Prototypical Backside Sn2 Reactions: a Reaction Force and Atomic Contribution Analysis.

PubMed

Pedraza-González, Laura Milena; Galindo, Johan Fabian; Gonzalez, Ronald; Reyes, Andrés

2016-10-09

The solvent effect on the nucleophile and leaving group atoms of the prototypical F - + CH 3 Cl → CH 3 F + Cl - backside bimolecular nucleophilic substitution reaction (S N 2) is analyzed employing the reaction force and the atomic contributions methods on the intrinsic reaction coordinate (IRC). Solvent effects were accounted for using the polarizable continuum solvent model. Calculations were performed employing eleven dielectric constants, ε, ranging from 1.0 to 78.5, to cover a wide spectrum of solvents. The reaction force data reveals that the solvent mainly influences the region of the IRC preceding the energy barrier, where the structural rearrangement to reach the transition state occurs. A detailed analysis of the atomic role in the reaction as a function of ε reveals that the nucleophile and the carbon atom are the ones that contribute the most to the energy barrier. In addition, we investigated the effect of the choice of nucleophile and leaving group on the ΔE 0 and ΔE ↕ of Y - + CH 3 X → YCH 3 + X - (X,Y= F, Cl, Br, I) in aqueous solution. Our analysis allowed us to find relationships between the atomic contributions to the activation energy and leaving group ability and nucleophilicity.

Nucleophilic substitution at phosphorus centers (SN2@p).

PubMed

van Bochove, Marc A; Swart, Marcel; Bickelhaupt, F Matthias

2007-12-03

We have studied the characteristics of archetypal model systems for bimolecular nucleophilic substitution at phosphorus (SN2@P) and, for comparison, at carbon (SN2@C) and silicon (SN2@Si) centers. In our studies, we applied the generalized gradient approximation (GGA) of density functional theory (DFT) at the OLYP/TZ2P level. Our model systems cover nucleophilic substitution at carbon in X(-)+CH3Y (SN2@C), at silicon in X(-)+SiH3Y (SN2@Si), at tricoordinate phosphorus in X(-)+PH2Y (SN2@P3), and at tetracoordinate phosphorus in X(-)+POH2Y (SN2@P4). The main feature of going from SN2@C to SN2@P is the loss of the characteristic double-well potential energy surface (PES) involving a transition state [X--CH3--Y]- and the occurrence of a single-well PES with a stable transition complex, namely, [X--PH2--Y]- or [X--POH2--Y](-). The differences between SN2@P3 and SN2@P4 are relatively small. We explored both the symmetric and asymmetric (i.e. X, Y=Cl, OH) SN2 reactions in our model systems, the competition between backside and frontside pathways, and the dependence of the reactions on the conformation of the reactants. Furthermore, we studied the effect, on the symmetric and asymmetric SN2@P3 and S(N)2@P4 reactions, of replacing hydrogen substituents at the phosphorus centers by chlorine and fluorine in the model systems X(-)+PR2Y and X(-)+POR2Y, with R=Cl, F. An interesting phenomenon is the occurrence of a triple-well PES not only in the symmetric, but also in the asymmetric SN2@P4 reactions of X(-)+POCl2--Y.

Barbier Continuous Flow Preparation and Reactions of Carbamoyllithiums for Nucleophilic Amidation.

PubMed

Ganiek, Maximilian A; Becker, Matthias R; Berionni, Guillaume; Zipse, Hendrik; Knochel, Paul

2017-08-01

An ambient temperature continuous flow method for nucleophilic amidation and thioamidation is described. Deprotonation of formamides by lithium diisopropylamine (LDA) affords carbamoyllithium intermediates that are quenched in situ with various electrophiles such as ketones, allyl bromides, Weinreb and morpholino amides. The nature of the reactive lithium intermediates and the thermodynamics of the metalation were further investigated by ab initio calculations and kinetic experiments. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nucleophilic substitution at silicon (SN2@Si) via a central reaction barrier.

PubMed

Bento, A Patrícia; Bickelhaupt, F Matthias

2007-03-16

It is textbook knowledge that nucleophilic substitution at carbon (SN2@C) proceeds via a central reaction barrier which disappears in the corresponding nucleophilic substitution reaction at silicon (SN2@Si). Here, we address the question why the central barrier disappears from SN2@C to SN2@Si despite the fact that these processes are isostructural and isoelectronic. To this end, we have explored and analyzed the potential energy surfaces (PES) of various Cl-+CR3Cl (R=H, CH3) and Cl-+SiR3Cl model reactions (R=H, CH3, C2H5, and OCH3). Our results show that the nature of the SN2 reaction barrier is in essence steric, but that it can be modulated by electronic factors. Thus, simply by increasing the steric demand of the substituents R around the silicon atom, the SN2@Si mechanism changes from its regular single-well PES (with a stable intermediate transition complex, TC), via a triple-well PES (with a pre- and a post-TS before and after the central TC), to a double-well PES (with a TS; R=OCH3), which is normally encountered for SN2@C reactions.

REVISITING NUCLEOPHILIC SUBSTITUTION REACTIONS: MICROWAVE-ASSISTED SYNTHESIS OF AZIDES, THIOCYANATES AND SULFONES IN AQUEOUS MEDIUM

EPA Science Inventory

A practical, rapid and efficient microwave (MW) promoted synthesis of various azides, thiocyanates and sulfones, is described in aqueous medium. This general and expeditious MW-enhanced nucleophilic substitution approach uses easily accessible starting materials such as halides o...

Counting ions and other nucleophiles at surfaces by chemical trapping.

PubMed

Cuccovia, Iolanda Midea; da Silva Lima, Filipe; Chaimovich, Hernan

2017-10-01

The interfaces of membranes and other aggregates are determined by the polarity, electrical charge, molecular volume, degrees of motional freedom and packing density of the head groups of the amphiphiles. These properties also determine the type of bound ion (ion selectivity) and its local density, i.e. concentration defined by choosing an appropriate volume element at the aggregate interface. Bulk and local ion concentrations can differ by orders of magnitude. The relationships between ion (or other compound) concentrations in the bulk solvent and in the interface are complex but, in some cases, well established. As the local ion concentration, rather than that in the bulk, controls a variety of properties of membranes, micelles, vesicles and other objects of theoretical and applied interests, measurement of local (interfacial, bound) ion concentrations is of relevance for understanding and characterizing such aggregates. Many experimental methods for estimating ion distributions between the bulk solution and the interface provide indirect estimates because they are based on concentration-dependent properties, rather than concentration measurements. Dediazoniation, i.e. the loss of N 2 , of a substituted diazophenyl derivative provides a tool for determining the number of nucleophiles (including neutral or negatively charged ions) surrounding the diazophenyl derivative prior to the dediazoniation event. This reaction, defined as chemical trapping, and the appropriate reference points obtained in bulk solution allow direct measurements of local concentrations of a variety of nucleophiles at the surface of membranes and other aggregates. Here we review our contributions of our research group to the use, and understanding, of this method and applications of chemical trapping to the description of local concentrations of ions and other nucleophiles in micelles, reverse micelles, vesicles and solvent mixtures. Among other results, we have shown that interfacial water

Organic Chemistry Students' Ideas about Nucleophiles and Electrophiles: The Role of Charges and Mechanisms

ERIC Educational Resources Information Center

Anzovino, Mary E.; Bretz, Stacey Lowery

2015-01-01

Organic chemistry students struggle with reaction mechanisms and the electron-pushing formalism (EPF) used by practicing organic chemists. Faculty have identified an understanding of nucleophiles and electrophiles as one conceptual prerequisite to mastery of the EPF, but little is known about organic chemistry students' knowledge of nucleophiles…

A Redox-Nucleophilic Dual-Reactable Probe for Highly Selective and Sensitive Detection of H2S: Synthesis, Spectra and Bioimaging

NASA Astrophysics Data System (ADS)

Zhang, Changyu; Wang, Runyu; Cheng, Longhuai; Li, Bingjie; Xi, Zhen; Yi, Long

2016-07-01

Hydrogen sulfide (H2S) is an important signalling molecule with multiple biological functions. The reported H2S fluorescent probes are majorly based on redox or nucleophilic reactions. The combination usage of both redox and nucleophilic reactions could improve the probe’s selectivity, sensitivity and stability. Herein we report a new dual-reactable probe with yellow turn-on fluorescence for H2S detection. The sensing mechanism of the dual-reactable probe was based on thiolysis of NBD (7-nitro-1,2,3-benzoxadiazole) amine (a nucleophilic reaction) and reduction of azide to amine (a redox reaction). Compared with its corresponding single-reactable probes, the dual-reactable probe has higher selectivity and fluorescence turn-on fold with magnitude of multiplication from that of each single-reactable probe. The highly selective and sensitive properties enabled the dual-reactable probe as a useful tool for efficiently sensing H2S in aqueous buffer and in living cells.

Detection and Structural Characterization of Nucleophiles Trapped Reactive Metabolites of Limonin Using Liquid Chromatography-Mass Spectrometry

PubMed Central

Deng, Yujie; Fu, Yudong; Xu, Shumin; Wang, Ping; Yang, Nailong; Li, Chengqian

2018-01-01

Limonin (LIM), a furan-containing limonoid, is one of the most abundant components of Dictamnus dasycarpus Turcz. Recent studies demonstrated that LIM has great potential for inhibiting the activity of drug-metabolizing enzymes. However, the mechanisms of LIM-induced enzyme inactivation processes remain unexplored. The main objective of this study was to identify the reactive metabolites of LIM using liquid chromatography-mass spectrometry. Three nucleophiles, glutathione (GSH), N-acetyl cysteine (NAC), and N-acetyl lysine (NAL), were used to trap the reactive metabolites of LIM in in vitro and in vivo models. Two different types of mass spectrometry, a hybrid quadrupole time-of-flight (Q-TOF) mass spectrometry and a LTQ velos Pro ion trap mass spectrometry, were employed to acquire structural information of nucleophile adducts of LIM. In total, six nucleophile adducts of LIM (M1–M6) with their isomers were identified; among them, M1 was a GSH and NAL conjugate of LIM, M2–M4 were glutathione adducts of LIM, M5 was a NAC and NAL conjugate of LIM, and M6 was a NAC adduct of LIM. Additionally, CYP3A4 was found to be the key enzyme responsible for the bioactivation of limonin. This metabolism study largely facilitates the understanding of mechanisms of limonin-induced enzyme inactivation processes. PMID:29850372

Synthesis and Late-Stage Functionalization of Complex Molecules through C–H Fluorination and Nucleophilic Aromatic Substitution

PubMed Central

2015-01-01

We report the late-stage functionalization of multisubstituted pyridines and diazines at the position α to nitrogen. By this process, a series of functional groups and substituents bound to the ring through nitrogen, oxygen, sulfur, or carbon are installed. This functionalization is accomplished by a combination of fluorination and nucleophilic aromatic substitution of the installed fluoride. A diverse array of functionalities can be installed because of the mild reaction conditions revealed for nucleophilic aromatic substitutions (SNAr) of the 2-fluoroheteroarenes. An evaluation of the rates for substitution versus the rates for competitive processes provides a framework for planning this functionalization sequence. This process is illustrated by the modification of a series of medicinally important compounds, as well as the increase in efficiency of synthesis of several existing pharmaceuticals. PMID:24918484

Poly(N-arylenebenzimidazole)s via aromatic nucleophilic displacement

NASA Technical Reports Server (NTRS)

Connell, John W. (Inventor); Hergenrother, Paul M. (Inventor); Smith, Jr., Joseph G. (Inventor)

1996-01-01

Novel poly(N-arylenebenzimidazole)s (PNABls) are prepared by the aromatic nucleophilic displacement reaction of novel di(hydroxyphenyl-N-arylene benzimidazole) monomers with activated aromatic dihalides or activated aromatic dinitro compounds. The polymerizations are carried out in polar aprotic solvents such as N-methyl-2-pyrrolidinone or N,N-dimethylacetamide using alkali metal bases such as potassium carbonate at elevated temperatures under nitrogen. The di(hydroxyphenyl-N-arylenebenzimidazole) monomers are synthesized by reacting phenyl-4-hydroxybenzoate with bis(2-aminoanilino)arylenes in diphenylsulfone. Moderate molecular weight PNABIs of new chemical structures were prepared that exhibit a favorable combination of physical and mechanical properties. The use of the novel di(hydroxyphenyI-N-arylenebenzimidazole)s permits a more economical and easier way to prepare PNABIs than previous routes.

Amination of electrophilic aromatic compounds by vicarious nucleophilic substitution

DOEpatents

Mitchell, Alexander R.; Pagoria, Philip F.; Schmidt, Robert D.

2000-01-01

The present invention relates to a process to aminate electrophilic aromatic compounds by vicarious nucleophilic substitution of hydrogen using quaternary hydrazinium salts. The use of trialkylhydrazinium halide, e.g., trimethylhydrazinium iodide, as well as hydroxylamine, alkoxylamines, and 4-amino-1,2,4-triazole to produce aminated aromatic structures, such as 1,3-diamino-2,4,6-trinitrobenzene (DATB), 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) and 3,5-diamino-2,4,6-trinitrotoluene (DATNT), is described. DATB and TATB are useful insensitive high explosives. TATB is also used for the preparation of benzenehexamine, a starting material for the synthesis of novel materials (optical imaging devices, liquid crystals, ferromagnetic compounds).

Nucleophilic ortho-Allylation of Pyrroles and Pyrazoles: An Accelerated Pummerer/Thio-Claisen Rearrangement Sequence

PubMed Central

2013-01-01

Arylsulfinyl groups direct the metal-free, regiospecific, nucleophilic ortho-allylation of pyrroles and pyrazoles. Mechanistic studies support the intermediacy of allylsulfonium salts that undergo facile thio-Claisen rearrangement onto the heterocyclic ring, giving products of coupling. The strategy has been adapted to allow regiospecific propargylation of the heterocyclic substrates. PMID:23855635

Catalysis of hydrolysis and nucleophilic substitution at the P-N bond of phosphoimidazolide-activated nucleotides in phosphate buffers

NASA Technical Reports Server (NTRS)

Kanavarioti, A.; Rosenbach, M. T.

1991-01-01

Phosphoimidazolide-activated derivatives of guanosine and cytidine 5'-monophosphates, henceforth called ImpN's, exhibit enhanced rates of degradation in the presence of aqueous inorganic phosphate in the range 4.0 < or = pH < or = 8.6. This degradation is been attributed to (i) nucleophilic substitution of the imidazolide and (ii) catalysis of the P-N bond hydrolysis by phosphate. The first reaction results in the formation of nucleoside 5'-diphosphate and the second in nucleoside 5'-monophosphate. Analysis of the observed rates as well as the product ratios as a function of pH and phosphate concentration allow distinction between various mechanistic possibilities. The results show that both H2PO4- and HPO4(2-) participate in both hydrolysis and nucleophilic substitution. Statistically corrected biomolecular rate constants indicate that the dianion is 4 times more effective as a general base than the monoanion, and 8 times more effective as nucleophile. The low Bronsted value beta = 0.15 calculated for these phosphate species, presumed to act as general bases in facilitating water attack, is consistent with the fact that catalysis of the hydrolysis of the P-N bond in ImpN's has not been detected before. The beta nuc = 0.35 calculated for water, H2PO4-, HPO4(2-), and hydroxide acting as nucleophiles indicates a more associative transition state for nucleotidyl (O2POR- with R = nucleoside) transfers than that observed for phosphoryl (PO3(2-)) transfers (beta nuc = 0.25). With respect to the stability/reactivity of ImpN's under prebiotic conditions, our study shows that these materials would not suffer additional degradation due to inorganic phosphate, assuming the concentrations of phosphate, Pi, on prebiotic Earth were similar to those in the present oceans ([Pi] approximately 2.25 micromoles).

Effect of carbonates/phosphates as nucleophilic catalysts in dimethylformamide for efficient cyanosilylation of aldehydes and ketones

PubMed Central

Prakash, G. K. Surya; Vaghoo, Habiba; Panja, Chiradeep; Surampudi, Vijayalakshmi; Kultyshev, Roman; Mathew, Thomas; Olah, George A.

2007-01-01

Cyanosilylation of aldehydes and aliphatic ketones can be carried out in dimethylformamide even without the use of any catalyst. In the presence of nucleophilic catalysts such as carbonate and phosphate salts, the reaction rate is significantly enhanced. PMID:17360603

Laboratory determination of the carbon kinetic isotope effects (KIEs) for reactions of methyl halides with various nucleophiles in solution

USGS Publications Warehouse

Baesman, S.M.; Miller, L.G.

2005-01-01

Large carbon kinetic isotope effects (KIEs) were measured for reactions of methyl bromide (MeBr), methyl chloride (MeCl), and methyl iodide (MeI) with various nucleophiles at 287 and 306 K in aqueous solutions. Rates of reaction of MeBr and MeI with H2O (neutral hydrolysis) or Cl- (halide substitution) were consistent with previous measurements. Hydrolysis rates increased with increasing temperature or pH (base hydrolysis). KIEs for hydrolysis were 51 ?? 6??? for MeBr and 38 ?? 8??? for MeI. Rates of halide substitution increased with increasing temperature and greater reactivity of the attacking nucleophile, with the fastest reaction being that of MeI with Br-. KIEs for halide substitution were independent of temperature but varied with the reactant methyl halide and the attacking nucleophile. KIEs were similar for MeBr substitution with Cl- and MeCl substitution with Br- (57 ?? 5 and 60 ?? 9??? respectively). The KIE for halide exchange of MeI was lower overall (33 ?? 8??? and was greater for substitution with Br- (46 ?? 6???) than with Cl- (29 ?? 6???). ?? Springer Science + Business Media, Inc. 2005.

A general ligand design for gold catalysis allowing ligand-directed anti-nucleophilic attack of alkynes.

PubMed

Wang, Yanzhao; Wang, Zhixun; Li, Yuxue; Wu, Gongde; Cao, Zheng; Zhang, Liming

2014-04-07

Most homogenous gold catalyses demand ≥ 0.5 mol% catalyst loading. Owing to the high cost of gold, these reactions are unlikely to be applicable in medium- or large-scale applications. Here we disclose a novel ligand design based on the privileged (1,1'-biphenyl)-2-ylphosphine framework that offers a potentially general approach to dramatically lowering catalyst loading. In this design, an amide group at the 3'-position of the ligand framework directs and promotes nucleophilic attack at the ligand gold complex-activated alkyne, which is unprecedented in homogenous gold catalysis considering the spatial challenge of using ligand to reach anti-approaching nucleophile in a linear P-Au-alkyne centroid structure. With such a ligand, the gold(I) complex becomes highly efficient in catalysing acid addition to alkynes, with a turnover number up to 99,000. Density functional theory calculations support the role of the amide moiety in directing the attack of carboxylic acid via hydrogen bonding.

A General Ligand Design for Gold Catalysis allowing Ligand-Directed Anti Nucleophilic Attack of Alkynes

PubMed Central

Wang, Yanzhao; Wang, Zhixun; Li, Yuxue; Wu, Gongde; Cao, Zheng; Zhang, Liming

2014-01-01

Most homogenous gold catalyses demand ≥0.5 mol % catalyst loading. Due to the high cost of gold, these reactions are unlikely to be applicable in medium or large scale applications. Here we disclose a novel ligand design based on the privileged biphenyl-2-phosphine framework that offers a potentially general approach to dramatically lowering catalyst loading. In this design, an amide group at the 3’ position of the ligand framework directs and promotes nucleophilic attack at the ligand gold complex-activated alkyne, which is unprecedented in homogeneous gold catalysis considering the spatial challenge of using ligand to reach antiapproaching nucleophile in a linear P-Au-alkyne centroid structure. With such a ligand, the gold(I) complex becomes highly efficient in catalyzing acid addition to alkynes, with a turnover number up to 99,000. Density functional theory calculations support the role of the amide moiety in directing the attack of carboxylic acid via hydrogen bonding. PMID:24704803

Phosphoester hydrolysis: the incoming substrate turns the bridging hydroxido nucleophile into a terminal one.

PubMed

Gouré, Eric; Carboni, Michaël; Troussier, Angélique; Lebrun, Colette; Pécaut, Jacques; Jacquot, Jean-François; Dubourdeaux, Patrick; Clémancey, Martin; Blondin, Geneviève; Latour, Jean-Marc

2015-05-26

Identifying the active nucleophile in hydrolysis reactions catalyzed by binuclear hydrolases is a recurrent problem and a matter of intense debate. We report on the phosphate ester hydrolysis by a Fe(III)Fe(II) complex of a binucleating ligand. This complex presents activities in the range of those observed for similar biomimetic compounds in the literature. The specific electronic properties of the Fe(III)Fe(II) complex allowed us to use (1)H NMR and Mössbauer spectroscopies to investigate the nature of the various species present in the solution in the pH range of 5-10. Both techniques showed that the hydrolysis activity is associated to a μ-hydroxido Fe(III)Fe(II) species. Further (1)H NMR experiments show that binding of anions or the substrate changes this bonding mode suggesting that a terminal hydroxide is the likely nucleophile in these hydrolysis reactions. This view is further supported by the structure determination of the hydrolysis product. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Probing the reactivation process of sarin-inhibited acetylcholinesterase with α-nucleophiles: hydroxylamine anion is predicted to be a better antidote with DFT calculations.

PubMed

Khan, Md Abdul Shafeeuulla; Lo, Rabindranath; Bandyopadhyay, Tusar; Ganguly, Bishwajit

2011-08-01

Inactivation of acetylcholinesterase (AChE) due to inhibition by organophosphorus (OP) compounds is a major threat to human since AChE is a key enzyme in neurotransmission process. Oximes are used as potential reactivators of OP-inhibited AChE due to their α-effect nucleophilic reactivity. In search of more effective reactivating agents, model studies have shown that α-effect is not so important for dephosphylation reactions. We report the importance of α-effect of nucleophilic reactivity towards the reactivation of OP-inhibited AChE with hydroxylamine anion. We have demonstrated with DFT [B3LYP/6-311G(d,p)] calculations that the reactivation process of sarin-serine adduct 2 with hydroxylamine anion is more efficient than the other nucleophiles reported. The superiority of hydroxylamine anion to reactivate the sarin-inhibited AChE with sarin-serine adducts 3 and 4 compared to formoximate anion was observed in the presence and absence of hydrogen bonding interactions of Gly121 and Gly122. The calculated results show that the rates of reactivation process of adduct 4 with hydroxylamine anion are 261 and 223 times faster than the formoximate anion in the absence and presence of such hydrogen bonding interactions. The DFT calculated results shed light on the importance of the adjacent carbonyl group of Glu202 for the reactivation of sarin-serine adduct, in particular with formoximate anion. The reverse reactivation reaction between hydroxylamine anion and sarin-serine adduct was found to be higher in energy compared to the other nucleophiles, which suggests that this α-nucleophile can be a good antidote agent for the reactivation process. Copyright © 2011 Elsevier Inc. All rights reserved.

Intramolecular hydrogen-bond activation for the addition of nucleophilic imines: 2-hydroxybenzophenone as a chemical auxiliary.

PubMed

Choubane, Houcine; Garrido-Castro, Alberto F; Alvarado, Cuauhtemoc; Martín-Somer, Ana; Guerrero-Corella, Andrea; Daaou, Mortada; Díaz-Tendero, Sergio; Carmen Maestro, M; Fraile, Alberto; Alemán, José

2018-03-29

The addition of nucleophilic imines, using 2-hydroxybenzophenone as a chemical auxiliary, is presented. An intramolecular six-membered ring via hydrogen bonding that enhances the reactivity and selectivity is the key of this strategy, which is supported by DFT calculations and experimental trials.

Improved Synthesis of and Nucleophilic Addition to 2-Formyl-2-Cyclohexenone

PubMed Central

Adary, Elan M.; Chang, Chih-wei; Auria, Damian T. D’; Nguyen, Phuc M.; Polewacz, Klaudyna; Reinicke, Justin A.; Seo, Hannah; Berger, Gideon O.

2014-01-01

A preparation of 2-formyl-2-cyclohexenone in nearly quantitative yield and purity of approximately 95% is described. It is scalable and has been extended to the synthesis of the 5- and 7-membered ring homologs with comparable yields. Conditions have also been developed for the successful conjugate addition of dimethylmalonate to 2-formyl-2-cyclohexenone, in good and scalable yield (60%). This result has been extended to 5 other nucleophile classes, and the dimethylmalonate conjugate addition has been demonstrated with 2-formyl-2-cyclopentenone and 2-formyl-2-cycloheptenone. PMID:25593375

Additional Nucleophile-Free FeCl3-Catalyzed Green Deprotection of 2,4-Dimethoxyphenylmethyl-Protected Alcohols and Carboxylic Acids.

PubMed

Sawama, Yoshinari; Masuda, Masahiro; Honda, Akie; Yokoyama, Hiroki; Park, Kwihwan; Yasukawa, Naoki; Monguchi, Yasunari; Sajiki, Hironao

2016-01-01

The deprotection of the methoxyphenylmethyl (MPM) ether and ester derivatives can be generally achieved by the combinatorial use of a catalytic Lewis acid and stoichiometric nucleophile. The deprotections of 2,4-dimethoxyphenylmethyl (DMPM)-protected alcohols and carboxylic acids were found to be effectively catalyzed by iron(III) chloride without any additional nucleophile to form the deprotected mother alcohols and carboxylic acids in excellent yields. Since the present deprotection proceeds via the self-assembling mechanism of the 2,4-DMPM protective group itself to give the hardly-soluble resorcinarene derivative as a precipitate, the rigorous purification process by silica-gel column chromatography was unnecessary and the sufficiently-pure alcohols and carboxylic acids were easily obtained in satisfactory yields after simple filtration.

Microsolvation effects on the reactivity of oxy-nucleophiles: the case of gas-phase SN2 reactions of YO-(CH3OH) n=1,2 towards CH3Cl.

PubMed

Yun-Yun, Liu; Fang-Zhou, Qiu; Jun, Zhu; Yi, Ren; Kai-Chung, Lau

2017-06-01

The modified G4(MP2) method was applied to explore microsolvation effects on the reactivity of four solvated normal oxy-nucleophiles YO - (CH 3 OH) n=1,2 (Y = CH 3 , C 2 H 5 , FC 2 H 4 , ClC 2 H 4 ), and five α-oxy-nucleophiles YO - (CH 3 OH) n=1,2 (Y = HO, CH 3 O, F, Cl, Br), in gas-phase S N 2 reactions towards the substrate CH 3 Cl. Based on a Brønsted-type plot, our calculations reveal that the overall activation barriers of five microsolvated α-oxy-nucleophiles are obviously smaller than the prediction from the correlation line constructed by four normal microsolvated ones to different degrees, and clearly demonstrate the existence of an α-effect in the presence of one or two methanol molecule(s). Moreover, it was found that the α-effect of the mono-methanol microsolvated α-nucleophile is stronger than that of the monohydrated α-nucleophile. However, the α-effect of YO - (CH 3 OH) 2 becomes weaker for Y = HO and CH 3 O, whereas it becomes stronger for Y = F, Cl, Br than that of YO - (H 2 O) 2 , which can be explained by analyses of the activation strain model in the two cases. It was also found that the rationale about the low ionization energy of α-nucleophile inducing the α-effect was not widely significant. Graphical abstract Variation of alpha-effect in the gas-phase S N 2 reaction with the microsolvation.

Evidence That Nucleophile Deprotonation Exceeds Bond Formation in the HDV Ribozyme Transition State.

PubMed

Lu, Jun; Koo, Selene C; Weissman, Benjamin P; Harris, Michael E; Li, Nan-Sheng; Piccirilli, Joseph A

2018-06-26

Steric constraints imposed by the active sites of protein and RNA enzymes pose major challenges to the investigation of structure-function relationships within these systems. As a strategy to circumvent such constraints in the HDV ribozyme, we have synthesized phosphoramidites from propanediol derivatives and incorporated them at the 5'-termini of RNA and DNA oligonucleotides to generate a series of novel substrates with nucleophiles perturbed electronically through geminal fluorination. In nonenzymatic, hydroxide-catalyzed intramolecular transphosphorylation of the DNA substrates, pH-rate profiles revealed that fluorine substitution reduces the maximal rate and the kinetic p K a , consistent with the expected electron-withdrawing effect. In HDV ribozyme reactions, we observed that the RNA substrates undergo transphosphorylation relatively efficiently, suggesting that the conformational constraints imposed by a ribofuranose ring are not strictly required for ribozyme catalysis. In contrast to the nonenzymatic reactions, however, substrate fluorination modestly increases the ribozyme reaction rate, consistent with a mechanism in which (1) the 2'-hydroxyl nucleophile exists predominantly in its neutral, protonated form in the ground state and (2) the 2'-hydroxyl bears some negative charge in the rate-determining step, consistent with a transition state in which the extent of 2'-OH deprotonation exceeds the extent of P-O bond formation.

Synthesis of a Fluorescent Acridone Using a Grignard Addition, Oxidation, and Nucleophilic Aromatic Substitution Reaction Sequence

ERIC Educational Resources Information Center

Goodrich, Samuel; Patel, Miloni; Woydziak, Zachary R.

2015-01-01

A three-pot synthesis oriented for an undergraduate organic chemistry laboratory was developed to construct a fluorescent acridone molecule. This laboratory experiment utilizes Grignard addition to an aldehyde, alcohol oxidation, and iterative nucleophilic aromatic substitution steps to produce the final product. Each of the intermediates and the…

Fine-tuning the nucleophilic reactivities of boron ate complexes derived from aryl and heteroaryl boronic esters.

PubMed

Berionni, Guillaume; Leonov, Artem I; Mayer, Peter; Ofial, Armin R; Mayr, Herbert

2015-02-23

Boron ate complexes derived from thienyl and furyl boronic esters and aryllithium compounds have been isolated and characterized by X-ray crystallography. Products and mechanisms of their reactions with carbenium and iminium ions have been analyzed. Kinetics of these reactions were monitored by UV/Vis spectroscopy, and the influence of the aryl substituents, the diol ligands (pinacol, ethylene glycol, neopentyl glycol, catechol), and the counterions on the nucleophilic reactivity of the boron ate complexes were examined. A Hammett correlation confirmed the polar nature of their reactions with benzhydrylium ions, and the correlation lg k(20 °C)=sN (E+N) was employed to determine the nucleophilicities of the boron ate complexes and to compare them with those of other borates and boronates. The neopentyl and ethylene glycol derivatives were found to be 10(4) times more reactive than the pinacol and catechol derivatives. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Tyrosyl-DNA Phosphodiesterase I Catalytic Mutants Reveal an Alternative Nucleophile That Can Catalyze Substrate Cleavage*

PubMed Central

Comeaux, Evan Q.; Cuya, Selma M.; Kojima, Kyoko; Jafari, Nauzanene; Wanzeck, Keith C.; Mobley, James A.; Bjornsti, Mary-Ann; van Waardenburg, Robert C. A. M.

2015-01-01

Tyrosyl-DNA phosphodiesterase I (Tdp1) catalyzes the repair of 3′-DNA adducts, such as the 3′-phosphotyrosyl linkage of DNA topoisomerase I to DNA. Tdp1 contains two conserved catalytic histidines: a nucleophilic His (Hisnuc) that attacks DNA adducts to form a covalent 3′-phosphohistidyl intermediate and a general acid/base His (Hisgab), which resolves the Tdp1-DNA linkage. A Hisnuc to Ala mutant protein is reportedly inactive, whereas the autosomal recessive neurodegenerative disease SCAN1 has been attributed to the enhanced stability of the Tdp1-DNA intermediate induced by mutation of Hisgab to Arg. However, here we report that expression of the yeast HisnucAla (H182A) mutant actually induced topoisomerase I-dependent cytotoxicity and further enhanced the cytotoxicity of Tdp1 Hisgab mutants, including H432N and the SCAN1-related H432R. Moreover, the HisnucAla mutant was catalytically active in vitro, albeit at levels 85-fold less than that observed with wild type Tdp1. In contrast, the HisnucPhe mutant was catalytically inactive and suppressed Hisgab mutant-induced toxicity. These data suggest that the activity of another nucleophile when Hisnuc is replaced with residues containing a small side chain (Ala, Asn, and Gln), but not with a bulky side chain. Indeed, genetic, biochemical, and mass spectrometry analyses show that a highly conserved His, immediately N-terminal to Hisnuc, can act as a nucleophile to catalyze the formation of a covalent Tdp1-DNA intermediate. These findings suggest that the flexibility of Tdp1 active site residues may impair the resolution of mutant Tdp1 covalent phosphohistidyl intermediates and provide the rationale for developing chemotherapeutics that stabilize the covalent Tdp1-DNA intermediate. PMID:25609251

Hydrolysis and nucleophilic substitution of model and ultimate carcinogens

DOE Office of Scientific and Technical Information (OSTI.GOV)

Helmick, J.S.

1992-01-01

The hydrolysis reaction of the Model Carcinogen O-pivaloyl-N-(4-chlorophenyl)hydroxylamine in aqueous buffer (pH 7.0-10.0) proceeds by was of a nitrenium ion intermediate. The products formed from this process are predominately 2,4-dichloroaniline, and 2-hydroxy-4-chloro-pivalanilide. At pH 10-13 the rate becomes dependent upon hydroxide. The product that is formed is 4-chlorophenylhydroxylamine. 4-Chlorophenyl-hydroxylamine is formed by basic ester hydrolysis determined by an [sup 18]O GC-MS experiment. The reaction of O-pivaloyl-N-(4-chlorophenyl)hydroxylamine in an aqueous diethylamine (pH 11.3) buffer gave 4-chlorophenyl-N,N-diethylhydrazine as the substitution product in a 16% yield. The reaction of O-pivaloyl-N-(4-methylphenyl)hydroxylamine with diethylamine gave a 1% yield of the hydrazine product. The reaction ofmore » N,N-dimethylanline and aniline with ring-substituted O-pivaloyl-N-arylhydroxylamines in MeOH generates products of nucleophilic attack on the nitrogen of the hydroxylamine derivative. The hydrolysis of the ultimate carcinogen N-(sulfonatooxy)-N-4-aminobiphenyl proceeds by two consecutive pseudo-first-order processes and generates predominately a product of nucleophilic attack by chloride ion at the ortho position of the aromatic ring. A labile intermediate identified as N-acetypl-4-hydroxy-4-phenyl-2,5-cyclohexadienone imine has been detected by NMR. This intermediate rearranges to form 4-hydroxy-3-phenylacetanilide. The hydrolysis of N-benzoyl-4-hydroxy-4-hydroxy-4-phenyl-2,5-cyclohexadienone imine proceeds by way of two consecutive pseudo-first-order processes. The hydrolysis of N-benzoyl-4-methoxy-4-phenyl-2,5-cyclohexadienone imine also proceeds by two consecutive pseudo-first-order processes. Spectroscopic evidence of two diastereomeric intermediates formed from the hydrolysis of the N-benzoyl imines were tentatively identified as N-benzoyl-N-hydroxy-4-hydroxy-4-phenyl-2,5-cyclohexadienone imine.« less

Phosphorus-containing nucleophiles in reactions with polyfluorinated organic compounds

NASA Astrophysics Data System (ADS)

Furin, Georgii G.

1993-03-01

The review presents a compilation of new expelimental data on the reactions of phosphorus-containing nucleophiles [triphenylphosphine, trialkylphosphines, trialkyl phosphites, phosphorus tris(diethylamide), etc.] with perfluorinated olefins and aromatic and heterocyclic compounds, leading to substances both with and without a phosphorus atom. It is shown that the interaction of phosphorus tris(diethylamide) and trialkylphosphines with organic polyfluoro-compounds and perfluoroolefins leads to the formation of phosphoranes, the decomposition of which is accompanied by the generation of aryl and alkenyl anions. The reactions of these anions with C-electrophiles and compounds containing mobile halogen atoms are examined. In addition, the pathways in the Arbuzov reaction involving a series of unsaturated perfluorinated compounds are analysed. Possible applications of these reactions in organic synthesis are demonstrated. The bibliography includes 120 references.

Origin of Enhanced Reactivity of a Microsolvated Nucleophile in Ion Pair SN2 Reactions: The Cases of Sodium p-Nitrophenoxide with Halomethanes in Acetone.

PubMed

Li, Qiang-Gen; Xu, Ke; Ren, Yi

2015-04-30

In a kinetic experiment on the SN2 reaction of sodium p-nitrophenoxide with iodomethane in acetone-water mixed solvent, Humeres et al. (J. Org. Chem. 2001, 66, 1163) found that the reaction depends strongly on the medium, and the fastest rate constant was observed in pure acetone. The present work tries to explore why acetone can enhance the reactivity of the title reactions. Accordingly, we make a mechanistic study on the reactions of sodium p-nitrophenoxide with halomethanes (CH3X, X = Cl, Br, I) in acetone by using a supramolecular/continuum model at the PCM-MP2/6-311+G(d,p)//B3LYP/6-311+G(d,p) level, in which the ion pair nucleophile is microsolvated by one to three acetone molecules. We compared the reactivity of the microsolvated ion pair nucleophiles with solvent-free ion pair and anionic ones. Our results clearly reveal that the microsolvated ion pair nucleophile is favorable for the SN2 reactions; meanwhile, the origin of the enhanced reactivity induced by microsolvation of the nucleophile is discussed in terms of the geometries of transition state (TS) structures and activation strain model, suggesting that lower deformation energies and stronger interaction energies between the deformed reactants in the TS lead to the lower overall reaction barriers for the SN2 reaction of microsolvated sodium p-nitrophenoxide toward halomethanes in acetone.

Citrus Peel Additives for One-Pot Triazole Formation by Decarboxylation, Nucleophilic Substitution, and Azide-Alkyne Cycloaddition Reactions

ERIC Educational Resources Information Center

Mendes, Desiree E.; Schoffstall, Allen M.

2011-01-01

This undergraduate organic laboratory experiment consists of three different reactions occurring in the same flask: a cycloaddition reaction, preceded by decarboxylation and nucleophilic substitution reactions. The decarboxylation and cycloaddition reactions occur using identical Cu(I) catalyst and conditions. Orange, lemon, and other citrus fruit…

Nucleophilic substitution at centers other than carbon: reaction at the chlorine of N-chloroacetanilides with triethylamine as the nucleophile

DOE Office of Scientific and Technical Information (OSTI.GOV)

Underwood, G.R.; Dietze, P.E.

1984-12-28

The reaction between triethylamine (TEA) and a series of para-substituted N-chloroacetanilides has been studied in aqueous solution buffered to pHs between 1 and 5. The exclusive product derived from the aromatic moiety is the corresponding acetanilide. The reaction occurs via two parallel pseudo-second-order paths, one acid catalyzed (the Orton-like mechanism), the other uncatalyzed. The uncatalyzed reaction is accelerated by the presence of electron-withdrawing substituents on the aromatic ring and can best be represented as nucleophilic displacement at chlorine. It therefore appears to be the prototype of a convenient class of reactions for the study of displacement reactions at chlorine. Themore » rho value for this reaction is 3.87, indicating substantial negative charge buildup in the aromatic ring during of the transition state. The acid-catalyzed reaction is more complex, presumable involving a protonation equilibrium for the N-chloroacetanilide prior to the rate-determining step similar to that in the Orton reaction. 15 references, 2 figures, 3 tables.« less

Development of Selective Colorimetric Probes for Hydrogen Sulfide Based on Nucleophilic Aromatic Substitution

PubMed Central

Montoya, Leticia A.; Pearce, Taylor F.; Hansen, Ryan J.; Zakharov, Lev N.; Pluth, Michael D.

2013-01-01

Hydrogen sulfide is an important biological signalling molecule and an important environmental target for detection. A major challenge in developing H2S detection methods is separating the often similar reactivity of thiols and other nucleophiles from H2S. To address this need, the nucleophilic aromatic substitution (SNAr) reaction of H2S with electron-poor aromatic electrophiles was developed as a strategy to separate H2S and thiol reactivity. Treatment of aqueous solutions of nitrobenzofurazan (7-nitro-1,2,3-benzoxadiazole, NBD) thioethers with H2S resulted in thiol extrusion and formation of nitrobenzofurazan thiol (λmax = 534 nm). This reactivity allows for unwanted thioether products to be converted to the desired nitrobenzofurazan thiol upon reaction with H2S. The scope of the reaction was investigated using a Hammett linear free energy relationship study, and the determined ρ = +0.34 is consistent with the proposed SN2Ar reaction mechanism. The efficacy of the developed probes was demonstrated in buffer and in serum with associated sub-micromolar detection limits as low as 190 nM (buffer) and 380 nM (serum). Furthermore, the sigmoidal response of nitrobenzofurazan electrophiles with H2S can be fit to accurately quantify H2S. The developed detection strategy offers a manifold for H2S detection that we foresee being applied in various future applications. PMID:23735055

Development of selective colorimetric probes for hydrogen sulfide based on nucleophilic aromatic substitution.

PubMed

Montoya, Leticia A; Pearce, Taylor F; Hansen, Ryan J; Zakharov, Lev N; Pluth, Michael D

2013-07-05

Hydrogen sulfide is an important biological signaling molecule and an important environmental target for detection. A major challenge in developing H2S detection methods is separating the often similar reactivity of thiols and other nucleophiles from H2S. To address this need, the nucleophilic aromatic substitution (SNAr) reaction of H2S with electron-poor aromatic electrophiles was developed as a strategy to separate H2S and thiol reactivity. Treatment of aqueous solutions of nitrobenzofurazan (7-nitro-1,2,3-benzoxadiazole, NBD) thioethers with H2S resulted in thiol extrusion and formation of nitrobenzofurazan thiol (λmax = 534 nm). This reactivity allows for unwanted thioether products to be converted to the desired nitrobenzofurazan thiol upon reaction with H2S. The scope of the reaction was investigated using a Hammett linear free energy relationship study, and the determined ρ = +0.34 is consistent with the proposed SN2Ar reaction mechanism. The efficacy of the developed probes was demonstrated in buffer and in serum with associated submicromolar detection limits as low as 190 nM (buffer) and 380 nM (serum). Furthermore, the sigmoidal response of nitrobenzofurazan electrophiles with H2S can be fit to accurately quantify H2S. The developed detection strategy offers a manifold for H2S detection that we foresee being applied in various future applications.

4-alkyl-L-(Dehydro)proline biosynthesis in actinobacteria involves N-terminal nucleophile-hydrolase activity of γ-glutamyltranspeptidase homolog for C-C bond cleavage

NASA Astrophysics Data System (ADS)

Zhong, Guannan; Zhao, Qunfei; Zhang, Qinglin; Liu, Wen

2017-07-01

γ-Glutamyltranspeptidases (γ-GTs), ubiquitous in glutathione metabolism for γ-glutamyl transfer/hydrolysis, are N-terminal nucleophile (Ntn)-hydrolase fold proteins that share an autoproteolytic process for self-activation. γ-GT homologues are widely present in Gram-positive actinobacteria where their Ntn-hydrolase activities, however, are not involved in glutathione metabolism. Herein, we demonstrate that the formation of 4-Alkyl-L-(dehydro)proline (ALDP) residues, the non-proteinogenic α-amino acids that serve as vital components of many bioactive metabolites found in actinobacteria, involves unprecedented Ntn-hydrolase activity of γ-GT homologue for C-C bond cleavage. The related enzymes share a key Thr residue, which acts as an internal nucleophile for protein hydrolysis and then as a newly released N-terminal nucleophile for carboxylate side-chain processing likely through the generation of an oxalyl-Thr enzyme intermediate. These findings provide mechanistic insights into the biosynthesis of various ALDP residues/associated natural products, highlight the versatile functions of Ntn-hydrolase fold proteins, and particularly generate interest in thus far less-appreciated γ-GT homologues in actinobacteria.

Poly(1,3,4-oxadiazoles) via aromatic nucleophilic displacement

NASA Technical Reports Server (NTRS)

Connell, John W. (Inventor); Hergenrother, Paul M. (Inventor); Wolf, Peter (Inventor)

1992-01-01

Poly(1,3,4-oxadiazoles) (POX) are prepared by the aromatic nucleophilic displacement reaction of di(hydroxyphenyl) 1,3,4-oxadiazole monomers with activated aromatic dihalides or activated aromatic dinitro compounds. The polymerizations are carried out in polar aprotic solvents such as sulfolane or diphenylsulfone using alkali metal bases such as potassium carbonate at elevated temperatures under nitrogen. The di(hydroxyphenyl) 1,3,4-oxadiazole monomers are synthesized by reacting 4-hydroxybenzoic hydrazide with phenyl 4-hydrobenzoate in the melt and also by reacting aromatic dihydrazides with two moles of phenyl 4-hydroxybenzoate in the melt. This synthetic route has provided high molecular weight POX of new chemical structure, is economically and synthetically more favorable than other routes, and allows for facile chemical structure variation due to the large variety of activated aromatic dihalides which are available.

Transition-Metal Catalysis of Nucleophilic Substitution Reactions: A Radical Alternative to SN1 and SN2 Processes.

PubMed

Fu, Gregory C

2017-07-26

Classical methods for achieving nucleophilic substitutions of alkyl electrophiles (S N 1 and S N 2) have limited scope and are not generally amenable to enantioselective variants that employ readily available racemic electrophiles. Radical-based pathways catalyzed by chiral transition-metal complexes provide an attractive approach to addressing these limitations.

Transition-Metal Catalysis of Nucleophilic Substitution Reactions: A Radical Alternative to SN1 and SN2 Processes

PubMed Central

2017-01-01

Classical methods for achieving nucleophilic substitutions of alkyl electrophiles (SN1 and SN2) have limited scope and are not generally amenable to enantioselective variants that employ readily available racemic electrophiles. Radical-based pathways catalyzed by chiral transition-metal complexes provide an attractive approach to addressing these limitations. PMID:28776010

Ionizing power and nucleophilicity in water in oil AOT-based microemulsions.

PubMed

García-Río, Luis; Hervella, Pablo; Leis, José Ramón

2005-08-16

A study was carried out on the solvolysis of substituted phenyl chloroformates in AOT/isooctane/water microemulsions. (AOT is the sodium salt of bis(2-ethyhexyl)sulfosuccinate.) The results obtained have been interpreted by taking into account the distribution of the chloroformates between the continuous medium and the interface of the microemulsions, where the reactions take place. The values obtained for the rate constant in the interface, k(i), decreases as the water content of the microemulsions increases, as a consequence of the decrease in its nucleophilic capacity. This behavior is consistent with a rate-determining step of water addition to the carbonyl group. The values of k(i) allow us to obtain the slopes of the Hammett correlations at the interface of the microemulsions, rho = 2.25, whose values are greater than those obtained in an aqueous medium, rho = 0.82. This increase in the Hammett slope is similar to that observed in ethanol/water mixtures and is a consequence of a variation in the structure of the transition state of the reaction where there is a smaller extension of the expulsion of the leaving group. The values of the rate constants at the interface of the microemulsions have allowed us, by means of the Grunwald-Winstein equation, to obtain the solvent ionizing power and the nucleophilicity of the solvent. The values obtained for Y(Cl) increase together with the water content of the microemulsion, whereas the values of N(T) decrease. These variations are a consequence of the interaction between the AOT headgroups and the interfacial water, where the water molecules act like electronic acceptors. The intensity of this interaction is greater if the system has a small water content, which explains the variation of Y(Cl) and N(T).

Synthesis of Aryl-Substituted 2,4-Dinitrophenylamines: Nucleophilic Aromatic Substitution as a Problem-Solving and Collaborative-Learning Approach

ERIC Educational Resources Information Center

Santos, Elvira Santos; Garcia, Irma Cruz Gavilan; Gomez, Eva Florencia Lejarazo; Vilchis-Reyes, Miguel Angel

2010-01-01

A series of experiments based on problem-solving and collaborative-learning pedagogies are described that encourage students to interpret results and draw conclusions from data. Different approaches including parallel library synthesis, solvent variation, and leaving group variation are used to study a nucleophilic aromatic substitution of…

Synthesis, structure and reaction chemistry of a nucleophilic aluminyl anion.

PubMed

Hicks, Jamie; Vasko, Petra; Goicoechea, Jose M; Aldridge, Simon

2018-05-01

The reactivity of aluminium compounds is dominated by their electron deficiency and consequent electrophilicity; these compounds are archetypal Lewis acids (electron-pair acceptors). The main industrial roles of aluminium, and classical methods of synthesizing aluminium-element bonds (for example, hydroalumination and metathesis), draw on the electron deficiency of species of the type AlR 3 and AlCl 3 1,2 . Whereas aluminates, [AlR 4 ] - , are well known, the idea of reversing polarity and using an aluminium reagent as the nucleophilic partner in bond-forming substitution reactions is unprecedented, owing to the fact that low-valent aluminium anions analogous to nitrogen-, carbon- and boron-centred reagents of the types [NX 2 ] - , [CX 3 ] - and [BX 2 ] - are unknown 3-5 . Aluminium compounds in the +1 oxidation state are known, but are thermodynamically unstable with respect to disproportionation. Compounds of this type are typically oligomeric 6-8 , although monomeric systems that possess a metal-centred lone pair, such as Al(Nacnac) Dipp (where (Nacnac) Dipp  = (NDippCR) 2 CH and R =  t Bu, Me; Dipp = 2,6- i Pr 2 C 6 H 3 ), have also been reported 9,10 . Coordination of these species, and also of (η 5 -C 5 Me 5 )Al, to a range of Lewis acids has been observed 11-13 , but their primary mode of reactivity involves facile oxidative addition to generate Al(III) species 6-8,14-16 . Here we report the synthesis, structure and reaction chemistry of an anionic aluminium(I) nucleophile, the dimethylxanthene-stabilized potassium aluminyl [K{Al(NON)}] 2 (NON = 4,5-bis(2,6-diisopropylanilido)-2,7-di-tert-butyl-9,9-dimethylxanthene). This species displays unprecedented reactivity in the formation of aluminium-element covalent bonds and in the C-H oxidative addition of benzene, suggesting that it could find further use in both metal-carbon and metal-metal bond-forming reactions.

Probing the reactivity of nucleophile residues in human 2,3-diphosphoglycerate/deoxy-hemoglobin complex by aspecific chemical modifications.

PubMed

Scaloni, A; Ferranti, P; De Simone, G; Mamone, G; Sannolo, N; Malorni, A

1999-06-11

The use of aspecific methylation reaction in combination with MS procedures has been employed for the characterization of the nucleophilic residues present on the molecular surface of the human 2,3-diphosphoglycerate/deoxy-hemoglobin complex. In particular, direct molecular weight determinations by ESMS allowed to control the reaction conditions, limiting the number of methyl groups introduced in the modified globin chains. A combined LCESMS-Edman degradation approach for the analysis of the tryptic peptide mixtures yielded to the exact identification of methylation sites together with the quantitative estimation of their degree of modification. The reactivities observed were directly correlated with the pKa and the relative surface accessibility of the nucleophilic residues, calculated from the X-ray crystallographic structure of the protein. The results here described indicate that this methodology can be efficiently used in aspecific modification experiments directed to the molecular characterization of the surface topology in proteins and protein complexes.

How Do Nutritional Antioxidants Really Work: Nucleophilic Tone and Para-Hormesis Versus Free Radical Scavenging in vivo

PubMed Central

Forman, Henry Jay; Davies, Kelvin J. A.; Ursini, Fulvio

2013-01-01

We present arguments for an evolution in our understanding of how antioxidants in fruits and vegetables exert their health-protective effects. There is much epidemiological evidence for disease prevention by dietary antioxidants and chemical evidence that such compounds react in one-electron reactions with free radicals in vitro. Nonetheless, kinetic constraints indicate that in vivo scavenging of radicals is ineffective in antioxidant defense. Instead, enzymatic removal of non-radical electrophiles, such as hydroperoxides, in two-electron redox reactions is the major antioxidant mechanism. Furthermore, we propose that a major mechanism of action for nutritional antioxidants is the paradoxical oxidative activation of the Nrf2 (NF-E2-related factor 2) signaling pathway, which maintains protective oxidoreductases and their nucleophilic substrates. This maintenance of ‘Nucleophilic Tone,’ by a mechanism that can be called ‘Para-Hormesis,’ provides a means for regulating physiological non-toxic concentrations of the non-radical oxidant electrophiles that boost antioxidant enzymes, and damage removal and repair systems (for proteins, lipids, and DNA), at the optimal levels consistent with good health. PMID:23747930

Organic Chemistry Students' Fragmented Ideas about the Structure and Function of Nucleophiles and Electrophiles: A Concept Map Analysis

ERIC Educational Resources Information Center

Anzovino, Mary E.; Bretz, Stacey Lowery

2016-01-01

Organic chemistry students struggle with multiple aspects of reaction mechanisms and the curved arrow notation used by organic chemists. Many faculty believe that an understanding of nucleophiles and electrophiles, among other concepts, is required before students can develop fluency with the electronpushing formalism (EPF). An expert concept map…

Direct sp(3)C-H acroleination of N-aryl-tetrahydroisoquinolines by merging photoredox catalysis with nucleophilic catalysis.

PubMed

Feng, Zhu-Jia; Xuan, Jun; Xia, Xu-Dong; Ding, Wei; Guo, Wei; Chen, Jia-Rong; Zou, You-Quan; Lu, Liang-Qiu; Xiao, Wen-Jing

2014-04-07

Sequence catalysis merging photoredox catalysis (PC) and nucleophilic catalysis (NC) has been realized for the direct sp(3) C-H acroleination of N-aryl-tetrahydroisoquinoline (THIQ). The reaction was performed under very mild conditions and afforded products in 50-91% yields. A catalytic asymmetric variant was proved to be successful with moderate enantioselectivities (up to 83 : 17 er).

Theoretical studies of the nucleophilic substitution of halides and amine at a sulfonyl center.

PubMed

Sung, Dae Dong; Kim, Tae Joon; Lee, Ikchoon

2009-06-25

Gas-phase nucleophilic substitution reactions, F(-) + CH(3)SO(2)F, Cl(-) + CH(3)SO(2)Cl, Cl(-) + CH(3)SO(2)F, and NH(3) + CH(3)SO(2)Cl, have been investigated at the B3LYP/6-311+G** and MP2/6-31+G* levels of theory. A very shallow well for the reaction intermediate in a triple-well potential energy surface (PES) was observed for the identity fluoride exchange, but double well PESs were obtained for the other three reactions with three different PES profiles. NBO analyses of the transition states showed substantial charge transfer interactions in all cases which provided a much larger amount of stabilization energy compared with the corresponding species at the carbon center of methyl halides. This difference is primarily caused by the strong electropositive nature of the sulfur center. The F-S-F axial linkage in the distorted TBP type intermediate in the identity fluoride exchange reaction exhibited a weak three-center, four-electron omega-bonding, which is considered to provide stability of the intermediate. All the reactant (RC) and product complexes (PC) have Cs symmetry. The symmetry plane bisects angles HCH (of methyl group), OSO (of sulfonyl group), and HNH (of ammonia). Vicinal charge transfer interactions between the two out-of-plane C-H, S-O, and N-H bonds provide extra stabilization to the ion-dipole complexes together with H-bond formation of in-plane H atom with the nucleophile and/or leaving group.

Covalent binding of aniline to humic substances. 2. 15N NMR studies of nucleophilic addition reactions

USGS Publications Warehouse

Thorn, K.A.; Pettigrew, P.J.; Goldenberg, W.S.; Weber, E.J.

1996-01-01

Aromatic amines are known to undergo covalent binding with humic substances in the environment. Although previous studies have examined reaction conditions and proposed mechanisms, there has been no direct spectroscopic evidence for the covalent binding of the amines to the functional groups in humic substances. In order to further elucidate the reaction mechanisms, the Suwannee River and IHSS soil fulvic and humic acids were reacted with 15N-labeled aniline at pH 6 and analyzed using 15N NMR spectrometry. Aniline underwent nucleophilic addition reactions with the quinone and other carbonyl groups in the samples and became incorporated in the form of anilinohydroquinone, anilinoquinone, anilide, imine, and heterocyclic nitrogen, the latter comprising 50% or more of the bound amine. The anilide and anilinohydroquinone nitrogens were determined to be susceptible to chemical exchange by ammonia. In the case of Suwannee River fulvic acid, reaction under anoxic conditions and pretreatment with sodium borohydride or hydroxylamine prior to reaction under oxic conditions resulted in a decrease in the proportion of anilinohydroquinone nitrogen incorporated. The relative decrease in the incorporation of anilinohydroquinone nitrogen with respect to anilinoquinone nitrogen under anoxic conditions suggested that inter- or intramolecular redox reactions accompanied the nucleophilic addition reactions.

The development of catalytic nucleophilic additions of terminal alkynes in water.

PubMed

Li, Chao-Jun

2010-04-20

One of the major research endeavors in synthetic chemistry over the past two decades is the exploration of synthetic methods that work under ambient atmosphere with benign solvents, that maximize atom utilization, and that directly transform natural resources, such as renewable biomass, from their native states into useful chemical products, thus avoiding the need for protecting groups. The nucleophilic addition of terminal alkynes to various unsaturated electrophiles is a classical (textbook) reaction in organic chemistry, allowing the formation of a C-C bond while simultaneously introducing the alkyne functionality. A prerequisite of this classical reaction is the stoichiometric generation of highly reactive metal acetylides. Over the past decade, our laboratory and others have been exploring an alternative, the catalytic and direct nucleophilic addition of terminal alkynes to unsaturated electrophiles in water. We found that various terminal alkynes can react efficiently with a wide range of such electrophiles in water (or organic solvent) in the presence of simple and readily available catalysts, such as copper, silver, gold, iron, palladium, and others. In this Account, we describe the development of these synthetic methods, focusing primarily on results from our laboratory. Our studies include the following: (i) catalytic reaction of terminal alkynes with acid chloride, (ii) catalytic addition of terminal alkynes to aldehydes and ketones, (iii) catalytic addition of alkynes to C=N bonds, and (iv) catalytic conjugate additions. Most importantly, these reactions can tolerate various functional groups and, in many cases, perform better in water than in organic solvents, clearly defying classical reactivities predicated on the relative acidities of water, alcohols, and terminal alkynes. We further discuss multicomponent and enantioselective reactions that were developed. These methods provide an alternative to the traditional requirement of separate steps in

Nucleophilic addition of Grignard reagents to 3-acylindoles: stereoselective synthesis of highly substituted indoline scaffolds.

PubMed

Wang, Lu; Shao, Yushang; Liu, Yuanhong

2012-08-03

3-Acylindoles undergo nucleophilic-type reactions with Grignard reagents to efficiently afford either cis- or trans-substituted indolines, depending on the different quenching procedures. The enolate intermediate could be trapped by aryl acyl chlorides to provide indolines bearing a quaternary carbon center with high stereoselectivity. In contrast, the use of benzyl bromide as an electrophile results in the fragmentation of the indole ring. The indoline products could be easily transformed into indoles through oxidation with DDQ in a one-pot manner.

Synthesis and characterization of a high-valent heterobimetallic [CuIII(μ-O)2NiIII]2+ core involving nucleophilic oxo groups**

PubMed Central

Kundu, Subrata; Pfaff, Florian Felix; Miceli, Enrico; Zaharieva, Ivelina; Herwig, Christian; Yao, Shenglai; Farquhar, Erik R.; Kuhlmann, Uwe; Bill, Eckhard; Hildebrandt, Peter; Dau, Holger

2014-01-01

A heterobimetallic CuNi bis(μ-oxo) diamond core is shown to possess nucleophilic oxo groups, and has been demonstrated for the first time as a viable intermediate during the deformylation of fatty aldehydes by cyanobacterial aldehyde decarbonylase. PMID:23589478

Performance study of magnesium-sulfur battery using a graphene based sulfur composite cathode electrode and a non-nucleophilic Mg electrolyte.

PubMed

Vinayan, B P; Zhao-Karger, Zhirong; Diemant, Thomas; Chakravadhanula, Venkata Sai Kiran; Schwarzburger, Nele I; Cambaz, Musa Ali; Behm, R Jürgen; Kübel, Christian; Fichtner, Maximilian

2016-02-14

Here we report for the first time the development of a Mg rechargeable battery using a graphene-sulfur nanocomposite as the cathode, a Mg-carbon composite as the anode and a non-nucleophilic Mg based complex in tetraglyme solvent as the electrolyte. The graphene-sulfur nanocomposites are prepared through a new pathway by the combination of thermal and chemical precipitation methods. The Mg/S cell delivers a higher reversible capacity (448 mA h g(-1)), a longer cyclability (236 mA h g(-1) at the end of the 50(th) cycle) and a better rate capability than previously described cells. The dissolution of Mg polysulfides to the anode side was studied by X-ray photoelectron spectroscopy. The use of a graphene-sulfur composite cathode electrode, with the properties of a high surface area, a porous morphology, a very good electronic conductivity and the presence of oxygen functional groups, along with a non-nucleophilic Mg electrolyte gives an improved battery performance.

Is nucleophilic cleavage chemistry practical for 4-membered heterocycles?

PubMed

Banks, Harold D

2009-11-07

A computational study at the MP2(Full)/6-311++G(d,p)//MP2(Full)/6-31+G(d) level of the ammonolysis of halogen substituted azetidines, oxetanes and thietanes was performed in the gas phase and in the commonly used solvent, acetonitrile. Using the free energy of activation of a benchmark reaction for evaluation of synthetic viability, several haloazetidines and oxetanes that possessed the required reactivity were identified; however, no substituted thietane investigated herein was determined to be synthetically useful under the mild conditions selected for this study. In the case of the azetidines, the side reaction of displacement of halide ion was determined to be the preferred reaction course in acetonitrile; however, the amino product of the reactions of the 2-haloazetidines cleaved at an acceptable rate under mild conditions. For the oxetane derivatives investigated, 2-fluorooxetane proved to be a direct source of ring cleavage product. Nucleophilic cleavage of halogen-substituted azetidines and oxetanes is predicted to be a viable source of functionalized three-carbon moieties under mild conditions in organic synthesis.

Nucleophilic Participation in the Solvolyses of (Arylthio)methyl Chlorides and Derivatives: Application of Simple and Extended Forms of the Grunwald-Winstein Equations

PubMed Central

Kevill, Dennis N.; Park, Young Hoon; Park, Byoung-Chun; D’Souza, Malcolm J.

2012-01-01

The specific rates of solvolysis of chloromethyl phenyl sulfide [(phenylthio)methyl chloride] and its p-chloro-derivative have been determined at 0.0 °C in a wide range of hydroxylic solvents, including several containing a fluroalcohol. Treatment in terms of a two-term Grunwald-Winstein equation, incorporating terms based on solvent ionizing power (YCl) and solvent nucleophilicity (NT) suggest a mechanism similar to that for the solvolyses of tert-butyl chloride, involving in the rate-determining step a nucleophilic solvation of the incipient carbocation in an ionization process. A previous suggestion, that a third-term governed by the aromatic ring parameter (I) is required, is shown both for the new and for the previously studied related substrates to be an artifact, resulting from an appreciable degree of multicollinearity between I values and a linear combination of NT and YCl values. PMID:22711999

Deuterium and oxygen-18 isotope effects on nucleophilic displacement by monomeric water in aprotic solvents

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kurz, J.L.; Lee, J.

1980-07-30

The H/sub 2/O/D/sub 2/O rate-constant ratio for nucleophilic attack by water at a methyl carbon (eq 1) is reduced to very near unity when the water is a dilute solute in L/sub 2/O+CH/sub 3/X..-->..L/sub 2/O/sup +/CH/sub 3/+X/sup -/ a dipolar aprotic solvent. This effect was observed for three leaving groups (CH/sub 3/X equals 1-methylthiophenium ion (MeTh/sup +/), methyl perchlorate (MeOCl/sub 3/), and methyl trifluoromethanesulfonate (MeOTf)) and for two aprotic solvents acetonitrile (MeCn), and tetrahydrothiophene 1,1-dioxide (TMSO:'';sulfolane). It was also observed that the corresponding H/sub 2//sup 16/O/H/sub 2//sup 18/O rate-constant ratio is 1.002 +- 0.004 (95% confidence limits) for the reactionmore » of MeTh/sup +/ with dilute H/sub 2/O in TMSO/sub 2/ at 35/sup 0/C. Although alternative explanations exist (vide infra), these observations are consistent with a mechanism in which no significant positive charge is present on the L/sub 2/O oxygen in the rate-determining transition state and thus in which the rate-determining process does not involve (and is not preceded by) any significant covalent-bonding interaction between the nucleophile and the methyl carbon. All reactions were followed by uv spectroscopy in a Cary 16K spectrophotometer.« less

Crystal Structures of Apo and Liganded 4-Oxalocrotonate Decarboxylase Uncover a Structural Basis for the Metal-Assisted Decarboxylation of a Vinylogous β-Keto Acid.

PubMed

Guimarães, Samuel L; Coitinho, Juliana B; Costa, Débora M A; Araújo, Simara S; Whitman, Christian P; Nagem, Ronaldo A P

2016-05-10

The enzymes in the catechol meta-fission pathway have been studied for more than 50 years in several species of bacteria capable of degrading a number of aromatic compounds. In a related pathway, naphthalene, a toxic polycyclic aromatic hydrocarbon, is fully degraded to intermediates of the tricarboxylic acid cycle by the soil bacteria Pseudomonas putida G7. In this organism, the 83 kb NAH7 plasmid carries several genes involved in this biotransformation process. One enzyme in this route, NahK, a 4-oxalocrotonate decarboxylase (4-OD), converts 2-oxo-3-hexenedioate to 2-hydroxy-2,4-pentadienoate using Mg(2+) as a cofactor. Efforts to study how 4-OD catalyzes this decarboxylation have been hampered because 4-OD is present in a complex with vinylpyruvate hydratase (VPH), which is the next enzyme in the same pathway. For the first time, a monomeric, stable, and active 4-OD has been expressed and purified in the absence of VPH. Crystal structures for NahK in the apo form and bonded with five substrate analogues were obtained using two distinct crystallization conditions. Analysis of the crystal structures implicates a lid domain in substrate binding and suggests roles for specific residues in a proposed reaction mechanism. In addition, we assign a possible function for the NahK N-terminal domain, which differs from most of the other members of the fumarylacetoacetate hydrolase superfamily. Although the structural basis for metal-dependent β-keto acid decarboxylases has been reported, this is the first structural report for that of a vinylogous β-keto acid decarboxylase and the first crystal structure of a 4-OD.

Synthesis of 6-alkyluridines from 6-cyanouridine via zinc(II) chloride-catalyzed nucleophilic substitution with alkyl Grignard reagents.

PubMed

Shih, Yu-Chiao; Yang, Ya-Ying; Lin, Chun-Chi; Chien, Tun-Cheng

2013-04-19

6-Cyanouracil derivatives underwent a direct nucleophilic substitution reaction with alkyl Grignard reagents in the presence of zinc(II) chloride as a catalyst to form the corresponding 6-alkyluracils. This methodology is applicable to sugar-protected 6-cyanouridine and 6-cyano-2'-deoxyuridine without the protection at the N(3)-imide and provides a facile and general access to versatile 6-alkyluracil and 6-alkyluridine derivatives.

Use of phosphoimidazolide-activated guanosine to investigate the nucleophilicity of spermine and spermidine

NASA Technical Reports Server (NTRS)

Kanavarioti, A.; Baird, E. E.; Smith, P. J.

1995-01-01

Guanosine 5'-phosphate 2-methylimidazolide (2-MeImpG), a labile phosphoimidazolide analog of guanosine triphosphate, was used to test the reactivity of the natural polyamines (PAs), spermine (spm) and spermidine (spd). The products are the guanosine 5'-phosphate-polyamine derivatives (PA-pG: spd-pG and spm-pG) which are quite stable in the range 4 < pH < 11. Our study is the first of which we are aware that reports on the nucleophilicity of these amines. The main findings are as follows. (i) HPLC analysis of the products indicates the formation of only two of the three possible spd products and only one of the two possible spm products. These results can be explained if only the primary amino groups of the two polyamines are reactive, while the secondary amino groups are rendered unreactive by a steric effect. The reactions of 2-MeImpG and other phosphoimidazolide derivatives of nucleosides (ImpNs) with primary and secondary monoamines support this interpretation (Kanavarioti et al. J. Org. Chem. 1995, 60, 632). (ii) The product ratio of the two spd-pG adducts derived from the primary amino groups varies between 2.40 and 0.71 in the range 6.1 < or equal to pH < or equal to 11.9. Such small variation in the product ratio can only be rationalized by the similar, but not identical, basicity of the two primary amino groups and provides strong support for a previously reported model for polyamine ionization (Onasch et. al. Biophys. Chem. 1984, 19, 245). (iii) On the basis of our kinetic determinations conditions at which the nucleophilicity of these amines is at a minimum and at which other interactions with ImpNs could be tested can be chosen.

Constructing a Catalytic Cycle for C-F to C-X (X = O, S, N) Bond Transformation Based on Gold-Mediated Ligand Nucleophilic Attack.

PubMed

Hu, Ji-Yun; Zhang, Jing; Wang, Gao-Xiang; Sun, Hao-Ling; Zhang, Jun-Long

2016-03-07

A tricoordinated gold(I) chloride complex, tBuXantphosAuCl, supported by a sterically bulky 9,9-dimethyl-4,5-bis(di-tert-butylphosphino)xanthene ligand (tBuXantphos) was synthesized. This complex features a remarkably longer Au-Cl bond length [2.632(1) Å] than bicoordinated linear gold complexes (2.27-2.30 Å) and tricoordinated XantphosAuCl [2.462(1) Å]. Single-crystal X-ray diffraction analysis of a cocrystal of tBuXantphosAuCl and pentafluoronitrobenzene (PFNB) and UV-vis spectroscopic titration experiments revealed the existence of an anion-π interaction between the Cl anion ligand and PFNB. Stoichiometric reaction between PFNB and tBuXantphosAuOtBu, after replacement of Cl by a more nucleophilic tBuO anion ligand, showed higher reactivity and para selectivity in the transformation of C-F to C-OtBu bond, distinctively different from that when only KOtBu was used (ortho selectivity) under the identical condition. Mechanistic studies including density functional theory calculations suggested a gold-mediated nucleophilic ligand attack of the C-F bond pathway via an SNAr process. On the basis of these results, using trimethylsilyl derivatives TMS-X (X = OMe, SEt, NEt2) as the nucleophilic ligand source and the fluorine acceptor, catalytic transformation of the C-F bond of aromatic substrates to the C-X (X = O, S, N) bond was achieved with tBuXantphosAuCl as the catalyst (up to 20 turnover numbers).

Oxidative cyclization reactions: controlling the course of a radical cation-derived reaction with the use of a second nucleophile.

PubMed

Redden, Alison; Perkins, Robert J; Moeller, Kevin D

2013-12-02

Construction of new ring systems: Oxidative cyclizations (see picture; RVC=reticulated vitreous carbon) have been conducted that use two separate intramolecular nucleophiles to trap an enol ether-derived radical cation intermediate. The reactions provide a means for rapidly trapping the radical cation intermediate in a manner that avoids competitive decomposition reactions. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Asymmetric nucleophilic monofluorobenzylation of carbonyl compounds: synthesis of enantiopure vic-fluorohydrins and α-fluorobenzylketones.

PubMed

Arroyo, Yolanda; Sanz-Tejedor, M Ascensión; Parra, Alejandro; García Ruano, José Luis

2012-04-23

Asymmetric nucleophilic monofluoroalkylation of a broad range of aldehydes with an α-fluoro-γ-sulfinylbenzyl carbanion takes place with complete control of the facial selectivity at the carbanion and good to high anti-diastereoselectivity to give easily separable mixtures of two optically pure 1,2-fluorohydrin derivatives (up to 24:1 anti/syn). Separation and removal of the p-tolylsulfinyl group with tBuLi provides enantiomerically pure anti-1,2-disubstituted-1,2-fluorohydrins, whereas α-fluorobenzylketones can be obtained by desulfinylation of the mixture followed by pyridinium chlorochromate oxidation (one-pot process). Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A colorimetric detection of acrylamide in potato chips based on nucleophile-initiated thiol-ene Michael addition.

PubMed

Hu, Qinqin; Fu, Yingchun; Xu, Xiahong; Qiao, Zhaohui; Wang, Ronghui; Zhang, Ying; Li, Yanbin

2016-02-07

Acrylamide (AA), a neurotoxin and a potential carcinogen, has been found in various thermally processed foods such as potato chips, biscuits, and coffee. Simple, cost-effective, and sensitive methods for the rapid detection of AA are needed to ensure food safety. Herein, a novel colorimetric method was proposed for the visual detection of AA based on a nucleophile-initiated thiol-ene Michael addition reaction. Gold nanoparticles (AuNPs) were aggregated by glutathione (GSH) because of a ligand-replacement, accompanied by a color change from red to purple. In the presence of AA, after the thiol-ene Michael addition reaction between GSH and AA with the catalysis of a nucleophile, the sulfhydryl group of GSH was consumed by AA, which hindered the subsequent ligand-replacement and the aggregation of AuNPs. Therefore, the concentration of AA could be determined by the visible color change caused by dispersion/aggregation of AuNPs. This new method showed high sensitivity with a linear range from 0.1 μmol L(-1) to 80 μmol L(-1) and a detection limit of 28.6 nmol L(-1), and especially revealed better selectivity than the fluorescence sensing method reported previously. Moreover, this new method was used to detect AA in potato chips with a satisfactory result in comparison with the standard methods based on chromatography, which indicated that the colorimetric method can be expanded for the rapid detection of AA in thermally processed foods.

An Unusual Salt Effect in an Interfacial Nucleophilic Substitution Reaction.

PubMed

Li, Shuheng; Mrksich, Milan

2018-06-12

This paper reports a kinetic characterization of the interfacial reaction of N-methylpyrrolidine with a self-assembled monolayer presenting an iodoalkyl group. SAMDI (self-assembled monolayers for matrix-assisted laser desorption/ionization) mass spectrometry was used to determine the extent of reaction for monolayers that were treated with a range of concentrations of the nucleophile for a range of times. These data revealed a second-order rate constant for the reaction that was approximately 100-fold greater than that for the analogous solution-phase reaction. However, addition of sodium iodide to the reaction mixture resulted in a 7-fold decrease in the reaction rate. Addition of bromide and chloride salts also gave slower rate constants for the reaction, but only at 100- and 1000-fold higher concentrations than was observed with iodide, respectively. The corresponding solution-phase reactions, by contrast, had rate constants that were unaffected by the concentration of halide salts. This work provides a well-characterized example illustrating the extent to which the kinetics and properties of an interfacial reaction can depart substantially from their better-understood solution-phase counterparts.

Nucleophilic substitution rates and solubilities for methyl halides in seawater

NASA Astrophysics Data System (ADS)

Elliott, Scott; Rowland, F. Sherwood

1993-06-01

Ozone depletion potentials indicate that methyl bromide is among halogen containing gases which may be scheduled for international level regulation. The oceanic component of its global budget is currently unquantifiable because of a lack of surface seawater measurements. Given values for internal removal and for solubility, marine mixed layer modelling can set bounds for air-sea transfer. Rate constants have been measured in seawater, 0.5m NaCl and distilled water for attack on methyl bromide by the chief oceanic nucleophiles chloride ion and H2O, over much of the oceanographic temperature range (0°C to 22°C). Henry's Law constants have been determined for the same conditions. All results are consistent with classical aqueous phase research adjusted for ionic strength effects. The lifetime of methyl bromide with respect to chemical decay in seawater is three weeks at average surface temperatures, and a factor of ten larger and smaller at the extremes. Its dimensionless solubility ranges from 0.1 to 0.3. Analogous experiments are reported for the other natural methyl halides, CH3Cl and CH3I.

In situ nucleophilic substitutional growth of methylammonium lead iodide polycrystals.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Acik, Muge; Alam, Todd M.; Guo, Fangmin

2017-01-01

Methylammonium lead iodide (MAPbIx) perovskites are organic-inorganic semiconductors that serve as the light-harvesting component of the photovoltaics, and are desirable with their long diffusion length yielding power conversion efficiencies of ≥22%. Conventional techniques grow perovskites by spin coating precursors on an oxide or a polymer substrate followed by annealing, however, use of high boiling point solvents and high temperatures hinder device stability and performance. Through a one-step, acid-catalyzed nucleophilic-substitutional crystal growth in polar protic solvents, we show evidence for the substrate- and annealing- free production of MAPbIx polycrystals that are metallic-lead-free with negligibly small amount of PbI2 precipitation (<10%). Onmore » the basis of this chemical composition, we have devised an in situ growth of highly air (upto ~1.5 months) and thermally-stable (≤300°C), tetragonal-phased, variable-sized polycrystals (~100 nm-10 μm) amendable for large-area deposition, and ultimately, large-scale manufacturing. This method is encouraging for stable optoelectronic devices, and leads to energy-efficient and low-cost processing.« less

Nucleophilic catalysis of acylhydrazone equilibration for protein-directed dynamic covalent chemistry

PubMed Central

Bhat, Venugopal T.; Caniard, Anne M.; Luksch, Torsten; Brenk, Ruth; Campopiano, Dominic J.; Greaney, Michael F.

2010-01-01

Dynamic covalent chemistry uses reversible chemical reactions to set up an equilibrating network of molecules at thermodynamic equilibrium, which can adjust its composition in response to any agent capable of altering the free energy of the system. When the target is a biological macromolecule, such as a protein, the process corresponds to the protein directing the synthesis of its own best ligand. Here, we demonstrate that reversible acylhydrazone formation is an effective chemistry for biological dynamic combinatorial library formation. In the presence of aniline as a nucleophilic catalyst, dynamic combinatorial libraries equilibrate rapidly at pH 6.2, are fully reversible, and may be switched on or off by means of a change in pH. We have interfaced these hydrazone dynamic combinatorial libraries with two isozymes from the glutathione S-transferase class of enzyme, and observed divergent amplification effects, where each protein selects the best-fitting hydrazone for the hydrophobic region of its active site. PMID:20489719

Electron transfer from nucleophilic species to N,N,N prime ,N prime -tetramethylbenzidine cation in micellar media: Effect of interfacial electrical potential on cation decay

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grand, D.; Hautecloque, S.

1990-01-25

Electron-transfer reaction between N,N,N{prime},N{prime}-tetramethylbenzidine cation (TMB{sup +}) and neutral nucleophiles, pyridine (Py) and triethylamine (Et{sub 3}N), is studied in NaLS micellar media. A biphasic decay of TMB{sup +} follows the laser-induced TMB photoionization. The very fast decay is attributed to an electron transfer between reactants located in the core of the micelle. The slow decay would correspond to an electron transfer from the nucleophile solubilized in the aqueous phase to TMB{sup +} embedded in the lipidic phase. The role of the electrical interfacial potential {Delta}{psi} is evidenced. The rate constant of the TMB{sup +} slow decay displays an exponential functionmore » of {Delta}{psi}. The effect of the localization and distance of the reactants is emphasized.« less

Nucleophilic modification of human complement protein C3: correlation of conformational changes with acquisition of C3b-like functional properties.

PubMed

Isenman, D E; Kells, D I; Cooper, N R; Müller-Eberhard, H J; Pangburn, M K

1981-07-21

Inactivation of C3 by enzymatic cleavage, nucleophilic addition, or slow freezing and thawing resulted in the acquisition of similar end-state conformations as judged by near-UV circular dichroism. Although inactivation by the two nonenzymatic processes involves no peptide bond scission, the inactivated C3 resembled C3b in that it possessed a free sulfhydryl group not present in the native protein and an increased surface hydrophobicity as evidenced by enhanced binding of the fluorophore 8-anilino-1-naphthalensulfonate (ANS). The C3b-like functional properties of modified C3 [Pangburn, M. K., & Müller-Eberhard, H. J. (1980) J. Exp. Med. 152, 1102-1114] may thus be understood in terms of the similarity of its conformation to that of C3b. The rate of the conformational change following proteolytic cleavage was fast and appeared to be limited by the rate of the enzymatic reaction. In contrast, the rate of conformational change following addition of methylamine was slow and rate limited by the conformational rearrangement itself, not by the chemical modification. A kinetic analysis of the changes in circular dichroism and ANS fluorescence enhancement suggested that the nucleophilic addition was spectroscopically undetectable and was followed by a minimally biphasic, spectroscopically demonstrable conformational rearrangement. The appearance of C3b-like functional activity in nucleophile-modified C3 largely parallels the time course of the spectroscopically detectable conformational change but is distinctly slower than the rate at which hemolytic activity is lost. While fully transconformed methylamine-inactivated C3 can bind factor B and is susceptible to cleavage by C3b inactivator and its cofactor beta 1H, this cleavage occurs at a substantially slower rate than the equivalent process in C3b. The implications of these findings in terms of the mechanism through which the alterative pathway of complement is initiated are discussed.

Replacing Conventional Carbon Nucleophiles with Electrophiles: Nickel-Catalyzed Reductive Alkylation of Aryl Bromides and Chlorides

PubMed Central

2012-01-01

A general method is presented for the synthesis of alkylated arenes by the chemoselective combination of two electrophilic carbons. Under the optimized conditions, a variety of aryl and vinyl bromides are reductively coupled with alkyl bromides in high yields. Under similar conditions, activated aryl chlorides can also be coupled with bromoalkanes. The protocols are highly functional-group tolerant (−OH, −NHTs, −OAc, −OTs, −OTf, −COMe, −NHBoc, −NHCbz, −CN, −SO2Me), and the reactions are assembled on the benchtop with no special precautions to exclude air or moisture. The reaction displays different chemoselectivity than conventional cross-coupling reactions, such as the Suzuki–Miyaura, Stille, and Hiyama–Denmark reactions. Substrates bearing both an electrophilic and nucleophilic carbon result in selective coupling at the electrophilic carbon (R–X) and no reaction at the nucleophilic carbon (R–[M]) for organoboron (−Bpin), organotin (−SnMe3), and organosilicon (−SiMe2OH) containing organic halides (X–R–[M]). A Hammett study showed a linear correlation of σ and σ(−) parameters with the relative rate of reaction of substituted aryl bromides with bromoalkanes. The small ρ values for these correlations (1.2–1.7) indicate that oxidative addition of the bromoarene is not the turnover-frequency determining step. The rate of reaction has a positive dependence on the concentration of alkyl bromide and catalyst, no dependence upon the amount of zinc (reducing agent), and an inverse dependence upon aryl halide concentration. These results and studies with an organic reductant (TDAE) argue against the intermediacy of organozinc reagents. PMID:22463689

Dechlorination of chloropicrin and 1,3-dichloropropene by hydrogen sulfide species: redox and nucleophilic substitution reactions.

PubMed

Zheng, Wei; Yates, Scott R; Papiernik, Sharon K; Guo, Mingxin; Gan, Jianying

2006-03-22

The chlorinated fumigants chloropicrin (trichloronitromethane) and 1,3-dichloropropene (1,3-D) are extensively used in agricultural production for the control of soilborne pests. The reaction of these two fumigants with hydrogen sulfide species (H2S and HS-) was examined in well-defined anoxic aqueous solutions. Chloropicrin underwent an extremely rapid redox reaction in the hydrogen sulfide solution. Transformation products indicated reductive dechlorination of chloropicrin by hydrogen sulfide species to produce dichloro- and chloronitromethane. The transformation of chloropicrin in hydrogen sulfide solution significantly increased with increasing pH, indicating that H2S is less reactive toward chloropicrin than HS- is. For both 1,3-D isomers, kinetics and transformation products analysis revealed that the reaction between 1,3-D and hydrogen sulfide species is an S(N)2 nucleophilic substitution process, in which the chlorine at C3 of 1,3-D is substituted by the sulfur nucleophile to form corresponding mercaptans. The 50% disappearance time (DT50) of 1,3-D decreased with increasing hydrogen sulfide species concentration at a constant pH. Transformation of 1,3-D was more rapid at high pH, suggesting that the reactivity of hydrogen sulfide species in the experimental system stems primarily from HS-. Because of the relatively low smell threshold values and potential environmental persistence of organic sulfur products yielded by the reaction of 1,3-D and HS-, the effects of reduced sulfide species should be considered in the development of alternative fumigation practices, especially in the integrated application of sulfur-containing fertilizers.

Determining the transition-state structure for different SN2 reactions using experimental nucleophile carbon and secondary alpha-deuterium kinetic isotope effects and theory.

PubMed

Westaway, Kenneth C; Fang, Yao-ren; MacMillar, Susanna; Matsson, Olle; Poirier, Raymond A; Islam, Shahidul M

2008-10-16

Nucleophile (11)C/ (14)C [ k (11)/ k (14)] and secondary alpha-deuterium [( k H/ k D) alpha] kinetic isotope effects (KIEs) were measured for the S N2 reactions between tetrabutylammonium cyanide and ethyl iodide, bromide, chloride, and tosylate in anhydrous DMSO at 20 degrees C to determine whether these isotope effects can be used to determine the structure of S N2 transition states. Interpreting the experimental KIEs in the usual fashion (i.e., that a smaller nucleophile KIE indicates the Nu-C alpha transition state bond is shorter and a smaller ( k H/ k D) alpha is found when the Nu-LG distance in the transition state is shorter) suggests that the transition state is tighter with a slightly shorter NC-C alpha bond and a much shorter C alpha-LG bond when the substrate has a poorer halogen leaving group. Theoretical calculations at the B3LYP/aug-cc-pVDZ level of theory support this conclusion. The results show that the experimental nucleophile (11)C/ (14)C KIEs can be used to determine transition-state structure in different reactions and that the usual method of interpreting these KIEs is correct. The magnitude of the experimental secondary alpha-deuterium KIE is related to the nucleophile-leaving group distance in the S N2 transition state ( R TS) for reactions with a halogen leaving group. Unfortunately, the calculated and experimental ( k H/ k D) alpha's change oppositely with leaving group ability. However, the calculated ( k H/ k D) alpha's duplicate both the trend in the KIE with leaving group ability and the magnitude of the ( k H/ k D) alpha's for the ethyl halide reactions when different scale factors are used for the high and the low energy vibrations. This suggests it is critical that different scaling factors for the low and high energy vibrations be used if one wishes to duplicate experimental ( k H/ k D) alpha's. Finally, neither the experimental nor the theoretical secondary alpha-deuterium KIEs for the ethyl tosylate reaction fit the trend found

Formation of difluorothionoacetyl-protein adducts by S-(1,1,2,2-tetrafluoroethyl)-L-cysteine metabolites: Nucleophilic catalysis of stable lysyl adduct formation by histidine and tyrosine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hayden, P.J.; McCann, D.J.; Stevens, J.L.

1991-06-18

{sup 19}F NMR spectorscopy was used in conjunction with isotopic labeling to demonstrate that difluorothionoacetyl-protein adducts are formed by metabolites of the nephrotoxic cysteine conjugate S(1,1,2,2-tetrafluoroethyl)-L-cysteine (TFEC). To determine which amino acid residues can be involved in adduct formation, the reactivity of TFEC metabolites with a variety of N-acetyl amino acids was also investigated. An N{sup {alpha}}-acetyl-N{sup {epsilon}}-(difluorothionoacetyl)lysine (DFTAL) adduct was isolated and characterized by {sup 19}F and {sup 13}C NMR spectroscopy and mass spectrometry. N{sup {alpha}}-Acetylhistidine and N-acetyltyrosine were found to act as nucleophilic catalysts to facilitate the formation of both the protein and DFTAL adducts. Adduct formation wasmore » greatly reduced when lysyl-modified protein was used as the substrate, indicating that lysyl residues are primary sites of adduct formation. However, N{sup a}-acetyllysine, at concentrations of >100-fold in excess compared to protein lysyl residues, was not effective in preventing binding of metabolites to protein. Therefore, nucleophilic catalysis at the surface of the protein may be an important mechanism for the binding of TFEC metabolites to specific lysyl residues in protein. TFEC metabolites were very reactive with the thiol nucleophiles glutathione and N-acetylcysteine. However, the predicted difluorodithioesters could not be isolated. Bothe stable difluorothioacetamide and less stable difluorodithioester protein adducts may play a role in TFEC-mediated enphrotoxicity.« less

Deuterium and oxygen-18 isotope effects on nucleophilic displacement by water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, J.

1981-01-01

Kinetic deuterium isotope effects (k/sub H/sub 2/O//k/sub D/sub 2/O/) have been measured for nucleophilic attack by water at primary alkyl carbon (S-methylthiophenium ion (MeTh+), methyl trifluoromethane-sulfonate (MeOTf), methyl and ethyl perchlorate (MeOClO/sub 3/, EtOClO/sub 3/)) in aprotic solvents (acetonitrile (MeCN) and tetrahydrothiophene-1, 1-dioxide (TMSO/sub 2/; solfolane)) and L/sub 2/O. In L/sub 2/O solvent k/sub H/sub 2/O//k/sub D/sub 2/O/ is significantly greater than unity while it is reduced to near unity in aprotic solvents. The oxygen-18 isotope effect has also been observed to be 1.002 +- 0.004 for the reaction of MeTh/sup +/ with dilute H/sub 2/O in TMSO/sub 2/ atmore » 35/sup 0/C. For the reaction of MeTh/sup +/ and MeOClO/sub 3/ in aprotic solvents the chemical reaction kinetics are discussed.« less

Nucleophilic substitution between polysulfides and binders unexpectedly stabilizing lithium sulfur battery

DOE PAGES

Ling, Min; Zhang, Liang; Zheng, Tianyue; ...

2017-05-10

Polysulfide shuttling has been the primary cause of failure in lithium-sulfur (Li-S) battery cycling. In this paper, we demonstrate an nucleophilic substitution reaction between polysulfides and binder functional groups can unexpectedly immobilizes the polysulfides. The substitution reaction is verified by UV–visible spectra and X-ray photoelectron spectra. The immobilization of polysulfide is in situ monitored by synchrotron based sulfur K-edge X-ray absorption spectra. The resulting electrodes exhibit initial capacity up to 20.4 mAh/cm 2, corresponding to 1199.1 mAh/g based on a micron-sulfur mass loading of 17.0 mg/cm 2. The micron size sulfur transformed into nano layer coating on the cathode bindermore » during cycling. Directly usage of nano-size sulfur promotes higher capacity of 33.7 mAh/cm 2, which is the highest areal capacity reported in Li-S battery. Finally, this enhance performance is due to the reduced shuttle effect by covalently binding of the polysulfide with the polymer binder.« less

Nucleophilic substitution between polysulfides and binders unexpectedly stabilizing lithium sulfur battery

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ling, Min; Zhang, Liang; Zheng, Tianyue

Polysulfide shuttling has been the primary cause of failure in lithium-sulfur (Li-S) battery cycling. In this paper, we demonstrate an nucleophilic substitution reaction between polysulfides and binder functional groups can unexpectedly immobilizes the polysulfides. The substitution reaction is verified by UV–visible spectra and X-ray photoelectron spectra. The immobilization of polysulfide is in situ monitored by synchrotron based sulfur K-edge X-ray absorption spectra. The resulting electrodes exhibit initial capacity up to 20.4 mAh/cm 2, corresponding to 1199.1 mAh/g based on a micron-sulfur mass loading of 17.0 mg/cm 2. The micron size sulfur transformed into nano layer coating on the cathode bindermore » during cycling. Directly usage of nano-size sulfur promotes higher capacity of 33.7 mAh/cm 2, which is the highest areal capacity reported in Li-S battery. Finally, this enhance performance is due to the reduced shuttle effect by covalently binding of the polysulfide with the polymer binder.« less

Heterobimetallic Pd-Sn catalysis: Michael addition reaction with C-, N-, O-, and S-nucleophiles and in situ diagnostics.

PubMed

Das, Debjit; Pratihar, Sanjay; Roy, Sujit

2013-03-15

An efficient Michael addition reaction of differently substituted enones with carbon, sulfur, oxygen, and nitrogen nucleophiles has been achieved by a new heterobimetallic "Pd-Sn" catalyst system. The nature of the catalytically relevant species and their interactions with the enone moiety has been examined by spectroscopy. The effect of ligand and the coordination mode of enone with "Pd-Sn" heterobimetallic system have been investigated by kinetics and DFT studies. A straightforward application of this methodology is shown in the synthesis of 1,4-oxathiepane core.

Subclass-specific labeling of protein-reactive natural products with customized nucleophilic probes.

PubMed

Rudolf, Georg C; Koch, Maximilian F; Mandl, Franziska A M; Sieber, Stephan A

2015-02-23

Natural products represent a rich source of bioactive compounds that constitute a large fraction of approved drugs. Among those are molecules with electrophilic scaffolds, such as Michael acceptors, β-lactams, and epoxides that irreversibly inhibit essential enzymes based on their catalytic mechanism. In the search for novel bioactive molecules, current methods are challenged by the frequent rediscovery of known chemical entities. Herein small nucleophilic probes that attack electrophilic natural products and enhance their detection by HPLC-UV and HPLC-MS are introduced. A screen of diverse probe designs revealed one compound with a desired selectivity for epoxide- and maleimide-based antibiotics. Correspondingly, the natural products showdomycin and phosphomycin could be selectively targeted in extracts of their natural producing organism, in which the probe-modified molecules exhibited superior retention and MS detection relative to their unmodified counterparts. This method may thus help to discover small, electrophilic molecules that might otherwise easily elude detection in complex samples. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Heterobimetallic Catalysis: Platinum-Gold-Catalyzed Tandem Cyclization/C-X Coupling Reaction of (Hetero)Arylallenes with Nucleophiles.

PubMed

Alonso, José Miguel; Muñoz, María Paz

2018-04-16

Heterobimetallic catalysis offers new opportunities for reactivity and selectivity but still presents challenges, and only a few metal combinations have been explored so far. Reported here is a Pt-Au heterobimetallic catalyst system for the synthesis of a family of multi-heteroaromatic structures through tandem cyclization/C-X coupling reaction. Au-catalyzed 6-endo-cyclization takes place as the first fast step. Pt-Au clusters are proposed to be responsible for the increased reactivity in the second step, that is, the intermolecular nucleophilic addition which occurs through an outer-sphere mechanism by hybrid homogeneous-heterogeneous catalysis. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Tandem SN2' nucleophilic substitution/oxidative radical cyclization of aryl substituted allylic alcohols with 1,3-dicarbonyl compounds.

PubMed

Zhang, Zhen; Li, Cheng; Wang, Shao-Hua; Zhang, Fu-Min; Han, Xue; Tu, Yong-Qiang; Zhang, Xiao-Ming

2017-04-11

A novel and efficient tandem S N 2' nucleophilic substitution/oxidative radical cyclization reaction of aryl substituted allylic alcohols with 1,3-dicarbonyl compounds has been developed by using Mn(OAc) 3 as an oxidant, which enables the expeditious synthesis of polysubstituted dihydrofuran (DHF) derivatives in moderate to high yields. The use of weakly acidic hexafluoroisopropanol (HFIP) as the solvent rather than AcOH has successfully improved the yields and expanded the substrate scope of this type of radical cyclization reactions. Mechanistic studies confirmed the cascade reaction process involving a final radical cyclization.

Stereocontrolled generation of nucleophilic (Z)- or (E)-α-fluoroalkenylchromium reagents via carbon-fluorine bond activation: highly stereoselective synthesis of (E)- or (Z)-β-fluoroallylic alcohols.

PubMed

Nihei, Takashi; Yokotani, Saya; Ishihara, Takashi; Konno, Tsutomu

2014-02-14

Highly nucleophilic (Z)- or (E)-α-fluoroalkenylchromium species could be generated in a stereoselective manner via C-F bond activation of CBrF2-containing molecules, and they reacted smoothly with various aldehydes to give (E)- or (Z)-β-fluoroallylic alcohol derivatives in high yields, respectively.

Tandem Cu-catalyzed ketenimine formation and intramolecular nucleophile capture: Synthesis of 1,2-dihydro-2-iminoquinolines from 1-(o-acetamidophenyl)propargyl alcohols

PubMed Central

Kant, Ruchir

2014-01-01

Summary The copper-catalyzed ketenimine formation reaction of 1-(o-acetamidophenyl)propargyl alcohols with various sulfonyl azides is found to undergo a concomitant intramolecular nucleophile attack to generate 1,2-dihydro-2-iminoquinolines after aromatization (via elimination of acetyl and hydroxy groups) and tautomerization. The reaction produces 4-substituted and 3,4-unsubstituted title compounds in moderate to good yields under mild reaction conditions. PMID:24991276

Temperature-dependent regioselectivity of nucleophilic aromatic photosubstitution. Evidence that activation energy controls reactivity.

PubMed

Wubbels, Gene G; Tamura, Ryo; Gannon, Emmett J

2013-05-17

Irradiation (λ > 330 nm) of 2-chloro-4-nitroanisole (1) at 25 °C in aqueous NaOH forms three substitution photoproducts: 2-methoxy-5-nitrophenol (2), 2-chloro-4-nitrophenol (3), and 3-chloro-4-methoxyphenol (4), in chemical yields of 69.2%, 14.3%, and 16.5%. The activation energies for the elementary steps from the triplet state at 25 °C were determined to be 1.8, 2.4, and 2.7 kcal/mol, respectively. The chemical yields of each of the three products were determined for exhaustive irradiations at 0, 35, and 70 °C. The variation with temperature of the experimental yields is reproduced almost exactly by the yields calculated with the Arrhenius equation. This indicates that activation energy is the fundamental property related to regioselectivity in nucleophilic aromatic photosubstitution of the S(N)2 Ar* type. The many methods proposed for predicting regioselectivity in reactions of this type have had limited success and have not been related to activation energy.

First example of a heterobimetallic 'Pd-Sn' catalyst for direct activation of alcohol: efficient allylation, benzylation and propargylation of arenes, heteroarenes, active methylenes and allyl-Si nucleophiles.

PubMed

Das, Debjit; Pratihar, Sanjay; Roy, Ujjal Kanti; Mal, Dipakranjan; Roy, Sujit

2012-06-21

Arenes, heteroarenes, 1,3-dicarbonyls and organosilicon nucleophiles undergo highly efficient alkylation with allylic, propargylic and benzylic alcohols in the presence of a new 'Pd-Sn' bimetallic catalyst in nitromethane; water being the sole byproduct. The plausible mechanism of alkylation and the intermediacy of ether has been enumerated.

Nucleophilic stabilization of water-based reactive ink for titania-based thin film inkjet printing

NASA Astrophysics Data System (ADS)

Gadea, C.; Marani, D.; Esposito, V.

2017-02-01

Drop on demand deposition (DoD) of titanium oxide thin films (<500 nm) is performed via a novel titanium-alkoxide-based solution that is tailored as a reactive ink for inkjet printing. The ink is developed as water-based solution by a combined use of titanium isopropoxide and n-methyldiethanolamine (MDEA) used as nucleophilic ligand. The function of the ligand is to control the fast hydrolysis/condensation reactions in water for the metal alkoxide before deposition, leading to formation of the TiO2 only after the jet process. The evolution of the titanium-ligand interactions at increasing amount of MDEA is here elucidated in terms of long term stability. The ink printability parameter (Z) is optimized, resulting in a reactive solution with printability, Z, >1, and chemical stability up to 600 h. Thin titanium oxide films (<500 nm) are proved on different substrates. Pure anatase phase is obtained after annealing at low temperature (ca. 400 °C).

Substituents on Quinone Methides Strongly Modulate Formation and Stability of Their Nucleophilic Adducts

PubMed Central

Weinert, Emily E.; Dondi, Ruggero; Colloredo-Melz, Stefano; Frankenfield, Kristen N.; Mitchell, Charles H.; Freccero, Mauro; Rokita, Steven E.

2008-01-01

Electronic perturbation of quinone methides (QM) greatly influences their stability and in turn alters the kinetics and product profile of QM reaction with deoxynucleosides. Consistent with the electron deficient nature of this reactive intermediate, electron-donating substituents are stabilizing and electron-withdrawing substituents are destabilizing. For example, a dC N3-QM adduct is made stable over the course of observation (7 days) by the presence of an electron-withdrawing ester group that inhibits QM regeneration. Conversely, a related adduct with an electron donating methyl group is very labile and regenerates its QM with a half-life of approximately 5 hr. The generality of these effects is demonstrated with a series of alternative quinone methide precursors (QMP) containing a variety of substituents attached at different positions with respect to the exocyclic methylene. The rates of nucleophilic addition to substituted QMs measured by laser flash photolysis similarly span five orders of magnitude with electron rich species reacting most slowly and electron deficient species reacting most quickly. The reversibility of QM reaction can now be predictably adjusted for any desired application. PMID:16953635

Iminoboronate Formation Leads to Fast and Reversible Conjugation Chemistry of α-Nucleophiles at Neutral pH

PubMed Central

Bandyopadhyay, Anupam

2015-01-01

Bioorthogonal reactions that are fast and reversible under physiologic conditions are in high demand for biological applications. Herein, we show that an ortho boronic acid substituent makes aryl ketones to rapidly conjugate with α-nucleophiles at neutral pH. Specifically, 2-acetylphenylboronic acid and derivatives were found to conjugate with phenylhydrazine with rate constants of 102 to 103 M−1 s−1, comparable to the fastest bioorthogonal conjugations known to date. 11B-NMR analysis reveals varied extent of iminoboronate formation of the conjugates, in which the imine nitrogen forms a dative bond with boron. The iminoboronate formation activates the imines for hydrolysis and exchange, rendering these oxime/hydrazone conjugations reversible and dynamic under physiologic conditions. The fast and dynamic nature of the iminoboronate chemistry should find wide applications in biology. PMID:26311464

Nucleophilic addition of nitrogen to aryl cations: mimicking Titan chemistry.

PubMed

Li, Anyin; Jjunju, Fred P M; Cooks, R Graham

2013-11-01

The reactivity of aryl cations toward molecular nitrogen is studied systematically in an ion trap mass spectrometer at 10(2) Pascal of nitrogen, the pressure of the Titan main haze layer. Nucleophilic addition of dinitrogen occurs and the nature of aryl group has a significant influence on the reactivity, through inductive effects and by changing the ground state spin multiplicity. The products of nitrogen activation, aryldiazonium ions, react with typical nitriles, aromatic amines, and alkynes (compounds that are relevant as possible Titan atmosphere constituents) to form covalently bonded heterocyclic products. Theoretical calculations at the level [DFT(B3LYP)/6-311++G(d,p)] indicate that the N2 addition reaction is exothermic for the singlet aryl cations but endothermic for their triplet spin isomers. The -OH and -NH2 substituted aryl ions are calculated to have triplet ground states, which is consistent with their decreased nitrogen addition reactivity. The energy needed for the generation of the aryl cations from their protonated precursors (ca. 340 kJ/mol starting with protonated aniline) is far less than that required to directly activate the nitrogen triple bond (the lowest energy excited state of N2 lies ca. 600 kJ/mol above the ground state). The formation of aza-aromatics via arene ionization and subsequent reactions provide a conceivable route to the genesis of nitrogen-containing organic molecules in the interstellar medium and Titan haze layers.

Mechanism of Oxidative Amidation of Nitroalkanes with Oxygen and Amine Nucleophiles by Using Electrophilic Iodine.

PubMed

Li, Jing; Lear, Martin J; Kwon, Eunsang; Hayashi, Yujiro

2016-04-11

Recently, we developed a direct method to oxidatively convert primary nitroalkanes into amides that entailed mixing an iodonium source with an amine, base, and oxygen. Herein, we systematically investigated the mechanism and likely intermediates of such methods. We conclude that an amine-iodonium complex first forms through N-halogen bonding. This complex reacts with aci-nitronates to give both α-iodo- and α,α-diiodonitroalkanes, which can act as alternative sources of electrophilic iodine and also generate an extra equimolar amount of I(+) under O2. In particular, evidence supports α,α-diiodonitroalkane intermediates reacting with molecular oxygen to form a peroxy adduct; alternatively, these tetrahedral intermediates rearrange anaerobically to form a cleavable nitrite ester. In either case, activated esters are proposed to form that eventually reacts with nucleophilic amines in a traditional fashion. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

N-Allyl-N-Sulfonyl Ynamides as Synthetic Precursors to Amidines and Vinylogous Amidines. An Unexpected N-to-C 1,3-Sulfonyl Shift in Nitrile Synthesis

PubMed Central

DeKorver, Kyle A.; Johnson, Whitney L.; Zhang, Yu; Hsung, Richard P.; Dai, Huifang; Deng, Jun; Lohse, Andrew G.; Zhang, Yan-Shi

2011-01-01

A detailed study of amidine synthesis from N-allyl-N-sulfonyl ynamides is described here. Mechanistically, this is a fascinating reaction consisting of diverging pathways that could lead to deallylation or allyl transfer depending upon the oxidation state of palladium catalysts, the nucleophilicity of amines, and the nature of the ligands. It essentially constitutes a Pd(0)-catalyzed aza-Claisen rearrangement of N-allyl ynamides, which can also be accomplished thermally. An observation of N-to-C 1,3-sulfonyl shift was made when examining these aza-Claisen rearrangements thermally. This represents a useful approach to nitrile synthesis. While attempts to render this 1,3-sulfonyl shift stereoselective failed, we uncovered another set of tandem sigmatropic rearrangements, leading to vinyl imidate formation. Collectively, this work showcases the rich array of chemistry one can discover using these ynamides. PMID:21563776

A quantum chemical study of molecular properties and QSPR modeling of oximes, amidoximes and hydroxamic acids with nucleophilic activity against toxic organophosphorus agents

NASA Astrophysics Data System (ADS)

Alencar Filho, Edilson B.; Santos, Aline A.; Oliveira, Boaz G.

2017-04-01

The proposal of this work includes the use of quantum chemical methods and cheminformatics strategies in order to understand the structural profile and reactivity of α-nucleophiles compounds such as oximes, amidoximes and hydroxamic acids, related to hydrolysis rate of organophosphates. Theoretical conformational study of 41 compounds were carried out through the PM3 semiempirical Hamiltonian, followed by the geometry optimization at the B3LYP/6-31+G(d,p) level of theory, complemented by Polarized Continuum Model (PCM) to simulate the aqueous environment. In line with the experimental hypothesis about hydrolytic power, the strength of the Intramolecular Hydrogen Bonds (IHBs) at light of the Bader's Quantum Theory of Atoms in Molecules (QTAIM) is related to the preferential conformations of α-nucleophiles. A set of E-Dragon descriptors (1,666) were submitted to a variable selection through Ordered Predictor Selection (OPS) algorithm. Five descriptors, including atomic charges obtained from the Natural Bond Orbitals (NBO) protocol jointly with a fragment index associated to the presence/absence of IHBs, provided a Quantitative Structure-Property Relationship (QSPR) model via Multiple Linear Regression (MLR). This model showed good validation parameters (R2 = 0.80, Qloo2 = 0.67 and Qext2 = 0.81) and allowed the identification of significant physicochemical features on the molecular scaffold in order to design compounds potentially more active against organophosphorus poisoning.

A Catalytic Mechanism for Cysteine N-Terminal Nucleophile Hydrolases, as Revealed by Free Energy Simulations

PubMed Central

Lodola, Alessio; Branduardi, Davide; De Vivo, Marco; Capoferri, Luigi; Mor, Marco; Piomelli, Daniele; Cavalli, Andrea

2012-01-01

The N-terminal nucleophile (Ntn) hydrolases are a superfamily of enzymes specialized in the hydrolytic cleavage of amide bonds. Even though several members of this family are emerging as innovative drug targets for cancer, inflammation, and pain, the processes through which they catalyze amide hydrolysis remains poorly understood. In particular, the catalytic reactions of cysteine Ntn-hydrolases have never been investigated from a mechanistic point of view. In the present study, we used free energy simulations in the quantum mechanics/molecular mechanics framework to determine the reaction mechanism of amide hydrolysis catalyzed by the prototypical cysteine Ntn-hydrolase, conjugated bile acid hydrolase (CBAH). The computational analyses, which were confirmed in water and using different CBAH mutants, revealed the existence of a chair-like transition state, which might be one of the specific features of the catalytic cycle of Ntn-hydrolases. Our results offer new insights on Ntn-mediated hydrolysis and suggest possible strategies for the creation of therapeutically useful inhibitors. PMID:22389698

Chiral aldehydes in hydrocarbons: diastereoselective nucleophilic addition, NMR, and CD spectroscopy reveal dynamic solvation effects.

PubMed

Cainelli, Gianfranco; Galletti, Paola; Pieraccini, Silvia; Quintavalla, Arianna; Giacomini, Daria; Piero Spada, Gian

2004-01-01

Temperature-dependent studies on the diastereoselective nucleophilic addition of n- BuLi to alpha-chiral aldehydes as (S)-O-(t-butyl-dimethylsilyl)lactal, (S)-O-(t-butyl-dimethylsilyl) mandelic aldehyde, and (R)-2-phenylpropanal in n-decane and n-dodecane reveal dynamic solvation phenomena with the presence of inversion temperatures (T(inv)) in the Eyring plots of ln (anti/syn) vs. 1/ T. These dynamic solvent effects were disclosed by temperature-dependent studies of the (13)C NMR, CD, and UV spectra of the starting aldehydes in solution of n-decane and n-dodecane. The concomitant presence of three peculiar temperatures T(CD), T(UV), and T(NMR), whose values are identical and match T(inv), clearly confirms our earlier interpretation of the solvent-dependent nature of T(inv). The inversion temperature, as well as T(CD), T(UV), and T(NMR) represents the interconversion temperature of two different solvation clusters which act as two different supramolecules with different stereoselectivities. Copyright 2003 Wiley-Liss, Inc.

Sulfur Denitrosylation by an Engineered Trx-like DsbG Enzyme Identifies Nucleophilic Cysteine Hydrogen Bonds as Key Functional Determinant.

PubMed

Lafaye, Céline; Van Molle, Inge; Tamu Dufe, Veronica; Wahni, Khadija; Boudier, Ariane; Leroy, Pierre; Collet, Jean-François; Messens, Joris

2016-07-15

Exposure of bacteria to NO results in the nitrosylation of cysteine thiols in proteins and low molecular weight thiols such as GSH. The cells possess enzymatic systems that catalyze the denitrosylation of these modified sulfurs. An important player in these systems is thioredoxin (Trx), a ubiquitous, cytoplasmic oxidoreductase that can denitrosylate proteins in vivo and S-nitrosoglutathione (GSNO) in vitro However, a periplasmic or extracellular denitrosylase has not been identified, raising the question of how extracytoplasmic proteins are repaired after nitrosative damage. In this study, we tested whether DsbG and DsbC, two Trx family proteins that function in reducing pathways in the Escherichia coli periplasm, also possess denitrosylating activity. Both DsbG and DsbC are poorly reactive toward GSNO. Moreover, DsbG is unable to denitrosylate its specific substrate protein, YbiS. Remarkably, by borrowing the CGPC active site of E. coli Trx-1 in combination with a T200M point mutation, we transformed DsbG into an enzyme highly reactive toward GSNO and YbiS. The pKa of the nucleophilic cysteine, as well as the redox and thermodynamic properties of the engineered DsbG are dramatically changed and become similar to those of E. coli Trx-1. X-ray structural insights suggest that this results from a loss of two direct hydrogen bonds to the nucleophilic cysteine sulfur in the DsbG mutant. Our results highlight the plasticity of the Trx structural fold and reveal that the subtle change of the number of hydrogen bonds in the active site of Trx-like proteins is the key factor that thermodynamically controls reactivity toward nitrosylated compounds. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Iminoboronate Formation Leads to Fast and Reversible Conjugation Chemistry of α-Nucleophiles at Neutral pH.

PubMed

Bandyopadhyay, Anupam; Gao, Jianmin

2015-10-12

Bioorthogonal reactions that are fast and reversible under physiological conditions are in high demand for biological applications. Herein, it is shown that an ortho boronic acid substituent makes aryl ketones rapidly conjugate with α-nucleophiles at neutral pH. Specifically, 2-acetylphenylboronic acid and derivatives were found to conjugate with phenylhydrazine with rate constants of 10(2) to 10(3) M(-1) s(-1) , comparable to the fastest bioorthogonal conjugations known to date. (11) B NMR analysis revealed the varied extent of iminoboronate formation of the conjugates, in which the imine nitrogen forms a dative bond with boron. The iminoboronate formation activates the imines for hydrolysis and exchange, rendering these oxime/hydrazone conjugations reversible and dynamic under physiological conditions. The fast and dynamic nature of the iminoboronate chemistry should find wide applications in biology. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

EXPEDITIOUS SYNTHETIC TRANSFORMATIONS USING MICROWAVES

EPA Science Inventory

Microwave-expedited solvent-free synthetic processes will be described for the synthesis of a variety of industrially significant compounds and intermediates namely, enamines, nitroalkenes, enones, oxidized sulfur compounds and ionic liquids. This solvent-free synthetic methodolo...

Steric Effect on the Nucleophilic Reactivity of Nickel(III) Peroxo Complexes.

PubMed

Kim, Jalee; Shin, Bongki; Kim, Hyunjeong; Lee, Junhyung; Kang, Joongoo; Yanagisawa, Sachiko; Ogura, Takashi; Masuda, Hideki; Ozawa, Tomohiro; Cho, Jaeheung

2015-07-06

A set of nickel(III) peroxo complexes bearing tetraazamacrocyclic ligands, [Ni(III)(TBDAP)(O2)](+) (TBDAP = N,N'-di-tert-butyl-2,11-diaza[3.3](2,6)pyridinophane) and [Ni(III)(CHDAP)(O2)](+) (CHDAP = N,N'-dicyclohexyl-2,11-diaza[3.3](2,6)pyridinophane), were prepared by reacting [Ni(II)(TBDAP)(NO3)(H2O)](+) and [Ni(II)(CHDAP)(NO3)](+), respectively, with H2O2 in the presence of triethylamine. The mononuclear nickel(III) peroxo complexes were fully characterized by various physicochemical methods, such as UV-vis, electrospray ionization mass spectrometry, resonance Raman, electron paramagnetic resonance, and X-ray analysis. The spectroscopic and structural characterization clearly shows that the NiO2 cores are almost identical where the peroxo ligand is bound in a side-on fashion. However, the different steric properties of the supporting ligands were confirmed by X-ray crystallography, where the CHDAP ligand gives enough space around the Ni core compared to the TBDAP ligand. The nickel(III) peroxo complexes showed reactivity in the oxidation of aldehydes. In the aldehyde deformylation reaction, the nucleophilic reactivity of the nickel(III) peroxo complexes was highly dependent on the steric properties of the macrocyclic ligands, with a reactivity order of [Ni(III)(TBDAP)(O2)](+) < [Ni(III)(CHDAP)(O2)](+). This result provides fundamental insight into the mechanism of the structure (steric)-reactivity relationship of metal peroxo intermediates.

Crystal structure of Thermoplasma acidophilum XerA recombinase shows large C-shape clamp conformation and cis-cleavage mode for nucleophilic tyrosine.

PubMed

Jo, Chang Hwa; Kim, Junsoo; Han, Ah-reum; Park, Sam Yong; Hwang, Kwang Yeon; Nam, Ki Hyun

2016-03-01

Site-specific Xer recombination plays a pivotal role in reshuffling genetic information. Here, we report the 2.5 Å crystal structure of XerA from the archaean Thermoplasma acidophilum. Crystallographic data reveal a uniquely open conformational state, resulting in a C-shaped clamp with an angle of ~ 48° and a distance of 57 Å between the core-binding and the catalytic domains. The catalytic nucleophile, Tyr264, is positioned in cis-cleavage mode by XerA's C-term tail that interacts with the CAT domain of a neighboring monomer without DNA substrate. Structural comparisons of tyrosine recombinases elucidate the dynamics of Xer recombinase. © 2016 Federation of European Biochemical Societies.

Aliphatic C-C Bond Cleavage in α-Hydroxy Ketones by a Dioxygen-Derived Nucleophilic Iron-Oxygen Oxidant.

PubMed

Bhattacharya, Shrabanti; Rahaman, Rubina; Chatterjee, Sayanti; Paine, Tapan K

2017-03-17

A nucleophilic iron-oxygen oxidant, formed in situ in the reaction between an iron(II)-benzilate complex and O 2 , oxidatively cleaves the aliphatic C-C bonds of α-hydroxy ketones. In the cleavage reaction, α-hydroxy ketones without any α-C-H bond afford a 1:1 mixture of carboxylic acid and ketone. Isotope labeling studies established that one of the oxygen atoms from dioxygen is incorporated into the carboxylic acid product. Furthermore, the iron(II) complex cleaves an aliphatic C-C bond of 17-α-hydroxyprogesterone affording androstenedione and acetic acid. The O 2 -dependent aliphatic C-C bond cleavage of α-hydroxy ketones containing no α-C-H bond bears similarity to the lyase activity of the heme enzyme, cytochrome P450 17A1 (CYP17A1). © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Differential nephrotoxicity of cisplatin and a novel series of traditional Chinese medicine-platinum anticancer agents correlates with their chemical reactivity towards sulfur-containing nucleophiles.

PubMed

To, Kenneth K W; Au-Yeung, Steve C F; Ho, Yee-Ping

2006-07-01

A series of novel traditional Chinese medicine-platinum compounds has been found to be active against a number of murine and human cancers both in vitro and in vivo. Their high potency and the lack of cisplatin cross-resistance are believed to be due to the inclusion of the protein phosphatase 2A-inhibiting demethylcantharidin in the novel structures. A simple reversed-phase high-performance liquid chromatographic method was developed and validated as a stability-indicating assay for the platinum compounds. Using cisplatin and carboplatin as reference compounds, the stability study agrees well with the literature-reported findings. The novel traditional Chinese medicine-platinum compounds were more stable than cisplatin in water and dextrose, but became unstable in normal saline, a characteristic similar to that of carboplatin. The developed assay was further applied to study the chemical reactivity of the novel platinum compounds towards physiologically important nucleophiles such as glutathione and cysteine. The novel compounds were considerably less reactive to the sulfur-containing nucleophiles than cisplatin. In-vitro cytotoxicity assay was performed in a porcine kidney LLC-PK1 cell line model to investigate the nephrotoxicity potential of the platinum compounds. The lower rate of hydrolysis and the decreased reactivity of the novel traditional Chinese medicine-platinum compounds towards sulfur-containing bionucleophiles appear to have reduced their toxicity when compared with cisplatin, yet the antitumor activities of the novel compounds have not been compromised.

Anionic polymerization of oxadiazole-containing 2-vinylpyridine by precisely tuning nucleophilicity and the polyelectrolyte characteristics of the resulting polymers

DOE PAGES

Goodwin, Andrew; Goodwin, Kimberly M.; Wang, Weiyu; ...

2016-09-01

Anionic polymerization is one of the most powerful techniques for preparation of well-defined polymers. However, this well-known and widely employed polymerization technique encounters major limitations for the polymerization of functional monomers containing heteroatoms. This work presents the anionic polymerization of 2-phenyl-5-(6-vinylpyridin-3-yl)-1,3,4-oxadiazole (VPyOzP), a heteroatom monomer that contains both oxadiazole and pyridine substituents within the same pendant group, using various initiating systems based on diphenylmethyl potassium (DPM-K) and triphenylmethyl potassium (TPM-K). Remarkably, well-defined poly(2-phenyl-5-(6-vinylpyridin-3-yl)-1,3,4-oxadiazole) (PVPyOzP) polymers having predicted molecular weights (MW) ranging from 2200 to 21 100 g/mol and polydispersity indices (PDI) ranging from 1.11 to 1.15 were prepared with TPM-K,more » without any additional additives, at –78 °C. The effect of temperature on the polymerization of PVPyOzP was also studied at –78, –45, 0, and 25 °C, and it was observed that increasing the polymerization temperature produced materials with unpredictable MW’s and broader molecular weight distributions. Furthermore, the nucleophilicity of PVPyOzP was investigated through copolymerization with methyl methacrylate and acrylonitrile, where only living poly(methyl methacrylate) (PMMA) prepared by DPM-K/VPPy and in the absence of additives such as lithium chloride (LiCl) and diethyl zinc (ZnEt 2) could be used to produce the well-defined block copolymer of PMMA-b-PVPyOzP. It was also demonstrated by sequential monomer addition that the nucleophilicity of living PVPyOzP is located between that of living PMMA and polyacrylonitrile (PAN). Here, the pyridine moiety of the pendant group also allowed for quaternization and produced PQVPyOzP homopolymer using methyl iodide (CH 3I) and bis(trifluoromethylsulfonyl)amide [Tf 2N –]. The resulting charged polymer and counterion complexes were manipulated and

Anionic polymerization of oxadiazole-containing 2-vinylpyridine by precisely tuning nucleophilicity and the polyelectrolyte characteristics of the resulting polymers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goodwin, Andrew; Goodwin, Kimberly M.; Wang, Weiyu

Anionic polymerization is one of the most powerful techniques for preparation of well-defined polymers. However, this well-known and widely employed polymerization technique encounters major limitations for the polymerization of functional monomers containing heteroatoms. This work presents the anionic polymerization of 2-phenyl-5-(6-vinylpyridin-3-yl)-1,3,4-oxadiazole (VPyOzP), a heteroatom monomer that contains both oxadiazole and pyridine substituents within the same pendant group, using various initiating systems based on diphenylmethyl potassium (DPM-K) and triphenylmethyl potassium (TPM-K). Remarkably, well-defined poly(2-phenyl-5-(6-vinylpyridin-3-yl)-1,3,4-oxadiazole) (PVPyOzP) polymers having predicted molecular weights (MW) ranging from 2200 to 21 100 g/mol and polydispersity indices (PDI) ranging from 1.11 to 1.15 were prepared with TPM-K,more » without any additional additives, at –78 °C. The effect of temperature on the polymerization of PVPyOzP was also studied at –78, –45, 0, and 25 °C, and it was observed that increasing the polymerization temperature produced materials with unpredictable MW’s and broader molecular weight distributions. Furthermore, the nucleophilicity of PVPyOzP was investigated through copolymerization with methyl methacrylate and acrylonitrile, where only living poly(methyl methacrylate) (PMMA) prepared by DPM-K/VPPy and in the absence of additives such as lithium chloride (LiCl) and diethyl zinc (ZnEt 2) could be used to produce the well-defined block copolymer of PMMA-b-PVPyOzP. It was also demonstrated by sequential monomer addition that the nucleophilicity of living PVPyOzP is located between that of living PMMA and polyacrylonitrile (PAN). Here, the pyridine moiety of the pendant group also allowed for quaternization and produced PQVPyOzP homopolymer using methyl iodide (CH 3I) and bis(trifluoromethylsulfonyl)amide [Tf 2N –]. The resulting charged polymer and counterion complexes were manipulated and

O–O bond formation in ruthenium-catalyzed water oxidation: single-site nucleophilic attack vs. O–O radical coupling

DOE PAGES

Shaffer, David W.; Xie, Yan; Concepcion, Javier J.

2017-09-01

In this review we discuss at the mechanistic level the different steps involved in water oxidation catalysis with ruthenium-based molecular catalysts. We have chosen to focus on ruthenium-based catalysts to provide a more coherent discussion and because of the availability of detailed mechanistic studies for these systems but many of the aspects presented in this review are applicable to other systems as well. The water oxidation cycle has been divided in four major steps: water oxidative activation, O–O bond formation, oxidative activation of peroxide intermediates, and O 2 evolution. A significant portion of the review is dedicated to the O–Omore » bond formation step as the key step in water oxidation catalysis. As a result, the two main pathways to accomplish this step, single-site water nucleophilic attack and O–O radical coupling, are discussed in detail and compared in terms of their potential use in photoelectrochemical cells for solar fuels generation.« less

O–O bond formation in ruthenium-catalyzed water oxidation: single-site nucleophilic attack vs. O–O radical coupling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shaffer, David W.; Xie, Yan; Concepcion, Javier J.

In this review we discuss at the mechanistic level the different steps involved in water oxidation catalysis with ruthenium-based molecular catalysts. We have chosen to focus on ruthenium-based catalysts to provide a more coherent discussion and because of the availability of detailed mechanistic studies for these systems but many of the aspects presented in this review are applicable to other systems as well. The water oxidation cycle has been divided in four major steps: water oxidative activation, O–O bond formation, oxidative activation of peroxide intermediates, and O 2 evolution. A significant portion of the review is dedicated to the O–Omore » bond formation step as the key step in water oxidation catalysis. As a result, the two main pathways to accomplish this step, single-site water nucleophilic attack and O–O radical coupling, are discussed in detail and compared in terms of their potential use in photoelectrochemical cells for solar fuels generation.« less

O-O bond formation in ruthenium-catalyzed water oxidation: single-site nucleophilic attack vs. O-O radical coupling.

PubMed

Shaffer, David W; Xie, Yan; Concepcion, Javier J

2017-10-16

In this review we discuss at the mechanistic level the different steps involved in water oxidation catalysis with ruthenium-based molecular catalysts. We have chosen to focus on ruthenium-based catalysts to provide a more coherent discussion and because of the availability of detailed mechanistic studies for these systems but many of the aspects presented in this review are applicable to other systems as well. The water oxidation cycle has been divided in four major steps: water oxidative activation, O-O bond formation, oxidative activation of peroxide intermediates, and O 2 evolution. A significant portion of the review is dedicated to the O-O bond formation step as the key step in water oxidation catalysis. The two main pathways to accomplish this step, single-site water nucleophilic attack and O-O radical coupling, are discussed in detail and compared in terms of their potential use in photoelectrochemical cells for solar fuels generation.

Novel organophosphorus scaffolds of urease inhibitors obtained by substitution of Morita-Baylis-Hillman adducts with phosphorus nucleophiles.

PubMed

Ntatsopoulos, Vassilis; Vassiliou, Stamatia; Macegoniuk, Katarzyna; Berlicki, Łukasz; Mucha, Artur

2017-06-16

The reactivity of Morita-Baylis-Hillman allyl acetates was employed to introduce phosphorus-containing functionalities to the side chain of the cinnamic acid conjugated system by nucleophilic displacement. The proximity of two acidic groups, the carboxylate and phosphonate/phosphinate groups, was necessary to form interactions in the active site of urease by recently described inhibitor frameworks. Several organophosphorus scaffolds were obtained and screened for inhibition of the bacterial urease, an enzyme that is essential for survival of urinary and gastrointestinal tract pathogens. α-Substituted phosphonomethyl- and 2-phosphonoethyl-cinnamate appeared to be the most potent and were further optimized. As a result, one of the most potent organophosphorus inhibitors of urease, α-phosphonomethyl-p-methylcinnamic acid, was identified, with K i  = 0.6 μM for Sporosarcina pasteurii urease. High complementarity to the enzyme active site was achieved with this structure, as any further modifications significantly decreased its affinity. Finally, this work describes the challenges faced in developing ligands for urease. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

One-pot facile synthesis of 4-amino-1,8-naphthalimide derived Tröger's bases via a nucleophilic displacement approach.

PubMed

Shanmugaraju, Sankarasekaran; McAdams, Deirdre; Pancotti, Francesca; Hawes, Chris S; Veale, Emma B; Kitchen, Jonathan A; Gunnlaugsson, Thorfinnur

2017-09-13

We report here a novel one-pot synthetic strategy for the synthesis of a family of N-alkyl-1,8-naphthalimide based Tröger's bases via a nucleophilic substitution reaction of a common 'precursor' (or a 'synthon') N-aryl-1,8-naphthalimide Tröger's base heated at 80 °C in neat aliphatic primary amine, in overall yield of 65-96%. This methodology provides an efficient and one-step facile route to design 1,8-naphthalimide derived Tröger's base structures in analytically pure form without the use of column chromatography purification, that can be used in medicinal chemistry and as supramolecular scaffolds. We also report the formation of the corresponding anhydride, and the crystallographic analysis of two of the resulting products, that of the N-phenyl-4-amino-1,8-naphthalimide and the anhydride derived Tröger's bases.

Unexpected Reactivity of [(η(5) -1,2,4-tBu3 C5 H2 )Ni(η(3) -P3 )] towards Main Group Nucleophiles and by Reduction.

PubMed

Mädl, Eric; Balázs, Gábor; Peresypkina, Eugenia V; Scheer, Manfred

2016-06-27

The reduction of [Cp'''Ni(η(3) -P3 )] (1; Cp'''=η(5) -1,2,4-tBu3 C5 H2 ) with potassium produces the complex anion [(Cp'''Ni)2 (μ,η(2:2) -P8 )](2-) (2), which contains a realgar-like P8 unit. The anionic triple-decker sandwich complex [(Cp'''Ni)2 (μ,η(3:3) -P3 )](-) (3) with a cyclo-P3 middle deck is obtained when 1 is treated with NaNH2 as a nucleophile. Na[3] can subsequently be oxidized with AgOTf to the neutral triple-decker complex [(Cp'''Ni)2 (μ,η(3:3) -P3 )] (4). In contrast, 1 reacts with LiPPh2 to give the anionic compound [(Cp'''Ni)2 (μ,η(2:2) -P6 PPh2 )](-) (5), a complex containing a bicyclic P7 fragment capped by two Cp'''Ni units. Protonation of Li[5] with HBF4 leads to the neutral complex [(Cp'''Ni)2 (μ,η(2:2) -(HP6 PPh2 )] (6). Adding LiNMe2 to 1 results in [Cp'''Ni(η(2) -P3 NMe2 )](-) (7) becoming accessible, a complex which forms as a result of nucleophilic attack at the cyclo-P3 ring of 1. The complexes K2 [2], Na[3], 4, 6, and Li[7] were fully characterized and their structures determined by single-crystal X-ray diffraction. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Controlled Expansion of a Strong-Field Iron Nitride Cluster: Multi-Site Ligand Substitution as a Strategy for Activating Interstitial Nitride Nucleophilicity.

PubMed

Drance, Myles J; Mokhtarzadeh, Charles C; Melaimi, Mohand; Agnew, Douglas W; Moore, Curtis E; Rheingold, Arnold L; Figueroa, Joshua S

2018-05-02

Multimetallic clusters have long been investigated as molecular surrogates for reactive sites on metal surfaces. In the case of the μ 4 -nitrido cluster [Fe 4 (μ 4 -N)(CO) 12 ] - , this analogy is limited owing to the electron-withdrawing effect of carbonyl ligands on the iron nitride core. Described here is the synthesis and reactivity of [Fe 4 (μ 4 -N)(CO) 8 (CNAr Mes2 ) 4 ] - , an electron-rich analogue of [Fe 4 (μ 4 -N)(CO) 12 ] - , where the interstitial nitride displays significant nucleophilicity. This characteristic enables rational expansion with main-group and transition-metal centers to yield unsaturated sites. The resulting clusters display surface-like reactivity through coordination-sphere-dependent atom rearrangement and metal-metal cooperativity. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The effect of varying the anion of an ionic liquid on the solvent effects on a nucleophilic aromatic substitution reaction.

PubMed

Hawker, Rebecca R; Haines, Ronald S; Harper, Jason B

2018-05-09

A variety of ionic liquids, each containing the same cation but a different anion, were examined as solvents for a nucleophilic aromatic substitution reaction. Varying the proportion of ionic liquid was found to increase the rate constant as the mole fraction of ionic liquid increased demonstrating that the reaction outcome could be controlled through varying the ionic liquid. The solvent effects were correlated with the hydrogen bond accepting ability (β) of the ionic liquid anion allowing for qualitative prediction of the effect of changing this component of the solute. To determine the microscopic origins of the solvent effects, activation parameters were determined through temperature-dependent kinetic analyses and shown to be consistent with previous studies. With the knowledge of the microscopic interactions in solution, an ionic liquid was rationally chosen to maximise rate enhancement demonstrating that an ionic solvent can be selected to control reaction outcome for this reaction type.

Reactions of l-ergothioneine and some other aminothiones with 2,2′- and 4,4′-dipyridyl disulphides and of l-ergothioneine with iodoacetamide. 2-Mercaptoimidazoles, 2- and 4-thiopyridones, thiourea and thioacetamide as highly reactive neutral sulphur nucleophiles

PubMed Central

Carlsson, Jan; Kierstan, Marek P. J.; Brocklehurst, Keith

1974-01-01

1. The reactions of 2,2′- and 4,4′-dipyridyl disulphide (2-Py–S–S–2-Py and 4-Py–S–S–4-Py) with l-ergothioneine (2-mercapto-l-histidine betaine), 2-mercaptoimidazole, 1-methyl-2-mercaptoimidazole, thiourea, thioacetamide, 2-thiopyridone (Py–2-SH) and 4-thiopyridone (Py–4-SH) were investigated spectrophotometrically in the pH range approx. 1–9. 2. These reactions involve two sequential reversible thiol–disulphide interchanges. 3. The reaction of l-ergothioneine with 2-Py–S–S–2-Py and/or with the l-ergothioneine–Py–2-SH mixed disulphide, both of which provide Py–2-SH, is characterized by at least three reactive protonic states. This provides definitive evidence that neutral l-ergothioneine is a reactive nucleophile, particularly towards the highly electrophilic protonated disulphides. 4. A similar situation appears to obtain in the reactions of l-ergothioneine and Py–2-SH with 4-Py–S–S–4-Py and in the reactions of the other 2-mercaptoimidazoles, thiourea and Py–4-SH with 2-Py–S–S–2-Py. The nucleophilic reactivity of Py–4-SH suggests that general base catalysis provided by the disulphide in a cyclic or quasi-cyclic transition state is not necessary to generate nucleophilic reactivity in the other amino-thiones whose geometry could permit such catalysis. 5. The existence of a positive deuterium isotope effect in the l-ergothioneine–2-Py–S–S–2-Py system at pH6–7 provides no evidence for general base catalysis but is in accord with a mechanism involving specific acid catalysis and post-transition-state proton transfer. 6. The pH-dependences of the overall equilibrium positions of the various thiol–disulphide interchanges are described. 7. Reaction of thioacetamide with a stoicheiometric quantity of 2-Py–S–S–2-Py at pH1 provides 2 molecules of Py–2-SH per molecule of thioacetamide and elemental sulphur; these findings can be accounted for by thiol–disulphide interchange to provide a thioacetamide�

Approaches to N-Methylwelwitindolinone C Isothiocyanate: Facile Synthesis of the Tetracyclic Core

PubMed Central

Heidebrecht, Richard W.; Gulledge, Brian; Martin, Stephen F.

2010-01-01

The synthesis of a functionalized, tetracyclic core of N-methylwelwitindolinone C isothiocyanate is reported. The approach features a convergent coupling between an indole iminium ion and a highly functionalized vinylogous silyl ketene acetal followed by an intramolecular palladium-catalyzed cyclization that proceeds via an enolate arylation. PMID:20446675

Weakly nucleophilic potassium aryltrifluoroborates in palladium-catalyzed Suzuki-Miyaura reactions: relative reactivity of K[4-RC6F4BF3] and the role of silver-assistance in acceleration of transmetallation.

PubMed

Bardin, Vadim V; Shabalin, Anton Yu; Adonin, Nicolay Yu

2015-01-01

Small differences in the reactivity of weakly nucleophilic potassium aryltrifluoroborates are revealed in the silver-assisted Pd-catalyzed cross-coupling of K[4-RC6F4BF3] (R = H, Bu, MeO, EtO, PrO, iPrO, BuO, t-BuO, CH2=CHCH2O, PhCH2O, PhCH2CH2O, PhO, F, pyrazol-1-yl, pyrrol-1-yl, and indol-1-yl) with ArX (4-BrC6H4CH3, 4-IC6H4F and 3-IC6H4F). An assumed role of silver(I) compounds Ag m Y (Y = O, NO3, SO4, BF4, F) consists in polarization of the Pd-X bond in neutral complex ArPdL n X with the generation of the related transition state or formation of [ArPdL n ][XAg m Y] with a highly electrophilic cation and subsequent transmetallation with the weakly nucleophilic borate. Efficiency of Ag m Y as a polarizing agent decreases in order Ag2O > AgNO3 ≈ Ag2SO4 > Ag[BF4] > AgF. No clear correlation between the reactivity of K[4-RC6F4BF3] and substituent electron parameters, σI and σR°, of the aryl group 4-RC6F4 was found.

Weakly nucleophilic potassium aryltrifluoroborates in palladium-catalyzed Suzuki–Miyaura reactions: relative reactivity of K[4-RC6F4BF3] and the role of silver-assistance in acceleration of transmetallation

PubMed Central

Bardin, Vadim V; Shabalin, Anton Yu

2015-01-01

Summary Small differences in the reactivity of weakly nucleophilic potassium aryltrifluoroborates are revealed in the silver-assisted Pd-catalyzed cross-coupling of K[4-RC6F4BF3] (R = H, Bu, MeO, EtO, PrO, iPrO, BuO, t-BuO, CH2=CHCH2O, PhCH2O, PhCH2CH2O, PhO, F, pyrazol-1-yl, pyrrol-1-yl, and indol-1-yl) with ArX (4-BrC6H4CH3, 4-IC6H4F and 3-IC6H4F). An assumed role of silver(I) compounds AgmY (Y = O, NO3, SO4, BF4, F) consists in polarization of the Pd–X bond in neutral complex ArPdLnX with the generation of the related transition state or formation of [ArPdLn][XAgmY] with a highly electrophilic cation and subsequent transmetallation with the weakly nucleophilic borate. Efficiency of AgmY as a polarizing agent decreases in order Ag2O > AgNO3 ≈ Ag2SO4 > Ag[BF4] > AgF. No clear correlation between the reactivity of K[4-RC6F4BF3] and substituent electron parameters, σI and σR°, of the aryl group 4-RC6F4 was found. PMID:26124862

Conformation and recognition of DNA modified by a new antitumor dinuclear PtII complex resistant to decomposition by sulfur nucleophiles

PubMed Central

Zerzankova, Lenka; Suchankova, Tereza; Vrana, Oldrich; Farrell, Nicholas P.; Brabec, Viktor; Kasparkova, Jana

2011-01-01

Reported herein is a detailed biochemical and molecular biophysics study of the molecular mechanism of action of antitumor dinuclear PtII complex [{PtCl(DACH)}2-μ-Y]4+ [DACH = 1,2-diaminocyclohexane, Y =H2N(CH2)6NH2(CH2)2NH2(CH2)6NH2] (complex 1). This new, long-chain bifunctional dinuclear PtII complex is resistant to metabolic decomposition by sulfur-containing nucleophiles. The results show that DNA adducts of 1 can largely escape repair and yet inhibit very effectively transcription so that they should persist longer than those of conventional cisplatin. Hence, they could trigger a number of downstream cellular effects different from those triggered in cancer cells by DNA adducts of cisplatin. This might lead to the therapeutic effects that could radically improve chemotherapy by platinum complexes. In addition, the findings of the present work make new insights into mechanisms associated with antitumor effects of dinuclear/trinuclear PtII complexes possible. PMID:19682435

Understanding thio-effects in simple phosphoryl systems: role of solvent effects and nucleophile charge† †Electronic supplementary information (ESI) available: A breakdown of calculated activation free energies shown in Table 1, as well as absolute energies and Cartesian coordinates of all key species in this work are presented as ESI. See DOI: 10.1039/c5ob00309a Click here for additional data file.

PubMed Central

Carvalho, Alexandra T. P.; O'Donoghue, AnnMarie C.; Hodgson, David R. W.

2015-01-01

Recent experimental work (J. Org. Chem., 2012, 77, 5829) demonstrated pronounced differences in measured thio-effects for the hydrolysis of (thio)phosphodichloridates by water and hydroxide nucleophiles. In the present work, we have performed detailed quantum chemical calculations of these reactions, with the aim of rationalizing the molecular bases for this discrimination. The calculations highlight the interplay between nucleophile charge and transition state solvation in SN2(P) mechanisms as the basis of these differences, rather than a change in mechanism. PMID:25797408

Rhodium Carbenoid Approach for Introduction of 4-Substituted (Z)-Pent-2-enoates into Sterically Encumbered Pyrroles and Indoles

PubMed Central

Lian, Yajing; Davies, Huw M. L.

2010-01-01

An unusual rhodium-carbenoid approach for introduction of 4-substituted (Z)-pent-2-enoates into sterically encumbered pyrroles and indoles is described. These studies show that (Z)-vinylcarbenoids have a greater tendency than (E)-vinylcarbenoids to react at the vinylogous position of the carbenoid rather than at the carbenoid center. PMID:20121078

Asymmetric Synthesis of Spiropyrazolones by Sequential Organo- and Silver Catalysis

PubMed Central

Hack, Daniel; Dürr, Alexander B; Deckers, Kristina; Chauhan, Pankaj; Seling, Nico; Rübenach, Lukas; Mertens, Lucas; Raabe, Gerhard; Schoenebeck, Franziska; Enders, Dieter

2016-01-01

A stereoselective one-pot synthesis of spiropyrazolones through an organocatalytic asymmetric Michael addition and a formal Conia-ene reaction has been developed. Depending on the nitroalkene, the 5-exo-dig-cyclization could be achieved by silver-catalyzed alkyne activation or by oxidation of the intermediate enolate. The mechanistic pathways have been investigated using computational chemistry and mechanistic experiments. PMID:26676875

Pyrimidine Nucleosides with a Reactive (β-Chlorovinyl)sulfone or (β-Keto)sulfone Group at the C5 Position, Their Reactions with Nucleophiles and Electrophiles, and Their Polymerase-Catalyzed Incorporation into DNA

PubMed Central

2018-01-01

Transition-metal-catalyzed chlorosulfonylation of 5-ethynylpyrimidine nucleosides provided (E)-5-(β-chlorovinyl)sulfones A, which undergo nucleophilic substitution with amines or thiols affording B. The treatment of vinyl sulfones A with ammonia followed by acid-catalyzed hydrolysis of the intermediary β-sulfonylvinylamines gave 5-(β-keto)sulfones C. The latter reacts with electrophiles, yielding α-carbon-alkylated or -sulfanylated analogues D. The 5′-triphosphates of A and C were incorporated into double-stranded DNA, using open and one-nucleotide gap substrates, by human or Escherichia coli DNA-polymerase-catalyzed reactions. PMID:29732453

Unusual reaction paths of SN2 nucleophile substitution reactions CH4 + H- → CH4 + H- and CH4 + F- → CH3F + H-: Quantum chemical calculations

NASA Astrophysics Data System (ADS)

Minyaev, Ruslan M.; Quapp, Wolfgang; Schmidt, Benjamin; Getmanskii, Ilya V.; Koval, Vitaliy V.

2013-11-01

Quantum chemical (CCSD(full)/6-311++G(3df,3pd), CCSD(T)(full)/6-311++G(3df,3pd)) and density function theory (B3LYP/6-311++G(3df,3pd)) calculations were performed for the SN2 nucleophile substitution reactions CH4 + H- → CH4 + H- and CH4 + F- → CH3F + H-. The calculated gradient reaction pathways for both reactions have an unusual behavior. An unusual stationary point of index 2 lies on the gradient reaction path. Using Newton trajectories for the reaction path, we can detect VRI point at which the reaction path branches.

Assessing the superelectrophilic dimension through sigma-complexation, SNAr and Diels-Alder reactivity.

PubMed

Buncel, Erwin; Terrier, François

2010-05-21

In the domain of organic chemistry, S(N)Ar substitutions represent a class of reactions of overwhelming importance, both in synthesis and in the understanding of structure-reactivity relationships, especially the role of sigma-complex intermediates. The primary factor necessary for achievement of S(N)Ar reactions is the presence of a good leaving group, which allows facile rearomatization of the ring undergoing nucleophilic attack. Consistent is the finding that the superelectrophilic chloronitrobenzofuroxans--or furazans--exhibit a very high S(N)Ar reactivity, allowing a number of C-C, C-N, C-O couplings to be achieved that are not accessible with the classical series of nitro-substituted aromatics. Of particular interest is the synthesis of a number of indoles, indolizines, pyrroles and extended pi-excessive aromatic structures like azulene substituted by superelectrophilic moieties. The remarkable driving force for the facile completion of these reactions is the 10 orders of magnitude greater reactivity of 10pi-electron-deficient heteroaromatics such as 4,6-dinitrobenzofuroxan (DNBF) than of the most reactive trinitrobenzene derivatives in sigma-adduct complexation. Among the factors that have been recognized as governing superelectrophilicity, there is the poor aromaticity of 6-membered 10pi-electron structures investigated, with a common origin for sigma-complexation and pericyclic processes. A remarkable capacity of these structures is actually to contribute to a variety of Diels-Alder reactions. As an example, the DNBF molecule formally behaves as a nitroalkene, being susceptible to act as a dienophile as well as a heterodiene. Another remarkable Diels-Alder pathway is the capacity of the 6-membered carbocyclic ring of DNBF to act as a carbodiene. Also noteworthy is the successful Diels-Alder trapping of the dinitroso intermediate associated with 1-oxide/3-oxide tautomerism of the furoxan moiety of 4-aza-6-nitrobenzofuroxan. A point of fundamental importance

Concise total syntheses of (+/-)-strychnine and (+/-)-akuammicine.

PubMed

Sirasani, Gopal; Paul, Tapas; Dougherty, William; Kassel, Scott; Andrade, Rodrigo B

2010-05-21

Concise total syntheses of Strychnos alkaloids strychnine (1) and akuammicine (2) have been realized in 13 and 6 operations, respectively. Key steps include (1) the vinylogous Mannich reaction; (2) a novel, sequential one-pot spirocyclization/intramolecular aza-Baylis-Hillman reaction; and (3) a Heck cyclization. The synthesis of 1 proceeds via the Wieland-Gumlich aldehyde (26).

A Catalytic Asymmetric Synthesis of Polysubstituted Piperidines Using a Rhodium (I) Catalyzed [2+2+2] Cycloaddition Employing a Cleavable Tether

PubMed Central

Martin, Timothy J.; Rovis, Tomislav

2013-01-01

An enantioselective rhodium (I) catalyzed [2+2+2] cycloaddition with a cleavable tether has been developed. The reaction proceeds with a variety of alkyne substrates in good yield and high enantioselectivity. Upon reduction of the vinylogous amide in high diastereoselectivity (>19:1) and cleavage of the tether, N-methylpiperidine products with functional group handles can be accessed. PMID:23606664

Reinterpretation of curved Hammett plots in reaction of nucleophiles with aryl benzoates: change in rate-determining step or mechanism versus ground-state stabilization.

PubMed

Um, Ik-Hwan; Han, Hyun-Joo; Ahn, Jung-Ae; Kang, Swan; Buncel, Erwin

2002-11-29

A kinetic study is reported for the reaction of the anionic nucleophiles OH-, CN-, and N 3 - with aryl benzoates containing substituents on the benzoyl as well as the aryloxy moiety, in 80 mol % H2O - 20 mol % dimethyl sulfoxide at 25.0 degrees C. Hammett log k vs sigma plots for these systems are consistently nonlinear. However, a possible traditional explanation in terms of a mechanism involving a tetrahedral intermediate with curvature resulting from a change in rate-determining step is considered but rejected. The proposed explanation involves ground-state stabilization through resonance interaction between the benzoyl substituent and the electrophilic carbonyl center in the two-stage mechanism. Accordingly, the data are nicely accommodated on the basis of the Yukawa-Tsuno equation, which gives linear plots for all three nuceophiles. Literature reports of the mechanism of acyl transfer processes are reconsidered in this light.

Preparation and characterization of poly (arylene ether isoxazole)s by fluoride ion-mediated aromatic nucleophilic displacement reactions

NASA Technical Reports Server (NTRS)

Herbert, C. G.; Bass, R. G.

1994-01-01

As part of a continuing effort to prepare novel thermally stable high-performance polymers, poly(arylene ether isoxazole)s have been prepared by fluoride ion-catalyzed aromatic nucleophilic substitution reactions with bis(trimethylsiloxyphenyl) isoxazoles and activated bisarylhalides in diphenyl sulfone. Initial investigation involving the preparation of these materials with isoxazole bisphenols and activated bisarylhalides in the presence of potassium carbonate indicated that, under reaction conditions necessary to prepare high-molecular-weight materials, the isoxazole monomer was converted to an enamino ketone. This side reaction was avoided by using fluoride as a base. However, trimethylsilyl ether derivatives of the isoxazole bisphenols were required in these polymerizations for the preparation of high-molecular-weight materials. Moderate to high inherent viscosity eta(sub inh): 0.43-0.87 dl/g) materials with good thermal stability (air: 409-477 C, helium: 435-512 C) can be prepared by the silyl ether method. Glass transition temperatures ranged from 182 to 225 C for polymers with phenyl pendants and from 170 to 214 C for those without. Molecular weight control by 2% endcapping and the incorporation of a phenyl pendant at the 4 position of the isoxazole is necessary to yield polymers soluble in polar aprotic solvents at room temperature. There is evidence, however, indicating the existence of crosslinks between the polymer chains when the silyl ether approach is utilized.

Easy access to fully functionalized chiral tetrahydro-β-carboline alkaloids.

PubMed

Arai, Takayoshi; Wasai, Makiko; Yokoyama, Naota

2011-04-15

A four-step synthetic route to fully substituted chiral tetrahydro-β-carbolines (THBCs) is described. Starting from the (R,S,S)-Friedel-Crafts/Henry adduct obtained from three-component coupling of an indole, nitroalkene, and aldehyde catalyzed by imidazoline-aminophenol-CuOTf, the (1S,3S,4R)-THBCs were readily synthesized in a three-step operation including reduction of the nitro-functionality and Pictet-Spengler cyclization.

Synthesis and antiproliferative activity of peracetylated 2-amino-1,2-dideoxy-1-nitro-d-glycero-l-manno and d-glycero-d-talo heptitols.

PubMed

Luque-Agudo, Verónica; González Gutiérrez, Ana María; Lagunes, Irene; López Galindo, Federico; Padrón, José M; Román, Emilio; Serrano, José Antonio; Gil, María Victoria

2016-12-01

Michael additions between carbohydrate derived nitroalkenes and several aliphatic and aromatic amines proceeded in a stereoselective way, leading to peracetylated 2-amino-1,2-dideoxy-1-nitro-heptitols. In addition, the antiproliferative activity of some of the new adducts has been studied. The results allowed to identify lead compounds which show GI 50 values in the range 1.7-19μM. Copyright © 2016 Elsevier Inc. All rights reserved.

Antioxidant activity of selenenamide-based mimic as a function of the aromatic thiols nucleophilicity, a DFT-SAPE model.

PubMed

Kheirabadi, Ramesh; Izadyar, Mohammad

2018-05-18

The mechanism of action of the selenenamide 1 as a mimic of the glutathione peroxidase (GPx) was investigated by the density functional theory. The solvent-assisted proton exchange procedure was applied to model the catalytic behavior and antioxidant activity of this mimic. To have an insight into the charge transfer effect, different aromatic thiols, including electron donating substituents on the phenyl ring were considered. The catalytic behavior of the selenenamide was modeled in a four-step mechanism, described by the oxidation of the mimic, the reduction of the obtained product, selenoxide, the reduction of the selenenylsulfide and dehydration of selenenic acid. On the basis of the activation parameters, the final step of the proposed mechanism is the rate determining states of the catalytic cycle. Turnover frequency (TOF) analysis showed that the electron donating groups at the para-position of the phenyl ring of the PhSH do not affect the catalytic activity of the selenenamide in contrast to p-methyl thiophenol which indicates the highest nucleophilicity. The evaluation of the electronic contribution of the various donating groups on the phenyl ring of the aromatic thiols shows that the antioxidant activity of the selenenamide sufficiently increases in the presence of the electron-donating substitutions. Finally, the charge transfer process at the rate-determining state was investigated based on the natural bond orbital analysis. Copyright © 2018 Elsevier Ltd. All rights reserved.

Construction of a 3D model of nattokinase, a novel fibrinolytic enzyme from Bacillus natto. A novel nucleophilic catalytic mechanism for nattokinase.

PubMed

Zheng, Zhong-liang; Zuo, Zhen-yu; Liu, Zhi-gang; Tsai, Keng-chang; Liu, Ai-fu; Zou, Guo-lin

2005-01-01

A three-dimensional structural model of nattokinase (NK) from Bacillus natto was constructed by homology modeling. High-resolution X-ray structures of Subtilisin BPN' (SB), Subtilisin Carlsberg (SC), Subtilisin E (SE) and Subtilisin Savinase (SS), four proteins with sequential, structural and functional homology were used as templates. Initial models of NK were built by MODELLER and analyzed by the PROCHECK programs. The best quality model was chosen for further refinement by constrained molecular dynamics simulations. The overall quality of the refined model was evaluated. The refined model NKC1 was analyzed by different protein analysis programs including PROCHECK for the evaluation of Ramachandran plot quality, PROSA for testing interaction energies and WHATIF for the calculation of packing quality. This structure was found to be satisfactory and also stable at room temperature as demonstrated by a 300ps long unconstrained molecular dynamics (MD) simulation. Further docking analysis promoted the coming of a new nucleophilic catalytic mechanism for NK, which is induced by attacking of hydroxyl rich in catalytic environment and locating of S221.

Oxidation of a guanine derivative coordinated to a Pt(IV) complex initiated by intermolecular nucleophilic attacks.

PubMed

Choi, Sunhee; Personick, Michelle L; Bogart, Justin A; Ryu, DaWeon; Redman, Romany M; Laryea-Walker, Edith

2011-03-28

In this study we report that fac-[Pt(IV)(dach)(9-EtG)Cl(3)](+) (dach = d,l-1,2-diaminocyclohexane, 9-EtG = 9-ethylguanine) in high pH (pH 12) or phosphate solution (pH 7.4) produces 8-oxo-9-EtG and Pt(II) species. The reaction in H(2)(18)O revealed that the oxygen atom in hydroxide or phosphate ends up at the C8 position of 8-oxo-G. The kinetics of the redox reaction was first order with respect to both Pt(IV)-G and free nucleophiles (OH(-) and phosphate). The oxidation of G initiated by hydroxide was approximately 30∼50 times faster than by phosphate in 100 mM NaCl solutions. The large entropy of activation of OH(-1) (ΔS(‡) = 26.6 ± 4.3 J mol(-1) K(-1)) due to the smaller size of OH(-) is interpreted to be responsible for the faster kinetics compared to phosphate (ΔS(‡) = -195.5 ± 11.1 J mol(-1) K(-1)). The enthalpy of activation for phosphate reaction is more favorable relative to the OH(-) reaction (ΔH(‡) = 35.4 ± 3.5 kJ mol(-1) for phosphate vs. 96.6 ± 11.4 kJ mol(-1) for OH(-1)). The kinetic isotope effect of H8 was determined to be 7.2 ± 0.2. The rate law, kinetic isotope effect, and isotopic labeling are consistent with a mechanism involving proton ionization at the C8 position as the rate determining step followed by two-electron transfer from G to Pt(IV).

Cytochrome p450 architecture and cysteine nucleophile placement impact raloxifene-mediated mechanism-based inactivation.

PubMed

VandenBrink, Brooke M; Davis, John A; Pearson, Josh T; Foti, Robert S; Wienkers, Larry C; Rock, Dan A

2012-11-01

The propensity for cytochrome P450 (P450) enzymes to bioactivate xenobiotics is governed by the inherent chemistry of the xenobiotic itself and the active site architecture of the P450 enzyme(s). Accessible nucleophiles in the active site or egress channels of the P450 enzyme have the potential of sequestering reactive metabolites through covalent modification, thereby limiting their exposure to other proteins. Raloxifene, a drug known to undergo CYP3A-mediated reactive metabolite formation and time-dependent inhibition in vitro, was used to explore the potential for bioactivation and enzyme inactivation of additional P450 enzymes (CYP1A2, CYP2C8, CYP2C9, CYP2C19, CYP2D6, CYP2E1, and CYP3A5). Every P450 tested except CYP2E1 was capable of raloxifene bioactivation, based on glutathione adduct formation. However, raloxifene-mediated time-dependent inhibition only occurred in CYP2C8 and CYP3A4. Comparable inactivation kinetics were achieved with K(I) and k(inact) values of 0.26 μM and 0.10 min(-1) and 0.81 μM and 0.20 min(-1) for CYP2C8 and CYP3A4, respectively. Proteolytic digests of CYP2C8 and CYP3A4 Supersomes revealed adducts to Cys225 and Cys239 for CYP2C8 and CYP3A4, respectively. For each P450 enzyme, proposed substrate/metabolite access channels were mapped and active site cysteines were identified, which revealed that only CYP2C8 and CYP3A4 possess accessible cysteine residues near the active site cavities, a result consistent with the observed kinetics. The combined data suggest that the extent of bioactivation across P450 enzymes does not correlate with P450 inactivation. In addition, multiple factors contribute to the ability of reactive metabolites to form apo-adducts with P450 enzymes.

Asymmetric Synthesis of Spiropyrazolones by Sequential Organo- and Silver Catalysis.

PubMed

Hack, Daniel; Dürr, Alexander B; Deckers, Kristina; Chauhan, Pankaj; Seling, Nico; Rübenach, Lukas; Mertens, Lucas; Raabe, Gerhard; Schoenebeck, Franziska; Enders, Dieter

2016-01-26

A stereoselective one-pot synthesis of spiropyrazolones through an organocatalytic asymmetric Michael addition and a formal Conia-ene reaction has been developed. Depending on the nitroalkene, the 5-exo-dig-cyclization could be achieved by silver-catalyzed alkyne activation or by oxidation of the intermediate enolate. The mechanistic pathways have been investigated using computational chemistry and mechanistic experiments. © 2015 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Tandem 1,5-hydride shift/1,5-S,N-cyclization with ethylene extrusion of 1,3-oxathiolane-substituted ketenimines and carbodiimides. An experimental and computational study.

PubMed

Alajarin, Mateo; Bonillo, Baltasar; Sanchez-Andrada, Pilar; Vidal, Angel

2010-06-04

Under thermal activation in solution, N-[2-(1,3-oxathiolan-2-yl)]phenyl ketenimines and carbodiimides were converted into 2,1-benzisothiazol-3-ones bearing a pendant N-styryl or imidoyl fragment, respectively. These processes should occur with the concomitant formation of ethylene as result of the fragmentation of the 1,3-oxathiolane ring. The conversions of ketenimines took place under softer thermal conditions, toluene 110 degrees C, than those of carbodiimides, o-xylene 160 degrees C. A computational DFT study unveiled the mechanistic course of these transformations, rare tandem processes consisting of an initial 1,5-hydride shift of the acetalic hydrogen atom to the central carbon atom of the heterocumulene function leading to the respective o-azaxylylene. This transient intermediate then converts, in a single step, into ethylene and the experimentally isolated benzisothiazolone. This latter stage of the mechanism is rather peculiar, combining a 1,5-cyclization by S-N bond formation, aromaticity recovery at the benzene nucleus, and the fragmentation of the oxathiolane framework originating a new carbonyl group. It can be related with a vinylogous retro-ene reaction and shows pseudopericyclic characteristics. The computations also revealed that the alternative 6pi electrocyclization of the transient o-azaxylylenes cannot compete, on kinetic and thermodynamic grounds, with the experimentally observed reaction channel. The two alternative reaction paths of a number of ketenimines and carbodiimides were computationally scrutinized, the results being in accord with the experimental outcomes. In addition, sulfur extrusion from the benzisothiazolones by the action of triphenylphosphine under two different reaction conditions led to three different types of heterocyclic products, 4(3H)-quinolones, quinolino[2,1-b]quinazolin-5,12-diones, and dibenzo[b,f][1,5]diazocin-6,12-diones, whose formation is explained by the initial formation of an intermediate imidoylketene

Protein alkylation, transcriptional responses and cytochrome c release during acrolein toxicity in A549 cells: influence of nucleophilic culture media constituents.

PubMed

Thompson, Colin A; Burcham, Philip C

2008-06-01

Acrolein is a toxic combustion product that elicits apoptotic and/or necrotic cell death depending on the conditions under which exposure occurs. As a strong electrophile, side-reactions with nucleophilic media constituents seem likely to accompany study of its toxicity in vitro, but these reactions are poorly characterized. We have thus examined the effect of media composition on the toxicity of acrolein in A549 cells. Cells were exposed to acrolein in either Dulbecco's buffered saline (DBS) or F12 supplemented with various concentrations of fetal bovine serum. Cell viability was assessed using the MTT assay, while heme oxygenase-1 (HO-1) and cytoplasmic cytochrome c were measured as respective markers of transcriptional response and apoptosis. Protein damage was evaluated using the protein carbonyl assay. Compared to F12 media (with or without serum), maximal cell death as evaluated using the MTT assay, as well as adduction of intracellular proteins, occurred when cells were exposed to acrolein in DBS. In contrast, cytochrome c release was maximal in cells exposed to acrolein in serum-containing F12, conditions which inhibited protein modification and overt cell death. These findings highlight the need for careful attention to experimental conditions when conducting in vitro toxicological studies of reactive substances.

A General Asymmetric Formal Synthesis of Aza-Baylis-Hillman Type Products under Bifunctional Catalysis.

PubMed

Frías, María; Carrasco, Ana Cristina; Fraile, Alberto; Alemán, José

2018-03-02

A new organocatalytic strategy for the synthesis of enantioenriched aza-Baylis-Hillman type products via a frustrated vinylogous reaction is presented. This process proceeds under mild conditions with good yields, completed Z/E selectivity and excellent enantioselectivities. Moreover, easy derivatizations of the final products led to important building blocks of organic synthesis such as 1,3-aminoalcohols and Lewis base catalysts. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Inhibition of crystallin ascorbylation by nucleophilic compounds in the hSVCT2 mouse model of lenticular aging.

PubMed

Fan, Xingjun; Monnier, Vincent M

2008-11-01

Senile cataracts are associated with oxidation, fragmentation, cross-linking, insolubilization, and yellow pigmentation of lens crystallins. This process is partially explained by advanced glycation end products (AGEs) from ascorbic acid (ASA), as the authors unequivocally demonstrated in an hSVCT2 transgenic mouse. The authors present the first pharmacologic intervention study against ascorbylation in these mice. Five groups of mice from 2 to 9 months of age (10 mice/group) were fed a diet containing 0.1% (wt/wt) aminoguanidine, pyridoxamine, penicillamine, and nucleophilic compounds NC-I and NC-II. AGEs were determined in crystallin digests using high-performance liquid chromatography, liquid chromatography-mass spectrometry, or gas chromatography-mass spectrometry. Lens protein extract was incubated in vitro with ASA or dehydroascorbic acid. The ASA level increased approximately 10-fold in all groups and was unaffected by treatment. AGEs were increased several-fold in transgenic compared with control lenses. Body weight, food intake, lenticular glutathione, and glycated lysine level were unaltered. In vitro, all compounds inhibited AGE formation. In vivo, NC-I and NC-II significantly decreased protein fluorescence at lambda(ex)335/(em)385 (P = 0.045, P = 0.017, respectively) and lambda(ex)370/(em)440 (P = 0.029, P = 0.007, respectively). Other inhibitors had no effect. After 7 months, only NC-I and NC-II induced a 50% reduction in pentosidine (P = NS for NC-I; P = 0.035 for NC-II). NC-I also decreased carboxymethyllysine (P = 0.032) and carboxyethyllysine (P = NS). Fluorescent cross-link K2P was decreased by NC-I, NC-II, aminoguanidine, and pyridoxamine (P = NS). Pharmacologically blocking protein ascorbylation with absorbable guanidino compounds is feasible and may represent a new strategy for the delay of age-related nuclear sclerosis of the lens.

Mechanistic studies on the phosphoramidite coupling reaction in oligonucleotide synthesis. I. Evidence for nucleophilic catalysis by tetrazole and rate variations with the phosphorus substituents.

PubMed Central

Dahl, B H; Nielsen, J; Dahl, O

1987-01-01

Tetrazole catalyzed reactions of a series of phosphoramidites, 5'-O-DMTdT-3'-O-P(OR1)NR2(2) (1a-h), with 3'-O-SiButPh2-6-N-benzoyl-dA (2a) in acetonitrile solution have been studied. It is found that the coupling rate depends very much on whether tetrazole is added before or after 2a, and that dialkylammonium tetrazolide salts are inhibitors. These and other facts are evidence that the reactions are subjected to nucleophilic catalysis by tetrazole, in addition to acid catalysis. The rate variations with phosphorus substituents of 1a-h are NEt2 greater than NPri2 greater than N(CH2CH2)O greater than NMePh, and OMe greater than OCH2CH2CN greater than OCHMeCH2CN greater than OCMe2CH2CN much greater than OC6H4Cl. The inhibitor properties of dialkylammonium tetrazolides have practical consequences for the efficiency of DNA syntheses, when in situ prepared phosphoramidites are used; the same would apply for segmented, simultaneous syntheses or syntheses where recycling is performed. PMID:3822837

Electrophilic-Nucleophilic Dualism of Nickel(II) toward Ni···I Noncovalent Interactions: Semicoordination of Iodine Centers via Electron Belt and Halogen Bonding via σ-Hole.

PubMed

Bikbaeva, Zarina M; Ivanov, Daniil M; Novikov, Alexander S; Ananyev, Ivan V; Bokach, Nadezhda A; Kukushkin, Vadim Yu

2017-11-06

The nitrosoguanidinate complex [Ni{NH═C(NMe 2 )NN(O)} 2 ] (1) was cocrystallized with I 2 and sym-trifluorotriiodobenzene (FIB) to give associates 1·2I 2 and 1·2FIB. Structures of these solid species were studied by XRD followed by topological analysis of the electron density distribution within the framework of Bader's approach (QTAIM) at the M06/DZP-DKH level of theory and Hirshfeld surface analysis. Our results along with inspection of XRD (CCDC) data, accompanied by the theoretical calculations, allowed the identification of three types of Ni···I contacts. The Ni···I semicoordination of the electrophilic nickel(II) center with electron belt of I 2 was observed in 1·2I 2 , the metal-involving halogen bonding between the nucleophilic nickel(II)-d z 2 center and σ-hole of iodine center was recognized and confirmed theoretically in the structure of [FeNi(CN) 4 (IPz)(H 2 O)] n (IPz = 4-N-coordinated 2-I-pyrazine), whereas the arrangement of FIB in 1·2FIB provides a boundary case between the semicoordination and the halogen Ni···I bondings. In 1·2I 2 and 1·2FIB, noncovalent interactions were studied by variable temperature XRD detecting the expansion of noncovalent contacts with preservation of covalent bond lengths upon the temperature increase from 100 to 300 K. The nature and energies of all identified types of the Ni···I noncovalent interactions in the obtained (1·2I 2 and 1·2FIB) and in the previously reported ([FeNi(CN) 4 (IPz)(H 2 O)] n , [NiL 2 ](I 3 ) 2 ·2I 2 (L = o-phenylene-bis(dimethylphosphine), [NiL]I 2 (L = 1,4,8,11-tetra-azacyclotetradecane), Ni(en) 2 ] n [AgI 2 ] 2n (en = ethylenediamine), and [NiL](ClO 4 ) (L = 4-iodo-2-((2-(2-(2-pyridyl)ethylsulfanyl)ethylimino)methyl)-phenolate)) structures were studied theoretically. The estimated strengths of these Ni···I noncovalent contacts vary from 1.6 to 4.1 kcal/mol and, as expected, become weaker on heating. This work is the first emphasizing electrophilic-nucleophilic dualism

Materials For Second and Third Order Nonlinear Optical Applications.

DTIC Science & Technology

1996-02-05

the ,Ieneral reaction scheme below in Fig. 1 is reminiscent of the synthetic method of Jutz, using Grignard reagents which were treated with N-methyl...N- phenylpropen-l-al (1[1]) or its higher vinylog, 1[2] in yields of 5-95%. In our procedure, we used a wide variety of organolithium reagents ...be synthesized from a facile high yield procedure for bromination of julolidine. Here we demonstrated that organolithium reagents add to known co-N,N

Regiospecific attack of nitrogen and sulfur nucleophiles on quinones derived from poison oak/ivy catechols (urushiols) and analogues as models for urushiol-protein conjugate formation.

PubMed

Liberato, D J; Byers, V S; Dennick, R G; Castagnoli, N

1981-01-01

Attempts to characterize potential biologically important covalent interactions between electrophilic quinones derived from catechols present in poison oak/ivy (urushiol) and biomacromolecules have led to the analysis of model reactions involving sulfur and amino nucleophiles with 3-heptadecylbenzoquinone. Characterization of the reaction products indicates that this quinone undergoes regiospecific attack by (S)-N-acetylcysteine at C-6 and by 1-aminopentane at C-5. The red solid obtained with 1-aminopentane proved to be 3-heptadecyl-5-(pentylamino)-1,2-benzoquinone. Analogous aminobenzoquinones were obtained with the quinones derived from the 4- and 6-methyl analogues of 3-pentadecylcatechol. All three adducts absorbed visible light at different wavelengths. When the starting catechols were incubated with human serum albumin almost identical chromophores were formed. These results establish that cathechols responsible for the production of the poison oak/ivy contact dermatitis in humans undergo a sequence of reactions in the presence of human serum albumin that lead to covalent attachment of the catechols to the protein via carbon-nitrogen bonds. Estimations of the extent of this binding indicate that, at least with human serum albumin, the reaction is quantitative.

Oxygen-atom transfer reactivity of axially ligated Mn(V)-oxo complexes: evidence for enhanced electrophilic and nucleophilic pathways.

PubMed

Neu, Heather M; Yang, Tzuhsiung; Baglia, Regina A; Yosca, Timothy H; Green, Michael T; Quesne, Matthew G; de Visser, Sam P; Goldberg, David P

2014-10-01

Addition of anionic donors to the manganese(V)-oxo corrolazine complex Mn(V)(O)(TBP8Cz) has a dramatic influence on oxygen-atom transfer (OAT) reactivity with thioether substrates. The six-coordinate anionic [Mn(V)(O)(TBP8Cz)(X)](-) complexes (X = F(-), N3(-), OCN(-)) exhibit a ∼5 cm(-1) downshift of the Mn-O vibrational mode relative to the parent Mn(V)(O)(TBP8Cz) complex as seen by resonance Raman spectroscopy. Product analysis shows that the oxidation of thioether substrates gives sulfoxide product, consistent with single OAT. A wide range of OAT reactivity is seen for the different axial ligands, with the following trend determined from a comparison of their second-order rate constants for sulfoxidation: five-coordinate ≈ thiocyanate ≈ nitrate < cyanate < azide < fluoride ≪ cyanide. This trend correlates with DFT calculations on the binding of the axial donors to the parent Mn(V)(O)(TBP8Cz) complex. A Hammett study was performed with p-X-C6H4SCH3 derivatives and [Mn(V)(O)(TBP8Cz)(X)](-) (X = CN(-) or F(-)) as the oxidant, and unusual "V-shaped" Hammett plots were obtained. These results are rationalized based upon a change in mechanism that hinges on the ability of the [Mn(V)(O)(TBP8Cz)(X)](-) complexes to function as either an electrophilic or weak nucleophilic oxidant depending upon the nature of the para-X substituents. For comparison, the one-electron-oxidized cationic Mn(V)(O)(TBP8Cz(•+)) complex yielded a linear Hammett relationship for all substrates (ρ = -1.40), consistent with a straightforward electrophilic mechanism. This study provides new, fundamental insights regarding the influence of axial donors on high-valent Mn(V)(O) porphyrinoid complexes.

New natural product -an efficient antimicrobial applications of new newly synthesized pyrimidine derivatives by the electrochemical oxidation of hydroxyl phenol in the presence of 2-mercapto-6-(trifluoromethyl) pyrimidine-4-ol as nucleophile.

PubMed

Khan, Zia Ul Haq; Khan, Amjad; Wan, Pingyu; Khan, Arif Ullah; Tahir, Kamran; Muhammad, Nawshad; Khan, Faheem Ullah; Shah, Hidayat Ullah; Khan, Zia Ullah

2018-05-01

Some new pyrimidine derivatives have been synthesised by electrochemical oxidation of catechol (1a) in the existence of 2-mercapto-6-(trifluoromethyl) pyrimidine-4-ol (3) as a nucleophile in aqueous solution using Cyclic Voltammetric and Controlled Potential Coulometry. The catechol has been oxidised to o-quinone through electrochemical method and participative in Michael addition reaction, leading to the development of some new pyrimidine derivatives. The products were achieved in good yield with high pureness. The mechanism of the reaction has been conformed from the Cyclic Voltammetric data and Controlled Potential Coulometry. After purification, the compounds were characterised using modern techniques. The synthesised materials were screened for antimicrobial actions using Gram positive and Gram negative strain of bacteria. These new synthesised pyrimidine derivatives showed very good antimicrobial activity.

A new family of nucleophiles for photoinduced, copper-catalyzed cross-couplings via single-electron transfer: reactions of thiols with aryl halides under mild conditions (O °C).

PubMed

Uyeda, Christopher; Tan, Yichen; Fu, Gregory C; Peters, Jonas C

2013-06-26

Building on the known photophysical properties of well-defined copper-carbazolide complexes, we have recently described photoinduced, copper-catalyzed N-arylations and N-alkylations of carbazoles. Until now, there have been no examples of the use of other families of heteroatom nucleophiles in such photoinduced processes. Herein, we report a versatile photoinduced, copper-catalyzed method for coupling aryl thiols with aryl halides, wherein a single set of reaction conditions, using inexpensive CuI as a precatalyst without the need for an added ligand, is effective for a wide range of coupling partners. As far as we are aware, copper-catalyzed C-S cross-couplings at 0 °C have not previously been achieved, which renders our observation of efficient reaction of an unactivated aryl iodide at -40 °C especially striking. Mechanistic investigations are consistent with these photoinduced C-S cross-couplings following a SET/radical pathway for C-X bond cleavage (via a Cu(I)-thiolate), which contrasts with nonphotoinduced, copper-catalyzed processes wherein a concerted mechanism is believed to occur.

A Highly Stereocontrolled, One-Pot Approach toward Pyrrolobenzoxazinones and Pyrroloquinazolinones through a Lewis Acid-Catalyzed [3 + 2]-Cycloannulation Process.

PubMed

Boomhoff, Michael; Ukis, Rostyslav; Schneider, Christoph

2015-08-21

We report herein a stereocontrolled [3 + 2]-cycloheteroannulation of bis-silyl dienediolate 1 with 2-aminobenzoic acid- and 2-aminobenzamide-derived imines to furnish highly substituted pyrrolo[1,2-a]benzoxazinones 3 and pyrrolo[1,2-a]quinazolinones 4, respectively, in good overall yields. This one-pot process rapidly generates molecular complexity and comprises a Lewis acid-catalyzed, vinylogous Mannich reaction of 1 followed by an intramolecular N,O-acetal- and N,N-aminal formation, respectively, which proceeds with good to excellent stereocontrol.

Asymmetric Synthesis of Rauhut-Currier type Products by a Regioselective Mukaiyama Reaction under Bifunctional Catalysis.

PubMed

Frias, María; Mas-Ballesté, Rubén; Arias, Saira; Alvarado, Cuauhtemoc; Alemán, José

2017-01-18

The reactivity and the regioselective functionalization of silyl-diene enol ethers under a bifunctional organocatalyst provokes a dramatic change in the regioselectivity, from the 1,5- to the 1,3-functionalization. This variation makes possible the 1,3-addition of silyl-dienol ethers to nitroalkenes, giving access to the synthesis of tri- and tetrasubstituted double bonds in Rauhut-Currier type products. The process takes place under smooth conditions, nonanionic conditions, and with a high enantiomeric excess. A rational mechanistic pathway is presented based on DFT and mechanistic experiments.

β-Amino acid catalyzed asymmetric Michael additions: design of organocatalysts with catalytic acid/base dyad inspired by serine proteases.

PubMed

Yang, Hui; Wong, Ming Wah

2011-09-16

A new type of chiral β-amino acid catalyst has been computationally designed, mimicking the enzyme catalysis of serine proteases. Our catalyst approach is based on the bioinspired catalytic acid/base dyad, namely, a carboxyl and imidazole pair. DFT calculations predict that this designed organocatalyst catalyzes Michael additions of aldehydes to nitroalkenes with excellent enantioselectivities and remarkably high anti diastereoselectivities. The unusual stacked geometry of the enamine intermediate, hydrogen bonding network, and the adoption of an exo transition state are the keys to understand the stereoselectivity. © 2011 American Chemical Society

Probing the substrate specificity of Golgi alpha-mannosidase II by use of synthetic oligosaccharides and a catalytic nucleophile mutant.

PubMed

Zhong, Wei; Kuntz, Douglas A; Ember, Brian; Singh, Harminder; Moremen, Kelley W; Rose, David R; Boons, Geert-Jan

2008-07-16

Inhibition of Golgi alpha-mannosidase II (GMII), which acts late in the N-glycan processing pathway, provides a route to blocking cancer-induced changes in cell surface oligosaccharide structures. To probe the substrate requirements of GMII, oligosaccharides were synthesized that contained an alpha(1,3)- or alpha(1,6)-linked 1-thiomannoside. Surprisingly, these oligosaccharides were not observed in X-ray crystal structures of native Drosophila GMII (dGMII). However, a mutant enzyme in which the catalytic nucleophilic aspartate was changed to alanine (D204A) allowed visualization of soaked oligosaccharides and led to the identification of the binding site for the alpha(1,3)-linked mannoside of the natural substrate. These studies also indicate that the conformational change of the bound mannoside to a high-energy B 2,5 conformation is facilitated by steric hindrance from, and the formation of strong hydrogen bonds to, Asp204. The observation that 1-thio-linked mannosides are not well tolerated by the catalytic site of dGMII led to the synthesis of a pentasaccharide containing the alpha(1,6)-linked Man of the natural substrate and the beta(1,2)-linked GlcNAc moiety proposed to be accommodated by the extended binding site of the enzyme. A cocrystal structure of this compound with the D204A enzyme revealed the molecular interactions with the beta(1,2)-linked GlcNAc. The structure is consistent with the approximately 80-fold preference of dGMII for the cleavage of substrates containing a nonreducing beta(1,2)-linked GlcNAc. By contrast, the lysosomal mannosidase lacks an equivalent GlcNAc binding site and kinetic analysis indicates oligomannoside substrates without non-reducing-terminal GlcNAc modifications are preferred, suggesting that selective inhibitors for GMII could exploit the additional binding specificity of the GlcNAc binding site.

A study of the reactivity of S(VI)-F containing warheads with nucleophilic amino-acid side chains under physiological conditions.

PubMed

Mukherjee, H; Debreczeni, J; Breed, J; Tentarelli, S; Aquila, B; Dowling, J E; Whitty, A; Grimster, N P

2017-11-22

Sulfonyl fluorides (SFs) have recently emerged as a promising warhead for the targeted covalent modification of proteins. Despite numerous examples of the successful deployment of SFs as covalent probe compounds, a detailed exploration of the factors influencing the stability and reactivity of SFs has not yet appeared. In this work we present an extensive study on the influence of steric and electronic factors on the reactivity and stability of the SF and related S VI -F groups. While SFs react rapidly with N-acetylcysteine, the resulting adducts were found to be unstable, rendering SFs inappropriate for the durable covalent inhibition of cysteine residues. In contrast, SFs afforded stable adducts with both N-acetyltyrosine and N-acetyllysine; furthermore, we show that the reactivity of arylsulfonyl fluorides towards these nucleophilic amino acids can be predictably modulated by adjusting the electronic properties of the warhead. These trends were largely conserved when the covalent reaction occurred within a protein binding pocket. We have also obtained a crystal structure depicting covalent modification of the catalytic lysine of a tyrosine kinase (FGFR1) by the ATP analog 5'-O-3-((fluorosulfonyl)benzoyl)adenosine (m-FSBA). Highly reactive warheads were demonstrated to be unstable with respect to hydrolysis in buffered aqueous solutions, indicating that warhead reactivity must be carefully tuned to provide optimal rates of protein modification. Our results demonstrate that the reactivity of SFs complements that of more commonly studied acrylamides, and we hope that this work spurs the rational design of novel SF-containing covalent probe compounds and inhibitors, particularly in cases where a suitably positioned cysteine residue is not present.

Total Synthesis of Tiacumicin A. Total Synthesis, Relay Synthesis, and Degradation Studies of Fidaxomicin (Tiacumicin B, Lipiarmycin A3).

PubMed

Hattori, Hiromu; Kaufmann, Elias; Miyatake-Ondozabal, Hideki; Berg, Regina; Gademann, Karl

2018-04-12

The commercial macrolide antibiotic fidaxomicin was synthesized in a highly convergent manner. Salient features of this synthesis include a β-selective noviosylation, a β-selective rhamnosylation, a ring-closing metathesis, a Suzuki coupling, and a vinylogous Mukaiyama aldol reaction. Careful choice of protecting groups and fine-tuning of the glycosylation reactions led to the first total synthesis of fidaxomicin. In addition, a relay synthesis of fidaxomicin was established, which gives access to a conveniently protected intermediate from the natural material for derivatization. The first total synthesis of a related congener, tiacumicin A, is presented.

An efficient and practical synthesis of [2- 11C]indole via superfast nucleophilic [ 11C]cyanation and RANEY® Nickel catalyzed reductive cyclization

DOE PAGES

So Jeong Lee; Fowler, Joanna S.; Alexoff, David; ...

2015-09-21

We developed a rapid method for the synthesis of carbon-11 radiolabeled indole using a sub-nanomolar quantity of no-carrier-added [ 11C]cyanide as radio-precursor. Based upon a reported synthesis of 2-(2-nitrophenyl)acetonitrile (2), a highly reactive substrate 2-nitrobenzyl bromide (1) was evaluated for nucleophilic [ 11C]cyanation. Additionally, related reaction conditions were explored with the goal of obtaining of highly reactive 2-(2-nitrophenyl)-[1- 11C]acetonitrile ([ 11C]-2) while inhibiting its rapid conversion to 2,3-bis(2-nitrophenyl)-[1- 11C]propanenitrile ([ 11C]-3). Next, a Raney Nickel catalyzed reductive cyclization method was utilized for synthesizing the desired [2- 11C]indole with hydrazinium monoformate as the active reducing agent. Extensive and iterative screening ofmore » basicity, temperature and stoichiometry was required to overcome the large stoichiometry bias that favored 2-nitrobenzylbromide (1) over [ 11C]cyanide, which both caused further alkylation of the desired nitrile and poisoned the Raney Nickel catalyst. The result is an efficient two-step, streamlined method to reliably synthesize [2- 11C]indole with an entire radiochemical yield of 21 ± 2.2% (n = 5, ranging from 18 – 24%). The radiochemical purity of the final product was > 98% and specific activity was 176 ± 24.8 GBq/μmol (n = 5, ranging from 141 – 204 GBq/μmol). The total radiosynthesis time including product purification by semi-preparative HPLC was 50 – 55 min from end of cyclotron bombardment.« less

An efficient and practical synthesis of [2- 11C]indole via superfast nucleophilic [ 11C]cyanation and RANEY® Nickel catalyzed reductive cyclization

DOE Office of Scientific and Technical Information (OSTI.GOV)

So Jeong Lee; Fowler, Joanna S.; Alexoff, David

We developed a rapid method for the synthesis of carbon-11 radiolabeled indole using a sub-nanomolar quantity of no-carrier-added [ 11C]cyanide as radio-precursor. Based upon a reported synthesis of 2-(2-nitrophenyl)acetonitrile (2), a highly reactive substrate 2-nitrobenzyl bromide (1) was evaluated for nucleophilic [ 11C]cyanation. Additionally, related reaction conditions were explored with the goal of obtaining of highly reactive 2-(2-nitrophenyl)-[1- 11C]acetonitrile ([ 11C]-2) while inhibiting its rapid conversion to 2,3-bis(2-nitrophenyl)-[1- 11C]propanenitrile ([ 11C]-3). Next, a Raney Nickel catalyzed reductive cyclization method was utilized for synthesizing the desired [2- 11C]indole with hydrazinium monoformate as the active reducing agent. Extensive and iterative screening ofmore » basicity, temperature and stoichiometry was required to overcome the large stoichiometry bias that favored 2-nitrobenzylbromide (1) over [ 11C]cyanide, which both caused further alkylation of the desired nitrile and poisoned the Raney Nickel catalyst. The result is an efficient two-step, streamlined method to reliably synthesize [2- 11C]indole with an entire radiochemical yield of 21 ± 2.2% (n = 5, ranging from 18 – 24%). The radiochemical purity of the final product was > 98% and specific activity was 176 ± 24.8 GBq/μmol (n = 5, ranging from 141 – 204 GBq/μmol). The total radiosynthesis time including product purification by semi-preparative HPLC was 50 – 55 min from end of cyclotron bombardment.« less

Can hydroxylamine be a more potent nucleophile for the reactivation of tabun-inhibited AChE than prototype oxime drugs? An answer derived from quantum chemical and steered molecular dynamics studies.

PubMed

Lo, Rabindranath; Ganguly, Bishwajit

2014-07-29

Organophosphorus nerve agents are highly toxic compounds which strongly inhibit acetylcholinesterase (AChE) in the blood and in the central nervous system (CNS). Tabun is one of the highly toxic organophosphorus (OP) compounds and is resistant to many oxime drugs formulated for the reactivation of AChE. The reactivation mechanism of tabun-conjugated AChE with various drugs has been examined with density functional theory and ab initio quantum chemical calculations. The presence of a lone-pair located on the amidic group resists the nucleophilic attack at the phosphorus center of the tabun-conjugated AChE. We have shown that the newly designed drug candidate N-(pyridin-2-yl)hydroxylamine, at the MP2/6-31+G*//M05-2X/6-31G* level in the aqueous phase with the polarizable continuum solvation model (PCM), is more effective in reactivating the tabun-conjugated AChE than typical oxime drugs. The rate determining activation barrier with N-(pyridin-2-yl)hydroxylamine was found to be ∼1.7 kcal mol(-1), which is 7.2 kcal mol(-1) lower than the charged oxime trimedoxime (one of the most efficient reactivators in tabun poisonings). The greater nucleophilicity index (ω(-)) and higher CHelpG charge of pyridinylhydroxylamine compared to TMB4 support this observation. Furthermore, we have also examined the reactivation process of tabun-inhibited AChE with some other bis-quaternary oxime drug candidates such as methoxime (MMB4) and obidoxime. The docking analysis suggests that charged bis-quaternary pyridinium oximes have greater binding affinity inside the active-site gorge of AChE compared to the neutral pyridinylhydroxylamine. The peripheral ligand attached to the neutral pyridinylhydroxylamine enhanced the binding with the aromatic residues in the active-site gorge of AChE through effective π-π interactions. Steered molecular dynamics (SMD) simulations have also been performed with the charged oxime (TMB4) and the neutral hydroxylamine. From protein-drug interaction

C-C bond formation and related reactions at the CNC backbone in (smif)FeX (smif = 1,3-di-(2-pyridyl)-2-azaallyl): dimerizations, 3 + 2 cyclization, and nucleophilic attack; transfer hydrogenations and alkyne trimerization (X = N(TMS)2, dpma = (di-(2-pyridyl-methyl)-amide)).

PubMed

Frazier, Brenda A; Williams, Valerie A; Wolczanski, Peter T; Bart, Suzanne C; Meyer, Karsten; Cundari, Thomas R; Lobkovsky, Emil B

2013-03-18

Molecular orbital analysis depicts the CNC(nb) backbone of the smif (1,3-di-(2-pyridyl)-2-azaallyl) ligand as having singlet diradical and/or ionic character where electrophilic or nucleophilic attack is plausible. Reversible dimerization of (smif)Fe{N(SiMe3)2} (1) to [{(Me3Si)2N}Fe]2(μ-κ(3),κ(3)-N,py2-smif,smif) (2) may be construed as diradical coupling. A proton transfer within the backbone-methylated, and o-pyridine-methylated smif of putative ((b)Me2(o)Me2smif)FeN(SiMe3)2 (8) provides a route to [{(Me3Si)2N}Fe]2(μ-κ(4),κ(4)-N,py2,C-((b)Me,(b)CH2,(o)Me2(smif)H))2 (9). A 3 + 2 cyclization of ditolyl-acetylene occurs with 1, leading to the dimer [{2,5-di(pyridin-2-yl)-3,4-di-(p-tolyl-2,5-dihydropyrrol-1-ide)}FeN(SiMe3)2]2 (11), and the collateral discovery of alkyne cyclotrimerization led to a brief study that identified Fe(N(SiMe3)2(THF) as an effective catalyst. Nucleophilic attack by (smif)2Fe (13) on (t)BuNCO and (2,6-(i)Pr2C6H3)NCO afforded (RNHCO-smif)2Fe (14a, R = (t)Bu; 14b, 2,6-(i)PrC6H3). Calculations suggested that (dpma)2Fe (15) would favorably lose dihydrogen to afford (smif)2Fe (13). H2-transfer to alkynes, olefins, imines, PhN═NPh, and ketones was explored, but only stoichiometric reactions were affected. Some physical properties of the compounds were examined, and X-ray structural studies on several dinuclear species were conducted.

Protective Effects of 10-nitro-oleic Acid in a Hypoxia-Induced Murine Model of Pulmonary Hypertension

PubMed Central

Klinke, Anna; Möller, Annika; Pekarova, Michaela; Ravekes, Thorben; Friedrichs, Kai; Berlin, Matthias; Scheu, Katrin M.; Kubala, Lukas; Kolarova, Hana; Ambrozova, Gabriela; Schermuly, Ralph T.; Woodcock, Steven R.; Freeman, Bruce A.; Rosenkranz, Stephan; Baldus, Stephan; Rudolph, Volker

2014-01-01

Pulmonary arterial hypertension (PAH) is characterized by adverse remodeling of pulmonary arteries. Although the origin of the disease and its underlying pathophysiology remain incompletely understood, inflammation has been identified as a central mediator of disease progression. Oxidative inflammatory conditions support the formation of electrophilic fatty acid nitroalkene derivatives, which exert potent anti-inflammatory effects. The current study investigated the role of 10-nitro-oleic acid (OA-NO2) in modulating the pathophysiology of PAH in mice. Mice were kept for 28 days under normoxic or hypoxic conditions, and OA-NO2 was infused subcutaneously. Right ventricular systolic pressure (RVPsys) was determined, and right ventricular and lung tissue was analyzed. The effect of OA-NO2 on cultured pulmonary artery smooth muscle cells (PASMCs) and macrophages was also investigated. Changes in RVPsys revealed increased pulmonary hypertension in mice on hypoxia, which was significantly decreased by OA-NO2 administration. Right ventricular hypertrophy and fibrosis were also attenuated by OA-NO2 treatment. The infiltration of macrophages and the generation of reactive oxygen species were elevated in lung tissue of mice on hypoxia and were diminished by OA-NO2 treatment. Moreover, OA-NO2 decreased superoxide production of activated macrophages and PASMCs in vitro. Vascular structural remodeling was also limited by OA-NO2. In support of these findings, proliferation and activation of extracellular signal-regulated kinases 1/2 in cultured PASMCs was less pronounced on application of OA-NO2.Our results show that the oleic acid nitroalkene derivative OA-NO2 attenuates hypoxia-induced pulmonary hypertension in mice. Thus, OA-NO2 represents a potential therapeutic agent for the treatment of PAH. PMID:24521348

Magnesium-based energy storage systems and methods having improved electrolytes

DOEpatents

Liu, Tianbiao; Li, Guosheng; Liu, Jun; Shao, Yuyan

2016-12-20

Electrolytes for Mg-based energy storage devices can be formed from non-nucleophilic Mg.sup.2+ sources to provide outstanding electrochemical performance and improved electrophilic susceptibility compared to electrolytes employing nucleophilic sources. The instant electrolytes are characterized by high oxidation stability (up to 3.4 V vs Mg), improved electrophile compatibility and electrochemical reversibility (up to 100% coulombic efficiency). Synthesis of the Mg.sup.2+ electrolytes utilizes inexpensive and safe magnesium dihalides as non-nucleophilic Mg.sup.2+ sources in combination with Lewis acids, MR.sub.aX.sub.3-a (for 3.gtoreq.a.gtoreq.1). Furthermore, addition of free-halide-anion donors can improve the coulombic efficiency of Mg electrolytes from nucleophilic or non-nucleophilic Mg.sup.2+ sources.

Total Synthesis of Strychnine.

PubMed

Lee, Geun Seok; Namkoong, Gil; Park, Jisook; Chen, David Y-K

2017-11-16

The total synthesis of the flagship Strychnos indole alkaloid, strychnine, has been accomplished. The developed synthetic sequence features a novel vinylogous 1,4-addition, a challenging iodinium salt mediated silyl enol ether arylation, a palladium-catalyzed Heck reaction, and a streamlined late-stage conversion to strychnine. Furthermore, an application of asymmetric counterion-directed catalysis (ACDC) in the context of target-oriented organic synthesis has been rendered access to an optically active material. The synthetic sequence described herein represents the most concise entry to optically active strychnine to date. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Asymmetric Total Synthesis of (-)-(3 R)-Inthomycin C.

PubMed

Balcells, Sandra; Haughey, Maxwell B; Walker, Johannes C L; Josa-Culleré, Laia; Towers, Christopher; Donohoe, Timothy J

2018-06-04

A short (10 step) and efficient (15% overall yield) synthesis of the natural product (-)-(3 R)-inthomycin C is reported. The key steps comprise three C-C bond-forming reactions: (i) a vinylogous Mukaiyama aldol, (ii) an olefin cross-metathesis reaction, and (iii) an asymmetric Mukaiyama-Kiyooka aldol. This route is notable for its brevity and has the advantage of lacking stoichiometric tin-promoted cross-coupling reactions present in previous approaches. Initial investigations on the biological activity of (-)-(3 R)-inthomycin C and structural analogues on human cancer cell lines are also described for the first time.

No Acid Required: 4π and 6π Electrocyclization Reactions of Dienyl Diketones for the Synthesis of Cyclopentenones and 2H-Pyrans

PubMed Central

2015-01-01

The 1,6-conjugate addition of nucleophiles to dienyl diketones produces either cyclopentenone or 2H-pyran products with high selectivity through either Nazarov (4π) or 6π electrocyclization, respectively. The outcome of the reaction is dependent upon the nature of the nucleophile used. Nucleophiles that are anionic or easily deprotonated exclusively produce cyclopentenones via Nazarov cyclization, whereas the neutral nucleophile DABCO promotes 6π cyclization to afford 2H-pyrans. Experimental evidence is presented for both retro-4π and -6π electrocyclization in these systems, lending support to the bifurcated mechanistic hypothesis proposed for these cyclizations. PMID:25325706

Nitro-fatty acid metabolome: saturation, desaturation, beta-oxidation, and protein adduction.

PubMed

Rudolph, Volker; Schopfer, Francisco J; Khoo, Nicholas K H; Rudolph, Tanja K; Cole, Marsha P; Woodcock, Steven R; Bonacci, Gustavo; Groeger, Alison L; Golin-Bisello, Franca; Chen, Chen-Shan; Baker, Paul R S; Freeman, Bruce A

2009-01-16

identified. In aggregate, these findings show that electrophilic FA nitroalkene derivatives (a) acquire an extended half-life by undergoing reversible and exchangeable electrophilic reactions with nucleophilic targets and (b) are metabolized predominantly via saturation of the double bond and beta-oxidation reactions that terminate at the site of acyl-chain nitration.

Gas-Phase Chemistry of Trimethyl Phosphite,

DTIC Science & Technology

keywords include: Flowing afterglow; Trimethyl phosphite ; Reaction mechanisms; Phosphorous ; and Nucleophilic displacement....The reactions of trimethyl phosphite were investigated with a series of nucleophiles. Products, branching ratios, and reaction rate constants are...of methoxide to form a new ion-dipole complex (CH3O-(CH3O)2PZ). If an additional acidic hydrogen is available on the nucleophile, the major products

The trans influence in the modulation of platinum anticancer agent biology: the effect of nitrite leaving group on aquation, reactions with S-nucleophiles and DNA binding of dinuclear and trinuclear compounds.

PubMed

Montero, Eva I; Zhang, Junyong; Moniodis, Joseph J; Berners-Price, Susan J; Farrell, Nicholas P

2010-08-09

To examine the effect of leaving group and trans influence on the general reactivity of polynuclear platinum antitumor agents we investigated substitution of the chloride leaving groups with nitrite ion, which forms strong bonds to Pt. It was of interest to explore whether nitrite could be used to modulate biological properties of these agents, in particular the deactivating reactions that occur on reaction with S-nucleophiles, involving loss of the linking diamine under the trans influence of sulfur. Reported herein is a study of the synthesis, aquation, DNA binding and reactions with glutathione (GSH), methionine (Met) and acetylmethione (AcMet) of nitrito derivatives of di- and trinuclear platinum antitumor compounds: [{trans-PtNO(2)(NH(3))(2)}(2)(mu-NH(2)(CH(2))(6)NH(2))](NO(3))(2) (1-NO(2)) and [{trans-PtNO(2)(NH(3))(2)}(2)(mu-trans-Pt(NH(3))(2){NH(2)(CH(2))(6)NH(2)}(2))](NO(3))(4) (1'-NO(2)). {(1)H,(15)N}-HSQC NMR studies revealed that 1-NO(2) is inert to aquation reactions, even after prolonged incubation at physiological pH. Monitoring of the interaction of 1-NO(2) with the duplex 5'-d(ATATGTACATAT)(2) (I) showed only unreacted complex, consistent with activation by aquation being a requirement for covalent DNA binding. The reaction of 1-NO(2) with GSH was studied by (1)H, (195)Pt, (15)N and {(1)H,(15)N}-HSQC NMR spectroscopy. For the parent dichlorido compounds (1 and 1') substitution of chloride by GS(-) leads to drug degradation involving liberation of the diamine linker. While the same final products trans-[Pt(SG)(2)(NH(3))(2)] (5) and trans-[{Pt(SG)(NH(3))(2)}(2)-mu-SG] (6) are formed, different mechanisms are involved, consistent with the trans influence NO(2)(-) > Cl(-); the half-life is slightly longer for 1-NO(2) (1.8 h) compared with 1 (1.3 h). Identification of the intermediate trans-[Pt(NH(3))(2)(NO(2))(SG)] (4) shows that the nitrito group remains coordinated while the linker amine is substituted by coordination of GS(-), and then trans

Activation of the SN2 Reaction by Adjacent π Systems: The Critical Role of Electrostatic Interactions and of Dissociative Character.

PubMed

Robiette, Raphaël; Trieu-Van, Tran; Aggarwal, Varinder K; Harvey, Jeremy N

2016-01-27

The activation of the SN2 reaction by π systems is well documented in textbooks. It has been shown previously that this is not primarily due to classical (hyper)conjugative effects. Instead, π-conjugated substituents enhance favorable substrate-nucleophile electrostatic interactions, with electron-withdrawing groups (EWG) on the sp(2) system leading to even stronger activation. Herein we report computational and experimental results which show that this activation by sp(2) EWG-substitution only occurs in a fairly limited number of cases, when the nucleophile involves strong electrostatic interactions (usually strongly basic negatively charged nucleophiles). In other cases, where bond breaking is more advanced than bond making at the transition state, electrophile-nucleophile electrostatic interactions are less important. In such cases, (hyper)conjugative electronic effects determine the reactivity, and EWG-substitution leads to decreased reactivity. The basicity of the nucleophile as well as solvent effects can help to determine which of these two regimes occurs for a given electrophile.

Synthesis and biological evaluation of vinylogous combretastatin A-4 derivatives.

PubMed

Kaffy, Julia; Pontikis, Renée; Florent, Jean-Claude; Monneret, Claude

2005-07-21

Stereospecific syntheses of the Z-E and E-Z vinylogues of combretastatin A-4, and two B-ring related analogues, were achieved through a Suzuki-Miyaura coupling. As compared to CA4, the derivative with a phenyl moiety has shown increased potency in its ability to inhibit tubulin polymerisation.

Chemical dynamics simulations of X- + CH3Y → XCH3 + Y- gas-phase S(N)2 nucleophilic substitution reactions. Nonstatistical dynamics and nontraditional reaction mechanisms.

PubMed

Manikandan, Paranjothy; Zhang, Jiaxu; Hase, William L

2012-03-29

Extensive classical chemical dynamics simulations of gas-phase X(-) + CH(3)Y → XCH(3) + Y(-) S(N)2 nucleophilic substitution reactions are reviewed and discussed and compared with experimental measurements and predictions of theoretical models. The primary emphasis is on reactions for which X and Y are halogen atoms. Both reactions with the traditional potential energy surface (PES), which include pre- and postreaction potential energy minima and a central barrier, and reactions with nontraditional PESs are considered. These S(N)2 reactions exhibit important nonstatistical atomic-level dynamics. The X(-) + CH(3)Y → X(-)---CH(3)Y association rate constant is less than the capture model as a result of inefficient energy transfer from X(-)+ CH(3)Y relative translation to CH(3)Y rotation and vibration. There is weak coupling between the low-frequency intermolecular modes of the X(-)---CH(3)Y complex and higher frequency CH(3)Y intramolecular modes, resulting in non-RRKM kinetics for X(-)---CH(3)Y unimolecular decomposition. Recrossings of the [X--CH(3)--Y](-) central barrier is important. As a result of the above dynamics, the relative translational energy and temperature dependencies of the S(N)2 rate constants are not accurately given by statistical theory. The nonstatistical dynamics results in nonstatistical partitioning of the available energy to XCH(3) +Y(-) reaction products. Besides the indirect, complex forming atomic-level mechanism for the S(N)2 reaction, direct mechanisms promoted by X(-) + CH(3)Y relative translational or CH(3)Y vibrational excitation are possible, e.g., the roundabout mechanism.

Five- and six-membered ring opening of pyroglutamic diketopiperazine.

PubMed

Parrish, Dennis A; Mathias, Lon J

2002-03-22

A variety of ring-opening reactions of pyroglutamic diketopiperazine at both the five-membered and six-membered rings is described. Mild, basic conditions facilitate nucleophilic attack by amines at the diketopiperazine carbonyls giving pyroglutamides in excellent yield. Reaction with nucleophiles under acidic conditions give bis-glutamate derivatives of 2,5-diketopiperazine (DKP). These reactions provide simple, two-step sequences to pyroglutamides and symmetrical diketopiperazines from commercial pyroglutamic acid with control of product dictated by reaction conditions, catalyst, and nucleophile.

Regio- and Enantioselective N-Allylations of Imidazole, Benzimidazole, and Purine Heterocycles Catalyzed by Single-Component Metallacyclic Iridium Complexes

PubMed Central

Stanley, Levi M.

2010-01-01

Highly regio- and enantioselective iridium-catalyzed N-allylations of benzimidazoles, imidazoles, and purines have been developed. N-Allylated benzimidazoles and imidazoles were isolated in high yields (up to 97%) with high branched-to-linear selectivity (up to 99:1) and enantioselectivity (up to 98% ee) from the reactions of benzimidazole and imidazole nucleophiles with unsymmetrical allylic carbonates in the presence of single component, ethylene-bound, metallacyclic iridium catalysts. N-Allylated purines were also obtained in high yields (up to 91%) with high N9:N7 selectivity (up to 96:4), high branched-to-linear selectivity (98:2), and high enantioselectivity (up to 98% ee) under similar conditions. The reactions encompass a range of benzimidazole, imidazole, and purine nucleophiles, as well as a variety of unsymmetrical aryl, heteroaryl, and aliphatic allylic carbonates. Competition experiments between common amine nucleophiles and the heterocyclic nitrogen nucleophiles studied in this work illustrate the effect of nucleophile pKa on the rate of iridium-catalyzed N-allylation reactions. Kinetic studies on the allylation of benzimidazole catalyzed by metallacyclic iridium-phosphoramidite complexes, in combination with studies on the deactivation of these catalysts in the presence of heterocyclic nucleophiles, provide insight into the effects of the structure of the phosphoramidite ligands on the stability of the metallacyclic catalysts. The data obtained from these studies has led to the development of N-allylations of benzimidazoles and imidazoles in the absence of an exogenous base. PMID:19480431

The Preparation of Lucigenin.

ERIC Educational Resources Information Center

Amiet, R. G.

1982-01-01

Outlines and discusses procedures for the preparation of lucigenin, a powerfully chemiluminescent compound. Major techniques (requiring three 4-hour sessions) involving nucleophilic and electrophilic aromatic substitution, nucleophilic aliphatic substitution, reductive coupling, and oxidation reactions include steam distillation, decolorization…

Direct displacement of alkoxy groups of vinylogous esters by Grignard reagents.

PubMed

Brockway, Anthony J; González-López, Marcos; Fettinger, James C; Shaw, Jared T

2011-05-06

The direct displacement of alkoxy groups from the β position of aromatic and unsaturated esters and ketones is described. The reaction is chemo- and regioselective, displaying wide substrate scope. © 2011 American Chemical Society

Direct Displacement of Alkoxy Groups of Vinylogous Esters by Grignard Reagents

PubMed Central

Brockway, Anthony J.; González-López, Marcos; Fettinger, James C.

2011-01-01

The direct displacement of alkoxy groups from the beta position of aromatic and unsaturated esters and ketones is described. The reaction is chemo- and regioselective, displaying wide substrate scope. PMID:21446670

A generalized operational formula based on total electronic densities to obtain 3D pictures of the dual descriptor to reveal nucleophilic and electrophilic sites accurately on closed-shell molecules.

PubMed

Martínez-Araya, Jorge I

2016-09-30

By means of the conceptual density functional theory, the so-called dual descriptor (DD) has been adapted to be used in any closed-shell molecule that presents degeneracy in its frontier molecular orbitals. The latter is of paramount importance because a correct description of local reactivity will allow to predict the most favorable sites on a molecule to undergo nucleophilic or electrophilic attacks; on the contrary, an incomplete description of local reactivity might have serio us consequences, particularly for those experimental chemists that have the need of getting an insight about reactivity of chemical reagents before using them in synthesis to obtain a new compound. In the present work, the old approach based only on electronic densities of frontier molecular orbitals is replaced by the most accurate procedure that implies the use of total electronic densities thus keeping consistency with the essential principle of the DFT in which the electronic density is the fundamental variable and not the molecular orbitals. As a result of the present work, the DD will be able to properly describe local reactivities only in terms of total electronic densities. To test the proposed operational formula, 12 very common molecules were selected as the original definition of the DD was not able to describe their local reactivities properly. The ethylene molecule was additionally used to test the capability of the proposed operational formula to reveal a correct local reactivity even in absence of degeneracy in frontier molecular orbitals. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Gas Phase Reactivity of Carboxylates with N-Hydroxysuccinimide Esters

PubMed Central

Peng, Zhou; McGee, William M.; Bu, Jiexun; Barefoot, Nathan Z.; McLuckey, Scott A.

2015-01-01

N-hydroxysuccinimide (NHS) esters have been used for gas phase conjugation reactions with peptides at nucleophilic sites, such as primary amines (N-terminus, ε-amine of lysine) or guanidines, by forming amide bonds through a nucleophilic attack on the carbonyl carbon. The carboxylate has recently been found to also be a reactive nucleophile capable of initiating a similar nucleophilic attack to form a labile anhydride bond. The fragile bond is easily cleaved, resulting in an oxygen transfer from the carboxylate-containing species to the reagent, nominally observed as a water transfer. This reactivity is shown for both peptides and non-peptidic species. Reagents isotopically labeled with O18 were used to confirm reactivity. This constitutes an example of distinct differences in reactivity of carboxylates between the gas-phase, where they are shown to be reactive, and the solution-phase, where they are not regarded as reactive with NHS esters. PMID:25338221

Nitro-fatty Acid Metabolome: Saturation, Desaturation, β-Oxidation, and Protein Adduction*

PubMed Central

Rudolph, Volker; Schopfer, Francisco J.; Khoo, Nicholas K. H.; Rudolph, Tanja K.; Cole, Marsha P.; Woodcock, Steven R.; Bonacci, Gustavo; Groeger, Alison L.; Golin-Bisello, Franca; Chen, Chen-Shan; Baker, Paul R. S.; Freeman, Bruce A.

2009-01-01

identified. In aggregate, these findings show that electrophilic FA nitroalkene derivatives (a) acquire an extended half-life by undergoing reversible and exchangeable electrophilic reactions with nucleophilic targets and (b) are metabolized predominantly via saturation of the double bond and β-oxidation reactions that terminate at the site of acyl-chain nitration. PMID:19015269

Metal ion-promoted cleavage of nucleoside diphosphosugars: a model for reactions of phosphodiester bonds in carbohydrates.

PubMed

Dano, Meisa; Elmeranta, Marjukka; Hodgson, David R W; Jaakkola, Juho; Korhonen, Heidi; Mikkola, Satu

2015-12-01

Cleavage of five different nucleoside diphosphosugars has been studied in the presence of Cu(2+) and Zn(2+) complexes. The results show that metal ion catalysts promote the cleavage via intramolecular transesterification whenever a neighbouring HO group can adopt a cis-orientation with respect to the phosphate. The HO group attacks the phosphate and two monophosphate products are formed. If such a nucleophile is not available, Cu(2+) complexes are able to promote a nucleophilic attack of an external nucleophile, e.g. a water molecule or metal ion coordinated HO ligand, on phosphate. With the Zn(2+) complex, this was not observed.

Divergent palladium iodide catalyzed multicomponent carbonylative approaches to functionalized isoindolinone and isobenzofuranimine derivatives.

PubMed

Mancuso, Raffaella; Ziccarelli, Ida; Armentano, Donatella; Marino, Nadia; Giofrè, Salvatore V; Gabriele, Bartolo

2014-04-18

2-Alkynylbenzamides underwent different reaction pathways when allowed to react under PdI2-catalyzed oxidative carbonylation conditions, depending on the nature of the external nucleophile and reaction conditions. Thus, oxidative carbonylation of 2-ethynylbenzamides, bearing a terminal triple bond, carried out in the presence of a secondary amine as external nucleophile, selectively led to the formation of 3-[(dialkylcarbamoyl)methylene]isoindolin-1-ones through the intermediate formation of the corresponding 2-ynamide derivatives followed by intramolecular nucleophilic attack by the nitrogen of the benzamide moiety on the conjugated triple bond. On the other hand, 3-[(alkoxycarbonyl)methylene]isobenzofuran-1(3H)imines were selectively obtained when the oxidative carbonylation of 2-alkynylbenzamides, bearing a terminal or an internal triple bond, was carried out in the presence of an alcohol R'OH (such as methanol or ethanol) as the external nucleophile and HC(OR')3 as a dehydrating agent, necessary to avoid substrate hydrolysis. In this latter case, the reaction pathway leading to the isobenzofuranimine corresponded to the 5-exo-dig intramolecular nucleophilic attack of the oxygen of the benzamide moiety on the triple bond coordinated to the metal center followed by alkoxycarbonylation. The structures of representative products have been confirmed by X-ray crystallographic analysis.

Palladium-Catalyzed Asymmetric Alkylation in the Synthesis of Cyclopentanoid and Cycloheptanoid Core Structures Bearing All-Carbon Quaternary Stereocenters

PubMed Central

Hong, Allen Y.; Bennett, Nathan B.; Krout, Michael R.; Jensen, Thomas; Harned, Andrew. M.

2011-01-01

General catalytic asymmetric routes toward cyclopentanoid and cycloheptanoid core structures embedded in numerous natural products have been developed. The central stereoselective transformation in our divergent strategies is the enantioselective decarboxylative alkylation of seven-membered β-ketoesters to form α-quaternary vinylogous esters. Recognition of the unusual reactivity of β-hydroxyketones resulting from the addition of hydride or organometallic reagents enabled divergent access to γ-quaternary acylcyclopentenes through a ring contraction pathway or γ-quaternary cycloheptenones through a carbonyl transposition pathway. Synthetic applications of these compounds were explored through the preparation of mono-, bi-, and tricyclic derivatives that can serve as valuable intermediates for the total synthesis of complex natural products. This work complements our previous work with cyclohexanoid systems. PMID:22347731

Attempts to counteract phosgene-induced acute lung injury by instant high-dose aerosol exposure to hexamethylenetetramine, cysteine or glutathione.

PubMed

Pauluhn, Jürgen; Hai, Chun Xue

2011-01-01

Phosgene is an important high-production-volume intermediate with widespread industrial use. Consistent with other lung irritants causing ALI (acute lung injury), mode-of-action-based countermeasures remain rudimentary. This study was conducted to analyze whether extremely short high-level exposure to phosgene gas could be mitigated using three different inhaled nucleophiles administered by inhalation instantly after exposure to phosgene. Groups of young adult male Wistar rats were acutely exposed to carbonyl chloride (phosgene) using a directed-flow nose-only mode of exposure of 600 mg/m³ for 1.5 min (225 ppm × min). Immediately after exposure to phosgene gas the rats were similarly exposed to three strong nucleophiles with and without antioxidant properties for 5 or 15 min. The following nucleophiles were used: hexamethylenetetramine (HMT), l-cysteine (Cys), and l-glutathione (GSH). The concentration of the aerosol (mass median aerodynamic diameter 1.7-2 µm) was targeted to be in the range of 1 mg/L. Cys and GSH have antioxidant properties in addition. The calculated alveolar molar dosage of phosgene was 9 µmol/kg. At 15-min exposure duration, the respective inhaled dose of HMT, Csy, and GSH were 111, 103, and 46 µmol/kg, respectively. The alveolar dose of drugs was ~10-times lower. The efficacy of treatment was judged by protein concentrations in bronchoalveolar lavage fluid (BALF) collected 1 day post-exposure. In spite of using optimized aerosolization techniques, none of the nucleophiles chosen had any mitigating effect on BALF-protein extravasation. This finding appear to suggest that inhaled phosgene gas acylates instantly nucleophilic moieties at the site of initial deposition and that the resultant reaction products can not be reactivated even following instant inhalation treatment with competing nucleophilic agents. In spite of using maximal technically attainable concentrations, it appears to be experimentally challenging to deliver

Molecular titanium nitrides: nucleophiles unleashed

DOE PAGES

Grant, Lauren N.; Pinter, Balazs; Kurogi, Takashi; ...

2017-01-30

In this contribution we present reactivity studies of a rare example of a titanium salt, in the form of [μ 2-K(OEt 2)] 2[(PN) 2Timore » $$\\equiv$$N] 2 (1) (PN - = N-(2-(diisopropylphosphino)-4-methylphenyl)-2,4,6-trimethylanilide) to produce a series of imide moieties including rare examples such as methylimido, borylimido, phosphonylimido, and a parent imido. For the latter, using various weak acids allowed us to narrow the pK a range of the NH group in (PN) 2Ti$$\\equiv$$NH to be between 26–36. Complex 1 could be produced by a reductively promoted elimination of N 2 from the azide precursor (PN) 2TiN 3, whereas reductive splitting of N 2 could not be achieved using the complex (PN) 2Ti$$\\equiv$$N$$\\equiv$$N$$\\equiv$$Ti(PN) 2 (2) and a strong reductant. Complete N-atom transfer reactions could also be observed when 1 was treated with ClC(O) tBu and OCCPh 2 to form NC tBu and KNCCPh 2, respectively, along with the terminal oxo complex (PN) 2Ti$$\\equiv$$O, which was also characterized. A combination of solid state 15N NMR (MAS) and theoretical studies allowed us to understand the shielding effect of the counter cation in dimer 1, the monomer [K(18-crown-6)][(PN) 2Ti$$\\equiv$$N], and the discrete salt [K(2,2,2-Kryptofix)][(PN) 2Ti$$\\equiv$$N] as well as the origin of the highly downfield 15N NMR resonance when shifting from dimer to monomer to a terminal nitride (discrete salt). The upfield shift of 15N nitride resonance in the 15N NMR spectrum was found to be linked to the K + induced electronic structural change of the titanium-nitride functionality by using a combination of MO analysis and quantum chemical analysis of the corresponding shielding tensors.« less

Polybenzoxazole via aromatic nucleophilic displacement

NASA Technical Reports Server (NTRS)

Hergenrother, Paul M. (Inventor); Connell, John W. (Inventor); Smith, Joseph G., Jr. (Inventor)

1993-01-01

Polybenzoxazoles (PBO) are heterocyclic macromolecules which were first synthesized in a two-step process by the initial formation of aromatic diacid chlorides with bis(o-aminophenol)s through solution condensation of aromatic diacid chlorides with bis(o-aminophenol)s followed by thermal cyclodehydration. Since then several methods were utilized in their synthesis. The most common synthetic method for PBO involves a polycondensation of bis(o-aminophenol)s with aromatic diacid diphenyl esters. Another preparative route involves the solution polycondensation of the hydrochloride salts of bis(o-amino phenol)s with aromatic diacids in polyphosphoric acid. Another synthetic method involves the initial formation of poly(o-hydroxy amide)s from silylated bis(o-aminophenol)s with aromatic diacid chlorides followed by thermal cyclodehydration to PBO. A recent preparative route involves the reaction of aromatic bisphenols with bis(fluorophenyl) benzoxazoles by the displacement reaction to form PBO. The novelty of the present invention is that high molecular weight PBO of new chemical structures are prepared that exhibit a favorable combination of physical and mechanical properties.

Catalytic Nucleophilic Glyoxylation of Aldehydes

PubMed Central

Steward, Kimberly M.; Johnson, Jeffrey S.

2010-01-01

β-Silyloxy-α-ketoesters are prepared through a cyanide-catalyzed benzoin-type reaction with silyl glyoxylates and aldehydes. The products undergo a dynamic kinetic resolution to provide enantioenriched orthogonally protected alcohols and can be converted to the corresponding β-silyloxy-α-aminoesters. PMID:20481613

First kinetic discrimination between carbon and oxygen reactivity of enols.

PubMed

García-Río, Luis; Mejuto, Juan C; Parajó, Mercedes; Pérez-Lorenzo, Moisés

2008-11-07

Nitrosation of enols shows a well-differentiated behavior depending on whether the reaction proceeds through the carbon (nucleophilic catalysis is observed) or the oxygen atom (general acid-base catalysis is observed). This is due to the different operating mechanisms for C- and O-nitrosation. Nitrosation of acetylacetone (AcAc) shows a simultaneous nucleophilic and acid-base catalysis. This simultaneous catalysis constitutes the first kinetic evidence of two independent reactions on the carbon and oxygen atom of an enol. The following kinetic study allows us to determine the rate constants for both reaction pathways. A similar reactivity of the nucleophilic centers with the nitrosonium ion is observed.

Evaluation of the Commercial off-the-shelf (COTS) Low Temperature Powder Coating (LTPC)

DTIC Science & Technology

2017-11-15

isothiazolin- 3-one (OIT) 26530-20-1 120°C 4.9x10-3 (25°C) Isothiazolinone; Mode of Action: Electrophilic active agent. Reacts with nucleophiles (e.g...Action: Electrophilic active agent with activated N-S bond and vinyl activated halogens; reacts with nucleophilic elements of cell proteins

The α-Effect and Competing Mechanisms: The Gas-Phase Reactions of Microsolvated Anions with Methyl Formate

NASA Astrophysics Data System (ADS)

Thomsen, Ditte L.; Nichols, Charles M.; Reece, Jennifer N.; Hammerum, Steen; Bierbaum, Veronica M.

2014-02-01

The enhanced reactivity of α-nucleophiles, which contain an electron lone pair adjacent to the reactive site, has been demonstrated in solution and in the gas phase and, recently, for the gas-phase SN2 reactions of the microsolvated HOO-(H2O) ion with methyl chloride. In the present work, we continue to explore the significance of microsolvation on the α-effect as we compare the gas-phase reactivity of the microsolvated α-nucleophile HOO-(H2O) with that of microsolvated normal alkoxy nucleophiles, RO-(H2O), in reactions with methyl formate, where three competing reactions are possible. The results reveal enhanced reactivity of HOO-(H2O) towards methyl formate, and clearly demonstrate the presence of an overall α-effect for the reactions of the microsolvated α-nucleophile. The association of the nucleophiles with a single water molecule significantly lowers the degree of proton abstraction and increases the SN2 and BAC2 reactivity compared with the unsolvated analogs. HOO-(H2O) reacts with methyl formate exclusively via the BAC2 channel. While microsolvation lowers the overall reaction efficiency, it enhances the BAC2 reaction efficiency for all anions compared with the unsolvated analogs. This may be explained by participation of the solvent water molecule in the BAC2 reaction in a way that continuously stabilizes the negative charge throughout the reaction.

Application of the Hard and Soft, Acids and Bases (HSAB) theory to toxicant--target interactions.

PubMed

Lopachin, Richard M; Gavin, Terrence; Decaprio, Anthony; Barber, David S

2012-02-20

Many chemical toxicants and/or their active metabolites are electrophiles that cause cell injury by forming covalent bonds with nucleophilic targets on biological macromolecules. Covalent reactions between nucleophilic and electrophilic reagents are, however, discriminatory since there is a significant degree of selectivity associated with these interactions. Over the course of the past few decades, the theory of Hard and Soft, Acids and Bases (HSAB) has proven to be a useful tool in predicting the outcome of such reactions. This concept utilizes the inherent electronic characteristic of polarizability to define, for example, reacting electrophiles and nucleophiles as either hard or soft. These HSAB definitions have been successfully applied to chemical-induced toxicity in biological systems. Thus, according to this principle, a toxic electrophile reacts preferentially with biological targets of similar hardness or softness. The soft/hard classification of a xenobiotic electrophile has obvious utility in discerning plausible biological targets and molecular mechanisms of toxicity. The purpose of this perspective is to discuss the HSAB theory of electrophiles and nucleophiles within a toxicological framework. In principle, covalent bond formation can be described by using the properties of their outermost or frontier orbitals. Because these orbital energies for most chemicals can be calculated using quantum mechanical models, it is possible to quantify the relative softness (σ) or hardness (η) of electrophiles or nucleophiles and to subsequently convert this information into useful indices of reactivity. This atomic level information can provide insight into the design of corroborative laboratory research and thereby help investigators discern corresponding molecular sites and mechanisms of toxicant action. The use of HSAB parameters has also been instrumental in the development and identification of potential nucleophilic cytoprotectants that can scavenge toxic

APPLICATION OF THE HARD AND SOFT, ACIDS AND BASES (HSAB) THEORY TO TOXICANT-TARGET INTERACTIONS

PubMed Central

LoPachin, Richard M.; Gavin, Terrence; DeCaprio, Anthony; Barber, David S.

2011-01-01

Many chemical toxicants and/or their active metabolites are electrophiles that cause cell injury by forming covalent bonds with nucleophilic targets on biological macromolecules. Covalent reactions between nucleophilic and electrophilic reagents are however discriminatory, since there is a significant degree of selectivity associated with these interactions. Over the course of the past few decades, the theory of Hard and Soft, Acid and Bases (HSAB) has proven to be a useful tool in predicting the outcome of such reactions. This concept utilizes the inherent electronic characteristic of polarizability to define, for example, reacting electrophiles and nucleophiles as either hard or soft. These HSAB definitions have been successfully applied to chemical-induced toxicity in biological systems. Thus, according to this principle, a toxic electrophile reacts preferentially with biological targets of similar hardness or softness. The soft/hard classification of a xenobiotic electrophile has obvious utility in discerning plausible biological targets and molecular mechanisms of toxicity. The purpose of this Perspective is to discuss the HSAB theory of electrophiles and nucleophiles within a toxicological framework. In principle, covalent bond formation can be described by using the properties of their outermost or frontier orbitals. Because these orbital energies for most chemicals can be calculated using quantum mechanical models, it is possible to quantify the relative softness (σ) or hardness (η) of electrophiles or nucleophiles and to subsequently convert this information into useful indices of reactivity. This atomic level information can provide insight into the design of corroborative laboratory research and thereby help investigators discern corresponding molecular sites and mechanisms of toxicant action. The use of HSAB parameters has also been instrumental in the development and identification of potential nucleophilic cytoprotectants that can scavenge toxic

Some chemical and physical properties of nisin, a small-protein antibiotic produced by Lactococcus lactis.

PubMed Central

Liu, W; Hansen, J N

1990-01-01

Nisin is a small gene-encoded antimicrobial protein produced by Lactococcus lactis that contains unusual dehydroalanine and dehydrobutyrine residues. The reactivity of these residues toward nucleophiles was explored by reacting nisin with a variety of mercaptans. The kinetics of reaction with 2-mercaptoethane-sulfonate and thioglycolate indicated that the reaction pathway includes a binding step. Reaction of nisin at high pH resulted in the formation of multimeric products, apparently as a result of intramolecular and intermolecular reactions between nucleophilic groups and the dehydro residues. One of the nucleophiles had a pKa of about 9.8. The unique vinyl protons of the dehydro residues that give readily identifiable proton nuclear magnetic resonances were used to observe the addition of nucleophiles to the dehydro moiety. After reaction with nucleophiles, nisin lost its antibiotic activity and no longer showed the dehydro resonances, indicating that the dehydro groups had been modified. The effect of pH on the solubility of nisin was determined; the solubility was quite high at low pH (57 mg/ml at pH 2) and was much lower at high pH (0.25 mg/ml at pH 8 to 12), as measured before significant pH-induced chemical modification had occurred. High-performance liquid chromatography on a C18 column was an effective technique for separating unmodified nisin from its reaction products. The cyanogen bromide cleavage products of nisin were about 90% less active toward inhibition of bacterial spore outgrowth than was native nisin. These results are consistent with earlier observations, which suggested that the dehydro residues of nisin have a role in the mechanism of antibiotic action, in which they act as electrophilic Michael acceptors toward nucleophiles in the cellular target. Images PMID:2119570

The α-effect in gas-phase SN2 reactions of microsolvated anions: methanol as a solvent.

PubMed

Thomsen, Ditte L; Reece, Jennifer N; Nichols, Charles M; Hammerum, Steen; Bierbaum, Veronica M

2014-09-18

The α-effect, an enhanced reactivity of nucleophiles with a lone-pair adjacent to the reaction center, has been studied in solution for several decades. The gas-phase α-effect has recently been documented in studies of SN2 reactions as well as in competing reactions for both bare and microhydrated anions. In the present work we extend our studies of the significance of microsolvation on the α-effect, employing methanol as the solvent, in the expectation that the greater stability of the methanol cluster relative to the water cluster will lower the reactivity and thereby allow studies over a wider efficiency range. We compare the gas-phase reactivity of the microsolvated α-nucleophile HOO(-)(CH3OH) to that of microsolvated normal alkoxy nucleophiles, RO(-)(CH3OH) in reactions with CH3Cl and CH3Br. The results reveal enhanced reactivity of HOO(-)(CH3OH) toward both methyl halides relative to the normal nucleophiles, and clearly demonstrate the presence of an α-effect for the microsolvated α-nucleophile. The highly exothermic reactions with methyl bromide result in a smaller Brønsted βnuc value than observed for methyl chloride, and the α-effect in turn influences the reactions with methyl chloride more than with methyl bromide. Computational investigations reveal that reactions with methyl bromide proceed through earlier transition states with less advanced bond formation compared to the related reactions of methyl chloride. In addition, solvent interactions for HOO(-) are quite different from those with the normal nucleophiles at the transition state, indicating that differential solvation may well contribute to the α-effect. The greater thermodynamic and kinetic stability of the anion-methanol clusters relative to the anion-water clusters accounts well for the differences in the influence of solvation with the two protic polar solvents.

Navy-ASEE (American Society for Engineering Education) Summer Faculty Research Program for 1983 with a Summary of Statistics and a Cumulative Compilation of Data on Later Research Fallouts from the First Five Years of the Program, 1979-1983.

DTIC Science & Technology

1983-01-01

POLYMER FORMATION VIA NUCLEOPHILIC ADDITION TO ACETYLENES Carl L. Bumgardner Department of Chemistry North Carolina...State University Raleigh, North Carolina ABSTRACT Utilizing the ability of acetylenes to add nucleophiles, two new polymer - forming reactions were...examined. The first involved hydroquinone and 1, 4-diethynylbenzene, which, under base calatysis, gave a new semiconducting polymer having the

Grunwald-Winstein Analysis - Isopropyl Chloroformate Solvolysis Revisited

PubMed Central

D’Souza, Malcolm J.; Reed, Darneisha N.; Erdman, Kevin J.; Kyong, Jin Burm; Kevill, Dennis N.

2009-01-01

Specific rates of solvolysis at 25 °C for isopropyl chloroformate (1) in 24 solvents of widely varying nucleophilicity and ionizing power, plus literature values for studies in water and formic acid, are reported. Previously published solvolytic rate constants at 40.0 °C are supplemented with two additional values in the highly ionizing fluoroalcohols. These rates are now are analyzed using the one and two-term Grunwald-Winstein Equations. In the more ionizing solvents including ten fluoroalcohols negligible sensitivities towards changes in solvent nucleophilicity (l) and very low sensitivities towards changes in solvent ionizing power (m) values are obtained, evocative to those previously observed for 1-adamantyl and 2-adamantyl chloroformates 2 and 3. These observations are rationalized in terms of a dominant solvolysis-decomposition with loss of the CO2 molecule. In nine of the more nucleophilic pure alchohols and aqueous solutions an association-dissociation mechanism is believed to be operative. Deficiencies in the acid production indicate 2-33% isopropyl chloride formation, with the higher values in less nucleophilic solvents. PMID:19399225

Deciphering Front-Side Complex Formation in SN2 Reactions via Dynamics Mapping.

PubMed

Szabó, István; Olasz, Balázs; Czakó, Gábor

2017-07-06

Due to their importance in organic chemistry, the atomistic understanding of bimolecular nucleophilic substitution (S N 2) reactions shows exponentially growing interest. In this publication, the effect of front-side complex (FSC) formation is uncovered via quasi-classical trajectory computations combined with a novel analysis method called trajectory orthogonal projection (TOP). For both F - + CH 3 Y [Y = Cl,I] reactions, the lifetime distributions of the F - ···YCH 3 front-side complex revealed weakly trapped nucleophiles (F - ). However, only the F - + CH 3 I reaction features strongly trapped nucleophiles in the front-side region of the prereaction well. Interestingly, both back-side and front-side attack show propensity to long-lived FSC formation. Spatial distributions of the nucleophile demonstrate more prominent FSC formation in case of the F - + CH 3 I reaction compared to F - + CH 3 Cl. The presence of front-side intermediates and the broad spatial distribution in the back-side region may explain the indirect nature of the F - + CH 3 I reaction.

Dietary nitrates, nitrites, and cardiovascular disease.

PubMed

Hord, Norman G

2011-12-01

Dietary nitrate (NO(3)), nitrite (NO(2)), and arginine can serve as sources for production of NO(x) (a diverse group of metabolites including nitric oxide, nitrosothiols, and nitroalkenes) via ultraviolet light exposure to skin, mammalian nitrate/nitrite reductases in tissues, and nitric oxide synthase enzymes, respectively. NO(x) are responsible for the hypotensive, antiplatelet, and cytoprotective effects of dietary nitrates and nitrites. Current regulatory limits on nitrate intakes, based on concerns regarding potential risk of carcinogenicity and methemoglobinemia, are exceeded by normal daily intakes of single foods, such as soya milk and spinach, as well as by some recommended dietary patterns such as the Dietary Approaches to Stop Hypertension diet. This review includes a call for regulatory bodies to consider all available data on the beneficial physiologic roles of nitrate and nitrite in order to derive rational bases for dietary recommendations.

Reversible double oxidation and protonation of the non-innocent bridge in a nickel(II) salophen complex.

PubMed

de Bellefeuille, David; Askari, Mohammad S; Lassalle-Kaiser, Benedikt; Journaux, Yves; Aukauloo, Ally; Orio, Maylis; Thomas, Fabrice; Ottenwaelder, Xavier

2012-12-03

Substitution on the aromatic bridge of a nickel(II) salophen complex with electron-donating dimethylamino substituents creates a ligand with three stable, easily and reversibly accessible oxidation states. The one-electron-oxidized product is characterized as a nickel(II) radical complex with the radical bore by the central substituted aromatic ring, in contrast to other nickel(II) salen or salophen complexes that oxidize on the phenolate moieties. The doubly oxidized product, a singlet species, is best described as having an iminobenzoquinone bridge with a vinylogous distribution of bond lengths between the dimethylamino substituents. Protonation of the dimethylamino substituents inhibits these redox processes on the time scale of cyclovoltammetry, but electrolysis and chemical oxidation are consistent with deprotonation occurring concomitantly with electron transfer to yield the mono- and dioxidized species described above.

Nucleophilicities of Lewis Bases B and Electrophilicities of Lewis Acids A Determined from the Dissociation Energies of Complexes B⋯A Involving Hydrogen Bonds, Tetrel Bonds, Pnictogen Bonds, Chalcogen Bonds and Halogen Bonds.

PubMed

Alkorta, Ibon; Legon, Anthony C

2017-10-23

It is shown that the dissociation energy D e for the process B⋯A = B + A for 250 complexes B⋯A composed of 11 Lewis bases B (N₂, CO, HC≡CH, CH₂=CH₂, C₃H₆, PH₃, H₂S, HCN, H₂O, H₂CO and NH₃) and 23 Lewis acids (HF, HCl, HBr, HC≡CH, HCN, H₂O, F₂, Cl₂, Br₂, ClF, BrCl, H₃SiF, H₃GeF, F₂CO, CO₂, N₂O, NO₂F, PH₂F, AsH₂F, SO₂, SeO₂, SF₂, and SeF₂) can be represented to good approximation by means of the equation D e = c ' N B E A , in which N B is a numerical nucleophilicity assigned to B, E A is a numerical electrophilicity assigned to A, and c ' is a constant, conveniently chosen to have the value 1.00 kJ mol -1 here. The 250 complexes were chosen to cover a wide range of non-covalent interaction types, namely: (1) the hydrogen bond; (2) the halogen bond; (3) the tetrel bond; (4) the pnictogen bond; and (5) the chalcogen bond. Since there is no evidence that one group of non-covalent interaction was fitted any better than the others, it appears the equation is equally valid for all the interactions considered and that the values of N B and E A so determined define properties of the individual molecules. The values of N B and E A can be used to predict the dissociation energies of a wide range of binary complexes B⋯A with reasonable accuracy.

A General Diastereoselective Catalytic Vinylogous Aldol Reaction Among Tetramic Acid-Derived Pyrroles

PubMed Central

2015-01-01

A catalytic diastereoselective aldol reaction has been developed for N1-arylated/C2-O-silylated/C3-methylated and brominated/C4-O-methylated pyrroles in its reactions with various aldehydes. Syn adducts emerge with regard to the vicinal nitrogen and oxygen heteroatom substituents. The N1-aryl residue undergoes oxidative cleavage, and the C3-bromine atom undergoes palladium-mediated coupling reactions, both without disturbing the newly created stereocenters. PMID:25119431

Action mechanism of tyrosinase on meta- and para-hydroxylated monophenols.

PubMed

Fenoll, L G; Rodríguez-López, J N; Varón, R; García-Ruiz, P A; García-Cánovas, F; Tudela, J

2000-04-01

The relationship between the structure and activity of meta- and para-hydroxylated monophenols was studied during their tyrosinase-catalysed hydroxylation and the rate-limiting steps of the reaction mechanism were identified. The para-hydroxylated substrates permit us to study the effect of a substituent (R) in the carbon-1 position (C-1) of the benzene ring on the nucleophilic attack step, while the meta group permits a similar study of the effect on the electrophilic attack step. Substrates with a -OCH3 group on C-1, as p-hydroxyanisol (4HA) and m-hydroxyanisol (3HA), or with a -CH2OH group, as p-hydroxybenzylalcohol (4HBA) and m-hydroxybenzylalcohol (3HBA), were used because the effect of the substituent (R) size was assumed to be similar. However, the electron-donating effect of the -OCH3 group means that the carbon-4 position (C-4) is favoured for nucleophilic attack (para-hydroxylated substrates) or for electrophilic attack (meta-hydroxylated substrates). The electron-attracting effect of the -CH2OH group has the opposite effect, hindering nucleophilic (para) or electrophilic (meta) attack of C-4. The experimental data point to differences between the maximum steady-state rate (V(M)Max) of the different substrates, the value of this parameter depends on the nucleophilic and electrophilic attack. However, differences are greatest in the Michaelis constants (K(M)m), with the meta-hydroxylated substrates having very large values. The catalytic efficiency k(M)cat/K(M)m is much greater for thepara-hydroxylated substrates although it varies greatly between one substrate and the other. However, it varies much less in the meta-hydroxylated substrates since this parameter describes the power of the nucleophilic attack, which is weaker in the meta OH. The large increase in the K(M)m of the meta-hydroxylated substrates might suggest that the phenolic OH takes part in substrate binding. Since this is a weaker nucleophil than the para-hydroxylated substrates, the binding

α-Carbamoylsulfides as N-Carbamoylimine Precursors in the Visible Light Photoredox-Catalyzed Synthesis of α,α-Disubstituted Amines.

PubMed

Lebée, Clément; Languet, Morgan; Allain, Clémence; Masson, Géraldine

2016-03-18

A general and practical photoredox-promoted addition of nucleophiles to N-acylimines generated in situ from α-amidosulfides using Ru(bpy)3(PF6)2 as the photocatalyst is reported. The broad scope of the reaction toward various nucleophiles and amidosulfide derivatives was explored. This novel protocol provides a rapid, mild, and efficient access to valuable α,α-disubstituted amines in respectable yields.

Complications of modeling glycosylation reactions: can the anomeric conformation of a donor determine the glycopyranosyl oxacarbenium ring conformation?

PubMed

Whitfield, Dennis M

2012-07-15

That the ring conformation of glycopyranosyl oxacarbenium ions can influence the stereochemical outcome of glycosylation reactions has been postulated for some time. Some new ionization calculations show that the ultimate conformation (4)H(3) or (5)S(1) of D-glucopyranosyl oxacarbenium ions depends on the initial ϕ(H) (CH-1-C-1-S(+)-SCH(3)) conformation of anomeric thiosulfonium ions. Evidence is also presented that nucleophile:electrophile hydrogen bonded complexes, 1,6-anhydro-carbenium ions and electron rich carbon nucleophile:oxacarbenium ion complexes are all probably artifacts of neglecting counter ions or nucleophiles in the DFT calculation. All three cationic species are likely important for glycosylation reaction side reactions but not as productive species. Copyright © 2012. Published by Elsevier Ltd.

Hydrolysis of the quinone methide of butylated hydroxytoluene in aqueous solutions.

PubMed

Willcockson, Maren Gulsrud; Toteva, Maria M; Stella, Valentino J

2013-10-01

Butylated hydroxytoluene or BHT is an antioxidant commonly used in pharmaceutical formulations. BHT upon oxidation forms a quinone methide (QM). QM is a highly reactive electrophilic species that can undergo nucleophilic addition. Here, the kinetic reactivity of QM with water at various apparent pH values in a 50% (v/v) water-acetonitrile solution at constant ionic strength of I = 0.5 (NaCl)4 , was studied. The hydrolysis of QM in the presence of added acid, base, sodium chloride, and phosphate buffer resulted in the formation of only one product--the corresponding 3,5-di-tert-butyl-4-hydroxybenzyl alcohol (BA). The rate of BA formation was catalyzed by the addition of acid and base, but not chloride and phosphate species. Nucleophilic excipients, used in the pharmaceutical formulation, or nucleophilic groups on active pharmaceutical ingredient molecule may form adducts with QM, the immediate oxidative product of BHT degradation, thus having implications for drug product impurity profiles. Because of these considerations, BHT should be used with caution in formulations containing drugs or excipients capable of acting as nucleophiles. © 2013 Wiley Periodicals, Inc. and the American Pharmacists Association.

Hydrogen/Chlorine exchange reactions of gaseous carbanions.

PubMed

Chen, Hao; Cooks, R Graham; Meurer, Eduardo C; Eberlin, Marcos N

2005-12-01

Gas-phase reactions of three typical carbanions CH(2)NO(2)(-), CH(2)CN(-), and CH(2)S(O)CH(3)(-) with the chloromethanes CH(2)Cl(2), CHCl(3), and CCl(4), examined by tandem mass spectrometry, show a novel hydrogen/chlorine exchange reaction. For example, reaction between the nitromethyl anion CH(2)NO(2)(-) and carbon tetrachloride CCl(4) forms the ion CHClNO(2)(-). The suggested reaction mechanism involves nucleophilic attack by CH(2)NO(2)(-) at the chlorine of CCl(4) followed by proton transfer within the resulting complex [CH(2)ClNO(2) + CCl(3)(-)] to form CHClNO(2)(-) and CHCl(3). Two other carbanions CH(2)CN(-) and CH(2)S(O)CH(3)(-) also undergo the novel hydrogen/chlorine exchange reactions with CCl(4) but to a much smaller extent, their higher nucleophilicities favoring competitive nucleophilic attack reactions. Proton abstraction is the exclusive pathway in the reactions of these carbanions with CHCl(3). While CH(2)CN(-) and CH(2)S(O)CH(3)(-) promote mainly proton abstraction and nucleophilic displacement in reactions with CH(2)Cl(2), CH(2)NO(2)(-) does not react.

Structure and reactivity of boron-ate complexes derived from primary and secondary boronic esters.

PubMed

Feeney, Kathryn; Berionni, Guillaume; Mayr, Herbert; Aggarwal, Varinder K

2015-06-05

Boron-ate complexes derived from primary and secondary boronic esters and aryllithiums have been isolated, and the kinetics of their reactions with carbenium ions studied. The second-order rate constants have been used to derive nucleophilicity parameters for the boron-ate complexes, revealing that nucleophilicity increased with (i) electron-donating aromatics on boron, (ii) neopentyl glycol over pinacol boronic esters, and (iii) 12-crown-4 ether.

Probing the importance of the hemilabile site of bis(phosphine) monoxide ligands in the copper-catalyzed addition of diethylzinc to N-phosphinoylimines: discovery of new effective chiral ligands.

PubMed

Bonnaventure, Isabelle; Charette, André B

2008-08-15

The hemilabile ligand Me-DuPHOS(O) 2 has proven to be a successful ligand for the copper-catalyzed addition of diethylzinc to N-phosphinoylimines. The corresponding alpha-chiral amines were obtained in high yields (80-98%) and enantiomeric ratios (19.0:1 to 99.0:1 er). Furthermore, this Cu* 2 catalytic system has been shown to be effective in the addition of diethylzinc to nitroalkenes and in the reduction of beta,beta-disubstituted vinyl phenyl sulfones. This paper describes a general structure/selectivity study in which the three ligand subunits (chiral phospholane-linker-labile coordinating group (Z)) are systematically modified and tested in the copper-catalyzed addition of diethylzinc to the N-phosphinoylimine 1 derived from benzaldehyde. This study led to the discovery of a new class of effective chiral ligands that combine a chiral phospholane unit and an achiral phosphine oxide.

Phosphine-Catalyzed Doubly Stereoconvergent γ-Additions of Racemic Heterocycles to Racemic Allenoates: The Catalytic Enantioselective Synthesis of Protected α,α-Disubstituted α-Amino Acid Derivatives.

PubMed

Kalek, Marcin; Fu, Gregory C

2015-07-29

Methods have recently been developed for the phosphine-catalyzed asymmetric γ-addition of nucleophiles to readily available allenoates and alkynoates to generate useful α,β-unsaturated carbonyl compounds that bear a stereogenic center in either the γ or the δ position (but not both) with high stereoselectivity. The utility of this approach would be enhanced considerably if the stereochemistry at both termini of the new bond could be controlled effectively. In this report, we describe the achievement of this objective, specifically, that a chiral phosphepine can catalyze the stereoconvergent γ-addition of a racemic nucleophile to a racemic electrophile; through the choice of an appropriate heterocycle as the nucleophilic partner, this new method enables the synthesis of protected α,α-disubstituted α-amino acid derivatives in good yield, diastereoselectivity, and enantioselectivity.

Biogenetically inspired approach to the Strychnos alkaloids. Concise syntheses of (+/-)-akuammicine and (+/-)-strychnine.

PubMed

Ito, M; Clark, C W; Mortimore, M; Goh, J B; Martin, S F

2001-08-22

A linear synthesis of the indole alkaloid (+/-)-akuammicine (2) was completed by a novel sequence of reactions requiring only 10 steps from commercially available starting materials. The approach features a tandem vinylogous Mannich addition and an intramolecular hetero Diels-Alder reaction to rapidly assemble the pentacyclic heteroyohimboid derivative 8 from the readily available hydrocarboline 6. Oxidation of the E ring of 8 gave the lactone 9 that was converted into deformylgeissoschizine (11). The subsequent elaboration of 11 into 2 was effected by a biomimetically patterned transformation that involved sequential oxidation and base-induced skeletal reorganization. A variation of these tactics was then applied to the synthesis of the C(18) hydroxylated akuammicine derivative 36. Because 36 had previously been converted into strychnine (1) in four steps, its preparation constitutes a concise, formal synthesis of this complex alkaloid.

Virtually complete control of simple and face diastereoselectivity in the Michael addition reactions between achiral equivalents of a nucleophilic glycine and (S)- or (R)-3-(E-enoyl)-4-phenyl-1,3-oxazolidin-2-ones: practical method for preparation of beta-substituted pyroglutamic acids and prolines.

PubMed

Soloshonok, Vadim A; Ueki, Hisanori; Tiwari, Rohit; Cai, Chaozhong; Hruby, Victor J

2004-07-23

This study demonstrates a new strategy for controlling the stereochemical outcome of the Michael addition reactions between nucleophilic glycine equivalents and alpha,beta-unsaturated carboxylic acid derivatives: The addition reactions between achiral Ni(II)-complex of the Schiff base of glycine with o-[N-alpha-pycolylamino]acetophenone and (S)- or (R)-3-(E-enoyl)-4-phenyl-1,3-oxazolidin-2-ones were shown to occur at room temperature in the presence of nonchelating organic bases and, most notably, with very high stereoselectivity at both newly formed stereogenic centers. Thus, the chiral 4-phenyl-1,3-oxazolidin-2-one moiety was found to control efficiently both face diastereoselectivities of the glycine derived enolate and the C,C double bond of the Michael acceptor. The new strategy developed in this work is methodologically superior to previous methods, most notably in terms of generality and synthetic efficiency. Excellent chemical yields and diastereoselectivities, combined with the simplicity of the experimental procedures, render the present method of immediate use for preparing various 3-substituted pyroglutamic acids and related amino acids (glutamic acids, glutamines, prolines, etc.) available via conventional transformations of the former.

ProPhenol-Catalyzed Asymmetric Additions by Spontaneously Assembled Dinuclear Main Group Metal Complexes

PubMed Central

2016-01-01

Conspectus The development of catalytic enantioselective transformations has been the focus of many research groups over the past half century and is of paramount importance to the pharmaceutical and agrochemical industries. Since the award of the Nobel Prize in 2001, the field of enantioselective transition metal catalysis has soared to new heights, with the development of more efficient catalysts and new catalytic transformations at increasing frequency. Furthermore, catalytic reactions that allow higher levels of redox- and step-economy are being developed. Thus, alternatives to asymmetric alkene dihydroxylation and the enantioselective reduction of α,β-unsaturated ketones can invoke more strategic C–C bond forming reactions, such as asymmetric aldol reactions of an aldehyde with α-hydroxyketone donors or enantioselective alkynylation of an aldehyde, respectively. To facilitate catalytic enantioselective addition reactions, including the aforementioned aldol and alkynylation reactions, our lab has developed the ProPhenol ligand. In this Account, we describe the development and application of the ProPhenol ligand for asymmetric additions of both carbon- and heteroatom-based nucleophiles to various electrophiles. The ProPhenol ligand spontaneously forms chiral dinuclear metal complexes when treated with an alkyl metal reagent, such as Et2Zn or Bu2Mg. The resulting complex contains both a Lewis acidic site to activate an electrophile and a Brønsted basic site to deprotonate a pronucleophile. Initially, our research focused on the use of Zn-ProPhenol complexes to facilitate the direct aldol reaction. Fine tuning of the reaction through ligand modification and the use of additives enabled the direct aldol reaction to proceed in high yields and stereoselectivities with a broad range of donor substrates, including acetophenones, methyl ynones, methyl vinyl ketone, acetone, α-hydroxy carbonyl compounds, and glycine Schiff bases. Additionally, an analogous

Characterization of labelling and de-labelling reagents for detection and recovery of tyrosine residue in peptide.

PubMed

Toyo'oka, Toshimasa; Mantani, Tomomi; Kato, Masaru

2003-01-01

This paper characterized the labelling and de-labelling reagents for reversible labelling of tyrosine (Tyr)-containing peptide, which involves detection and recovery. The phenolic hydroxyl group (-OH) in Tyr structure reacted with 4-fluoro-7-nitro-2,1,3-benzoxadiazole (NBD-F), 4-(N,N-dimethylaminosulfonyl)-7-fluoro-2,1,3-benzoxadiazole (DBD-F), and 1-fluoro-2,4-dinitrobenzene (DNFB) under mild conditions at room temperature at pH 9.3. The labels in the resulting derivatives were removed with the treatment of nucleophiles, such as thiols (cysteine, N-acetyl-L-cysteine and dithiothreitol) and amines (dimethylamine, methylamine, diethylamine, ethylamine and pyrrolidine). The de-labelling reactions of NBD-labelled N-acetyl-L-tyrosine (N-AcTyr) with the nucleophiles produced N-AcTyr, accompanied by NBD-nucleophile. Although DBD-F and DNFB also successfully labeled the -OH group in N-AcTyr, the efficiency of Cbond;O bond cleavage and recovery of N-AcTyr by the nucleophiles was relatively low compared with NBD-label. Among the de-labelling reagents, N-acetyl-L-cysteine and dimethylamine were recommended for the elimination of NBD moiety, with respect to the reaction rate, the side reaction, and the yield of recovery. The proposed procedure, which includes the labelling with NBD-F and the removal of NBD moiety by the nucleophiles, was successfully applied to the reversible labelling of N-terminal amine-blocked peptides, i.e. N-AcTyr-Val-Gly, Z-Glu-Tyr, Z-Phe-Tyr, N-Formyl-Met-Leu-Tyr, and N-AcArg-Pro-Pro-Gly-Phe-Ser-Pro-Tyr-Arg. Copyright 2003 John Wiley & Sons, Ltd.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Christopher M. Leavitt; Garold L. Gresham; Michael T. Benson

Diphenyldithiophosphinate (DTP) ligands modified with electron-withdrawing trifluoromethyl (TFM) substitutents are of high interest because they have demonstrated potential for exceptional separation of Am3+ from lanthanide3+ cations. Specifically, the bis(ortho-TFM) (L1-) and (ortho-TFM)(meta-TFM) (L2-) derivatives have shown excellent separation selectivity, while the bis(meta-TFM) (L3)- and unmodified DTP (Lu-) did not. Factors responsible for selective coordination have been investigated using density functional theory (DFT) calculations in concert with competitive dissociation reactions in the gas phase. To evaluate the role of (DTP+H) acidity, density functional calculations were used to predict pKa values, which followed the trend of L3 < L2 < L1 nucleophilicity. The relative nucleophilicities of the DTP anions were evaluated by forming metal-mixed ligand complexes in a trapped ion mass spectrometer, and then fragmenting them using competitive collision induced dissociation. Relative to Na+, the unmodified Lu- anion was the strongest nucleophile. Comparing the TFM derivatives, the bis(ortho-TFM) derivative L1- was found to be the strongest nucleophile, while the bis(meta-TFM) L3- was the weakest, a trend consistent with the pKa calculations. DFT modeling of the Na+ complexes suggested that the elevated cation affinity of the L1- and L2- anions was due to donation of electron density from fluorine atoms to the metal center, which was occurring in rotational conformers where the TFM moiety was proximate to the Na+-dithiophosphinate group. Competitive dissociation experiments were performed with the dithiophosphinate anions complexed with europium nitrate species; ionic dissociation of these complexes always produced the TFM-modified dithiophosphinate

Chemical Modification of Polysaccharides

PubMed Central

Cumpstey, Ian

2013-01-01

This review covers methods for modifying the structures of polysaccharides. The introduction of hydrophobic, acidic, basic, or other functionality into polysaccharide structures can alter the properties of materials based on these substances. The development of chemical methods to achieve this aim is an ongoing area of research that is expected to become more important as the emphasis on using renewable starting materials and sustainable processes increases in the future. The methods covered in this review include ester and ether formation using saccharide oxygen nucleophiles, including enzymatic reactions and aspects of regioselectivity; the introduction of heteroatomic nucleophiles into polysaccharide chains; the oxidation of polysaccharides, including oxidative glycol cleavage, chemical oxidation of primary alcohols to carboxylic acids, and enzymatic oxidation of primary alcohols to aldehydes; reactions of uronic-acid-based polysaccharides; nucleophilic reactions of the amines of chitosan; and the formation of unsaturated polysaccharide derivatives. PMID:24151557

Felinine stability in the presence of selected urine compounds.

PubMed

Rutherfurd, S M; Kitson, T M; Woolhouse, A D; McGrath, M C; Hendriks, W H

2007-02-01

The stability of felinine, an amino acid present in feline urine, was investigated. Synthetic felinine was unstable in the urine of a selection of mammals. Felinine was found to stable in feline urine in which urea had been degraded. Synthetic felinine was found to react specifically with urea and did not react with urea analogues such as biuret or thiourea or other nucleophilic compounds such as ammonia which is more nucleophilic or acetamide and water which are less nucleophilic than urea. The reaction of urea and felinine was independent of pH over the range of 3-10. Urea did not react with N-acetyl-felinine suggesting a felinine N-terminal interaction with urea. Mass spectral analysis of the reaction products showed the presence of carbamylated felinine and fragmentation ions derived from carbamyl-felinine. The physiological relevance of felinine carbamylation is yet to be determined.

Transition State Analysis of Thymidine Hydrolysis by Human Thymidine Phosphorylase*

PubMed Central

Schwartz, Phillip A.; Vetticatt, Mathew; Schramm, Vern L.

2010-01-01

Human thymidine phosphorylase (hTP) is responsible for thymidine (dT) homeostasis and its action promotes angiogenesis. In the absence of phosphate, hTP catalyzes a slow hydrolytic depyrimidination of dT yielding thymine and 2-deoxyribose (dRib). Its transition state was characterized using multiple kinetic isotope effect (KIE) measurements. Isotopically enriched thymidines were synthesized enzymatically from glucose or (deoxy)ribose and intrinsic KIEs were used to interpret the transition state structure. KIEs from [1′-14C]-, [1-15N]-, [1′-3H]-, [2′R-3H]-, [2′S-3H]-, [4′-3H]-, [5′-3H]dTs provided values of 1.033 ± 0.002, 1.004 ± 0.002, 1.325 ± 0.003, 1.101 ± 0.004, 1.087 ± 0.005, 1.040 ± 0.003, and 1.033 ± 0.003, respectively. Transition state analysis revealed a stepwise mechanism with a 2-deoxyribocation formed early and a higher energetic barrier for nucleophilic attack of a water molecule on the high energy intermediate. An equilibrium exists between the deoxyribocation and reactants prior to the irreversible nucleophilic attack by water. The results establish activation of the thymine leaving group without requirement for phosphate. A transition state constrained to match the intrinsic KIEs was found using density functional theory. An active site histidine (His116) is implicated as the catalytic base for activation of the water nucleophile at the rate-limiting transition state. The distance between the water nucleophile and the anomeric carbon (rC-O) is predicted to be 2.3 Å at the transition state. The transition state model predicts that deoxyribose adopts a mild 3′-endo confirmation during nucleophilic capture. These results differ from the concerted bimolecular mechanism reported for the arsenolytic reaction PMID:20804144

Redox homeostasis: The Golden Mean of healthy living

PubMed Central

Ursini, Fulvio; Maiorino, Matilde; Forman, Henry Jay

2016-01-01

The notion that electrophiles serve as messengers in cell signaling is now widely accepted. Nonetheless, major issues restrain acceptance of redox homeostasis and redox signaling as components of maintenance of a normal physiological steady state. The first is that redox signaling requires sudden switching on of oxidant production and bypassing of antioxidant mechanisms rather than a continuous process that, like other signaling mechanisms, can be smoothly turned up or down. The second is the misperception that reactions in redox signaling involve “reactive oxygen species” rather than reaction of specific electrophiles with specific protein thiolates. The third is that hormesis provides protection against oxidants by increasing cellular defense or repair mechanisms rather than by specifically addressing the offset of redox homeostasis. Instead, we propose that both oxidant and antioxidant signaling are main features of redox homeostasis. As the redox shift is rapidly reversed by feedback reactions, homeostasis is maintained by continuous signaling for production and elimination of electrophiles and nucleophiles. Redox homeostasis, which is the maintenance of nucleophilic tone, accounts for a healthy physiological steady state. Electrophiles and nucleophiles are not intrinsically harmful or protective, and redox homeostasis is an essential feature of both the response to challenges and subsequent feedback. While the balance between oxidants and nucleophiles is preserved in redox homeostasis, oxidative stress provokes the establishment of a new radically altered redox steady state. The popular belief that scavenging free radicals by antioxidants has a beneficial effect is wishful thinking. We propose, instead, that continuous feedback preserves nucleophilic tone and that this is supported by redox active nutritional phytochemicals. These nonessential compounds, by activating Nrf2, mimic the effect of endogenously produced electrophiles (parahormesis). In summary

The relationship between RNA catalytic processes

NASA Astrophysics Data System (ADS)

Cedergren, Robert; Lang, B. Franz; Gravel, Denis

1988-09-01

Proposals that an RNA-based genetic system preceeded DNA, stem from the ability of RNA to store genetic information and to promote simple catalysis. However, to be a valid basis for the RNA world, RNA catalysis must demonstrate or be related to intrinsic chemical properties which could have existed in primordial times. We analyze this question by first classifying RNA catalysis and related processes according to their mechanism. We define: (A) thedisjunct nucleophile class which leads to 5'-phosphates. These include Group I and II intron splicing, nuclear mRNA splicing and RNase P reactions. Although Group I introns and its excision mechanism is likely to have existed in primordial times, present-day examples have arisen independently in different phyla much more recently. Comparative methodology indicates that RNase P catalysis originated before the divergence of the major kingdoms. In addition, alldisjunct nucleophile reactions can be interrelated by a proposed mechanism involving a distant 2-OH nucleophile. (B) theconjunct nucleophile class leading to 3'-phosphates. This class is composed of self-cleaving RNAs found in plant viruses and the newt. We propose that tRNA splicing is related to this mechanism rather than the previous one. The presence of introns in tRNA genes of eukaryotes and archaebacteria supports the idea that tRNA splicing predates the divergence of these cell types.

Key factors regulating protein carbonylation by α,β unsaturated carbonyls: A structural study based on a retrospective meta-analysis.

PubMed

Vistoli, Giulio; Mantovani, Chiara; Gervasoni, Silvia; Pedretti, Alessandro; Aldini, Giancarlo

2017-11-01

Protein carbonylation represents one of the most important oxidative-based modifications involving nucleophilic amino acids and affecting protein folding and function. Protein carbonylation is induced by electrophilic carbonyl species and is an highly selective process since few nucleophilic residues are carbonylated within each protein. While considering the great interest for protein carbonylation, few studies investigated the factors which render a nucleophilic residue susceptible to carbonylation. Hence, the present study is aimed to delve into the factors which modulate the reactivity of cysteine, histidine and lysine residues towards α,β unsaturated carbonyls by a retrospective analysis of the available studies which identified the adducted residues for proteins, the structure of which was resolved. Such an analysis involved different parameters including exposure, nucleophilicity, surrounding residues and capacity to attract carbonyl species (as derived by docking simulations). The obtained results allowed a meaningful clustering of the analyzed proteins suggesting that on average carbonylation selectivity increases with protein size. The comparison between adducted and unreactive residues revealed differences in all monitored parameters which are markedly more pronounced for cysteines compared to lysines and histidines. Overall, these results suggest that cysteine's carbonylation is a finely (and reasonably purposely) modulated process, while the carbonylation of lysines and histidines seems to be a fairly random event in which limited differences influence their reactivity. Copyright © 2017 Elsevier B.V. All rights reserved.

Surface-active ionic liquids in micellar catalysis: impact of anion selection on reaction rates in nucleophilic substitutions† †Electronic supplementary information (ESI) available: Formulae for calculating aggregation parameters and fitting of kinetic constants and copies of NMR spectra. See DOI: 10.1039/c6cp00493h Click here for additional data file.

PubMed Central

Cognigni, Alice; Gaertner, Peter; Zirbs, Ronald; Peterlik, Herwig; Prochazka, Katharina; Schröder, Christian

2016-01-01

A series of surface-active ionic liquids based on the 1-dodecyl-3-methylimidazolium cation and different anions such as halides and alkylsulfates was synthesized. The aggregation behavior of these ionic liquids in water was characterized by surface tension, conductivity measurements and UV-Vis spectroscopy in order to determine the critical micelle concentration (CMC) and to provide aggregation parameters. The determination of surface activity and aggregation properties of amphiphilic ionic liquids was accompanied by SAXS studies on selected surface-active ionic liquids. The application of these surface-active ionic liquids with different anions was tested in nucleophilic substitution reactions for the degradation of organophosphorus compounds. Kinetic studies via UV-Vis spectrophotometry showed a strong acceleration of the reaction in the micellar system compared to pure water. In addition, an influence of the anion was observed, resulting in a correlation between the anion binding to the micelle and the reaction rate constants, indicating that the careful choice of the surface-active ionic liquid can considerably affect the outcome of reactions. PMID:27121134

Heterobimetallic Pd-Sn catalysis: a Suzuki, tandem ring-closing sequence toward indeno[2,1-b]thiophenes and indeno[2,1-b]indoles.

PubMed

Das, Debjit; Pratihar, Sanjay; Roy, Sujit

2012-09-21

Indeno[2,1-b]thiophene and indeno[1,2-b]indole motifs have been obtained in moderate to good yields from easily available substituted boronic acids, 2-bromo aryl/vinyl aldehydes, and nucleophiles such as arenes/heteroarenes and others using a catalytic combination of bimetallic "Pd-Sn" and AgPF(6). This formal three-component coupling involves a Suzuki reaction followed by nucleophile assisted tandem ring closure. The sequential synthesis of substituted heterocycle-fused indenes, benzofluorene, and fluorenes was also accomplished.

Applications of the Conceptual Density Functional Theory Indices to Organic Chemistry Reactivity.

PubMed

Domingo, Luis R; Ríos-Gutiérrez, Mar; Pérez, Patricia

2016-06-09

Theoretical reactivity indices based on the conceptual Density Functional Theory (DFT) have become a powerful tool for the semiquantitative study of organic reactivity. A large number of reactivity indices have been proposed in the literature. Herein, global quantities like the electronic chemical potential μ, the electrophilicity ω and the nucleophilicity N indices, and local condensed indices like the electrophilic P k + and nucleophilic P k - Parr functions, as the most relevant indices for the study of organic reactivity, are discussed.

Electrochemical capture and release of carbon dioxide

DOE PAGES

Rheinhardt, Joseph H.; Singh, Poonam; Tarakeshwar, Pilarisetty; ...

2017-01-18

Understanding the chemistry of carbon dioxide is key to affecting changes in atmospheric concentrations. One area of intense interest is CO 2 capture in chemically reversible cycles relevant to carbon capture technologies. Most CO 2 capture methods involve thermal cycles in which a nucleophilic agent captures CO 2 from impure gas streams (e.g., flue gas), followed by a thermal process in which pure CO 2 is released. Several reviews have detailed progress in these approaches. A less explored strategy uses electrochemical cycles to capture CO 2 and release it in pure form. These cycles typically rely on electrochemical generation ofmore » nucleophiles that attack CO 2 at the electrophilic carbon atom, forming a CO 2 adduct. Then, CO 2 is released in pure form via a subsequent electrochemical step. In this Perspective, we describe electrochemical cycles for CO 2 capture and release, emphasizing electrogenerated nucleophiles. As a result, we also discuss some advantages and disadvantages inherent in this general approach.« less

Design of activated serine-containing catalytic triads with atomic level accuracy

PubMed Central

Rajagopalan, Sridharan; Wang, Chu; Yu, Kai; Kuzin, Alexandre P.; Richter, Florian; Lew, Scott; Miklos, Aleksandr E.; Matthews, Megan L.; Seetharaman, Jayaraman; Su, Min; Hunt, John. F.; Cravatt, Benjamin F.; Baker, David

2014-01-01

A challenge in the computational design of enzymes is that multiple properties must be simultaneously optimized -- substrate-binding, transition state stabilization, and product release -- and this has limited the absolute activity of successful designs. Here, we focus on a single critical property of many enzymes: the nucleophilicity of an active site residue that initiates catalysis. We design proteins with idealized serine-containing catalytic triads, and assess their nucleophilicity directly in native biological systems using activity-based organophosphate probes. Crystal structures of the most successful designs show unprecedented agreement with computational models, including extensive hydrogen bonding networks between the catalytic triad (or quartet) residues, and mutagenesis experiments demonstrate that these networks are critical for serine activation and organophosphate-reactivity. Following optimization by yeast-display, the designs react with organophosphate probes at rates comparable to natural serine hydrolases. Co-crystal structures with diisopropyl fluorophosphate bound to the serine nucleophile suggest the designs could provide the basis for a new class of organophosphate captures agents. PMID:24705591

Identification of ortho-Substituted Benzoic Acid/Ester Derivatives via the Gas-Phase Neighboring Group Participation Effect in (+)-ESI High Resolution Mass Spectrometry.

PubMed

Blincoe, William D; Rodriguez-Granillo, Agustina; Saurí, Josep; Pierson, Nicholas A; Joyce, Leo A; Mangion, Ian; Sheng, Huaming

2018-04-01

Benzoic acid/ester/amide derivatives are common moieties in pharmaceutical compounds and present a challenge in positional isomer identification by traditional tandem mass spectrometric analysis. A method is presented for exploiting the gas-phase neighboring group participation (NGP) effect to differentiate ortho-substituted benzoic acid/ester derivatives with high resolution mass spectrometry (HRMS 1 ). Significant water/alcohol loss (>30% abundance in MS 1 spectra) was observed for ortho-substituted nucleophilic groups; these fragment peaks are not observable for the corresponding para and meta-substituted analogs. Experiments were also extended to the analysis of two intermediates in the synthesis of suvorexant (Belsomra) with additional analysis conducted with nuclear magnetic resonance (NMR), density functional theory (DFT), and ion mobility spectrometry-mass spectrometry (IMS-MS) studies. Significant water/alcohol loss was also observed for 1-substituted 1, 2, 3-triazoles but not for the isomeric 2-substituted 1, 2, 3-triazole analogs. IMS-MS, NMR, and DFT studies were conducted to show that the preferred orientation of the 2-substituted triazole rotamer was away from the electrophilic center of the reaction, whereas the 1-subtituted triazole was oriented in close proximity to the center. Abundance of NGP product was determined to be a product of three factors: (1) proton affinity of the nucleophilic group; (2) steric impact of the nucleophile; and (3) proximity of the nucleophile to carboxylic acid/ester functional groups. Graphical Abstract ᅟ.

Unravelling the reaction mechanism of matrix metalloproteinase 3 using QM/MM calculations

NASA Astrophysics Data System (ADS)

Feliciano, Gustavo Troiano; da Silva, Antônio José Roque

2015-07-01

The matrix metalloproteinase family (MMP) constitutes a family of zinc (Zn) proteases that catalyze the breaking of peptide bonds in proteins. These enzymes are very promising drug targets, since they are involved in remodeling and degradation of the extracellular matrix, which is a key process required for cancer metastasis, and thus, their reaction mechanism has been an area of intensive research. Early proposal based on acid base catalyzed hydrolysis, suggested that a conserved zinc bound water molecule acted as the nucleophile attacking the peptide bond carbon, after being activated by essential glutamate. The possibility of a direct nucleophilic attack by the enzyme, performed by the glutamate was also suggested. These are the key yet unsolved issues about MMP reaction mechanism. In the present work, we used hybrid quantum/classical calculations to analyze the structure and energetics of different possible hydrolysis reaction paths. The results support a water mediated mechanism, where both the nucleophile water molecule and the carbonyl oxygen of the scissile peptide bond are coordinated to zinc in the reactive configuration, while the essential glutamate acts as the base accepting the proton from the nucleophilic water. Formation of the carbon-oxygen bond and breaking of carbon-nitrogen bond were found to be concerted events, with a computed barrier of 14.8 kcal/mol. Substrate polarization was found to be important for the observed reaction mechanism, and a substantial change in the metal coordination environment was observed, particularly, regarding the zinc-histidine coordination.

Generation of N-Heterocycles via Tandem Reactions of N '-(2-Alkynylbenzylidene)hydrazides.

PubMed

Qiu, Guanyinsheng; Wu, Jie

2016-02-01

As a powerful synthon, N '-(2-alkynylbenzylidene)hydrazides have been utilized efficiently for the construction of N-heterocycles. Since N '-(2-alkynylbenzylidene)hydrazides can easily undergo intramolecular 6-endo cyclization promoted by silver triflate or electrophiles, the resulting isoquinolinium-2-yl amides can proceed through subsequent transformations including [3 + 2] cycloaddition, nucleophilic addition, and [3 + 3] cycloaddition. Several unexpected rearrangements via radical processes were observed in some cases, which afforded nitrogen-containing heterocycles with molecular complexity. Reactive partners including internal alkynes, arynes, ketenimines, ketenes, allenoates, and activated alkenes reacted through [3 + 2] cycloaddition and subsequent aromatization, leading to diverse H-pyrazolo[5,1-a]isoquinolines with high efficiency. Nucleophilic addition to the in situ generated isoquinolinium-2-yl amide followed by aromatization also produced H-pyrazolo[5,1-a]isoquinoline derivatives when terminal alkynes, carbonyls, enamines, and activated methylene compounds were used as nucleophiles. Isoquinoline derivatives were obtained when indoles or phosphites were employed as nucleophiles in the reactions of N '-(2-alkynylbenzylidene)hydrazides. A tandem 6-endo cyclization and [3 + 3] cycloaddition of cyclopropane-1,1-dicarboxylates with N '-(2-alkynylbenzylidene)hydrazides was observed as well. Small libraries of these compounds were constructed. Biological evaluation suggested that some compounds showed promising activities for inhibition of CDC25B, TC-PTP, HCT-116, and PTP1B. © 2015 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Identification of ortho-Substituted Benzoic Acid/Ester Derivatives via the Gas-Phase Neighboring Group Participation Effect in (+)-ESI High Resolution Mass Spectrometry

NASA Astrophysics Data System (ADS)

Blincoe, William D.; Rodriguez-Granillo, Agustina; Saurí, Josep; Pierson, Nicholas A.; Joyce, Leo A.; Mangion, Ian; Sheng, Huaming

2018-02-01

Benzoic acid/ester/amide derivatives are common moieties in pharmaceutical compounds and present a challenge in positional isomer identification by traditional tandem mass spectrometric analysis. A method is presented for exploiting the gas-phase neighboring group participation (NGP) effect to differentiate ortho-substituted benzoic acid/ester derivatives with high resolution mass spectrometry (HRMS1). Significant water/alcohol loss (>30% abundance in MS1 spectra) was observed for ortho-substituted nucleophilic groups; these fragment peaks are not observable for the corresponding para and meta-substituted analogs. Experiments were also extended to the analysis of two intermediates in the synthesis of suvorexant (Belsomra) with additional analysis conducted with nuclear magnetic resonance (NMR), density functional theory (DFT), and ion mobility spectrometry-mass spectrometry (IMS-MS) studies. Significant water/alcohol loss was also observed for 1-substituted 1, 2, 3-triazoles but not for the isomeric 2-substituted 1, 2, 3-triazole analogs. IMS-MS, NMR, and DFT studies were conducted to show that the preferred orientation of the 2-substituted triazole rotamer was away from the electrophilic center of the reaction, whereas the 1-subtituted triazole was oriented in close proximity to the center. Abundance of NGP product was determined to be a product of three factors: (1) proton affinity of the nucleophilic group; (2) steric impact of the nucleophile; and (3) proximity of the nucleophile to carboxylic acid/ester functional groups. [Figure not available: see fulltext.

A Sensitive Gel-based Method Combining Distinct Cyclophellitol-based Probes for the Identification of Acid/Base Residues in Human Retaining β-Glucosidases*

PubMed Central

Kallemeijn, Wouter W.; Witte, Martin D.; Voorn-Brouwer, Tineke M.; Walvoort, Marthe T. C.; Li, Kah-Yee; Codée, Jeroen D. C.; van der Marel, Gijsbert A.; Boot, Rolf G.; Overkleeft, Herman S.; Aerts, Johannes M. F. G.

2014-01-01

Retaining β-exoglucosidases operate by a mechanism in which the key amino acids driving the glycosidic bond hydrolysis act as catalytic acid/base and nucleophile. Recently we designed two distinct classes of fluorescent cyclophellitol-type activity-based probes (ABPs) that exploit this mechanism to covalently modify the nucleophile of retaining β-glucosidases. Whereas β-epoxide ABPs require a protonated acid/base for irreversible inhibition of retaining β-glucosidases, β-aziridine ABPs do not. Here we describe a novel sensitive method to identify both catalytic residues of retaining β-glucosidases by the combined use of cyclophellitol β-epoxide- and β-aziridine ABPs. In this approach putative catalytic residues are first substituted to noncarboxylic amino acids such as glycine or glutamine through site-directed mutagenesis. Next, the acid/base and nucleophile can be identified via classical sodium azide-mediated rescue of mutants thereof. Selective labeling with fluorescent β-aziridine but not β-epoxide ABPs identifies the acid/base residue in mutagenized enzyme, as only the β-aziridine ABP can bind in its absence. The Absence of the nucleophile abolishes any ABP labeling. We validated the method by using the retaining β-glucosidase GBA (CAZy glycosylhydrolase family GH30) and then applied it to non-homologous (putative) retaining β-glucosidases categorized in GH1 and GH116: GBA2, GBA3, and LPH. The described method is highly sensitive, requiring only femtomoles (nanograms) of ABP-labeled enzymes. PMID:25344605

Synthesis and stereochemical analysis of β-nitromethane substituted γ-amino acids and peptides.

PubMed

Ganesh Kumar, Mothukuri; Mali, Sachitanand M; Gopi, Hosahudya N

2013-02-07

The high diastereoselectivity in the Michael addition of nitromethane to α,β-unsaturated γ-amino esters, crystal conformations of β-nitromethane substituted γ-amino acids and peptides are studied. Results suggest that the N-Boc protected amide NH, conformations of α,β-unsaturated γ-amino esters and alkyl side chains play a crucial role in dictating the high diastereoselectivity of nitromethane addition to E-vinylogous amino esters. Investigation of the crystal conformations of both α,β-unsaturated γ-amino esters and the Michael addition products suggests that an H-C(γ)-C(β)=C(α) eclipsed conformer of the unsaturated amino ester leads to the major (anti) product compared to that of an N-C(γ)-C(β)=C(α) eclipsed conformer. The major diastereomers were separated and subjected to the peptide synthesis. The single crystal analysis of the dipeptide containing β-nitromethane substituted γ-amino acids reveals a helical type of folded conformation with an isolated H-bond involving a nine-atom pseudocycle.

UV-Vis absorption spectra and electronic structure of merocyanines in the gas phase

NASA Astrophysics Data System (ADS)

Ishchenko, Alexander A.; Kulinich, Andrii V.; Bondarev, Stanislav L.; Raichenok, Tamara F.

2018-02-01

Gas-phase absorption spectra of a merocyanine vinylogous series have been studied for the first time. In vapour, their long-wavelength absorption bands were found to be considerably shifted hypsochromically, broader, more symmetrical, less intense, and their vinylene shift much smaller than even in low-polarity n-hexane. This indicates that in the gas phase their electronic structure closely approaches the nonpolar polyene limiting structure. The TDDFT calculations of the long-wavelength electronic transitions in the studied merocyanines in vacuo demonstrated good-to-excellent correlation - depending on the functional used - with the obtained experimental data. For comparison, the solvent effects was accounted for using the polarizable continuum model (PCM) with n-hexane and ethanol as low-polarity and high-polarity media, and compared with the UV-Vis spectral data in these solvents. In this case, the discrepancy between theory and experiment was much greater, increasing at that with the polymethine chain length.

C9/12 Ribbon-Like Structures in Hybrid Peptides Alternating α- and Thiazole-Based γ-Amino Acids.

PubMed

Bonnel, Clément; Legrand, Baptiste; Simon, Matthieu; Martinez, Jean; Bantignies, Jean-Louis; Kang, Young Kee; Wenger, Emmanuel; Hoh, Francois; Masurier, Nicolas; Maillard, Ludovic T

2017-12-11

According to their restricted conformational freedom, heterocyclic γ-amino acids are usually considered to be related to Z-vinylogous γ-amino acids. In this context, oligomers alternating α-amino acids and thiazole-based γ-amino acids (ATCs) were expected to fold into a canonical 12-helical shape as described for α/γ-hybrid peptides composed of cis-α/β-unsaturated γ-amino acids. However, through a combination of X-ray crystallography, NMR spectroscopy, FTIR experiments, and DFT calculations, it was determined that the folding behavior of ATC-containing hybrid peptides is much more complex. The homochiral α/(S)-ATC sequences were unable to adopt a stable conformation, whereas the heterochiral α/(R)-ATC peptides displayed novel ribbon structures stabilized by unusual C 9/12 -bifurcated hydrogen bonds. These ribbon structures could be considered as a succession of pre-organized γ/α dipeptides and may provide the basis for designing original α-helix mimics. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Secondary benzylation with benzyl alcohols catalyzed by a high-valent heterobimetallic Ir-Sn complex.

PubMed

Podder, Susmita; Choudhury, Joyanta; Roy, Sujit

2007-04-13

A highly efficient secondary benzylation procedure has been demonstrated using a high-valent heterobimetallic complex [Ir2(COD)2(SnCl3)2(Cl)2(mu-Cl)2] 1 as the catalyst in 1,2-dichloroethane to afford the corresponding benzylated products in moderate to excellent yields. The reaction was performed not only with carbon nucleophiles (arenes and heteroarenes) but also with oxygen (alcohol), nitrogen (amide and sulfonamide), and sulfur (thiol) nucleophiles. Mechanistic investigation showed the intermediacy of the ether in this reaction. An electrophilic mechanism is proposed from Hammett correlation.

The role of an active site Mg(2+) in HDV ribozyme self-cleavage: insights from QM/MM calculations.

PubMed

Mlýnský, Vojtěch; Walter, Nils G; Šponer, Jiří; Otyepka, Michal; Banáš, Pavel

2015-01-07

The hepatitis delta virus (HDV) ribozyme is a catalytic RNA motif embedded in the human pathogenic HDV RNA. It catalyzes self-cleavage of its sugar-phosphate backbone with direct participation of the active site cytosine C75. Biochemical and structural data support a general acid role of C75. Here, we used hybrid quantum mechanical/molecular mechanical (QM/MM) calculations to probe the reaction mechanism and changes in Gibbs energy along the ribozyme's reaction pathway with an N3-protonated C75H(+) in the active site, which acts as the general acid, and a partially hydrated Mg(2+) ion with one deprotonated, inner-shell coordinated water molecule that acts as the general base. We followed eight reaction paths with a distinct position and coordination of the catalytically important active site Mg(2+) ion. For six of them, we observed feasible activation barriers ranging from 14.2 to 21.9 kcal mol(-1), indicating that the specific position of the Mg(2+) ion in the active site is predicted to strongly affect the kinetics of self-cleavage. The deprotonation of the U-1(2'-OH) nucleophile and the nucleophilic attack of the resulting U-1(2'-O(-)) on the scissile phosphodiester are found to be separate steps, as deprotonation precedes the nucleophilic attack. This sequential mechanism of the HDV ribozyme differs from the concerted nucleophilic activation and attack suggested for the hairpin ribozyme. We estimate the pKa of the U-1(2'-OH) group to range from 8.8 to 11.2, suggesting that it is lowered by several units from that of a free ribose, comparable to and most likely smaller than the pKa of the solvated active site Mg(2+) ion. Our results thus support the notion that the structure of the HDV ribozyme, and particularly the positioning of the active site Mg(2+) ion, facilitate deprotonation and activation of the 2'-OH nucleophile.

Redox homeostasis: The Golden Mean of healthy living.

PubMed

Ursini, Fulvio; Maiorino, Matilde; Forman, Henry Jay

2016-08-01

The notion that electrophiles serve as messengers in cell signaling is now widely accepted. Nonetheless, major issues restrain acceptance of redox homeostasis and redox signaling as components of maintenance of a normal physiological steady state. The first is that redox signaling requires sudden switching on of oxidant production and bypassing of antioxidant mechanisms rather than a continuous process that, like other signaling mechanisms, can be smoothly turned up or down. The second is the misperception that reactions in redox signaling involve "reactive oxygen species" rather than reaction of specific electrophiles with specific protein thiolates. The third is that hormesis provides protection against oxidants by increasing cellular defense or repair mechanisms rather than by specifically addressing the offset of redox homeostasis. Instead, we propose that both oxidant and antioxidant signaling are main features of redox homeostasis. As the redox shift is rapidly reversed by feedback reactions, homeostasis is maintained by continuous signaling for production and elimination of electrophiles and nucleophiles. Redox homeostasis, which is the maintenance of nucleophilic tone, accounts for a healthy physiological steady state. Electrophiles and nucleophiles are not intrinsically harmful or protective, and redox homeostasis is an essential feature of both the response to challenges and subsequent feedback. While the balance between oxidants and nucleophiles is preserved in redox homeostasis, oxidative stress provokes the establishment of a new radically altered redox steady state. The popular belief that scavenging free radicals by antioxidants has a beneficial effect is wishful thinking. We propose, instead, that continuous feedback preserves nucleophilic tone and that this is supported by redox active nutritional phytochemicals. These nonessential compounds, by activating Nrf2, mimic the effect of endogenously produced electrophiles (parahormesis). In summary

Preparative HSCCC isolation of phloroglucinolysis products from grape seed polymeric proanthocyanidins as new powerful antioxidants.

PubMed

Zhang, Shuting; Cui, Yan; Li, Lingxi; Li, Yuanyuan; Zhou, Peiyu; Luo, Lanxin; Sun, Baoshan

2015-12-01

Polymeric proanthocyanidins isolated from a grape seed phenolic extract were hydrolysed in the presence of phloroglucinol into monomer catechins and their nucleophile derivatives. Each of the phloroglucinolysis products was successfully separated and isolated in large amount by semi-preparative HSCCC technique under the optimized conditions based on a selection of suitable solvent system. The optimized solvent system consisted of n-hexane-ethyl acetate-water (1:80:80, v/v/v) with a combination of head-tail and tail-head elution modes. By only one-step HSCCC separation, the purity of each obtained phloroglucinolysis product, including monomer catechins and their nucleophile derivatives was above 76%, verified by UPLC. The structures of these products were tentatively identified by UPLC based on their retention time and further confirmed by MS and (1)H NMR analysis. Furthermore, by DPPH, ABTS and FRAP assays, it was verified that all these phloroglucinolysis products possessed strong antioxidant activities, being catechin-nucleophile derivatives more powerful than free catechins. Copyright © 2015 Elsevier Ltd. All rights reserved.

A Pictet-Spengler ligation for protein chemical modification

PubMed Central

Agarwal, Paresh; van der Weijden, Joep; Sletten, Ellen M.; Rabuka, David; Bertozzi, Carolyn R.

2013-01-01

Aldehyde- and ketone-functionalized proteins are appealing substrates for the development of chemically modified biotherapeutics and protein-based materials. Their reactive carbonyl groups are typically conjugated with α-effect nucleophiles, such as substituted hydrazines and alkoxyamines, to generate hydrazones and oximes, respectively. However, the resulting C=N linkages are susceptible to hydrolysis under physiologically relevant conditions, which limits the utility of such conjugates in biological systems. Here we introduce a Pictet-Spengler ligation that is based on the classic Pictet-Spengler reaction of aldehydes and tryptamine nucleophiles. The ligation exploits the bioorthogonal reaction of aldehydes and alkoxyamines to form an intermediate oxyiminium ion; this intermediate undergoes intramolecular C–C bond formation with an indole nucleophile to form an oxacarboline product that is hydrolytically stable. We used the reaction for site-specific chemical modification of glyoxyl- and formylglycine-functionalized proteins, including an aldehyde-tagged variant of the therapeutic monoclonal antibody Herceptin. In conjunction with techniques for site-specific introduction of aldehydes into proteins, the Pictet-Spengler ligation offers a means to generate stable bioconjugates for medical and materials applications. PMID:23237853

Ferrier rearrangement promoted by an electrochemically generated zirconium catalyst.

PubMed

Stevanović, Dragana; Pejović, Anka; Damljanović, Ivan; Minić, Aleksandra; Bogdanović, Goran A; Vukićević, Mirjana; Radulović, Niko S; Vukićević, Rastko D

2015-04-30

In situ generated zirconium catalyst from a sacrificial zirconium anode was successfully applied to promote Ferrier rearrangement of 3,4,5-tri-O-acetyl-D-glucal and 6-deoxy-3,4-di-O-acetyl-L-glucal (3,4-di-O-acetyl-L-rhamnal) in the presence of three thiols and eleven thiophenols as nucleophiles. A simple constant current electrolysis (20 mA, 0.4 F mol(-1)) of an acetonitrile solution of lithium perchlorate (0.1 M) containing the corresponding glycal and S-nucleophiles, using a zirconium anode and a platinum cathode resulted in the successful synthesis of the corresponding 2,3-unsaturated peracetylated thioglycosides (with an average anomer ratio α/β=4.129 in the case of peracetylated D-glucal and 8.740 in the case of L-rhamnal). The same procedure proved to be appropriate in synthesizing dihydropyran derivatives ('C-glycosides') using allyltrimethylsilane as the nucleophile (only 'α-anomers' were obtained). All new compounds were fully characterized by spectral data, whereas single-crystal X-ray analysis was performed for two thioglycosides. Copyright © 2015 Elsevier Ltd. All rights reserved.

The scope and limitations of intramolecular Nicholas and Pauson-Khand reactions for the synthesis of tricyclic oxygen- and nitrogen-containing heterocycles.

PubMed

Closser, Kristina D; Quintal, Miriam M; Shea, Kevin M

2009-05-15

We studied the scope and limitations of a tandem intramolecular Nicholas/Pauson-Khand strategy for the synthesis of tricyclic oxygen- and nitrogen-containing heterocycles. This methodology enables conversion of simple acyclic starting materials into a series of previously unknown heterocyclic architectures. For the preparation of cyclic ethers (Z = O), tricyclic [5,6,5]- through [5,9,5]-systems (m = 1, n = 1-4) are available with the [5,7,5]- and [5,8,5]-systems amenable to quick and efficient synthesis. Tricyclic [5,7,5]- and [5,8,5]-amine-containing (Z = NTs) heterocycles can be successfully prepared. Attempts to make larger ring systems (Z = O, m = 2; Z = O, n = 5; or Z = NTs, n = 4-5) or prepare lactones via Nicholas reactions with carboxylic acid nucleophiles (available via oxidation of alcohol nucleophiles, Z = O) result in decomposition or dimerization. The latter process enables formation of 14-, 16-, and 18-membered ring diolides when using carboxylic acid nucleophiles. We also investigated the use of chiral amine promoters in the Pauson-Khand step but found no asymmetric induction.

δ-Deuterium Isotope Effects as Probes for Transition-State Structures of Isoprenoid Substrates

PubMed Central

2015-01-01

The biosynthetic pathways to isoprenoid compounds involve transfer of the prenyl moiety in allylic diphosphates to electron-rich (nucleophilic) acceptors. The acceptors can be many types of nucleophiles, while the allylic diphosphates only differ in the number of isoprene units and stereochemistry of the double bonds in the hydrocarbon moieties. Because of the wide range of nucleophilicities of naturally occurring acceptors, the mechanism for prenyltransfer reactions may be dissociative or associative with early to late transition states. We have measured δ-secondary kinetic isotope effects operating through four bonds for substitution reactions with dimethylallyl derivatives bearing deuterated methyl groups at the distal (C3) carbon atom in the double bond under dissociative and associative conditions. Computational studies with density functional theory indicate that the magnitudes of the isotope effects correlate with the extent of bond formation between the allylic moiety and the electron-rich acceptor in the transition state for alkylation and provide insights into the structures of the transition states for associative and dissociative alkylation reactions. PMID:24665882

Theoretical characterization on the size-dependent electron and hole trapping activity of chloride-passivated CdSe nanoclusters

NASA Astrophysics Data System (ADS)

Cui, Yingqi; Cui, Xianhui; Zhang, Li; Xie, Yujuan; Yang, Mingli

2018-04-01

Ligand passivation is often used to suppress the surface trap states of semiconductor quantum dots (QDs) for their continuous photoluminescence output. The suppression process is related to the electrophilic/nucleophilic activity of surface atoms that varies with the structure and size of QD and the electron donating/accepting nature of ligand. Based on first-principles-based descriptors and cluster models, the electrophilic/nucleophilic activities of bare and chloride-coated CdSe clusters were studied to reveal the suppression mechanism of Cl-passivated QDs and compared to experimental observations. The surface atoms of bare clusters have higher activity than inner atoms and their activity decreases with cluster size. In the ligand-coated clusters, the Cd atom remains as the electrophilic site, while the nucleophilic site of Se atoms is replaced by Cl atoms. The activities of Cd and Cl atoms in the coated clusters are, however, remarkably weaker than those in bare clusters. Cluster size, dangling atoms, ligand coverage, electronegativity of ligand atoms, and solvent (water) were found to have considerable influence on the activity of surface atoms. The suppression of surface trap states in Cl-passivated QDs was attributed to the reduction of electrophilic/nucleophilic activity of Cd/Se/Cl atoms. Both saturation to under-coordinated surface atoms and proper selection for the electron donating/accepting strength of ligands are crucial for eliminating the charge carrier traps. Our calculations predicted a similar suppressing effect of chloride ligands with experiments and provided a simple but effective approach to assess the charge carrier trapping behaviors of semiconductor QDs.

Kinetic Studies that Evaluate the Solvolytic Mechanisms of Allyl and Vinyl Chloroformate Esters

PubMed Central

D’Souza, Malcolm J.; Givens, Aaron F.; Lorchak, Peter A.; Greenwood, Abigail E.; Gottschall, Stacey L.; Carter, Shannon E.; Kevill, Dennis N.

2013-01-01

At 25.0 °C the specific rates of solvolysis for allyl and vinyl chloroformates have been determined in a wide mix of pure and aqueous organic mixtures. In all the solvents studied, vinyl chloroformate was found to react significantly faster than allyl chloroformate. Multiple correlation analyses of these rates are completed using the extended (two-term) Grunwald-Winstein equation with incorporation of literature values for solvent nucleophilicity (NT) and solvent ionizing power (YCl). Both substrates were found to solvolyze by similar dual bimolecular carbonyl-addition and unimolecular ionization channels, each heavily dependent upon the solvents nucleophilicity and ionizing ability. PMID:23549265

The thriving chemistry of ketenimines.

PubMed

Lu, Ping; Wang, Yanguang

2012-09-07

Ketenimines are an important class of reactive species and useful synthetic intermediates. During the last two decades several practical and versatile approaches to ketenimines have been developed, leading to exhaustive investigations on ketenimine chemistry and the discovery of a variety of highly efficient reactions. Five types of reactions for ketenimines have been reported, including nucleophilic additions (ketenimines can be used as both electrophiles and nucleophiles), radical additions, cycloaddition reactions, electrocyclic ring closure reactions, and σ rearrangements. Furthermore, numerous complex organic compounds, particularly the biologically interesting heterocycles, have been constructed using these methodologies. The review of these accomplishments is presented here.

α-Oxo-Ketenimines from Isocyanides and α-Haloketones: Synthesis and Divergent Reactivity.

PubMed

Mamboury, Mathias; Wang, Qian; Zhu, Jieping

2017-09-18

The palladium-catalyzed reaction of α-haloketones with isocyanides afforded α-oxo-ketenimines through β-hydride elimination of the β-oxo-imidoyl palladium intermediates. Reaction of these relatively stable α-oxo-ketenimines with nucleophiles such as hydrazines, hydrazoic acid, amines, and Grignard reagent afforded pyrazoles, tetrazole, β-keto amidines, and enaminone, respectively, with high chemoselectivity. Whereas amines attack exclusively on the ketenimine functions, the formal [3+2] cycloaddition between N-monosubstituted hydrazines and α-oxo-ketenimines was initiated by nucleophilic addition to the carbonyl group. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Copper-Catalyzed Carbonylative Coupling of Cycloalkanes and Amides.

PubMed

Li, Yahui; Dong, Kaiwu; Zhu, Fengxiang; Wang, Zechao; Wu, Xiao-Feng

2016-06-13

Carbonylation reactions are a most powerful method for the synthesis of carbonyl-containing compounds. However, most known carbonylation procedures still require noble-metal catalysts and the use of activated compounds and good nucleophiles as substrates. Herein, we developed a copper-catalyzed carbonylative transformation of cycloalkanes and amides. Imides were prepared in good yields by carbonylation of a C(sp(3) )-H bond of the cycloalkane with the amides acting as weak nucleophiles. Notably, this is the first report of copper-catalyzed carbonylative C-H activation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Systematic Investigation of Quaternary Ammonium Ions as Asymmetric Phase Transfer Catalysts. Synthesis of Catalyst Libraries and Evaluation of Catalyst Activity

PubMed Central

Denmark, Scott E.; Gould, Nathan D.; Wolf, Larry M.

2011-01-01

Despite over three decades of research into asymmetric phase transfer catalysis (APTC), a fundamental understanding of the factors that affect the rate and stereoselectivity of this important process are still obscure. This paper describes the initial stages of a long-term program aimed at elucidating the physical organic foundations of APTC employing a chemoinformatic analysis of the alkylation of a protected glycine imine with a libraries of enantiomerically enriched quaternary ammonium ions. The synthesis of the quaternary ammonium ions follows a diversity oriented approach wherein the tandem inter[4+2]/intra[3+2] cycloaddition of nitroalkenes serves as the key transformation. A two part synthetic strategy comprised of: (1) preparation of enantioenriched scaffolds and (2) development of parallel synthesis procedures is described. The strategy allows for the facile introduction of four variable groups in the vicinity of a stereogenic quaternary ammonium ion. The quaternary ammonium ions exhibited a wide range of activity and to a lesser degree enantioselectivity. Catalyst activity and selectivity are rationalized in a qualitative way based on the effective positive potential of the ammonium ion. PMID:21446721

Oxidations of Organic and Inorganic Substrates by Superoxo-, hydroperoxo-, and oxo-compounds of the transition metals.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vasbinder, Michael John

2006-01-01

Chapters 1 and 2 dealt with the chemistry of superoxo-, hydroperoxo-, and oxo- complexes of chromium, rhodium and cobalt. Chapter 3 dealt with the mechanism of oxygen-atom transfer catalyzed by an oxo-complex of rhenium. In Chapter 1, it was shown that hydroperoxometal complexes of cobalt and rhodium react with superoxochromium and chromyl ions, generating reduced chromium species while oxidizing the hydroperoxometal ions to their corresponding superoxometal ions. It was shown that the chromyl and superoxochromium ions are the more powerful oxidants. Evidence supports hydrogen atom transfer from the hydroperoxometal ion to the oxidizing superoxochromium or chromyl ion as the reactionmore » mechanism. There is a significant H/D kinetic isotope effect. Comparisons to the rate constants of other known hydrogen atom transfer reactions show the expected correlation with bond dissociation energies. In Chapter 2, it was found that the superoxometal complexes Cr{sub aq}OO 2+ and Rh(NH 3) 4(H 2O)OO 2+ oxidize stable nitroxyl radicals of the TEMPO series with rate constants that correlate with the redox potentials of both the oxidant and reductant. These reactions fit the Marcus equation for electron transfer near the theoretical value. Acid catalysis is important to the reaction, especially the thermodynamically limited cases involving Rh(NH 3) 4(H 2O)OO 2+ as the oxidant. The rate constants are notably less than those measured in the reaction between the same nitroxyl radicals and other strong free-radical oxidants, an illustration of the delocalized and stabilized nature of the superoxometal ions. Chapter 3 showed that oxo-rhenium catalysts needed a nucleophile to complete the catalytic oxygen-atom transfer from substituted pyridine-N-oxides to triphenylphosphine. The reaction was studied by introducing various pyridine-derived nucleophiles and monitoring their effect on the rate, then fitting the observed rate constants to the Hammett correlation. It was found that the

Reactivity of nitrido complexes of ruthenium(VI), osmium(VI), and manganese(V) bearing Schiff base and simple anionic ligands.

PubMed

Man, Wai-Lun; Lam, William W Y; Lau, Tai-Chu

2014-02-18

Nitrido complexes (M≡N) may be key intermediates in chemical and biological nitrogen fixation and serve as useful reagents for nitrogenation of organic compounds. Osmium(VI) nitrido complexes bearing 2,2':6',2″-terpyridine (terpy), 2,2'-bipyridine (bpy), or hydrotris(1-pyrazolyl)borate anion (Tp) ligands are highly electrophilic: they can react with a variety of nucleophiles to generate novel osmium(IV)/(V) complexes. This Account describes our recent results studying the reactivity of nitridocomplexes of ruthenium(VI), osmium(VI), and manganese(V) that bear Schiff bases and other simple anionic ligands. We demonstrate that these nitrido complexes exhibit rich chemical reactivity. They react with various nucleophiles, activate C-H bonds, undergo N···N coupling, catalyze the oxidation of organic compounds, and show anticancer activities. Ruthenium(VI) nitrido complexes bearing Schiff base ligands, such as [Ru(VI)(N)(salchda)(CH3OH)](+) (salchda = N,N'-bis(salicylidene)o-cyclohexyldiamine dianion), are highly electrophilic. This complex reacts readily at ambient conditions with a variety of nucleophiles at rates that are much faster than similar reactions using Os(VI)≡N. This complex also carries out unique reactions, including the direct aziridination of alkenes, C-H bond activation of alkanes and C-N bond cleavage of anilines. The addition of ligands such as pyridine can enhance the reactivity of [Ru(VI)(N)(salchda)(CH3OH)](+). Therefore researchers can tune the reactivity of Ru≡N by adding a ligand L trans to nitride: L-Ru≡N. Moreover, the addition of various nucleophiles (Nu) to Ru(VI)≡N initially generate the ruthenium(IV) imido species Ru(IV)-N(Nu), a new class of hydrogen-atom transfer (HAT) reagents. Nucleophiles also readily add to coordinated Schiff base ligands in Os(VI)≡N and Ru(VI)≡N complexes. These additions are often stereospecific, suggesting that the nitrido ligand has a directing effect on the incoming nucleophile. M≡N is also

Alkali-metal-ion catalysis and inhibition in the nucleophilic displacement reaction of y-substituted phenyl diphenylphosphinates and diphenylphosphinothioates with alkali-metal ethoxides: effect of changing the electrophilic center from P=O to P=S.

PubMed

Um, Ik-Hwan; Shin, Young-Hee; Park, Jee-Eun; Kang, Ji-Sun; Buncel, Erwin

2012-01-16

A kinetic study of the nucleophilic substitution reaction of Y-substituted phenyl diphenylphosphinothioates 2 a-g with alkali-metal ethoxides (MOEt; M = Li, Na, K) in anhydrous ethanol at (25.0±0.1) °C is reported. Plots of pseudo-first-order rate constants (k(obsd)) versus [MOEt], the alkali ethoxide concentration, show distinct upward (KOEt) and downward (LiOEt) curvatures, respectively, pointing to the importance of ion-pairing phenomena and a differential reactivity of dissociated EtO(-) and ion-paired MOEt. Based on ion-pairing treatment of the kinetic data, the k(obsd) values were dissected into k EtO - and k(MOEt), the second-order rate constants for the reaction with the dissociated EtO(-) and ion-paired MOEt, respectively. The reactivity of MOEt toward 2 b (Y = 4-NO(2)) increases in the order LiOEtNaOEt>KOEt>EtO(-). The current study based on Yukawa-Tsuno analysis has revealed that the reactions of 2 a-g (P=S) and Y-substituted phenyl diphenylphosphinates 1 a-g (P=O) with MOEt proceed through the same concerted mechanism, which indicates that the contrasting selectivity patterns are not due to a difference in reaction mechanism. The P=O compounds 1 a-g are approximately 80-fold more reactive than the P=S compounds 2 a-g toward the dissociated EtO(-) (regardless of the electronic nature of substituent Y) but are up to 3.1×10(3)-fold more reactive toward ion-paired LiOEt. The origin of the contrasting selectivity patterns is further discussed on the basis of competing electrostatic effects and solvational requirements as a function of anionic electric field strength and cation size (Eisenman's theory). Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Changing the chemical and physical properties of high valent heterobimetallic bis-(μ-oxido) Cu-Ni complexes by ligand effects.

PubMed

Kafentzi, Maria-Chrysanthi; Orio, Maylis; Réglier, Marius; Yao, Shenglai; Kuhlmann, Uwe; Hildebrandt, Peter; Driess, Matthias; Simaan, A Jalila; Ray, Kallol

2016-10-12

Two new heterobimetallic [LNiO 2 Cu(RPY2)] + (RPY2 = N-substituted bis 2-pyridyl(ethylamine) ligands with R = indane, 3a or R = Me, 3b) complexes have been spectroscopically trapped at low temperatures. They were prepared by reacting the mononuclear side-on LNi II superoxo precursor bearing a β-diketiminate ligand (L = [HC-(CMeNC 6 H 3 (iPr) 2 ) 2 ]) with the Cu(i) complexes. In contrast to the oxo groups in known high-valent [M 2 (μ-O) 2 ] n+ (M = Fe, Co, Ni, Cu) cores that display electrophilic reactivities, 3a and 3b display rather nucleophilic oxo cores active in aldehyde deformylation reactions. However, the spectroscopic and reactivity properties of 3a/3b are found to be distinct relative to that of the previously reported [LNiO 2 Cu(MeAN)] + complex containing a more basic (nucleophilic) N,N,N',N',N'-pentamethyl-dipropylenetriamine (MeAN) ligand at the copper centre. The geometry and electronic properties of the copper ligands affect the electron density of the oxygen atoms of the heterodinuclear {Ni(μ-O) 2 } core and 3a/3b undergo slower nucleophilic and faster electrophilic reactions than the previously reported [LNiO 2 Cu(MeAN)] + intermediate. The present study therefore demonstrates the tuning of the electrophilicity/nucleophilicity of the oxygen atoms of the heterobimetallic [Ni(μ-O) 2 Cu] 2+ cores by controlling the electron donation from the ancillary ligands, and underlines the significance of subtle electronic changes in the physical and chemical properties of the biologically relevant heterobimetallic metal-dioxygen intermediates.

Analysis of the Active-Site Mechanism of Tyrosyl-DNA Phosphodiesterase I: A Member of the Phospholipase D Superfamily

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gajewski, Stefan; Comeaux, Evan Q.; Jafari, Nauzanene

2012-03-15

Tyrosyl-DNA phosphodiesterase I (Tdp1) is a member of the phospholipase D superfamily that hydrolyzes 3'-phospho-DNA adducts via two conserved catalytic histidines - one acting as the lead nucleophile and the second acting as a general acid/base. Substitution of the second histidine specifically to arginine contributes to the neurodegenerative disease spinocerebellar ataxia with axonal neuropathy (SCAN1). We investigated the catalytic role of this histidine in the yeast protein (His432) using a combination of X-ray crystallography, biochemistry, yeast genetics, and theoretical chemistry. The structures of wild-type Tdp1 and His432Arg both show a phosphorylated form of the nucleophilic histidine that is not observedmore » in the structure of His432Asn. The phosphohistidine is stabilized in the His432Arg structure by the guanidinium group that also restricts the access of nucleophilic water molecule to the Tdp1-DNA intermediate. Biochemical analyses confirm that His432Arg forms an observable and unique Tdp1-DNA adduct during catalysis. Substitution of His432 by Lys does not affect catalytic activity or yeast phenotype, but substitutions with Asn, Gln, Leu, Ala, Ser, and Thr all result in severely compromised enzymes and DNA topoisomerase I-camptothecin dependent lethality. Surprisingly, His432Asn did not show a stable covalent Tdp1-DNA intermediate that suggests another catalytic defect. Theoretical calculations revealed that the defect resides in the nucleophilic histidine and that the pK{sub a} of this histidine is crucially dependent on the second histidine and on the incoming phosphate of the substrate. This represents a unique example of substrate-activated catalysis that applies to the entire phospholipase D superfamily.« less

A theoretical investigation of substituent effects on the stability and reactivity of N-heterocyclic olefin carboxylates.

PubMed

Dong, Liang; Wen, Jun; Li, Weiyi

2015-08-21

A theoretical study of substituent effects on the stability and reactivity of novel synthesized N-heterocyclic olefin (NHO) carboxylates has been performed using a combination of density functional theory (DFT) calculations, molecular electrostatic potential (MESP) minimum and nucleophilicity index analyses. These calculations demonstrate that the nucleophilicity of free NHO is stronger than that of the NHO-CO2 adduct and, hence, the thermally unstable NHO-CO2 adduct should be a more efficient organocatalyst for nucleophile-mediated reactions. The stability of the NHO-CO2 adduct, as well as the reactivity of free NHO, is strongly dependent on the electronic and steric effects of the C- and N-substituents on the imidazole ring. This dependency is reflected by the measured MESP minimum for the carboxylate moiety, the NHO-CO2 adduct (Vmin1), and the terminal carbon atom of free NHO (Vmin2). C-Substituents exert only electronic effects while N-substituents exert both electronic and steric effects. In general, the electron-withdrawing groups on the C- and N-positions favor decarboxylation while weakening the reactivity of NHO. These positions favor decarboxylation due to the simultaneous decrease of the electronic density on the carboxyl moiety of the NHO-CO2 and the terminal carbon atom of olefins. Additionally, the balance between the stability of the NHO-CO2 and the reactivity of free NHO can be tuned by the combined effects of the C- and N-substituents. The introduction of weak electron-withdrawing groups at the C-position and aromatic substituents or similar ring-strained entities at the N-position favors decarboxylation of the NHO-CO2 adduct and ensures the free NHO as a strong nucleophile.

Analysis of the active site mechanism of Tyrosyl-DNA phosphodiesterase I: a member of the phospholipase D superfamily

PubMed Central

Gajewski, Stefan; Comeaux, Evan Q.; Jafari, Nauzanene; Bharatham, Nagakumar; Bashford, Donald; White, Stephen W.; van Waardenburg, Robert C.A.M.

2011-01-01

Tyrosyl DNA phosphodiesterase I (Tdp1) is a member of the phospholipase D superfamily and hydrolyzes 3′phospho-DNA adducts via two conserved catalytic histidines, one acting as the lead nucleophile and the second as a general acid/base. Substitution of the second histidine specifically to arginine contributes to the neurodegenerative disease SCAN1. We investigated the catalytic role of this histidine in the yeast protein (His432) using a combination of X-ray crystallography, biochemistry, yeast genetics and theoretical chemistry. The structures of wild type Tdp1 and His432Arg both show a phosphorylated form of the nucleophilic histidine that is not observed in the structure of His432Asn. The phosphohistidine is stabilized in the His432Arg structure by the guanidinium group that also restricts access of a nucleophilic water molecule to the Tdp1-DNA intermediate. Biochemical analyses confirm that His432Arg forms an observable and unique Tdp1-DNA adduct during catalysis. Substitution of His432 by Lys does not affect catalytic activity or yeast phenotype, but substitution with Asn, Gln, Leu, Ala, Ser and Thr all result in severely compromised enzymes and Top1-camptothecin dependent lethality. Surprisingly, His432Asn did not show a stable covalent Tdp1-DNA intermediate which suggests another catalytic defect. Theoretical calculations revealed that the defect resides in the nucleophilic histidine and that the pKa of this histidine is crucially dependent upon the second histidine and the incoming phosphate of the substrate. This represents a unique example of substrate-activated catalysis that applies to the entire phospholipase D superfamily. PMID:22155078

Mechanism of the sulfurisation of phosphines and phosphites using 3-amino-1,2,4-dithiazole-5-thione (xanthane hydride).

PubMed

Hanusek, Jirí; Russell, Mark A; Laws, Andrew P; Jansa, Petr; Atherton, John H; Fettes, Kevin; Page, Michael I

2007-02-07

Contrary to a previous report, the sulfurisation of phosphorus(III) derivatives by 3-amino-1,2,4-dithiazole-5-thione (xanthane hydride) does not yield carbon disulfide and cyanamide as the additional reaction products. The reaction of xanthane hydride with triphenyl phosphine or trimethyl phosphite yields triphenyl phosphine sulfide or trimethyl thiophosphate, respectively, and thiocarbamoyl isothiocyanate which has been trapped with nucleophiles. The reaction pathway involves initial nucleophilic attack of the phosphorus at sulfur next to the thiocarbonyl group of xanthane hydride followed by decomposition of the phosphonium intermediate formed to products. The Hammett rho-values for the sulfurisation of substituted triphenyl phosphines and triphenyl phosphites in acetonitrile are approximately -1.0. The entropies of activation are very negative (-114+/-15 J mol-1 K-1) with little dependence on solvent which is consistent with a bimolecular association step leading to the transition state. The negative values of DeltaS(not equal) and rho values indicate that the rate limiting step of the sulfurisation reaction is formation of the phosphonium ion intermediate which has an early transition state with little covalent bond formation. The site of nucleophilic attack has been also confirmed using computational calculations.

Assessing the issue of instability due to Michael adduct formation in novel chemical entities possessing a carbon-carbon double bond during early drug development--applicability of common laboratory analytical protocols.

PubMed

Polepally, Akshanth Reddy; Kumar, Venkata V Pavan; Bhamidipati, Ravikanth; Kota, Jagannath; Naveed, Shaik Abdul; Reddy, Karnati Harinder; Mamidi, Rao N V S; Selvakumar, N; Mullangi, Ramesh; Srinivas, Nuggehally R

2008-09-01

The discovery of small-molecule novel chemical entities (NCEs) is often a complex play between appropriate structural requirements and optimization of the desired efficacy, safety and pharmacokinetic properties. One of the typical structural variants such as having an active carbon-carbon double bond (alpha, beta-unsaturated carbonyl group) in xenobiotics may lead to stability issues. Such functionalities are extremely reactive, paving way to nucleophilic attack by endogenously occurring and ubiquitous nucleophiles like thiols. While it is easy to make a unilateral decision to not pursue the development of xenobiotics with such functionalities, we question the wisdom of such a decision. In this report, we present in vitro methodologies with appropriate examples to illustrate the ease of assessing the reactivity of the xenobiotics containing double bonds with a known nucleophile. The protocols involve simple reaction procedures followed by measurements using standard laboratory equipments (UV spectrophotometer, HPLC and LC-MS). Our data suggests that not all xenobiotics with carbon-carbon double bonds readily form a Michael's adduct product with glutathione. Hence, the criterion for dropping discovery compounds because of alpha,beta-unsaturated double bonds needs to be reconsidered.

Photometric Characterization of the Reductive Amination Scope of the Imine Reductases from Streptomyces tsukubaensis and Streptomyces ipomoeae.

PubMed

Matzel, Philipp; Krautschick, Lukas; Höhne, Matthias

2017-10-18

Imine reductases (IREDs) have emerged as promising enzymes for the asymmetric synthesis of secondary and tertiary amines starting from carbonyl substrates. Screening the substrate specificity of the reductive amination reaction is usually performed by time-consuming GC analytics. We found two highly active IREDs in our enzyme collection, IR-20 from Streptomyces tsukubaensis and IR-Sip from Streptomyces ipomoeae, that allowed a comprehensive substrate screening with a photometric NADPH assay. We screened 39 carbonyl substrates combined with 17 amines as nucleophiles. Activity data from 663 combinations provided a clear picture about substrate specificity and capabilities in the reductive amination of these enzymes. Besides aliphatic aldehydes, the IREDs accepted various cyclic (C 4 -C 8 ) and acyclic ketones, preferentially with methylamine. IR-Sip also accepted a range of primary and secondary amines as nucleophiles. In biocatalytic reactions, IR-Sip converted (R)-3-methylcyclohexanone with dimethylamine or pyrrolidine with high diastereoselectivity (>94-96 % de). The nucleophile acceptor spectrum depended on the carbonyl substrate employed. The conversion of well-accepted substrates could also be detected if crude lysates were employed as the enzyme source. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Donation and back-donation analyzed through a charge transfer model based on density functional theory.

PubMed

Orozco-Valencia, Ulises; Gázquez, José L; Vela, Alberto

2017-07-01

The net charge transfer process that occurs between two species, A and B, interacting with each other, may be decomposed into two processes: one in which A receives charge from B, which can be identified as the electrophilic channel for A or the nucleophilic channel for B, and a second in which A donates charge to B, which can be identified as the nucleophilic channel for A or the electrophilic channel for B. By determining the amount of charge associated with both processes through the minimization of the interaction energy associated with each case, the expressions for the amount of charge involved in each case can be expressed in terms of the directional chemical potentials and the hardnesses of the interacting species. The correlation between the charges obtained for the interaction between phosphine ligands of the type PRR'R'' and Ni, and the A 1 carbonyl stretching frequency provides support for their interpretation as measures of the electrophilicity and nucleophilicity of a chemical species, and, at the same time, allows one to describe the donation and back-donation processes in terms of the density functional theory of chemical reactivity.

Stereoinversion of tertiary alcohols to tertiary-alkyl isonitriles and amines.

PubMed

Pronin, Sergey V; Reiher, Christopher A; Shenvi, Ryan A

2013-09-12

The SN2 reaction (bimolecular nucleophilic substitution) is a well-known chemical transformation that can be used to join two smaller molecules together into a larger molecule or to exchange one functional group for another. The SN2 reaction proceeds in a very predictable manner: substitution occurs with inversion of stereochemistry, resulting from the 'backside attack' of the electrophilic carbon by the nucleophile. A significant limitation of the SN2 reaction is its intolerance for tertiary carbon atoms: whereas primary and secondary alcohols are viable precursor substrates, tertiary alcohols and their derivatives usually either fail to react or produce stereochemical mixtures of products. Here we report the stereochemical inversion of chiral tertiary alcohols with a nitrogenous nucleophile facilitated by a Lewis-acid-catalysed solvolysis. The method is chemoselective against secondary and primary alcohols, thereby complementing the selectivity of the SN2 reaction. Furthermore, this method for carbon-nitrogen bond formation mimics a putative biosynthetic step in the synthesis of marine terpenoids and enables their preparation from the corresponding terrestrial terpenes. We expect that the general attributes of the methodology will allow chiral tertiary alcohols to be considered viable substrates for stereoinversion reactions.

Substrate-Controlled Product Divergence: Conversion of CO2 into Heterocyclic Products.

PubMed

Rintjema, Jeroen; Epping, Roel; Fiorani, Giulia; Martín, Eddy; Escudero-Adán, Eduardo C; Kleij, Arjan W

2016-03-14

Substituted epoxy alcohols and amines allow substrate-controlled conversion of CO2 into a wide range of heterocyclic structures through different mechanistic manifolds. This new approach results in an unusual scope of CO2-derived products by initial activation of CO2 through either the amine or alcohol unit, thus providing nucleophiles for intramolecular epoxy ring opening under mild reaction conditions. Control experiments support the crucial role of the amine/alcohol fragment in this process with the nucleophile-assisted ring-opening step following an SN i pathway, and a 5-exo-tet cyclization, thus leading to heterocyclic scaffolds. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bond formations by intermolecular and intramolecular trappings of acylketenes and their applications in natural product synthesis†

PubMed Central

Reber, Keith P.; Tilley, S. David

2011-01-01

The reactive intermediates known as acylketenes exhibit a rich chemistry and have been extensively utilized for many types of inter- and intramolecular bond-forming reactions within the field of organic synthesis. Characteristic reactions of acylketenes include cycloadditions, carbon–carbon bond-forming reactions, and nucleophilic capture with alcohols or amines to give β-keto acid derivatives. In particular, the intramolecular capture of acylketene intermediates with pendant nucleophiles represents a powerful method for forming both medium-sized rings and macrocycles, often in high yield. This tutorial review examines the history, generation, and reactivity of acylketenes with a special focus on their applications in the synthesis of natural products. PMID:19847338

Water Assisted Reaction Mechanism of OH- with CCl4 in Aqueous Solution - Hybrid Quantum Mechanical and Molecular Mechanics Investigation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Jie; Yin, Hongyun; Wang, Dunyou

2013-02-20

The OH- (H2O) + CCl4 reaction in aqueous solution was investigated using the combined quantum mechanical and molecular mechanics approach. The reaction mechanism of OH- (H2O) + CCl4 consists of two concerted steps - formation of OH- in the favorable attack conformation via the proton transfer process, and the nucleophilic substitution process in which the newly formed OH- attacks the CCl4. The free energy activation barrier is 38.2 kcal/mol at CCSD(T)/MM level of theory for this reaction, which is about 10.3 kcal/mol higher than that of the direct nucleophilic substitution mechanism of the OH- + CCl4 reaction in aqueous solution.

Progress and developments in the turbo Grignard reagent i-PrMgCl·LiCl: a ten-year journey.

PubMed

Bao, Robert Li-Yuan; Zhao, Rong; Shi, Lei

2015-04-25

Over the past decade, the effectiveness of i-PrMgCl·LiCl has been constantly highlighted by a number of research groups. Its enhanced nucleophilicity brings prosperity to highly functionalized Grignard reagents, other useful bimetallic (alkali-metal) agents and nucleophilic alkylation products under mild reaction conditions. In this feature article, a comprehensive, systematical and in-depth overview of i-PrMgCl·LiCl is provided in a multidisciplinary idea. It involves the structural and kinetic perspectives of i-PrMgCl·LiCl as well as its unique reactivity and selectivity, with knowledge of the former helping to rationalize trends of the later.

Prediction of the chemo- and regioselectivity of Diels-Alder reactions of o-benzoquinone derivatives with thiophenes by means of DFT-based reactivity indices

NASA Astrophysics Data System (ADS)

Ghomri, Amina; Mekelleche, Sidi Mohamed

2014-03-01

Global and local reactivity indices derived from density functional theory were used to elucidate the regio- and chemoselectivity of Diels-Alder reactions of masked o-benzoquinones with thiophenes acting as dienophiles. The polarity of the studied reactions is evaluated in terms of the difference of electrophilicity powers between the diene and dienophile partners. Preferential cyclisation modes of these cycloadditions are predicted using Domingo's polar model based on the local electrophilicity index, ωk, of the electrophile and the local nucleophilicity index, Nuk, of the nucleophile. The theoretical calculations, carried out at the B3LYP/6-311G(d,p) level of theory, are in good agreement with experimental findings.

A model SN2 reaction ‘on water’ does not show rate enhancement

NASA Astrophysics Data System (ADS)

Nelson, Katherine V.; Benjamin, Ilan

2011-05-01

Molecular dynamics calculations of the benchmark nucleophilic substitution reaction (SN2) Cl- + CH3Cl are carried out at the water liquid/vapor interface. The reaction free energy profile and the activation free energy are determined as a function of the reactants' location normal to the surface. The activation free energy remains almost constant relative to that in bulk water, despite the fact that the barrier is expected to significantly decrease as the reaction is carried out near the vapor phase. We show that this is due to the combined effects of a clustering of water molecules around the nucleophile and a relatively weak hydration of the transition state.

Potent Inhibitors of Plasmodial Serine Hydroxymethyltransferase (SHMT) Featuring a Spirocyclic Scaffold.

PubMed

Schwertz, Geoffrey; Witschel, Matthias C; Rottmann, Matthias; Leartsakulpanich, Ubolsree; Chitnumsub, Penchit; Jaruwat, Aritsara; Amornwatcharapong, Watcharee; Ittarat, Wanwipa; Schäfer, Anja; Aponte, Raphael A; Trapp, Nils; Chaiyen, Pimchai; Diederich, François

2018-05-08

With the discovery that serine hydroxymethyltransferase (SHMT) is a druggable target for antimalarials, the aim of this study was to design novel inhibitors of this key enzyme in the folate biosynthesis cycle. Herein, 19 novel spirocyclic ligands based on either 2-indolinone or dihydroindene scaffolds and featuring a pyrazolopyran core are reported. Strong target affinities for Plasmodium falciparum (Pf) SHMT (14-76 nm) and cellular potencies in the low nanomolar range (165-334 nm) were measured together with interesting selectivity against human cytosolic SHMT1 (hSHMT1). Four co-crystal structures with Plasmodium vivax (Pv) SHMT solved at 2.2-2.4 Å resolution revealed the key role of the vinylogous cyanamide for anchoring ligands within the active site. The spirocyclic motif in the molecules enforces the pyrazolopyran core to adopt a substantially more curved conformation than that of previous non-spirocyclic analogues. Finally, solvation of the spirocyclic lactam ring of the receptor-bound ligands is discussed. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Importance of Nonclassical σ-Hole Interactions for the Reactivity of λ3-Iodane Complexes.

PubMed

Pinto de Magalhães, Halua; Togni, Antonio; Lüthi, Hans Peter

2017-11-17

Key for the observed reactivity of λ 3 -iodanes, powerful reagents for the selective transfer of functional groups to nucleophiles, are the properties of the 3-center-4-electron bond involving the iodine atom and the two linearly arranged ligands. This bond is also involved in the formation of the initial complex between the λ 3 -iodane and a nucleophile, which can be a solvent molecule or a reactant. The bonding in such complexes can be described by means of σ-hole interactions. In halogen compounds, σ-hole interaction was identified as a force in crystal packing or in the formation of supramolecular chains. More recently, σ-hole interactions were also shown to affect the reactivity of the iodine-based hypervalent reagents. Relative to their monovalent counterparts, where the σ-hole is located on the extension of the sigma-bond, in the hypervalent species our DFT calculations reveal the formation of a nonclassical σ-hole region with one or even two maxima. This observation is also made in fully relativistic calculations. The SAPT analysis shows that the σ-hole bond between the λ 3 -iodane and the nucleophile is not necessarily of purely electrostatic nature but may also contain a significant covalent component. This covalent component may facilitate chemical transformation of the compound by means of reductive elimination or other mechanisms and is therefore an indicator for its reactivity. Here, we also show that the shape, location, and strength of the σ-holes can be tuned by the choice of ligands and measures such as Brønsted activation of the iodane reagent. At the limit, the tuning transforms the nonclassical σ-hole regions into coordination sites, which allows us to control how a nucleophile will bind and react with the iodane.

Probing the Catalytic Mechanism of Vibrio harveyi GH20 β-N-Acetylglucosaminidase by Chemical Rescue

PubMed Central

Meekrathok, Piyanat; Suginta, Wipa

2016-01-01

Background Vibrio harveyi GH20 β-N-acetylglucosaminidase (VhGlcNAcase) is a chitinolytic enzyme responsible for the successive degradation of chitin fragments to GlcNAc monomers, activating the onset of the chitin catabolic cascade in marine Vibrios. Methods Two invariant acidic pairs (Asp303-Asp304 and Asp437-Glu438) of VhGlcNAcase were mutated using a site-directed mutagenesis strategy. The effects of these mutations were examined and the catalytic roles of these active-site residues were elucidated using a chemical rescue approach. Enhancement of the enzymic activity of the VhGlcNAcase mutants was evaluated by a colorimetric assay using pNP-GlcNAc as substrate. Results Substitution of Asp303, Asp304, Asp437 or Glu438 with Ala/Asn/Gln produced a dramatic loss of the GlcNAcase activity. However, the activity of the inactive D437A mutant was recovered in the presence of sodium formate. Our kinetic data suggest that formate ion plays a nucleophilic role by mimicking the β-COO-side chain of Asp437, thereby stabilizing the reaction intermediate during both the glycosylation and the deglycosylation steps. Conclusions Chemical rescue of the inactive D437A mutant of VhGlcNAcase by an added nucleophile helped to identify Asp437 as the catalytic nucleophile/base, and hence its acidic partner Glu438 as the catalytic proton donor/acceptor. General Significance Identification of the catalytic nucleophile of VhGlcNAcases supports the proposal of a substrate-assisted mechanism of GH20 GlcNAcases, requiring the catalytic pair Asp437-Glu438 for catalysis. The results suggest the mechanistic basis of the participation of β-N-acetylglucosaminidase in the chitin catabolic pathway of marine Vibrios. PMID:26870945

Micellar catalyzed degradation of fenitrothion, an organophosphorus pesticide, in solution and soils.

PubMed

Balakrishnan, Vimal K; Buncel, Erwin; Vanloon, Gary W

2005-08-01

We report on a study of the decomposition of fenitrothion (an organophosphorus pesticide that is a persistent contaminant in soils and groundwater) as catalyzed by cetyltrimethylammonium (CTA+) micelles. The CTA micelles were associated with two types of counterions: (1) inert counterions (e.g. CTABr) and (2) reactive counterions (e.g. CTAOH). The reactive counterion surfactants used were hydroxide anion (HO-) as a normal nucleophile and hydroperoxide anion (HOO-) and the anion of pyruvaldehyde oxime (MINA-) as two alpha-nucleophiles. The reactivity order followed: CTABr < CTAOH < CTAMINA < CTAOOH. Treatment of the rate data using the Pseudo-Phase Ion Exchange (PPIE) model of micellar catalysis showed the ratio k2M/k2w to be less than unity for all the surfactants employed. Rather than arising from a "true catalysis", we attributed the observed rate enhancements to a "concentration effect", where both pesticide and nucleophile were incorporated into the small micellar phase volume. Furthermore, the CTAOOH/CTAOH pair gave an alpha-effect of 57, showing that the alpha-effect can play an important role in micellar systems. We further investigated the effectiveness of reactive counterion surfactants in decontaminating selected environmental solids that were spiked with 27 ppb fenitrothion. The solids were as follows: the clay mineral montmorillonite and SO-1 and S0-2 soils (obtained from the Canadian Certified Reference Materials Project). The reactive counterion surfactant solutions significantly enhanced the rate of fenitrothion degradation in the spiked solids over that obtained when the spiked solid was placed in contact with either 0.02 M KOH or water. The rate enhancements followed the order CTAOOH > CTAMINA approximately CTAOH > KOH > water. We conclude that reactive counterion surfactants, especially with alpha-nucleophiles, hold great potential in terms of remediating soils contaminated by toxic organophosphorus esters.

Chemoselective covalent coupling of oligonucleotide probes to self-assembled monolayers.

PubMed

Devaraj, Neal K; Miller, Gregory P; Ebina, Wataru; Kakaradov, Boyko; Collman, James P; Kool, Eric T; Chidsey, Christopher E D

2005-06-22

A chemoselective route to routinely and rapidly attach oligonucleotide probes to well-defined surfaces is presented. Cu(I) tris(benzyltriazolylmethyl)amine-catalyzed coupling of terminal acetylenes to azides on a self-assembled monolayer is used instead of traditional nucleophilic-electrophilic coupling reactions. The reaction proceeds well even in the presence of purposely introduced nucleophilic and electrophilic impurities. The density of oligonucleotide probes can be controlled by controlling the amount of azide functionality. Although most of our work was done on gold surfaces, this technique should be readily applicable to any surface on which an azide-containing monolayer can be assembled as we have preliminarily demonstrated by derivatizing azidotrimethoxysilane-modified glass slides with fluorescein-containing oligonucleotides.

Enantioselective Decarboxylative Alkylation Reactions: Catalyst Development, Substrate Scope, and Mechanistic Studies

PubMed Central

Behenna, Douglas C.; Mohr, Justin T.; Sherden, Nathaniel H.; Marinescu, Smaranda C.; Harned, Andrew M.; Tani, Kousuke; Seto, Masaki; Ma, Sandy; Novák, Zoltán; Krout, Michael R.; McFadden, Ryan M.; Roizen, Jennifer L.; Enquist, John A.; White, David E.; Levine, Samantha R.; Petrova, Krastina V.; Iwashita, Akihiko; Virgil, Scott C.; Stoltz, Brian M.

2012-01-01

α-Quaternary ketones are accessed through novel enantioselective alkylations of allyl and propargyl electrophiles by unstabilized prochiral enolate nucleophiles in the presence of palladium complexes with various phosphinooxazoline (PHOX) ligands. Excellent yields and high enantiomeric excesses are obtained from three classes of enolate precursors: enol carbonates, enol silanes, and racemic β-ketoesters. Each of these substrate classes functions with nearly identical efficiency in terms of yield and enantioselectivity. Catalyst discovery and development, the optimization of reaction conditions, the exploration of reaction scope, and applications in target-directed synthesis are reported. Experimental observations suggest that these alkylation reactions occur through an unusual inner-sphere mechanism involving binding of the prochiral enolate nucleophile directly to the palladium center. PMID:22083969

Chiral Brønsted Acid‐Catalyzed Enantioselective α‐Amidoalkylation Reactions: A Joint Experimental and Predictive Study

PubMed Central

Aranzamendi, Eider; Arrasate, Sonia; Sotomayor, Nuria

2016-01-01

Abstract Enamides with a free NH group have been evaluated as nucleophiles in chiral Brønsted acid‐catalyzed enantioselective α‐amidoalkylation reactions of bicyclic hydroxylactams for the generation of quaternary stereocenters. A quantitative structure–reactivity relationship (QSRR) method has been developed to find a useful tool to rationalize the enantioselectivity in this and related processes and to orient the catalyst choice. This correlative perturbation theory (PT)‐QSRR approach has been used to predict the effect of the structure of the substrate, nucleophile, and catalyst, as well as the experimental conditions, on the enantioselectivity. In this way, trends to improve the experimental results could be found without engaging in a long‐term empirical investigation. PMID:28032023

Redox and Lewis acid relay catalysis: a titanocene/zinc catalytic platform in the development of multicomponent coupling reactions.

PubMed

Gianino, Joseph B; Campos, Catherine A; Lepore, Antonio J; Pinkerton, David M; Ashfeld, Brandon L

2014-12-19

A titanocene-catalyzed multicomponent coupling is described herein. Using catalytic titanocene, phosphine, and zinc dust, zinc acetylides can be generated from the corresponding iodoalkynes to affect sequential nucleophilic additions to aromatic aldehydes. The intermediate propargylic alkoxides are trapped in situ with acetic anhydride, which are susceptible to a second nucleophilic displacement upon treatment with a variety of electron-rich species, including acetylides, allyl silanes, electron-rich aromatics, silyl enol ethers, and silyl ketene acetals. Additionally, employing cyclopropane carboxaldehydes led to ring-opened products resulting from iodine incorporation. Taken together, these results form the basis for a new mode of three-component coupling reactions, which allows for rapid access to value added products in a single synthetic operation.

Structural basis of metallo-β-lactamase, serine-β-lactamase and penicillin-binding protein inhibition by cyclic boronates

NASA Astrophysics Data System (ADS)

Brem, Jürgen; Cain, Ricky; Cahill, Samuel; McDonough, Michael A.; Clifton, Ian J.; Jiménez-Castellanos, Juan-Carlos; Avison, Matthew B.; Spencer, James; Fishwick, Colin W. G.; Schofield, Christopher J.

2016-08-01

β-Lactamases enable resistance to almost all β-lactam antibiotics. Pioneering work revealed that acyclic boronic acids can act as `transition state analogue' inhibitors of nucleophilic serine enzymes, including serine-β-lactamases. Here we report biochemical and biophysical analyses revealing that cyclic boronates potently inhibit both nucleophilic serine and zinc-dependent β-lactamases by a mechanism involving mimicking of the common tetrahedral intermediate. Cyclic boronates also potently inhibit the non-essential penicillin-binding protein PBP 5 by the same mechanism of action. The results open the way for development of dual action inhibitors effective against both serine- and metallo-β-lactamases, and which could also have antimicrobial activity through inhibition of PBPs.

Predicting Hydride Donor Strength via Quantum Chemical Calculations of Hydride Transfer Activation Free Energy.

PubMed

Alherz, Abdulaziz; Lim, Chern-Hooi; Hynes, James T; Musgrave, Charles B

2018-01-25

We propose a method to approximate the kinetic properties of hydride donor species by relating the nucleophilicity (N) of a hydride to the activation free energy ΔG ⧧ of its corresponding hydride transfer reaction. N is a kinetic parameter related to the hydride transfer rate constant that quantifies a nucleophilic hydridic species' tendency to donate. Our method estimates N using quantum chemical calculations to compute ΔG ⧧ for hydride transfers from hydride donors to CO 2 in solution. A linear correlation for each class of hydrides is then established between experimentally determined N values and the computationally predicted ΔG ⧧ ; this relationship can then be used to predict nucleophilicity for different hydride donors within each class. This approach is employed to determine N for four different classes of hydride donors: two organic (carbon-based and benzimidazole-based) and two inorganic (boron and silicon) hydride classes. We argue that silicon and boron hydrides are driven by the formation of the more stable Si-O or B-O bond. In contrast, the carbon-based hydrides considered herein are driven by the stability acquired upon rearomatization, a feature making these species of particular interest, because they both exhibit catalytic behavior and can be recycled.

Density functional theory and surface reactivity study of bimetallic AgnYm (n+m = 10) clusters

NASA Astrophysics Data System (ADS)

Hussain, Riaz; Hussain, Abdullah Ijaz; Chatha, Shahzad Ali Shahid; Hussain, Riaz; Hanif, Usman; Ayub, Khurshid

2018-06-01

Density functional theory calculations have been performed on pure silver (Agn), yttrium (Ym) and bimetallic silver yttrium clusters AgnYm (n + m = 2-10) for reactivity descriptors in order to realize sites for nucleophilic and electrophilic attack. The reactivity descriptors of the clusters, studied as a function of cluster size and shape, reveal the presence of different type of reactive sites in a cluster. The size and shape of the pure silver, yttrium and bimetallic silver yttrium cluster (n = 2-10) strongly influences the number and position of active sites for an electrophilic and/or nucleophilic attack. The trends of reactivities through reactivity descriptors are confirmed through comparison with experimental data for CO binding with silver clusters. Moreover, the adsorption of CO on bimetallic silver yttrium clusters is also evaluated. The trends of binding energies support the reactivity descriptors values. Doping of pure cluster with the other element also influence the hardness, softness and chemical reactivity of the clusters. The softness increases as we increase the number of silver atoms in the cluster, whereas the hardness decreases. The chemical reactivity increases with silver doping whereas it decreases by increasing yttrium concentration. Silver atoms are nucleophilic in small clusters but changed to electrophilic in large clusters.

A front-face 'SNi synthase' engineered from a retaining 'double-SN2' hydrolase.

PubMed

Iglesias-Fernández, Javier; Hancock, Susan M; Lee, Seung Seo; Khan, Maola; Kirkpatrick, Jo; Oldham, Neil J; McAuley, Katherine; Fordham-Skelton, Anthony; Rovira, Carme; Davis, Benjamin G

2017-08-01

S N i-like mechanisms, which involve front-face leaving group departure and nucleophile approach, have been observed experimentally and computationally in chemical and enzymatic substitution at α-glycosyl electrophiles. Since S N i-like, S N 1 and S N 2 substitution pathways can be energetically comparable, engineered switching could be feasible. Here, engineering of Sulfolobus solfataricus β-glycosidase, which originally catalyzed double S N 2 substitution, changed its mode to S N i-like. Destruction of the first S N 2 nucleophile through E387Y mutation created a β-stereoselective catalyst for glycoside synthesis from activated substrates, despite lacking a nucleophile. The pH profile, kinetic and mutational analyses, mechanism-based inactivators, X-ray structure and subsequent metadynamics simulations together suggest recruitment of substrates by π-sugar interaction and reveal a quantum mechanics-molecular mechanics (QM/MM) free-energy landscape for the substitution reaction that is similar to those of natural, S N i-like glycosyltransferases. This observation of a front-face mechanism in a β-glycosyltransfer enzyme highlights that S N i-like pathways may be engineered in catalysts with suitable environments and suggests that 'β-S N i' mechanisms may be feasible for natural glycosyltransfer enzymes.

Linear free energy relationship and deuterium kinetic isotope effect observed on phospho and thiophosphoryl transfer reactions in some organophosphorous compounds

NASA Astrophysics Data System (ADS)

Lumbiny, B. J.; Hui, Z.; Islam, M. A.; Quader, M. A.; Rahman, M.

2014-04-01

Tetracoordinated organophosphorous compounds were synthesized, characterized and nucleophilic substitution reaction were investigated by varying substituents around phosphorous centre or in nucleophile considering its utility in biological and environmental system. The reactivity is expressed in terms of second-order rate constant, k2 and measured conductometrically. Linear Free Energy Relationship (LFER) tools mainly Hammett (ρ), Brönsted (β) LFER coefficients and deuterium kinetic isotope effects (KIEs) being determined for the pyridinolysis of 4 - chlorophenyl 4 - methoxy phenyl chlorophosphate, 1 in acetonitrile at 5.0 °C. The experimental data's were compared with those of structurally similar organophosphorous compounds reported earlier in quest for the mechanistic information. Nice linear correlation being found for Hammett (logk2 vs σx), having negative value of the ρX = -5.85 and Brönsted (logk2 vs pKa(x)) plots having large positive value for βX = 1.18 for 1 can be interpreted as SN2 process with greater extent of bond formation in transition state (TS) of 1. The observed kH/kD values of 1 is 1.00 ± 0.05 and net KIE, 1.32 suggests the primary KIE and indicates frontside nucleophilic attack through the partial deprotonation of pyridine occurs by the hydrogen bonding in the rate-determining step.

Optimization of the biotechnological production of a novel class of anti-MRSA antibiotics from Chitinophaga sancti.

PubMed

Beckmann, Amelie; Hüttel, Stephan; Schmitt, Viktoria; Müller, Rolf; Stadler, Marc

2017-08-17

Recently, the discovery of the elansolids, a group of macrolides, was reported. The molecules show activity against methicillin-resistant Staphylococcus aureus as well as other gram-positive organisms. This fact renders those substances a promising starting point for future chemical development. The active atropisomers A1/A2 are formed by macrolactonization of the biosynthesis product A3 but are prone to ring opening and subsequent formation of several unwanted side products. Recently it could be shown that addition of different nucleophiles to culture extracts of Chitinophaga sancti enable the formation of new stable elansolid derivatives. Furthermore, addition of such a nucleophile directly into the culture led exclusively to formation of a single active elansolid derivative. Due to low product yields, methods for production of gram amounts of these molecules have to be established to enable further development of this promising compound class. Production of elansolid A2 by C. sancti was enabled using a synthetic medium with sucrose as carbon source to a final concentration of 18.9 mg L -1 . A fed-batch fermentation was ensued that resulted in an elansolid A2 concentration of 55.3 mg L -1 . When using glucose as carbon source in a fed-batch fermentation only 34.4 mg L -1 elansolid A2 but 223.1 mg L -1 elansolid C1 were produced. This finding was not unexpected since elansolids A1/A2 and A3 have been reported to easily react with nucleophiles like anthranilic acid, a precursor of tryptophan biosynthesis. Due to the fact that nucleophiles can be incorporated in vivo, a fed-batch cultivation under identical conditions, with addition of anthranilic acid was carried out and lead to almost exclusive formation of elansolid C1 (257.5 mg L -1 ). Reproducible elansolid A2 and C1 production is feasible in different synthetic media at relatively high concentrations that will allow further investigation and semi-synthetic optimization. The feeding of anthranilic

Synthesis, X-ray crystallography, and computational analysis of 1-azafenestranes.

PubMed

Denmark, Scott E; Montgomery, Justin I; Kramps, Laurenz A

2006-09-06

The tandem [4+2]/[3+2] cycloaddition of nitroalkenes has been employed in the synthesis of 1-azafenestranes, molecules of theoretical interest because of planarizing distortion of their central carbon atoms. The synthesis of c,c,c,c-[5.5.5.5]-1-azafenestrane was completed in good yield from a substituted nitrocyclopentene, and its borane adduct was analyzed through X-ray crystallography, which showed a moderate distortion from ideal tetrahedral geometry. The syntheses of two members of the [4.5.5.5] family of 1-azafenestranes are also reported, including one with a trans fusion at a bicyclic ring junction which brings about considerable planarization of one of the central angles (16.8 degrees deviation from tetrahedral geometry). While investigating the [4.5.5.5]-1-azafenestranes, a novel dyotropic rearrangement that converts nitroso acetals into tetracyclic aminals was discovered. Through conformational analysis, a means to prevent this molecular reorganization was formulated and realized experimentally with the use of a bulky vinyl ether in the key [4+2] cycloaddition reaction. Finally, DFT calculations on relative strain energy for the 1-azafenestranes, as well as their predicted central angles, are disclosed.

Boosting Chemical Stability, Catalytic Activity, and Enantioselectivity of Metal-Organic Frameworks for Batch and Flow Reactions.

PubMed

Chen, Xu; Jiang, Hong; Hou, Bang; Gong, Wei; Liu, Yan; Cui, Yong

2017-09-27

A key challenge in heterogeneous catalysis is the design and synthesis of heterogeneous catalysts featuring high catalytic activity, selectivity, and recyclability. Here we demonstrate that high-performance heterogeneous asymmetric catalysts can be engineered from a metal-organic framework (MOF) platform by using a ligand design strategy. Three porous chiral MOFs with the framework formula [Mn 2 L(H 2 O) 2 ] are prepared from enantiopure phosphono-carboxylate ligands of 1,1'-biphenol that are functionalized with 3,5-bis(trifluoromethyl)-, bismethyl-, and bisfluoro-phenyl substituents at the 3,3'-position. For the first time, we show that not only chemical stability but also catalytic activity and stereoselectivity of the MOFs can be tuned by modifying the ligand structures. Particularly, the MOF incorporated with -CF 3 groups on the pore walls exhibits enhanced tolerance to water, weak acid, and base compared with the MOFs with -F and -Me groups. Under both batch and flow reaction systems, the CF 3 -containing MOF demonstrated excellent reactivity, selectivity, and recyclability, affording high yields and enantioselectivities for alkylations of indoles and pyrrole with a range of ketoesters or nitroalkenes. In contrast, the corresponding homogeneous catalysts gave low enantioselectivity in catalyzing the tested reactions.

Spectroscopic Evidence for Covalent Binding of Sulfadiazine to Natural Soils via 1,4-nucleophilic addition (Michael Type Addition) studied by Spin Labeling ESR

NASA Astrophysics Data System (ADS)

Aleksandrova, Olga

2015-04-01

with different polarity. As shown by the spin labeling ESR experiment, molecules modeling SDZ were promptly bound to non-hydrolysable network of soil organic matter only via the aromatic amines that was accompanied by a prompt enlargement of humic particles binding aromatic amines, whereas binding of decomposition products of SDZ to humic acids of soil via the aliphatic amines was not observable. The ESR spectra obviously showed a single-phase process of covalent binding of the aromatic amines. Repeated washouts of labeled soil samples using distil water and ultrafiltration through the membrane of 5000 MWCO PES confirmed irreversible binding of the aromatic amines, and showed that via the aliphatic amines, binding of SDZ or decomposition products of SDZ to soil might also occur but reversibly and only to small soil molecules, which don't enter into the composition of non-hydrolysable part of soil organic matter. SL ESR experiments of different soils at the presence of Laccase highlighted that covalent binding of the aromatic amines to humic particles occurred in the specific hydrophobic areas of soil found as depleted in oxygen. All measured data evidenced that first, SDZ might be decomposed that allowed for measuring the same change of a paramagnetic signal of soil organic matter influenced by both aromatic and aliphatic amines as in the experiment of the interaction of soil with SDZ. Second, a decomposition product of SDZ with the aromatic amine might be bound to non-hydrolysable parts of soil organic matter under specific anaerobic conditions only via 1,4 - nucleophilic addition, Michael-type addition. Gulkowska, A., Thalmann, B., D., Hollender, J., & Krauss, M. (2014). Chemosphere, 107, 366 - 372. Müller, T., Rosendahl, I., Focks, A., Siemens, J., Klasmeier, J., & Matthies. (2013). Environmental Pollution, 172,180 - 185. Nowak, K.M., Miltner, A., Gehre, M., Schaeffer, A., & Kaestner, M. (2011). Environmental Science & Technology 45, 999 - 1006. Weber, E.J., Spidle

Ligand-Controlled Regioselective Copper-Catalyzed Trifluoromethylation To Generate (Trifluoromethyl)allenes.

PubMed

Ambler, Brett R; Peddi, Santosh; Altman, Ryan A

2015-05-15

"Cu-CF3" species have been used historically for a broad spectrum of nucleophilic trifluoromethylation reactions. Although recent advancements have employed ligands to stabilize and harness the reactivity of this key organometallic intermediate, the ability of a ligand to differentiate a regiochemical outcome of a Cu-CF3-mediated or -catalyzed reaction has not been previously reported. Herein, we report the first example of a Cu-catalyzed trifluoromethylation reaction in which a ligand controls the regiochemical outcome. More specifically, we demonstrate the ability of bipyridyl-derived ligands to control the regioselectivity of the Cu-catalyzed nucleophilic trifluoromethylation reactions of propargyl electrophiles to generate (trifluoromethyl)allenes. This method provides a variety of di-, tri-, and tetrasubstituted (trifluoromethyl)allenes, which can be further modified to generate complex fluorinated substructures.

C-glycosylation reactions of sulfur-substituted glycosyl donors: evidence against the role of neighboring-group participation.

PubMed

Beaver, Matthew G; Billings, Susan B; Woerpel, K A

2008-02-13

Nucleophilic substitution reactions of C-4 sulfur-substituted tetrahydropyran acetals revealed that neighboring-group participation does not control product formation. Spectroscopic evidence for the formation of an intermediate sulfonium ion is provided, as are data from nucleophilic substitution reactions demonstrating that products are formed from oxocarbenium ion intermediates. The selectivity was not sensitive to solvent or to which Lewis acid was employed. The identity of the heteroatom at the C-4 position also did not significantly impact diastereoselectivity. Consequently, neighboring-group participation was not responsible for the formation of either the major or the minor products. These studies implicate a Curtin-Hammett kinetic scenario in which the formation of a low-energy intermediate does not necessitate its involvement in the product-forming pathway.

N-Heterocyclic Olefins as Robust Organocatalyst for the Chemical Conversion of Carbon Dioxide to Value-Added Chemicals.

PubMed

Saptal, Vitthal B; Bhanage, Bhalchandra M

2016-08-09

In this report, the activity of N-heterocyclic olefins (NHOs) as a newly emerging class of organocatalyst is investigated for the chemical fixation of carbon dioxide through reactions with aziridines to form oxazolidinones and the N-formylation of amines with polymethylhydrosiloxane (PMHS) or 9-borabicyclo[3.3.1]nonane (9-BBN) as the reducing agent under mild conditions. The exocyclic carbon atoms of NHOs are highly nucleophilic owing to the electron-donating ability of the two nitrogen atoms. This high nucleophilicity of the NHOs activates CO2 molecules to form zwitterionic NHO-carboxylate (NHO-CO2 ) adducts, which are active in formylation reactions as well as the carboxylation of aziridines to oxazolidinones. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A New Domain of Reactivity for High-Valent Dinuclear [M(μ-O)2 M'] Complexes in Oxidation Reactions.

PubMed

Engelmann, Xenia; Yao, Shenglai; Farquhar, Erik R; Szilvási, Tibor; Kuhlmann, Uwe; Hildebrandt, Peter; Driess, Matthias; Ray, Kallol

2017-01-02

The strikingly different reactivity of a series of homo- and heterodinuclear [(M III )(μ-O) 2 (M III )'] 2+ (M=Ni; M'=Fe, Co, Ni and M=M'=Co) complexes with β-diketiminate ligands in electrophilic and nucleophilic oxidation reactions is reported, and can be correlated to the spectroscopic features of the [(M III )(μ-O) 2 (M III )'] 2+ core. In particular, the unprecedented nucleophilic reactivity of the symmetric [Ni III (μ-O) 2 Ni III ] 2+ complex and the decay of the asymmetric [Ni III (μ-O) 2 Co III ] 2+ core through aromatic hydroxylation reactions represent a new domain for high-valent bis(μ-oxido)dimetal reactivity. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Generation and exploitation of acyclic azomethine imines in chiral Brønsted acid catalysis

NASA Astrophysics Data System (ADS)

Hashimoto, Takuya; Kimura, Hidenori; Kawamata, Yu; Maruoka, Keiji

2011-08-01

Successful implementation of a catalytic asymmetric synthesis strategy to produce enantiomerically enriched compounds requires the adoption of suitable prochiral substrates. The combination of an azomethine imine electrophile with various nucleophiles could give straightforward access to a number of synthetically useful chiral hydrazines, but is used rarely. Here we report the exploitation of acyclic azomethine imines as a new type of prochiral electrophile. They can be generated in situ by the condensation of N‧-benzylbenzoylhydrazide with a variety of aldehydes in the presence of a catalytic amount of an axially chiral dicarboxylic acid. By trapping these electrophiles with alkyl diazoacetate or (diazomethyl)phosphonate nucleophiles, we produced a diverse array of chiral α-diazo-β-hydrazino esters and phosphonates with excellent enantioselectivities.

Presidential Green Chemistry Challenge: 1998 Greener Synthetic Pathways Award

EPA Pesticide Factsheets

Presidential Green Chemistry Challenge 1998 award winner, Flexsys America, developed nucleophilic aromatic substitution for hydrogen to eliminate waste from a common reaction and to produce 4-ADPA, a high-volume chemical.

Eco-friendly polyethylene glycol promoted Michael addition reactions of α,β-unsaturated carbonyl compounds

EPA Science Inventory

Abstract- Intra- and inter-nucleophilic addition reactions of different unsaturated compounds were found to be highly effective without any additives in PEG-400 as a recyclable reaction medium under neutral conditions.

Spirodi(iminohydantoin) Products from Oxidation of 2′-Deoxyguanosine in the Presence of NH4Cl in Nucleoside and Oligodeoxynucleotide Contexts

PubMed Central

2015-01-01

Upon oxidation of the heterocyclic ring in 2′-deoxyguanosine (dG), the initial electrophilic intermediate displays a wide range of reactivities with nucleophiles leading to many downstream products. In the present study, the product profiles were mapped when aqueous solutions of dG were allowed to react with NH4Cl in the presence of the photooxidants riboflavin and Rose Bengal as well as the diffusible one-electron oxidant Na2IrCl6. Product characterization identified the 2′-deoxyribonucleosides of spiroiminodihydantoin, 5-guanidinohydantoin, and oxazolone resulting from H2O as the nucleophile. When NH3 was the nucleophile, a set of constitutional isomers that are diastereotopic were also observed, giving characteristic masses of dG + 31. ESI+-MS/MS of these NH3 adducts identified them to be spirocycles with substitution of either the C5 or C8 carbonyl with an amine. The NH3 adducts exhibit acid-catalyzed hydrolysis to spiroiminodihydantoin. Quantification of the NH3 and H2O adducts resulting from oxidation of dG in the nucleoside, single-stranded, and duplex oligodeoxynucleotide contexts were monitored allowing mechanisms for product formation to be proposed. These data also provide a cautionary note to those who purify their oligonucleotide samples with ammonium salts before oxidation because this will lead to unwanted side reactions in which ammonia participates in product formation. PMID:25539403

Electron and Oxygen Atom Transfer Chemistry of Co(II) in a Proton Responsive, Redox Active Ligand Environment.

PubMed

Cook, Brian J; Pink, Maren; Pal, Kuntal; Caulton, Kenneth G

2018-05-21

The bis-pyrazolato pyridine complex LCo(PEt 3 ) 2 serves as a masked form of three-coordinate Co II and shows diverse reactivity in its reaction with several potential outer sphere oxidants and oxygen atom transfer reagents. N-Methylmorpholine N-oxide (NMO) oxidizes coordinated PEt 3 from LCo(PEt 3 ) 2 , but the final cobalt product is still divalent cobalt, in LCo(NMO) 2 . The thermodynamics of a variety of oxygen atom transfer reagents, including NMO, are calculated by density functional theory, to rank their oxidizing power. Oxidation of LCo(PEt 3 ) 2 with AgOTf in the presence of LiCl as a trapping nucleophile forms the unusual aggregate [LCo(PEt 3 ) 2 Cl(LiOTf) 2 ] 2 held together by Li + binding to very nucleophilic chloride on Co(III) and triflate binding to those Li + . In contrast, Cp 2 Fe + effects oxidation to trivalent cobalt, to form (HL)Co(PEt 3 ) 2 Cl + ; proton and the chloride originate from solvent in a rare example of CH 2 Cl 2 dehydrochlorination. An unexpected noncomplementary redox reaction is reported involving attack by 2e reductant PEt 3 nucleophile on carbon of the 1e oxidant radical Cp 2 Fe + , forming a P-C bond and H + ; this reaction competes in the reaction of LCo(PEt 3 ) 2 with Cp 2 Fe + .

Gold(III) chloride catalyzed synthesis of chiral substituted 3-formyl furans from carbohydrates: application in the synthesis of 1,5-dicarbonyl derivatives and furo[3,2-c]pyridine.

PubMed

Mal, Kanchan; Sharma, Abhinandan; Das, Indrajit

2014-09-08

This report describes a gold(III)-catalyzed efficient general route to densely substituted chiral 3-formyl furans under extremely mild conditions from suitably protected 5-(1-alkynyl)-2,3-dihydropyran-4-one using H2 O as a nucleophile. The reaction proceeds through the initial formation of an activated alkyne-gold(III) complex intermediate, followed by either a domino nucleophilic attack/anti-endo-dig cyclization, or the formation of a cyclic oxonium ion with subsequent attack by H2 O. To confirm the proposed mechanistic pathway, we employed MeOH as a nucleophile instead of H2 O to result in a substituted furo[3,2-c]pyran derivative, as anticipated. The similar furo[3,2-c]pyran skeleton with a hybrid carbohydrate-furan derivative has also been achieved through pyridinium dichromate (PDC) oxidation of a substituted chiral 3-formyl furan. The corresponding protected 5-(1-alkynyl)-2,3-dihydropyran-4-one can be synthesized from the monosaccharides (both hexoses and pentose) following oxidation, iodination, and Sonogashira coupling sequences. Furthermore, to demonstrate the potentiality of chiral 3-formyl furan derivatives, a TiBr4 -catalyzed reaction of these derivatives has been shown to offer efficient access to 1,5-dicarbonyl compounds, which on treatment with NH4 OAc in slightly acidic conditions afforded substituted furo[3,2-c]pyridine. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cascade rearrangement of furylcarbinols with hydroxylamines: practical access to densely functionalized cyclopentane derivatives.

PubMed

Veits, Gesine K; Wenz, Donald R; Palmer, Leoni I; St Amant, André H; Hein, Jason E; Read de Alaniz, Javier

2015-08-21

This article describes the aza-Piancatelli rearrangement with hydroxylamines to 4-aminocyclopentenones and subsequent transformations that highlight the versatility of the cyclopentene scaffold and the value of the hydroxylamine nucleophile in this transformation.

Hydrolytic Glycosidic Bond Cleavage in RNA Nucleosides: Effects of the 2'-Hydroxy Group and Acid-Base Catalysis.

PubMed

Lenz, Stefan A P; Kohout, Johnathan D; Wetmore, Stacey D

2016-12-22

Despite the inherent stability of glycosidic linkages in nucleic acids that connect the nucleobases to sugar-phosphate backbones, cleavage of these bonds is often essential for organism survival. The current study uses DFT (B3LYP) to provide a fundamental understanding of the hydrolytic deglycosylation of the natural RNA nucleosides (A, C, G, and U), offers a comparison to DNA hydrolysis, and examines the effects of acid, base, or simultaneous acid-base catalysis on RNA deglycosylation. By initially examining HCOO - ···H 2 O mediated deglycosylation, the barriers for RNA hydrolysis were determined to be 30-38 kJ mol -1 higher than the corresponding DNA barriers, indicating that the 2'-OH group stabilizes the glycosidic bond. Although the presence of HCOO - as the base (i.e., to activate the water nucleophile) reduces the barrier for uncatalyzed RNA hydrolysis (i.e., unactivated H 2 O nucleophile) by ∼15-20 kJ mol -1 , the extreme of base catalysis as modeled using a fully deprotonated water molecule (i.e., OH - nucleophile) decreases the uncatalyzed barriers by up to 65 kJ mol -1 . Acid catalysis was subsequently examined by selectively protonating the hydrogen-bond acceptor sites of the RNA nucleobases, which results in an up to ∼80 kJ mol -1 barrier reduction relative to the corresponding uncatalyzed pathway. Interestingly, the nucleobase proton acceptor sites that result in the greatest barrier reductions match sites typically targeted in enzyme-catalyzed reactions. Nevertheless, simultaneous acid and base catalysis is the most beneficial way to enhance the reactivity of the glycosidic bonds in RNA, with the individual effects of each catalytic approach being weakened, additive, or synergistic depending on the strength of the base (i.e., degree of water nucleophile activation), the nucleobase, and the hydrogen-bonding acceptor site on the nucleobase. Together, the current contribution provides a greater understanding of the reactivity of the glycosidic

Molecular Mechanisms of Aldehyde Toxicity: A Chemical Perspective

PubMed Central

2015-01-01

Aldehydes are electrophilic compounds to which humans are pervasively exposed. Despite a significant health risk due to exposure, the mechanisms of aldehyde toxicity are poorly understood. This ambiguity is likely due to the structural diversity of aldehyde derivatives and corresponding differences in chemical reactions and biological targets. To gain mechanistic insight, we have used parameters based on the hard and soft, acids and bases (HSAB) theory to profile the different aldehyde subclasses with respect to electronic character (softness, hardness), electrophilic reactivity (electrophilic index), and biological nucleophilic targets. Our analyses indicate that short chain aldehydes and longer chain saturated alkanals are hard electrophiles that cause toxicity by forming adducts with hard biological nucleophiles, e.g., primary nitrogen groups on lysine residues. In contrast, α,β-unsaturated carbonyl derivatives, alkenals, and the α-oxoaldehydes are soft electrophiles that preferentially react with soft nucleophilic thiolate groups on cysteine residues. The aldehydes can therefore be grouped into subclasses according to common electronic characteristics (softness/hardness) and molecular mechanisms of toxicity. As we will discuss, the toxic potencies of these subgroups are generally related to corresponding electrophilicities. For some aldehydes, however, predictions of toxicity based on electrophilicity are less accurate due to inherent physicochemical variables that limit target accessibility, e.g., steric hindrance and solubility. The unsaturated aldehydes are also members of the conjugated type-2 alkene chemical class that includes α,β-unsaturated amide, ketone, and ester derivatives. Type-2 alkenes are electrophiles of varying softness and electrophilicity that share a common mechanism of toxicity. Therefore, exposure to an environmental mixture of unsaturated carbonyl derivatives could cause “type-2 alkene toxicity” through additive interactions

Conceptual DFT Descriptors of Amino Acids with Potential Corrosion Inhibition Properties Calculated with the Latest Minnesota Density Functionals

PubMed Central

Frau, Juan; Glossman-Mitnik, Daniel

2017-01-01

Amino acids and peptides have the potential to perform as corrosion inhibitors. The chemical reactivity descriptors that arise from Conceptual DFT for the twenty natural amino acids have been calculated by using the latest Minnesota family of density functionals. In order to verify the validity of the calculation of the descriptors directly from the HOMO and LUMO, a comparison has been performed with those obtained through ΔSCF results. Moreover, the active sites for nucleophilic and electrophilic attacks have been identified through Fukui function indices, the dual descriptor Δf(r) and the electrophilic and nucleophilic Parr functions. The results could be of interest as a starting point for the study of large peptides where the calculation of the radical cation and anion of each system may be computationally harder and costly. PMID:28361050

A Molecular Electron Density Theory Study of the Chemical Reactivity of Cis- and Trans-Resveratrol.

PubMed

Frau, Juan; Muñoz, Francisco; Glossman-Mitnik, Daniel

2016-12-01

The chemical reactivity of resveratrol isomers with the potential to play a role as inhibitors of the nonenzymatic glycation of amino acids and proteins, both acting as antioxidants and as chelating agents for metallic ions such as Cu, Al and Fe, have been studied by resorting to the latest family of Minnesota density functionals. The chemical reactivity descriptors have been calculated through Molecular Electron Density Theory encompassing Conceptual DFT. The active sites for nucleophilic and electrophilic attacks have been chosen by relating them to the Fukui function indices, the dual descriptor f ( 2 ) ( r ) and the electrophilic and nucleophilic Parr functions. The validity of "Koopmans' theorem in DFT" has been assessed by means of a comparison between the descriptors calculated through vertical energy values and those arising from the HOMO and LUMO values.

Conceptual DFT Descriptors of Amino Acids with Potential Corrosion Inhibition Properties Calculated with the Latest Minnesota Density Functionals.

PubMed

Frau, Juan; Glossman-Mitnik, Daniel

2017-01-01

Amino acids and peptides have the potential to perform as corrosion inhibitors. The chemical reactivity descriptors that arise from Conceptual DFT for the twenty natural amino acids have been calculated by using the latest Minnesota family of density functionals. In order to verify the validity of the calculation of the descriptors directly from the HOMO and LUMO, a comparison has been performed with those obtained through ΔSCF results. Moreover, the active sites for nucleophilic and electrophilic attacks have been identified through Fukui function indices, the dual descriptor Δf( r ) and the electrophilic and nucleophilic Parr functions. The results could be of interest as a starting point for the study of large peptides where the calculation of the radical cation and anion of each system may be computationally harder and costly.

Reactive Metabolites in the Biotransformation of Molecules Containing a Furan Ring

PubMed Central

Peterson, Lisa A.

2012-01-01

Many xenobiotics containing a furan ring are toxic and/or carcinogenic. The harmful effects of these compounds require furan ring oxidation. This reaction generates an electrophilic intermediate. Depending on the furan ring substituents, the intermediate is either an epoxide or a cis-enedione with more ring substitution favoring epoxide formation. Either intermediate reacts with cellular nucleophiles such as protein or DNA to trigger toxicities. The reactivity of the metabolite determines which cellular nucleophiles are targeted. The toxicity of a particular furan is also influenced by the presence of competing metabolic pathways or efficient detoxification routes. GSH plays an important role in modulating the harmful effects of this class of compound by reacting with the reactive metabolite. However, this may not represent a detoxification step in all cases. PMID:23061605

Acid-catalyzed ring-opening reactions of a cyclopropanated 3-aza-2-oxabicyclo[2.2.1]hept-5-ene with alcohols.

PubMed

Tait, Katrina; Horvath, Alysia; Blanchard, Nicolas; Tam, William

2017-01-01

The acid-catalyzed ring-opening reactions of a cyclopropanated 3-aza-2-oxabicylic alkene using alcohol nucleophiles were investigated. Although this acid-catalyzed ring-opening reaction did not cleave the cyclopropane unit as planned, this represent the first examples of ring-openings of cyclopropanated 3-aza-2-oxabicyclo[2.2.1]alkenes that lead to the cleavage of the C-O bond instead of the N-O bond. Different acid catalysts were tested and it was found that pyridinium toluenesulfonate in methanol gave the best yields in the ring-opening reactions. The scope of the reaction was successfully expanded to include primary, secondary, and tertiary alcohol nucleophiles. Through X-ray crystallography, the stereochemistry of the product was determined which confirmed an S N 2-like mechanism to form the ring-opened product.

Hydroxide as general base in the saponification of ethyl acetate.

PubMed

Mata-Segreda, Julio F

2002-03-13

The second-order rate constant for the saponification of ethyl acetate at 30.0 degrees C in H(2)O/D(2)O mixtures of deuterium atom fraction n (a proton inventory experiment) obeys the relation k(2)(n) = 0.122 s(-1) M(-1) (1 - n + 1.2n) (1 - n + 0.48n)/(1 - n + 1.4n) (1 - n + 0.68n)(3). This result is interpreted as a process where formation of the tetrahedral intermediate is the rate-determining step and the transition-state complex is formed via nucleophilic interaction of a water molecule with general-base assistance from hydroxide ion, opposite to the direct nucleophilic collision commonly accepted. This mechanistic picture agrees with previous heavy-atom kinetic isotope effect data of Marlier on the alkaline hydrolysis of methyl formate.

Stereocontrolled Cyanohydrin Ether Synthesis through Chiral Brønsted Acid-Mediated Vinyl Ether Hydrocyanation

PubMed Central

Lu, Chunliang; Su, Xiaoge; Floreancig, Paul E.

2013-01-01

Vinyl ethers can be protonated to generate oxocarbenium ions that react with Me3SiCN to form cyanohydrin alkyl ethers. Reactions that form racemic products proceed efficiently upon converting the vinyl ether to an α-chloro ether prior to cyanide addition in a pathway that proceeds through Brønsted acid-mediated chloride ionization. Enantiomerically enriched products can be accessed by directly protonating the vinyl ether with a chiral Brønsted acid to form a chiral ion pair. Me3SiCN acts as the nucleophile and PhOH serves as a stoichiometric proton source in a rare example of an asymmetric bimolecular nucleophilic addition reaction into an oxocarbenium ion. Computational studies provide a model for the interaction between the catalyst and the oxocarbenium ion. PMID:23968162

Chemical reactivity indices for the complete series of chlorinated benzenes: solvent effect.

PubMed

Padmanabhan, J; Parthasarathi, R; Subramanian, V; Chattaraj, P K

2006-03-02

We present a comprehensive analysis to probe the effect of solvation on the reactivity of the complete series of chlorobenzenes through the conceptual density functional theory (DFT)-based global and local descriptors. We propose a multiphilic descriptor in this study to explore the nature of attack at a particular site in a molecule. It is defined as the difference between nucleophilic and electrophilic condensed philicity functions. This descriptor is capable of explaining both the nucleophilicity and electrophilicity of the given atomic sites in the molecule simultaneously. The predictive ability of this descriptor is tested on the complete series of chlorobenzenes in gas and solvent media. A structure-toxicity analysis of these entire sets of chlorobenzenes toward aquatic organisms demonstrates the importance of the electrophilicity index in the prediction of the reactivity/toxicity.

Cu/Mn bimetallic catalysis enables carbonylative Suzuki-Miyaura coupling with unactivated alkyl electrophiles.

PubMed

Pye, Dominic R; Cheng, Li-Jie; Mankad, Neal P

2017-07-01

A bimetallic system consisting of Cu-carbene and Mn-carbonyl co-catalysts was employed for carbonylative C-C coupling of arylboronic esters with alkyl halides, allowing for the convergent synthesis of ketones. The system operates under mild conditions and exhibits complementary reactivity to Pd catalysis. The method is compatible with a wide range of arylboronic ester nucleophiles and proceeds smoothly for both primary and secondary alkyl iodide electrophiles. Preliminary mechanistic experiments corroborate a hypothetical catalytic mechanism consisting of co-dependent cycles wherein the Cu-carbene co-catalyst engages in transmetallation to generate an organocopper nucleophile, while the Mn-carbonyl co-catalyst activates the alkyl halide electrophile by single-electron transfer and then undergoes reversible carbonylation to generate an acylmanganese electrophile. The two cycles then intersect with a heterobimetallic, product-releasing C-C coupling step.

Asymmetric synthesis of α-amino acids via homologation of Ni(II) complexes of glycine Schiff bases. Part 3: Michael addition reactions and miscellaneous transformations.

PubMed

Aceña, José Luis; Sorochinsky, Alexander E; Soloshonok, Vadim

2014-09-01

The major goal of this review is a critical discussion of the literature data on asymmetric synthesis of α-amino acids via Michael addition reactions involving Ni(II)-complexes of amino acids. The material covered is divided into two conceptually different groups dealing with applications of: (a) Ni(II)-complexes of glycine as C-nucleophiles and (b) Ni(II)-complexes of dehydroalanine as Michael acceptors. The first group is significantly larger and consequently subdivided into four chapters based on the source of stereocontrolling element. Thus, a chiral auxiliary can be used as a part of nucleophilic glycine Ni(II) complex, Michael acceptor or both, leading to the conditions of matching vs. mismatching stereochemical preferences. The particular focus of the review is made on the practical aspects of the methodology under discussion and mechanistic considerations.

Synthetic versatility of 2-substituted-6-methyl 2,3-dihydropyridinones in the synthesis of polyfunctional piperidine-based compounds and related β amino acid derivatives.

PubMed

Yang, Yang; Hardman, Clayton

2017-10-18

Chiral 2-substituted-6-methyl 2,3-dihydropyidinones 9, which can be facilely obtained from an asymmetric vinylogous Mannich reaction (VMR) with 1,3-bis-trimethysily enol ether, were used as versatile intermediates in constructing chiral polyfunctional piperidine-based compounds. The 6-methyl group of such compounds can be conveniently functionalized via alkylation and acylation reactions to provide efficient entries to the synthesis of a variety of chiral multi-substituted piperidine-based compounds. Further elaboration of the corresponding intermediates also provided access to polyfunctional indolizidine-based compounds. These methods were showcased in an asymmetric synthesis of 2,6-di-substituted piperidine compound 13, reported as the key intermediate in the synthesis of (+)-calvine and a natural alkaloid (-)-indolizidine 209D. Furthermore, selective C5 iodination of compound 9 enabled the installation of additional functional groups at this position. Finally, we demonstrated that the oxidative cleavage of 2-substituted-6-methyl-2,3-dihydropyidinones is a practical and efficient method for the enantioselective synthesis of β-amino acids, which can undergo further intra-molecular cyclization to give the corresponding chiral four-membered β-lactam derivatives.

Electrochemical synthesis of azanucleoside derivatives using a lithium perchlorate-nitromethane system.

PubMed

Kim, Shokaku; Shoji, Takao; Kitano, Yoshikazu; Chiba, Kazuhiro

2013-07-25

We have developed a highly efficient synthetic method for azanucleosides using a lithium perchlorate-nitromethane reaction medium, allowing direct and exclusive installation of various nucleophiles, including protected nucleobases into prolinol derivatives at the preferred 5-position.

Total synthesis and stereochemical assignment of the spiroisoxazoline natural product (+)-calafianin.

PubMed

Bardhan, Sujata; Schmitt, Daniel C; Porco, John A

2006-03-02

Synthesis of the spiroisoxazoline natural product (+)-calafianin is reported using asymmetric nucleophilic epoxidation and nitrile oxide cycloaddition as key steps. Synthesis and spectral analysis of all calafianin stereoisomers led to unambiguous assignment of relative and absolute stereochemistry.

Self-assembled bifunctional surface mimics an enzymatic and templating protein for the synthesis of a metal oxide semiconductor

PubMed Central

Kisailus, David; Truong, Quyen; Amemiya, Yosuke; Weaver, James C.; Morse, Daniel E.

2006-01-01

The recent discovery and characterization of silicatein, a mineral-synthesizing enzyme that assembles to form the filamentous organic core of the glassy skeletal elements (spicules) of a marine sponge, has led to the development of new low-temperature synthetic routes to metastable semiconducting metal oxides. These protein filaments were shown in vitro to catalyze the hydrolysis and structurally direct the polycondensation of metal oxides at neutral pH and low temperature. Based on the confirmation of the catalytic mechanism and the essential participation of specific serine and histidine residues (presenting a nucleophilic hydroxyl and a nucleophilicity-enhancing hydrogen-bonding imidazole nitrogen) in silicatein’s catalytic active site, we therefore sought to develop a synthetic mimic that provides both catalysis and the surface determinants necessary to template and structurally direct heterogeneous nucleation through condensation. Using lithographically patterned poly(dimethylsiloxane) stamps, bifunctional self-assembled monolayer surfaces containing the essential catalytic and templating elements were fabricated by using alkane thiols microcontact-printed on gold substrates. The interface between chemically distinct self-assembled monolayer domains provided the necessary juxtaposition of nucleophilic (hydroxyl) and hydrogen-bonding (imidazole) agents to catalyze the hydrolysis of a gallium oxide precursor and template the condensed product to form gallium oxohydroxide (GaOOH) and the defect spinel, gamma-gallium oxide (γ-Ga2O3). Using this approach, the production of patterned substrates for catalytic synthesis and templating of semiconductors for device applications can be envisioned. PMID:16585518

Fast and Selective Two-Stage Ratiometric Fluorescent Probes for Imaging of Glutathione in Living Cells.

PubMed

Gong, Deyan; Han, Shi-Chong; Iqbal, Anam; Qian, Jing; Cao, Ting; Liu, Wei; Liu, Weisheng; Qin, Wenwu; Guo, Huichen

2017-12-19

Two fluorescent, m-nitrophenol-substituted difluoroboron dipyrromethene dyes have been designed by nucleophilic substitution reaction of 3,5-dichloro-4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY). Nonsymmetric and symmetric probes, that is. BODIPY 1 (with one nitrophenol group at the position 3) and BODIPY 2 (with two nitrophenol groups at the positions 3 and 5) were applied to ratiometric fluorescent glutathione detection. The detection is based on the two-step nucleophilic aromatic substitution of the nitrophenol groups of the probes by glutathione in buffer solution containing CTAB. In the first stage, probe 1 showed ratiometric fluorescent color change from green (λ em = 530 nm) to yellow (λ em = 561 nm) because of monosubstitution with glutathione (I 561nm /I 530nm ). Addition of excess glutathione caused the second stage of ratiometric fluorescent color change from yellow to reddish orange (λ em = 596 nm, I 596nm /I 561nm ) due to disubstitution with glutathione. Therefore, different concentration ranges of glutathione (from less to excess) could be rapidly detected by the two-stage ratiometric fluorescent probe 1 in 5 min. While, probe 2 shows single-stage ratiometric fluorescent detection to GSH (from green to reddish orange, I 596nm /I 535nm ). Probes 1 and 2 exhibit excellent properties with sensitive, specific colorimetric response and ratiometric fluorescent response to glutathione over other sulfur nucleophiles. Application to cellular ratiometric fluorescence imaging indicated that the probes were highly responsive to intracellular glutathione.

Bonding reactivity descriptor from conceptual density functional theory and its applications to elucidate bonding formation

NASA Astrophysics Data System (ADS)

Zhou, Pan-Pan; Liu, Shubin; Ayers, Paul W.; Zhang, Rui-Qin

2017-10-01

Condensed-to-atom Fukui functions which reflect the atomic reactivity like the tendency susceptible to either nucleophilic or electrophilic attack demonstrate the bonding trend of an atom in a molecule. Accordingly, Fukui functions based concepts, that is, bonding reactivity descriptors which reveal the bonding properties of molecules in the reaction were put forward and then applied to pericyclic and cluster reactions to confirm their effectiveness and reliability. In terms of the results from the bonding descriptors, a covalent bond can readily be predicted between two atoms with large Fukui functions (i.e., one governs nucleophilic attack while the other one governs electrophilic attack, or both of them govern radical attacks) for pericyclic reactions. For SinOm clusters' reactions, the clusters with a low O atom ratio readily form a bond between two Si atoms with big values of their Fukui functions in which they respectively govern nucleophilic and electrophilic attacks or both govern radical attacks. Also, our results from bonding descriptors show that Si—Si bonds can be formed via the radical mechanism between two Si atoms, and formations of Si—O and O—O bonds are possible when the O content is high. These results conform with experimental findings and can help experimentalists design appropriate clusters to synthesize Si nanowires with high yields. The approach established in this work could be generalized and applied to study reactivity properties for other systems.

Double displacement: An improved bioorthogonal reaction strategy for templated nucleic acid detection.

PubMed

Kleinbaum, Daniel J; Miller, Gregory P; Kool, Eric T

2010-06-16

Quenched autoligation probes have been employed previously in a target-templated nonenzymatic ligation strategy for detecting nucleic acids in cells by fluorescence. A common source of background signal in such probes is the undesired reaction with water and other cellular nucleophiles. Here, we describe a new class of self-ligating probes, double displacement (DD) probes, that rely on two displacement reactions to fully unquench a nearby fluorophore. Three potential double displacement architectures, all possessing two fluorescence quencher/leaving groups (dabsylate groups), were synthesized and evaluated for templated reaction with nucleophile (phosphorothioate) probes both in vitro and in intact bacterial cells. All three DD probe designs provided substantially better initial quenching than a single-Dabsyl control. In isothermal templated reactions in vitro, double displacement probes yielded considerably lower background signal than previous single displacement probes; investigation into the mechanism revealed that one dabsylate acts as a sacrificial leaving group, reacting nonspecifically with water, but yielding little signal because another quencher group remains. Templated reaction with the specific nucleophile probe is required to activate a signal. The double displacement probes provided a ca. 80-fold turn-on signal and yielded a 2-4-fold improvement in signal/background over single Dabsyl probes. The best-performing probe architecture was demonstrated in a two-color, FRET-based two-allele discrimination system in vitro and was shown to be capable of discriminating between two closely related species of bacteria differing by a single nucleotide at an rRNA target site.

Phosphodiester Cleavage in Ribonuclease H Occurs via an Associative Two-Metal-Aided Catalytic Mechanism

PubMed Central

De Vivo, Marco; Dal Peraro, Matteo; Klein, Michael L.

2009-01-01

Ribonuclease H (RNase H) belongs to the nucleotidyl-transferase (NT) superfamily and hydrolyzes the phosphodiester linkages that form the backbone of the RNA strand in RNA·DNA hybrids. This enzyme is implicated in replication initiation and DNA topology restoration and represents a very promising target for anti-HIV drug design. Structural information has been provided by high-resolution crystal structures of the complex RNase H/RNA·DNA from Bacillus halodurans (Bh), which reveals that two metal ions are required for formation of a catalytic active complex. Here, we use classical force field-based and quantum mechanics/molecular mechanics calculations for modeling the nucleotidyl transfer reaction in RNase H, clarifying the role of the metal ions and the nature of the nucleophile (water versus hydroxide ion). During the catalysis, the two metal ions act cooperatively, facilitating nucleophile formation and stabilizing both transition state and leaving group. Importantly, the two Mg2+ metals also support the formation of a meta-stable phosphorane intermediate along the reaction, which resembles the phosphorane intermediate structure obtained only in the debated β-phosphoglucomutase crystal. The nucleophile formation (i.e., water deprotonation) can be achieved in situ, after migration of one proton from the water to the scissile phosphate in the transition state. This proton transfer is actually mediated by solvation water molecules. Due to the highly conserved nature of the enzymatic bimetal motif, these results might also be relevant for structurally similar enzymes belonging to the NT superfamily. PMID:18662000

Mapping the Reactivity and Selectivity of 2-Azidofucosyl Donors for the Assembly of N-Acetylfucosamine-Containing Bacterial Oligosaccharides.

PubMed

Hagen, Bas; Ali, Sara; Overkleeft, Herman S; van der Marel, Gijsbert A; Codée, Jeroen D C

2017-01-20

The synthesis of complex oligosaccharides is often hindered by a lack of knowledge on the reactivity and selectivity of their constituent building blocks. We investigated the reactivity and selectivity of 2-azidofucosyl (FucN 3 ) donors, valuable synthons in the synthesis of 2-acetamido-2-deoxyfucose (FucNAc) containing oligosaccharides. Six FucN 3 donors, bearing benzyl, benzoyl, or tert-butyldimethylsilyl protecting groups at the C3-O and C4-O positions, were synthesized, and their reactivity was assessed in a series of glycosylations using acceptors of varying nucleophilicity and size. It was found that more reactive nucleophiles and electron-withdrawing benzoyl groups on the donor favor the formation of β-glycosides, while poorly reactive nucleophiles and electron-donating protecting groups on the donor favor α-glycosidic bond formation. Low-temperature NMR activation studies of Bn- and Bz-protected donors revealed the formation of covalent FucN 3 triflates and oxosulfonium triflates. From these results, a mechanistic explanation is offered in which more reactive acceptors preferentially react via an S N 2-like pathway, while less reactive acceptors react via an S N 1-like pathway. The knowledge obtained in this reactivity study was then applied in the construction of α-FucN 3 linkages relevant to bacterial saccharides. Finally, a modular synthesis of the Staphylococcus aureus type 5 capsular polysaccharide repeating unit, a trisaccharide consisting of two FucNAc units, is described.

Clathrochelates meet phosphorus. New thio- and phosphorylation reactions of an iron(II) dichloroclathrochelate precursor and preparation of its first phosphorus(III)-containing macrobicyclic derivative.

PubMed

Artyushin, Oleg I; Matveeva, Ekaterina V; Vologzhanina, Anna V; Voloshin, Yan Z

2016-03-28

Phosphorylation reactions of an iron(II) dichloroclathrochelate FeBd2(Cl2Gm)(BF)2 (where Bd(2-) and Cl2Gm(2-) are α-benzildioxime and dichloroglyoxime dianions, respectively) with diphenylphosphine oxide and diethyl thiophosphite were performed under phase-transfer conditions. In the case of diethyl thiophosphite as a P-nucleophile, the best yields were obtained in the dichloromethane-50% NaOH aqueous solution-5 mol% triethylbenzylammonium chloride (TEBAC) system. The use of different molar ratios of a macrobicycle precursor and this thiophosphorylating agent allowed us to obtain both the mono- and the diphosphorylated cage complexes. Nucleophilic substitution with diphenylphosphine oxide was performed in the K2CO3-acetonitrile-5 mol% TEBAC system, giving only the corresponding monophosphorylated iron(II) complex in high yield even in the presence of an excess of this P-nucleophile. The phosphorus(v)-containing clathrochelate product was reduced with an excess of silicoform to give an iron(II) macrobicycle with an inherent diphenylphosphine group in an almost quantitative yield, which was then characterized by (31)P{(1)H} NMR and single-crystal X-ray diffraction; it easily undergoes re-oxidation to the initial clathrochelate. The synthesized phosphorus(v)-containing cage complexes were characterized using elemental analysis, MALDI-TOF mass, IR, UV-Vis, (1)H, (11)B, (13)C{(1)H}, (19)F{(1)H} and (31)P{(1)H} NMR spectra, and by single-crystal X-ray diffraction.

Rates of proton transfer to Fe-S-based clusters: comparison of clusters containing {MFe(mu(2)-S)(2)}n+ and {MFe(3)(mu(3)-S)(4)}n+ (M = Fe, Mo, or W) cores.

PubMed

Bates, Katie; Garrett, Brendan; Henderson, Richard A

2007-12-24

The rates of proton transfer from [pyrH]+ (pyr = pyrrolidine) to the binuclear complexes [Fe2S2Cl4]2- and [S2MS2FeCl2]2- (M = Mo or W) are reported. The reactions were studied using stopped-flow spectrophotometry, and the rate constants for proton transfer were determined from analysis of the kinetics of the substitution reactions of these clusters with the nucleophiles Br- or PhS- in the presence of [pyrH]+. In general, Br- is a poor nucleophile for these clusters, and proton transfer occurs before Br- binds, allowing direct measure of the rate of proton transfer from [pyrH]+ to the cluster. In contrast, PhS- is a better nucleophile, and a pathway in which PhS- binds preferentially to the cluster prior to proton transfer from [pyrH]+ usually operates. For the reaction of [Fe2S2Cl4]2- with PhS- in the presence of [pyrH]+ both pathways are observed. Comparison of the results presented in this paper with analogous studies reported earlier on cuboidal Fe-S-based clusters allows discussion of the factors which affect the rates of proton transfer in synthetic clusters including the nuclearity of the cluster core, the metal composition, and the nature of the terminal ligands. The possible relevance of these findings to the protonation sites of natural Fe-S-based clusters, including FeMo-cofactor from nitrogenase, are presented.

Alternative strategy for converting an inverting glycoside hydrolase into a glycosynthase.

PubMed

Honda, Yuji; Fushinobu, Shinya; Hidaka, Masafumi; Wakagi, Takayoshi; Shoun, Hirofumi; Taniguchi, Hajime; Kitaoka, Motomitsu

2008-04-01

The tyrosine residue Y198 is known to support a nucleophilic water molecule with the general base residue, D263, in the reducing-end xylose-releasing exo-oligoxylanase (Rex). A mutation in the tyrosine residue changing it into phenylalanine caused a drastic decrease in the hydrolytic activity and a small increase in the F(-) releasing activity from alpha-xylobiosyl fluoride in the presence of xylose. In contrast, mutations at D263 resulted in the decreased F(-) releasing activity. As a result of the high F(-) releasing activity and low hydrolytic activity, Y198F of Rex accumulates a large amount of product during the glycosynthase reaction. We propose a novel method for producing a glycosynthase from an inverting glycoside hydrolase by mutating a residue that holds the nucleophilic water molecule with the general base residue while keeping the general base residue intact.

Insertion of Isocyanides into N-Si Bonds: Multicomponent Reactions with Azines Leading to Potent Antiparasitic Compounds.

PubMed

Kishore, Kranti G; Ghashghaei, Ouldouz; Estarellas, Carolina; Mestre, M Mar; Monturiol, Cristina; Kielland, Nicola; Kelly, John M; Francisco, Amanda Fortes; Jayawardhana, Shiromani; Muñoz-Torrero, Diego; Pérez, Belén; Luque, F Javier; Gámez-Montaño, Rocío; Lavilla, Rodolfo

2016-07-25

Trimethylsilyl chloride is an efficient activating agent for azines in isocyanide-based reactions, which then proceed through a key insertion of the isocyanide into a N-Si bond. The reaction is initiated by N activation of the azine, followed by nucleophilic attack of an isocyanide in a Reissert-type process. Finally, a second equivalent of the same or a different isocyanide inserts into the N-Si bond leading to the final adduct. The use of distinct nucleophiles leads to a variety of α-substituted dihydroazines after a selective cascade process. Based on computational studies, a mechanistic hypothesis for the course of these reactions was proposed. The resulting products exhibit significant activity against Trypanosoma brucei and T. cruzi, featuring favorable drug-like properties and safety profiles. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cu/Mn bimetallic catalysis enables carbonylative Suzuki–Miyaura coupling with unactivated alkyl electrophiles† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc01170a Click here for additional data file.

PubMed Central

Pye, Dominic R.; Cheng, Li-Jie

2017-01-01

A bimetallic system consisting of Cu-carbene and Mn-carbonyl co-catalysts was employed for carbonylative C–C coupling of arylboronic esters with alkyl halides, allowing for the convergent synthesis of ketones. The system operates under mild conditions and exhibits complementary reactivity to Pd catalysis. The method is compatible with a wide range of arylboronic ester nucleophiles and proceeds smoothly for both primary and secondary alkyl iodide electrophiles. Preliminary mechanistic experiments corroborate a hypothetical catalytic mechanism consisting of co-dependent cycles wherein the Cu-carbene co-catalyst engages in transmetallation to generate an organocopper nucleophile, while the Mn-carbonyl co-catalyst activates the alkyl halide electrophile by single-electron transfer and then undergoes reversible carbonylation to generate an acylmanganese electrophile. The two cycles then intersect with a heterobimetallic, product-releasing C–C coupling step. PMID:28966784

Synthetic Studies on Tricyclic Diterpenoids: Direct Allylic Amination Reaction of Isopimaric Acid Derivatives†

PubMed Central

Timoshenko, Mariya A.; Kharitonov, Yurii V.; Shakirov, Makhmut M.; Bagryanskaya, Irina Yu.

2015-01-01

Abstract A selective synthesis of 7‐ or 14‐nitrogen containing tricyclic diterpenoids was completed according to a strategy in which the key step was the catalyzed direct allylic amination of methyl 14α‐hydroxy‐15,16‐dihydroisopimarate with a wide variety of nitrogenated nucleophiles. It was revealed that the selectivity of the reaction depends on the nature of nucleophile. The catalyzed reaction of the mentioned diterpenoid allylic alcohol with 3‐nitroaniline, 3‐(trifluoromethyl)aniline, and 4‐(trifluoromethyl)aniline yield the subsequent 7α‐, 7β‐ and 14αnitrogen‐containing diterpenoids. The reaction with 2‐nitroaniline, 4‐nitro‐2‐chloroaniline, 4‐methoxy‐2‐nitroaniline, phenylsulfamide, or tert‐butyl carbamate proceeds with the formation of 7α‐nitrogen‐substituted diterpenoids as the main products. PMID:27308214

Chirality Transfer in Gold(I)-Catalysed Direct Allylic Etherifications of Unactivated Alcohols: Experimental and Computational Study

PubMed Central

Barker, Graeme; Johnson, David G; Young, Paul C; Macgregor, Stuart A; Lee, Ai-Lan

2015-01-01

Gold(I)-catalysed direct allylic etherifications have been successfully carried out with chirality transfer to yield enantioenriched, γ-substituted secondary allylic ethers. Our investigations include a full substrate-scope screen to ascertain substituent effects on the regioselectivity, stereoselectivity and efficiency of chirality transfer, as well as control experiments to elucidate the mechanistic subtleties of the chirality-transfer process. Crucially, addition of molecular sieves was found to be necessary to ensure efficient and general chirality transfer. Computational studies suggest that the efficiency of chirality transfer is linked to the aggregation of the alcohol nucleophile around the reactive π-bound Au–allylic ether complex. With a single alcohol nucleophile, a high degree of chirality transfer is predicted. However, if three alcohols are present, alternative proton transfer chain mechanisms that erode the efficiency of chirality transfer become competitive. PMID:26248980

Using heteroaryl-lithium reagents as hydroxycarbonyl anion equivalents in conjugate addition reactions with (S,S)-(+)-pseudoephedrine as chiral auxiliary; enantioselective synthesis of 3-substituted pyrrolidines.

PubMed

Alonso, Beatriz; Ocejo, Marta; Carrillo, Luisa; Vicario, Jose L; Reyes, Efraim; Uria, Uxue

2013-01-18

We have developed an efficient protocol for carrying out the stereocontrolled formal conjugate addition of hydroxycarbonyl anion equivalents to α,β-unsaturated carboxylic acid derivatives using (S,S)-(+)-pseudoephedrine as chiral auxiliary, making use of the synthetic equivalence between the heteroaryl moieties and the carboxylate group. This protocol has been applied as key step in the enantioselective synthesis of 3-substituted pyrrolidines in which, after removing the chiral auxiliary, the heteroaryl moiety is converted into a carboxylate group followed by reduction and double nucleophilic displacement. Alternatively, the access to the same type of heterocyclic scaffold but with opposite absolute configuration has also been accomplished by making use of the regio- and diastereoselective conjugate addition of organolithium reagents to α,β,γ,δ-unsaturated amides derived from the same chiral auxiliary followed by chiral auxiliary removal, ozonolysis, and reductive amination/intramolecular nucleophilic displacement sequence.

Synthesis, crystal structures, computational studies and antimicrobial activity of new designed bis((5-aryl-1,3,4-oxadiazol-2-yl)thio)alkanes

NASA Astrophysics Data System (ADS)

Ahmed, Muhammad Naeem; Sadiq, Beenish; Al-Masoudi, Najim A.; Yasin, Khawaja Ansar; Hameed, Shahid; Mahmood, Tariq; Ayub, Khurshid; Tahir, Muhammad Nawaz

2018-03-01

A new series of bis((5-aryl-1,3,4-oxadiazol-2-yl)thio)alkanes 4-14 have been synthesized via nucleophilic substitution reaction of dihaloalkanes with respective 1,3,4-oxadiazole-2-thiols 3a-f, and characterized by spectroscopic techniques. The structures of 4 and 12 were unambiguously confirmed by single-crystal X-ray diffraction analysis. Density functional theory calculations at B3LYP/6-31 + G(d) level of theory were performed for comparison of X-ray geometric parameters, molecular electrostatic potential (MEP) and frontier molecular orbital analyses of synthesized compounds. MEP analysis revealed that these compounds are nucleophilic in nature. Frontier molecular orbitals (FMOs) analysis of 4-14 was performed for evaluation of kinetic stability. All synthesized compounds were screened in vitro for antimicrobial activity against three bacterial and three fungal strains and showed promising results.

A facile synthesis of the basic steroidal skeleton using a Pauson-Khand reaction as a key step.

PubMed

Kim, Do Han; Kim, Kwang; Chung, Young Keun

2006-10-13

A high-yield synthesis of steroid-type molecules under mild reaction conditions is achieved in two steps involving nucleophilic addition of alkynyl cerium reagent to an easily enolizable carbonyl compound (beta-tetralone) followed by an intramolecular Pauson-Khand reaction.

Synthesis of Unsymmetrical 3,4-Diaryl-3-pyrrolin-2-ones Utilizing Pyrrole Weinreb Amides

PubMed Central

Greger, Jessica G.; Yoon-Miller, Sarah J.P.; Bechtold, Nathan R.; Flewelling, Scott A.; MacDonald, Jacob P.; Downey, Catherine R.; Cohen, Eric A.; Pelkey, Erin T.

2011-01-01

A regiocontrolled synthesis of unsymmetrical 3,4-diaryl-3-pyrrolin-2-ones has been achieved in three steps from 1,2-diaryl-1-nitroethenes with pyrrole-2-carboxamides (pyrrole Weinreb amides) serving as the key linchpin intermediates. Two different methods for the preparation of the requisite nitroalkenes were investigated: (1) modified Henry reaction between arylnitromethanes and arylimines; and (2) Suzuki-Miyaura cross-coupling reaction of 2-aryl-1-bromo-1-nitroethenes with arylboronic acids. Some difficulty was encountered in the preparation of arylnitromethanes, thus leading to the exploration of a cross-coupling strategy that proved more useful. A Barton-Zard pyrrole cyclocondensation reaction between 1,2-diaryl-1-nitroethenes and N-methoxy-N-methyl-2-isocyanoacetamide gave the corresponding pyrrole Weinreb amides, which were then converted into the desired 3-pyrrolin-2-ones in two steps. Overall, this method allowed for the construction of 3,4-diaryl-3-pyrrolin-2-ones with complete regiocontrol of the substituents with respect to the lactam carbonyl. The utility of this synthetic methodology was demonstrated by the preparation of eight unsymmetrical and symmetrical 3,4-diaryl-3-pyrrolin-2-ones including the N-H lactam analog of the selective COX-II inhibitor, rofecoxib. PMID:21913662

Cu(3)(BTC)(2) as a viable heterogeneous solid catalyst for Friedel-Crafts alkylation of indoles with nitroalkenes.

PubMed

Nagaraj, Anbu; Amarajothi, Dhakshinamoorthy

2017-05-15

In the present work, Friedel-Crafts alkylation reaction of indole with β-nitrostyrene is examined using a readily available copper based metal-organic frameworks (MOFs) namely, Cu 3 (BTC) 2 (BTC: 1,3,5-benzenetricarboxylic acid) as solid catalyst under mild reaction conditions. Among the various catalysts screened for this reaction, Cu 3 (BTC) 2 exhibits higher activity under the optimized reaction conditions. Besides the absence of leaching of active sites, it is also observed that the catalyst can be reused for four cycles with a minimal decrease in its activity. Cu 3 (BTC) 2 is used as a catalyst to synthesise a series of heterocyclic compounds with different indole and β-nitrostyrene derivatives in moderate to high yields. The present catalytic system shows comparable activity against to recent reports but the advantage of Cu 3 (BTC) 2 is that it does not require any post-functionalization and above all it can be readily synthesised, thus contributing to the synthesis of heterocyclic compounds with high biological interest. Copyright © 2017 Elsevier Inc. All rights reserved.

Intramolecular Hydrogen Bond Activation: Thiourea-Organocatalyzed Enantioselective 1,3-Dipolar Cycloaddition of Salicylaldehyde-Derived Azomethine Ylides with Nitroalkenes.

PubMed

Esteban, Francisco; Cieślik, Wioleta; Arpa, Enrique M; Guerrero-Corella, Andrea; Díaz-Tendero, Sergio; Perles, Josefina; Fernández-Salas, José A; Fraile, Alberto; Alemán, José

2018-03-02

An organocatalytic strategy for the synthesis of tetrasubstituted pyrrolidines with monoactivated azomethine ylides in high enantiomeric excess and excellent exo/endo selectivity is presented. The key to success is the intramolecular activation via hydrogen bonding through an o -hydroxy group, which allows the dipolar cycloaddition to take place in the presence of azomethine ylides bearing only one activating group. The intramolecular hydrogen bond in the azomethine ylide and the intermolecular hydrogen bond with the catalyst have been demonstrated by DFT calculations and mechanistic proofs to be crucial for the reaction to proceed.

METABOLISM OF 1,1- AND 1,3- DICHLOROPROPENE: A MECHANISM OF BIOACTIVATION BY GLUTATHIONE

EPA Science Inventory

Glutathione transferases (GST) catalyze the reaction of glutathione (GSH) with haloalkenes via a nucleophilic vinylic substitution mechanism (SNV reaction). The source water contaminants 1,1-dichloropropene and 1,3-dichloropropene, which are under scrutiny by the U.S.EPA, were...

SEDIMENT-ASSOCIATED REACTIONS OF AROMATIC AMINES. 2. QSAR DEVELOPMENT

EPA Science Inventory

The fate of aromatic amines in soils and sediments is dominated by irreversible binding through nucleophilic addition and oxidative radical coupling. Despite the common occurrence of the aromatic amine functional group in organic chemicals, the molecular properties useful for pr...

Science Notes.

ERIC Educational Resources Information Center

Talbot, Chris; And Others

1991-01-01

Twenty science experiments are presented. Topics include recombinant DNA, physiology, nucleophiles, reactivity series, molar volume of gases, spreadsheets in chemistry, hydrogen bonding, composite materials, radioactive decay, magnetism, speed, charged particles, compression waves, heat transfer, Ursa Major, balloons, current, and expansion of…

Catechin-3-0-rhamoside chain procyanidins from mangrove bark

Treesearch

Suminar Achmadi; Gustini Syahbirin; Elvin T. Chonng; Richard W. Hemingway

1994-01-01

Acid-catalysed cleavage of 'purified' condensed tannin isolates from Bruguiera gymnorrhiza (tancang) bark in the presence of phloroglucinol as a capture nucleophile gave, in addition to the expected procyanidin- and prodelphinidin-phloroglucinol adducts, 3-O-α-L-rhamnopyranosyl-(+)-catechin-(4α...

Introducing Aliphatic Substitution with a Discovery Experiment Using Competing Electrophiles

ERIC Educational Resources Information Center

Curran, Timothy P.; Mostovoy, Amelia J.; Curran, Margaret E.; Berger, Clara

2016-01-01

A facile, discovery-based experiment is described that introduces aliphatic substitution in an introductory undergraduate organic chemistry curriculum. Unlike other discovery-based experiments that examine substitution using two competing nucleophiles with a single electrophile, this experiment compares two isomeric, competing electrophiles…

SOME CHEMICAL PROPERTIES UNDERLYING ARSENIC'S BIOLOGICAL ACTIVITY

EPA Science Inventory

ABSTRACT

In this paper some of the chemical properties of arsenicals (atomic
and molecular orbitals, electronegativity, valence state, changes between
valence state, nucleophilicity, the hard/soft acid/base principle) that may
account for some of the b...

Aromatic Substitution Reactions: When You've Said Ortho, Meta, and Para, You Haven't Said It All.

ERIC Educational Resources Information Center

Traynham, James G.

1983-01-01

Recent investigations show that the ipso position competes effectively with unsubstituted positions in many aromatic substitution reactions, regardless of charge type of reaction. Selected examples available for nucleophilic, electrophilic, and free radical reactions are reviewed to suggest the range of ipso reactions. (JN)

USING STRUCTURAL EFFECTS ON THE ORGANIZATION OF THE CYTOSKELETON OF RAINBOW TROUT HEPATOCYTES TO SORT PATHWAYS OF REACTIVE TOXICITY

EPA Science Inventory

Quinones have been shown to be more acutely toxic to aquatic organisms than chemicals that are not capable of either direct interaction with cellular nucleophiles or potentially metabolized free radicals. For the development of accurate QSAR models, in vitro toxicity assays are n...

Halogen, Hydroxy, Mercapto and Amino-Compounds: A Mechanistic Study--2

ERIC Educational Resources Information Center

Hanson, R. W.

1976-01-01

Compare reactions in which the functional groups of title compounds are displaced. The overall order of activity observed for alkyl halides, alcohols, thiels, and aliphatic amines acting as bases or nucleophiles is reversed when reactions involve displacement of the functional group. (MLH)

Characterization and thermal properties of polygenipin-crosslinked hide powders

USDA-ARS?s Scientific Manuscript database

Genipin is a naturally occurring iridoid compound, it is widely used as an ideal biological protein crosslinking agent due to its low toxicity compared to glutaraldehyde and formaldehyde. Under alkaline condition, genipin could undergo ring-opening polymerization via nucleophilic attack of hydroxyl ...

A Conversion of Methyl Ketones into Acetylenes: A Project for a Problem-Oriented or Microscale Organic Chemistry Course.

ERIC Educational Resources Information Center

Silveira, Augustine, Jr.; Orlando, Steven C.

1988-01-01

Describes a process for producing terminal or internal alkynes from ketones. Recommends using the experiment to aid in understanding acid-base strength, enolate anion chemistry, reaction at carbon versus oxygen, use of polar aprotic solvents, and elimination and nucleophilic substitution reactions. (ML)

Carbene Catalysts

NASA Astrophysics Data System (ADS)

Moore, Jennifer L.; Rovis, Tomislav

The use of N-heterocyclic carbenes as catalysts for organic transformations has received increased attention in the past 10 years. A discussion of catalyst development and nucleophilic characteristics precedes a description of recent advancements and new reactions using N-heterocyclic carbenes in catalysis.

N-heterocyclic carbene-catalyzed tandem aza-benzoin/Michael reactions: on site reversal of the reactivity of N-Boc imines.

PubMed

Wu, Ke-Jia; Li, Gong-Qiang; Li, Yi; Dai, Li-Xin; You, Shu-Li

2011-01-07

A tandem NHC-catalyzed aza-benzoin/Michael reaction has been developed as a method to efficiently produce dihydroindenones and pyrrolidinone-containing tricycles. The novel reaction pattern involves tert-butyl aryl(tosyl)methylcarbamates reacting as both electrophile and nucleophile on the same carbon.

Kinetics of degradation of sulfur mustard and sarin simulants on HKUST-1 metal organic framework.

PubMed

Roy, Anuradha; Srivastava, Avanish K; Singh, Beer; Shah, Dilip; Mahato, Timir Haran; Srivastava, Anchal

2012-10-28

The applicability of HKUST-1 for the degradation of sulfur mustard and sarin simulants was studied with and without coadsorbed water. Degradation was found to be via hydrolysis and dependent on the nucleophilic substitution reaction, vapour pressure and molecular diameter of the toxicants.

The Gabriel Synthesis of Benzylamine

ERIC Educational Resources Information Center

Nigh, W. G.

1975-01-01

Describes an undergraduate organic chemistry laboratory experiment which utilizes the Gabriel Synthesis to demonstrate the acidity of imides and to provide an example of nucleophilic substitution reactions. The experiment also demonstrates the laboratory techniques involved in simple and steam distillation, filtration, extraction, and…

Chemoproteomic profiling and discovery of protein electrophiles in human cells

NASA Astrophysics Data System (ADS)

Matthews, Megan L.; He, Lin; Horning, Benjamin D.; Olson, Erika J.; Correia, Bruno E.; Yates, John R.; Dawson, Philip E.; Cravatt, Benjamin F.

2017-03-01

Activity-based protein profiling (ABPP) serves as a chemical proteomic platform to discover and characterize functional amino acids in proteins on the basis of their enhanced reactivity towards small-molecule probes. This approach, to date, has mainly targeted nucleophilic functional groups, such as the side chains of serine and cysteine, using electrophilic probes. Here we show that 'reverse-polarity' (RP)-ABPP using clickable, nucleophilic hydrazine probes can capture and identify protein-bound electrophiles in cells. Using this approach, we demonstrate that the pyruvoyl cofactor of S-adenosyl-L-methionine decarboxylase (AMD1) is dynamically controlled by intracellular methionine concentrations. We also identify a heretofore unknown modification—an N-terminally bound glyoxylyl group—in the poorly characterized protein secernin-3. RP-ABPP thus provides a versatile method to monitor the metabolic regulation of electrophilic cofactors and discover novel types of electrophilic modifications on proteins in human cells.

Polar Diels-Alder reactions using electrophilic nitrobenzothiophenes. A combined experimental and DFT study

NASA Astrophysics Data System (ADS)

Della Rosa, Claudia D.; Mancini, Pedro M. E.; Kneeteman, Maria N.; Lopez Baena, Anna F.; Suligoy, Melisa A.; Domingo, Luis R.

2015-01-01

The reactions between 2- and 3-nitrobenzothiophenes with three dienes of different nucleophilicity, 1-methoxy-3-trimethylsilyloxy-1,3-butadiene, 1-trimethylsilyloxy-1,3-butadiene and isoprene developed in anhydrous benzene and alternative under microwave irradiation with molecular solvents or in free solvent conditions, respectively, for produce dibenzothiophenes permit to conclude that both nitroheterocycles act as electrophile with the cited dienes. In the cases of the dienes 1-methoxy-3-trimethylsilyloxy-1,3-butadiene and 1-trimethylsilyloxy-1,3-butadiene which posses major nucleophilicity the observed product is the normal cycloaddition one. However when the diene is isoprene the product with both electrophiles follow the hetero Diels-Alder way. These reactions are considered polar cycloaddition reactions and the yields are reasonables. Moreover the polar Diels-Alder reactions of nitrobenzothiophenes with electron rich dienes 1-trimethylsilyloxy-1,3-butadiene have been theoretically studied using DFT methods.

Chemical trapping and characterization of small oxoacids of sulfur (SOS) generated in aqueous oxidations of H2S.

PubMed

Kumar, Murugaeson R; Farmer, Patrick J

2018-04-01

Small oxoacids of sulfur (SOS) are elusive molecules like sulfenic acid, HSOH, and sulfinic acid, HS(O)OH, generated during the oxidation of hydrogen sulfide, H 2 S, in aqueous solution. Unlike their alkyl homologs, there is a little data on their generation and speciation during H 2 S oxidation. These SOS may exhibit both nucleophilic and electrophilic reactivity, which we attribute to interconversion between S(II) and S(IV) tautomers. We find that SOS may be trapped in situ by derivatization with nucleophilic and electrophilic trapping agents and then characterized by high resolution LC MS. In this report, we compare SOS formation from H 2 S oxidation by a variety of biologically relevant oxidants. These SOS appear relatively long lived in aqueous solution, and thus may be involved in the observed physiological effects of H 2 S. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Photoluminescent silicon nanocrystals with chlorosilane surfaces - synthesis and reactivity

NASA Astrophysics Data System (ADS)

Höhlein, Ignaz M. D.; Kehrle, Julian; Purkait, Tapas K.; Veinot, Jonathan G. C.; Rieger, Bernhard

2014-12-01

We present a new efficient two-step method to covalently functionalize hydride terminated silicon nanocrystals with nucleophiles. First a reactive chlorosilane layer was formed via diazonium salt initiated hydrosilylation of chlorodimethyl(vinyl)silane which was then reacted with alcohols, silanols and organolithium reagents. With organolithium compounds a side reaction is observed in which a direct functionalization of the silicon surface takes place.We present a new efficient two-step method to covalently functionalize hydride terminated silicon nanocrystals with nucleophiles. First a reactive chlorosilane layer was formed via diazonium salt initiated hydrosilylation of chlorodimethyl(vinyl)silane which was then reacted with alcohols, silanols and organolithium reagents. With organolithium compounds a side reaction is observed in which a direct functionalization of the silicon surface takes place. Electronic supplementary information (ESI) available: Detailed experimental procedures and additional NMR, PL, EDX, DLS and TEM data. See DOI: 10.1039/C4NR05888G

Modeling of Toxicity-Relevant Electrophilic Reactivity for Guanine with Epoxides: Estimating the Hard and Soft Acids and Bases (HSAB) Parameter as a Predictor.

PubMed

Zhang, Jing; Wang, Chenchen; Ji, Li; Liu, Weiping

2016-05-16

According to the electrophilic theory in toxicology, many chemical carcinogens in the environment and/or their active metabolites are electrophiles that exert their effects by forming covalent bonds with nucleophilic DNA centers. The theory of hard and soft acids and bases (HSAB), which states that a toxic electrophile reacts preferentially with a biological macromolecule that has a similar hardness or softness, clarifies the underlying chemistry involved in this critical event. Epoxides are hard electrophiles that are produced endogenously by the enzymatic oxidation of parent chemicals (e.g., alkenes and PAHs). Epoxide ring opening proceeds through a SN2-type mechanism with hard nucleophile DNA sites as the major facilitators of toxic effects. Thus, the quantitative prediction of chemical reactivity would enable a predictive assessment of the molecular potential to exert electrophile-mediated toxicity. In this study, we calculated the activation energies for reactions between epoxides and the guanine N7 site for a diverse set of epoxides, including aliphatic epoxides, substituted styrene oxides, and PAH epoxides, using a state-of-the-art density functional theory (DFT) method. It is worth noting that these activation energies for diverse epoxides can be further predicted by quantum chemically calculated nucleophilic indices from HSAB theory, which is a less computationally demanding method than the exacting procedure for locating the transition state. More importantly, the good qualitative/quantitative correlations between the chemical reactivity of epoxides and their bioactivity suggest that the developed model based on HSAB theory may aid in the predictive hazard evaluation of epoxides, enabling the early identification of mutagenicity/carcinogenicity-relevant SN2 reactivity.

Activation of Peroxymonosulfate by Subsurface Minerals.

PubMed

Yu, Miao; Teel, Amy L; Watts, Richard J

2016-08-01

In situ chemical oxidation (ISCO) has become a widely used technology for the remediation of soil and groundwater. Although peroxymonosulfate is not a common oxidant source for ISCO, its chemical structure is similar to the ISCO reagents hydrogen peroxide and persulfate, suggesting that peroxymonosulfate may have the beneficial properties of each of these oxidants. Peroxymonosulfate activation in the presence of subsurface minerals was examined as a basis for ISCO, and possible reactive species (hydroxyl radical, sulfate radical, and reductants+nucleophiles) generated in the mineral-activated peroxymonosulfate systems were investigated. Rates of peroxymonosulfate decomposition and generation rates of reactive species were studied in the presence of three iron oxides, one manganese oxide, and three soil fractions. The iron oxide hematite-activated peroxymonosulfate system most effectively degraded the hydroxyl radical probe nitrobenzene. Reductants+nucleophiles were not generated in mineral-activated peroxymonosulfate systems. Use of the probe compound anisole in conjunction with scavengers demonstrated that both sulfate radical and hydroxyl radical are generated in mineral-activated peroxymonosulfate systems. In order to confirm the activation of peroxymonosulfate by subsurface minerals, one natural soil and associated two soil fractions were evaluated as peroxymonosulfate catalysts. The natural soil did not effectively promote the generation of oxidants; however, the soil organic matter was found to promote the generation of reductants + nucleophiles. The results of this research show that peroxymonosulfate has potential as an oxidant source for ISCO applications, and would be most effective in treating halogenated contaminants when soil organic matter is present in the subsurface. Copyright © 2016. Published by Elsevier B.V.

The ligand effect on the hydrolytic reactivity of Zn(II) complexes toward phosphate diesters.

PubMed

Bonfá, Lodovico; Gatos, Maddalena; Mancin, Fabrizio; Tecilla, Paolo; Tonellato, Umberto

2003-06-16

The catalytic effects of the Zn(II) complexes of a series of poliaminic ligands in the hydrolysis of the activated phosphodiesters bis-p-nitrophenyl phosphate (BNP) and 2-hydroxypropyl-p-nitrophenyl phosphate (HPNP) have been investigated. The reactions show first-order rate dependency on both substrate and metal ion complex and a pH dependence which is diagnostic of the acid dissociation of the reactive species. The mechanism of the metal catalyzed transesterification of HPNP has been assessed by solvent isotopic kinetic effect studies and involves the intramolecular nucleophilic attack of the substrate alcoholic group, activated by metal ion coordination. The intrinsic reactivity of the different complexes is controlled by the nature and structure of the ligand: complexes of tridentate ligands, particularly if characterized by a facial coordination mode, are more reactive than those of tetradentate ligands which can hardly allow binding sites for the substrate. In the case of tridentate ligands that form complexes with a facial coordination mode, a linear Brønsted correlation between the reaction rate (log k) and the pK(a) of the active nucleophile is obtained. The beta(nuc) values are 0.75 for the HPNP transesterification and 0.20 for the BNP hydrolysis. These values are indicated as the result of the combination of two opposite Lewis acid effects of the Zn(II) ion: the activation of the substrate and the efficiency of the metal coordinated nucleophile. The latter factor apparently prevails in determining the intrinsic reactivity of the Zn(II) complexes.

Chameleonic reactivity of vicinal diazonium salt of acetylenyl-9,10-anthraquinones: synthetic application toward two heterocyclic targets.

PubMed

Stepanov, A A; Gornostaev, L M; Vasilevsky, S F; Arnold, E V; Mamatyuk, V I; Fadeev, D S; Gold, B; Alabugin, I V

2011-11-04

The nature of products in the diazotization of 1-amino-2-acetylenyl-9,10-anthraquinones strongly depends on the nature of substituents at both the alkyne and at the anthraquinone core. Donor substitution (NHAr, OH) at the fourth position stabilizes the diazonium salt at C1, decelerating electrophilic cyclization at the arylethynyl substituent at C2. This effect allows the replacement of the diazonium with azide group and subsequent closure into isoxazole ring with preservation of the alkyne. In contrast, electrophilic 5-exo-dig cyclizations to condensed pyrazoles is observed for the combination of donor substituents at the aryl alkyne moiety and an OAc substituent at C4. The latter process provides a new synthetic route to 3-ethynyl-[1,9-cd]isoxazol-6-ones that are difficult to access otherwise. DFT calculations suggest that donor substituents have only a minor effect on alkyne and diazonium polarization in the reactant but provide specific transition state stabilization by stabilizing the incipient vinyl cation. This analysis provides the first computational data on electrophilic 5-exo-dig cyclization in its parent form and the nucleophile-promoted version. This cyclization is a relatively fast but endothermic process that is rendered thermodynamically feasible by the enol-keto tautomerization with concomitant aromatization in the five-membered heteroaromatic ring. Computations suggest that the importance of nucleophilic assistance in the transition state for a relatively weak nucleophile such as water is minor because the energy gain due to the Lewis base coordination to the carbocationic center is more than compensated for by the unfavorable entropic term for the bimolecular proces.

A FACILE ONE-POT SYNTHESIS OF β-KETO SULFONES FROM KETONES UNDER SOLVENT-FREE CONDITIONS

EPA Science Inventory

An easy solvent-free method is described for the conversion of ketones into β-keto sulfones in high yields that involves in situ generation of α-tosyloxyketones followed by nucleophilic substitution with sodium arene sulfinate in presence of tetra-butylammonium bromide at ...

Organic Lecture Demonstrations.

ERIC Educational Resources Information Center

Silversmith, Ernest F.

1988-01-01

Provides a listing of 35 demonstrations designed to generate interest in organic chemistry and help put points across. Topics include opening lecture; molecular structure and properties; halogenation; nucleophilic substitution, alkenes and dienes, stereochemistry, spectroscopy, alcohols and phenols, aldehydes and ketones; carboxylic acids, amines,…

Nucleophilic catalysis of MeON-neoglycoside formation by aniline derivatives.

PubMed

Loskot, Steven A; Zhang, Jianjun; Langenhan, Joseph M

2013-12-06

Neoglycosylations are increasingly being employed in the synthesis of natural products, drug candidates, glycopeptide mimics, oligosaccharide analogues, and other applications, but the efficiency of these reactions is usually limited by slow reaction times. Here, we show that aniline derivatives such as 2-amino-5-methoxybenzoic acid enhance the rate of acid-catalyzed neoglycosylation for a range of sugar substrates up to a factor of 32 relative to the uncatalyzed reaction.

Nucleophilic Chiral Phosphines: Powerful and Versatile Catalysts for Asymmetric Annulations

PubMed Central

Xiao, Yumei; Guo, Hongchao; Kwon, Ohyun

2016-01-01

Recent advances in chiral-phosphine-catalyzed asymmetric annulation reactions; including annulations of allenes, alkynes, Morita–Baylis–Hillman (MBH) carbonates, and ketenes; and their applications in the synthesis of bioactive molecules and natural products are reviewed. PMID:28077882

Recent trends in ring opening of epoxides with sulfur nucleophiles.

PubMed

Ahmad, Sajjad; Zahoor, Ameer Fawad; Naqvi, Syed Ali Raza; Akash, Muhammad

2018-02-01

Thiolysis of epoxides offers an efficient and simple synthetic approach to access [Formula: see text]-hydroxy sulfides which are valuable scaffold in the synthesis of various important molecules in medicinal chemistry. This review article presents a recent compilation of the synthetic approaches developed after 2000 for the thiolysis of epoxides.

Synthesis and purification of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB)

DOEpatents

Mitchell, Alexander R [Livermore, CA; Coburn, Michael D [Santa Fe, NM; Lee, Gregory S [San Ramon, CA; Schmidt, Robert D [Livermore, CA; Pagoria, Philip F [Livermore, CA; Hsu, Peter C [Pleasanton, CA

2006-06-06

A method to convert surplus nitroarene explosives (picric acid, ammonium picrate,) into TATB is described. The process comprises three major steps: conversion of picric acid/ammonium picrate into picramide; conversion of picramide to TATB through vicarious nucleophilic substitution (VNS) of hydrogen chemistry; and purification of TATB.

Organic Reaction Mechanisms in the Sixth Form Part 2.

ERIC Educational Resources Information Center

Simpson, Peter

1989-01-01

Presents the mechanistic ideas underlying reactions between nucleophiles and carbonyl compounds as well as some popular misconceptions. Relates reactions of carboxylic acid derivatives to those of aldehydes and ketones. Discusses leaving group ability and the ability of carbonyl oxygen to accept a negative charge. (Author/MVL)

Karrikins force a rethink of strigolactone mode of action

PubMed Central

Waters, Mark T.; Scaffidi, Adrian; Flematti, Gavin R.; Smith, Steven M.

2012-01-01

Strigolactones (SL) and karrikins (KAR) both contain essential butenolide moieties, and both require the F-box protein MAX2 to control seed germination and photomorphogenesis in Arabidopsis thaliana. A new discovery that SL and KAR also require related α/β-hydrolase proteins for such activity suggests that they operate through a similar molecular mechanism. Based on structural similarity, a previously proposed mode of action for SL was also considered for KAR, but recent structure-activity studies suggest that this mechanism may not apply. Here we rationalise these observations into a hypothesis whereby different α/β-hydrolases distinguish SL and KAR by virtue of their non-butenolide moieties and catalyze nucleophilic attack on the butenolide. The products would be different for SL and KAR, and in the case of SL they have no biological activity. The inference is that nucleophilic attack on SL and KAR by α/β-hydrolases is required for their bioactivity, but the hydrolysis products are not. PMID:22827937

Global profiling of lysine reactivity and ligandability in the human proteome

NASA Astrophysics Data System (ADS)

Hacker, Stephan M.; Backus, Keriann M.; Lazear, Michael R.; Forli, Stefano; Correia, Bruno E.; Cravatt, Benjamin F.

2017-12-01

Nucleophilic amino acids make important contributions to protein function, including performing key roles in catalysis and serving as sites for post-translational modification. Electrophilic groups that target amino-acid nucleophiles have been used to create covalent ligands and drugs, but have, so far, been mainly limited to cysteine and serine. Here, we report a chemical proteomic platform for the global and quantitative analysis of lysine residues in native biological systems. We have quantified, in total, more than 9,000 lysines in human cell proteomes and have identified several hundred residues with heightened reactivity that are enriched at protein functional sites and can frequently be targeted by electrophilic small molecules. We have also discovered lysine-reactive fragment electrophiles that inhibit enzymes by active site and allosteric mechanisms, as well as disrupt protein-protein interactions in transcriptional regulatory complexes, emphasizing the broad potential and diverse functional consequences of liganding lysine residues throughout the human proteome.

Correlation of the Rates of Solvolysis of Neopentyl Chloroformate—A Recommended Protecting Agent

PubMed Central

D’Souza, Malcolm J.; Carter, Shannon E.; Kevill, Dennis N.

2011-01-01

The specific rates of solvolysis of neopentyl chloroformate (1) have been determined in 21 pure and binary solvents at 45.0 °C. In most solvents the values are essentially identical to those for ethyl and n-propyl chloroformates. However, in aqueous-1,1,1,3,3,3-hexafluoro-2-propanol mixtures (HFIP) rich in fluoroalcohol, 1 solvolyses appreciably faster than the other two substrates. Linear free energy relationship (LFER) comparison of the specific rates of solvolysis of 1 with those for phenyl chloroformate and those for n-propyl chloroformate are helpful in the mechanistic considerations, as is also the treatment in terms of the Extended Grunwald-Winstein equation. It is proposed that the faster reaction for 1 in HFIP rich solvents is due to the influence of a 1,2-methyl shift, leading to a tertiary alkyl cation, outweighing the only weak nucleophilic solvation of the cation possible in these low nucleophilicity solvents. PMID:21541050

Correlation of the rates of solvolysis of neopentyl chloroformate-a recommended protecting agent.

PubMed

D'Souza, Malcolm J; Carter, Shannon E; Kevill, Dennis N

2011-02-15

The specific rates of solvolysis of neopentyl chloroformate (1) have been determined in 21 pure and binary solvents at 45.0 °C. In most solvents the values are essentially identical to those for ethyl and n-propyl chloroformates. However, in aqueous-1,1,1,3,3,3-hexafluoro-2-propanol mixtures (HFIP) rich in fluoroalcohol, 1 solvolyses appreciably faster than the other two substrates. Linear free energy relationship (LFER) comparison of the specific rates of solvolysis of 1 with those for phenyl chloroformate and those for n-propyl chloroformate are helpful in the mechanistic considerations, as is also the treatment in terms of the Extended Grunwald-Winstein equation. It is proposed that the faster reaction for 1 in HFIP rich solvents is due to the influence of a 1,2-methyl shift, leading to a tertiary alkyl cation, outweighing the only weak nucleophilic solvation of the cation possible in these low nucleophilicity solvents.

Evidence for Interfacial Halogen Bonding.

PubMed

Swords, Wesley B; Simon, Sarah J C; Parlane, Fraser G L; Dean, Rebecca K; Kellett, Cameron W; Hu, Ke; Meyer, Gerald J; Berlinguette, Curtis P

2016-05-10

A homologous series of donor-π-acceptor dyes was synthesized, differing only in the identity of the halogen substituents about the triphenylamine (TPA; donor) portion of each molecule. Each Dye-X (X=F, Cl, Br, and I) was immobilized on a TiO2 surface to investigate how the halogen substituents affect the reaction between the light-induced charge-separated state, TiO2 (e(-) )/Dye-X(+) , with iodide in solution. Transient absorption spectroscopy showed progressively faster reactivity towards nucleophilic iodide with more polarizable halogen substituents: Dye-F < Dye-Cl < Dye-Br < Dye-I. Given that all other structural and electronic properties for the series are held at parity, with the exception of an increasingly larger electropositive σ-hole on the heavier halogens, the differences in dye regeneration kinetics for Dye-Cl, Dye-Br, and Dye-I are ascribed to the extent of halogen bonding with the nucleophilic solution species. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A comparative study on the experimentally derived electron densities of three protease inhibitor model compounds.

PubMed

Grabowsky, Simon; Pfeuffer, Thomas; Morgenroth, Wolfgang; Paulmann, Carsten; Schirmeister, Tanja; Luger, Peter

2008-07-07

In order to contribute to a rational design of optimised protease inhibitors which can covalently block the nucleophilic amino acids of the proteases' active sites, we have chosen three model compounds (aziridine , oxirane and acceptor-substituted olefin ) for the examination of their electron-density distribution. Therefore, high-resolution low temperature (9, 27 and 100 K) X-ray diffraction experiments on single-crystals were carried out with synchrotron and conventional X-radiation. It could be shown by the analysis of the electron density using mainly Bader's Theory of Atoms in Molecules, Volkov's EPMM method for interaction energies, electrostatic potentials and Gatti's Source Function that aziridine is most suitable for drug design in this field. A regioselective nucleophilic attack at carbon atom C1 could be predicted and even hints about the reaction's stereoselectivity could be obtained. Moreover, the comparison between two data sets of aziridine (conventional X-ray source vs. synchrotron radiation) gave an estimate concerning the reproducibility of the quantitative results.

Chemoenzymatic synthesis of new derivatives of glycyrrhetinic acid with antiviral activity. Molecular docking study.

PubMed

Zígolo, M Antonela; Salinas, Maximiliano; Alché, Laura; Baldessari, Alicia; Liñares, Guadalupe García

2018-08-01

We present an efficient approach to the synthesis of a series of glycyrrhetinic acid derivatives. Six derivatives, five of them new compounds, were obtained through chemoenzymatic reactions in very good to excellent yield. In order to find the optimal reaction conditions, the influence of various parameters such as enzyme source, nucleophile:substrate ratio, enzyme:substrate ratio, solvent and temperature was studied. The excellent results obtained by lipase catalysis made the procedure very efficient considering their advantages such as mild reaction conditions and low environmental impact. Moreover, in order to explain the reactivity of glycyrrhetinic acid and the acetylated derivative to different nucleophiles in the enzymatic reactions, molecular docking studies were carried out. In addition, one of the synthesized compounds exhibited remarkable antiviral activity against TK + and TK- strains of Herpes simplex virus type 1 (HSV-1), sensitive and resistant to acyclovir (ACV) treatment. Copyright © 2018 Elsevier Inc. All rights reserved.

Organocatalytic asymmetric arylation of indoles enabled by azo groups

NASA Astrophysics Data System (ADS)

Qi, Liang-Wen; Mao, Jian-Hui; Zhang, Jian; Tan, Bin

2018-01-01

Arylation is a fundamental reaction that can be mostly fulfilled by electrophilic aromatic substitution and transition-metal-catalysed aryl functionalization. Although the azo group has been used as a directing group for many transformations via transition-metal-catalysed aryl carbon-hydrogen (C-H) bond activation, there remain significant unmet challenges in organocatalytic arylation. Here, we show that the azo group can effectively act as both a directing and activating group for organocatalytic asymmetric arylation of indoles via formal nucleophilic aromatic substitution of azobenzene derivatives. Thus, a wide range of axially chiral arylindoles have been achieved in good yields with excellent enantioselectivities by utilizing chiral phosphoric acid as catalyst. Furthermore, highly enantioenriched pyrroloindoles bearing two contiguous quaternary chiral centres have also been obtained via a cascade enantioselective formal nucleophilic aromatic substitution-cyclization process. This strategy should be useful in other related research fields and will open new avenues for organocatalytic asymmetric aryl functionalization.

Organocatalytic asymmetric arylation of indoles enabled by azo groups.

PubMed

Qi, Liang-Wen; Mao, Jian-Hui; Zhang, Jian; Tan, Bin

2018-01-01

Arylation is a fundamental reaction that can be mostly fulfilled by electrophilic aromatic substitution and transition-metal-catalysed aryl functionalization. Although the azo group has been used as a directing group for many transformations via transition-metal-catalysed aryl carbon-hydrogen (C-H) bond activation, there remain significant unmet challenges in organocatalytic arylation. Here, we show that the azo group can effectively act as both a directing and activating group for organocatalytic asymmetric arylation of indoles via formal nucleophilic aromatic substitution of azobenzene derivatives. Thus, a wide range of axially chiral arylindoles have been achieved in good yields with excellent enantioselectivities by utilizing chiral phosphoric acid as catalyst. Furthermore, highly enantioenriched pyrroloindoles bearing two contiguous quaternary chiral centres have also been obtained via a cascade enantioselective formal nucleophilic aromatic substitution-cyclization process. This strategy should be useful in other related research fields and will open new avenues for organocatalytic asymmetric aryl functionalization.

Efficient chemo-enzymatic gluten detoxification: reducing toxic epitopes for celiac patients improving functional properties

PubMed Central

Ribeiro, Miguel; Nunes, Fernando M.; Guedes, Sofia; Domingues, Pedro; Silva, Amélia M.; Carrillo, Jose Maria; Rodriguez-Quijano, Marta; Branlard, Gérard; Igrejas, Gilberto

2015-01-01

Protein engineering of gluten, the exogenous effector in celiac disease, seeking its detoxification by selective chemical modification of toxic epitopes is a very attractive strategy and promising technology when compared to pharmacological treatment or genetic engineering of wheat. Here we present a simple and efficient chemo-enzymatic methodology that decreases celiac disease toxic epitopes of gluten proteins improving its technological value through microbial transglutaminase-mediated transamidation of glutamine with n-butylamine under reducing conditions. First, we found that using low concentrations of amine-nucleophile under non-reducing conditions, the decrease in toxic epitopes is mainly due to transglutaminase-mediated cross-linking. Second, using high amine nucleophile concentrations protein cross-linking is substantially reduced. Third, reducing conditions increase 7-fold the transamidation reaction further decreasing toxic epitopes amount. Fourth, using n-butylamine improves gluten hydrophobicity that strengthens the gluten network. These results open the possibility of tailoring gluten for producing hypoallergenic flours while still taking advantage of the unique viscoelastic properties of gluten. PMID:26691232

The Future of Polar Organometallic Chemistry Written in Bio-Based Solvents and Water.

PubMed

García-Álvarez, Joaquín; Hevia, Eva; Capriati, Vito

2018-06-19

There is a strong imperative to reduce the release of volatile organic compounds (VOCs) into the environment, and many efforts are currently being made to replace conventional hazardous VOCs in favour of safe, green and bio-renewable reaction media that are not based on crude petroleum. Recent ground-breaking studies from a few laboratories worldwide have shown that both Grignard and (functionalised) organolithium reagents, traditionally handled under strict exclusion of air and humidity and in anhydrous VOCs, can smoothly promote both nucleophilic additions to unsaturated substrates and nucleophilic substitutions in water and other bio-based solvents (glycerol, deep eutectic solvents), competitively with protonolysis, at room temperature and under air. The chemistry of polar organometallics in the above protic media is a complex phenomenon influenced by several factors, and understanding its foundational character is surely stimulating in the perspective of the development of a sustainable organometallic chemistry. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Preparation of a novel radiotracer targeting the EphB4 receptor via radiofluorination using spiro azetidinium salts as precursor.

PubMed

Wiemer, Jens; Steinbach, Jörg; Pietzsch, Jens; Mamat, Constantin

2017-08-01

The visualization of Eph receptors, which are overexpressed in various tumor entities, using selective small molecule Eph inhibitors by means of positron emission tomography is a promising approach for tumor imaging. N-(Pyrimidinyl)indazolamines represent a class of compounds, which are known to have high affinity especially for the EphB4 receptor. Radiofluorination of these compounds could provide a highly specific imaging agent and was investigated using a classical nucleophilic introduction of [ 18 F]fluoride as well as a less common nucleophilic ring-opening reaction of azetidinium salts. In the past, radiofluorinations using azetidinium precursors were demonstrated to result in high radiochemical yields in short periods. For this purpose, an azetidinium precursor based on the N-(pyrimidinyl)indazolamine lead compound was developed, and radiofluorination was successfully accomplished. The respective [ 18 F]radiotracer was quickly prepared with high radiochemical purity >97% and in a radiochemical yield of 34%. Copyright © 2017 John Wiley & Sons, Ltd.

β-Lactam Ring Opening: A Useful Entry to Amino Acids and Relevant Nitrogen-Containing Compounds

NASA Astrophysics Data System (ADS)

Palomo, C.; Oiarbide, M.

The main strategies for the ring opening of β-lactams by chemical means are described. The discovery of each approach is put into context, sometimes in connection to processes occurring in biological systems, and the synthetic opportunities each approach offers are shown. Thus, this β-lactam route affords a number of synthetically relevant building-blocks, including α-amino acids, β-amino acids, their derived peptides, and other nitrogen containing heterocycles and open chain molecules. The content, which encompases references to initial work, further major development, and the most relevant recent literature contributions, is categorized according to the ring bond cleavaged (N 1-C 2, C 2-C 3, C 3 -C 4 , N 1-C 4), to finish with ring opening strategies leading to large heterocyclic compounds. Within each category, distinction has been made according to the type of nucleophilic agent employed, principally O-, N-, and C-nucleophiles. Also, a variety of applications of the strategy to the synthesis of interesting target compounds are shown.

CO- and HCl-free synthesis of acid chlorides from unsaturated hydrocarbons via shuttle catalysis

NASA Astrophysics Data System (ADS)

Fang, Xianjie; Cacherat, Bastien; Morandi, Bill

2017-11-01

The synthesis of carboxylic acid derivatives from unsaturated hydrocarbons is an important process for the preparation of polymers, pharmaceuticals, cosmetics and agrochemicals. Despite its industrial relevance, the traditional Reppe-type carbonylation reaction using pressurized CO is of limited applicability to laboratory-scale synthesis because of: (1) the safety hazards associated with the use of CO, (2) the need for special equipment to handle pressurized gas, (3) the low reactivity of several relevant nucleophiles and (4) the necessity to employ different, often tailor-made, catalytic systems for each nucleophile. Herein we demonstrate that a shuttle-catalysis approach enables a CO- and HCl-free transfer process between an inexpensive reagent, butyryl chloride, and a wide range of unsaturated substrates to access the corresponding acid chlorides in good yields. This new transformation provides access to a broad range of carbonyl-containing products through the in situ transformation of the reactive acid chloride intermediate. In a broader context, this work demonstrates that isodesmic shuttle-catalysis reactions can unlock elusive catalytic reactions.

Mechanistic Basis for High Reactivity of (salen)Co–OTs in the Hydrolytic Kinetic Resolution of Terminal Epoxides

PubMed Central

Nielsen, Lars P. C.; Zuend, Stephan J.; Ford, David D.; Jacobsen, Eric N.

2012-01-01

The (salen)Co(III)-catalyzed hydrolytic kinetic resolution (HKR) of terminal epoxides is a bimetallic process with a rate controlled by partitioning between a nucleophilic (salen)Co–OH catalyst and a Lewis acidic (salen)Co–X catalyst. The commonly used (salen)Co–OAc and (salen)Co–Cl precatalysts undergo complete and irreversible counterion addition to epoxide during the course of the epoxide hydrolysis reaction, resulting in quantitative formation of weakly Lewis acidic (salen)Co–OH, and severely diminished reaction rates in the late stages of HKR reactions. In contrast, (salen)Co–OTs maintains high reactivity over the entire course of HKR reactions. We describe here an investigation of catalyst partitioning with different (salen)Co–X precatalysts, and demonstrate that counterion addition to epoxide is reversible in the case of the (salen)Co–OTs. This reversible counterion addition results in stable partitioning between nucleophilic and Lewis acidic catalyst species, allowing highly efficient catalysis throughout the course of the HKR reaction. PMID:22292515

Mechanistic basis for high reactivity of (salen)Co-OTs in the hydrolytic kinetic resolution of terminal epoxides.

PubMed

Nielsen, Lars P C; Zuend, Stephan J; Ford, David D; Jacobsen, Eric N

2012-03-02

The (salen)Co(III)-catalyzed hydrolytic kinetic resolution (HKR) of terminal epoxides is a bimetallic process with a rate controlled by partitioning between a nucleophilic (salen)Co-OH catalyst and a Lewis acidic (salen)Co-X catalyst. The commonly used (salen)Co-OAc and (salen)Co-Cl precatalysts undergo complete and irreversible counterion addition to epoxide during the course of the epoxide hydrolysis reaction, resulting in quantitative formation of weakly Lewis acidic (salen)Co-OH and severely diminished reaction rates in the late stages of HKR reactions. In contrast, (salen)Co-OTs maintains high reactivity over the entire course of HKR reactions. We describe here an investigation of catalyst partitioning with different (salen)Co-X precatalysts and demonstrate that counterion addition to epoxide is reversible in the case of the (salen)Co-OTs. This reversible counterion addition results in stable partitioning between nucleophilic and Lewis acidic catalyst species, allowing highly efficient catalysis throughout the course of the HKR reaction.

Aldolase-catalysed stereoselective synthesis of fluorinated small molecules.

PubMed

Windle, Claire L; Berry, Alan; Nelson, Adam

2017-04-01

The introduction of fluorine has been widely exploited to tune the biological functions of small molecules. Indeed, around 20% of leading drugs contain at least one fluorine atom. Yet, despite profound effects of fluorination on conformation, there is only a limited toolkit of reactions that enable stereoselective synthesis of fluorinated compounds. Aldolases are useful catalysts for the stereoselective synthesis of bioactive small molecules; however, despite fluoropyruvate being a viable nucleophile for some aldolases, the potential of aldolases to control the formation of fluorine-bearing stereocentres has largely been untapped. Very recently, it has been shown that aldolase-catalysed stereoselective carboncarbon bond formation with fluoropyruvate as nucleophile enable the synthesis of many α-fluoro β-hydroxy carboxyl derivatives. Furthermore, an understanding of the structural basis for the stereocontrol observed in these reactions is beginning to emerge. Here, we review the application of aldolase catalysis in the stereocontrolled synthesis of chiral fluorinated small molecules, and highlight likely areas for future developments. Copyright © 2017 Elsevier Ltd. All rights reserved.

Synthesis and analysis of 2-[211At]-L-phenylalanine and 4-[211At]-L-phenylalanine and their uptake in human glioma cell cultures in-vitro.

PubMed

Meyer, Geerd J; Walte, Almut; Sriyapureddy, Siva R; Grote, Michaela; Krull, Doris; Korkmaz, Zekiye; Knapp, Wolfram H

2010-06-01

2-[211At]-L-phenylalanine and 4-[211At]-L-phenylalanine were prepared from the corresponding iodo and bromo derivatives using the Cu(+)-assisted nucleophilic exchange. 4-[211At]-L-phenylalanine was additionally prepared by destannylation of the BOC-derivatized 4-tributylstannyl-L-phenylalanine. Radiochemical yields of 2-[211At]-L-phenylalanine and 4-[211At]-L-phenylalanine by nucleophilic exchange were 52-74% and 65-85%. Radiochemical yield of 4-[211At]-L-phenylalanine by electrophilic destannylation was 35-50%. HPLC sequence analysis showed that 2-[211At]-L-phenylalanine followed the halogen sequence (F

Discovery and characterization of a marine bacterial SAM-dependent chlorinase

PubMed Central

Eustáquio, Alessandra S; Pojer, Florence; Noel, Joseph P; Moore, Bradley S

2009-01-01

Halogen atom incorporation into a scaffold of bioactive compounds often amplifies biological activity, as is the case for the anticancer agent salinosporamide A (1), a chlorinated natural product from the marine bacterium Salinispora tropica. Significant effort in understanding enzymatic chlorination shows that oxidative routes predominate to form reactive electrophilic or radical chlorine species. Here we report the genetic, biochemical and structural characterization of the chlorinase SalL, which halogenates S-adenosyl-l-methionine (2) with chloride to generate 5′-chloro-5′-deoxyadenosine (3) and l-methionine (4) in a rarely observed nucleophilic substitution strategy analogous to that of Streptomyces cattleya fluorinase. Further metabolic tailoring produces a halogenated polyketide synthase substrate specific for salinosporamide A biosynthesis. SalL also accepts bromide and iodide as substrates, but not fluoride. High-resolution crystal structures of SalL and active site mutants complexed with substrates and products support the SN2 nucleophilic substitution mechanism and further illuminate halide specificity in this newly discovered halogenase family. PMID:18059261

Influence of the leaving group on the dynamics of a gas-phase SN2 reaction

NASA Astrophysics Data System (ADS)

Stei, Martin; Carrascosa, Eduardo; Kainz, Martin A.; Kelkar, Aditya H.; Meyer, Jennifer; Szabó, István; Czakó, Gábor; Wester, Roland

2016-02-01

In addition to the nucleophile and solvent, the leaving group has a significant influence on SN2 nucleophilic substitution reactions. Its role is frequently discussed with respect to reactivity, but its influence on the reaction dynamics remains unclear. Here, we uncover the influence of the leaving group on the gas-phase dynamics of SN2 reactions in a combined approach of crossed-beam imaging and dynamics simulations. We have studied the reaction F- + CH3Cl and compared it to F- + CH3I. For the two leaving groups, Cl and I, we find very similar structures and energetics, but the dynamics show qualitatively different features. Simple scaling of the leaving group mass does not explain these differences. Instead, the relevant impact parameters for the reaction mechanisms are found to be crucial and the differences are attributed to the relative orientation of the approaching reactants. This effect occurs on short timescales and may also prevail in solution-phase conditions.

Influence of the leaving group on the dynamics of a gas-phase SN2 reaction.

PubMed

Stei, Martin; Carrascosa, Eduardo; Kainz, Martin A; Kelkar, Aditya H; Meyer, Jennifer; Szabó, István; Czakó, Gábor; Wester, Roland

2016-02-01

In addition to the nucleophile and solvent, the leaving group has a significant influence on SN2 nucleophilic substitution reactions. Its role is frequently discussed with respect to reactivity, but its influence on the reaction dynamics remains unclear. Here, we uncover the influence of the leaving group on the gas-phase dynamics of SN2 reactions in a combined approach of crossed-beam imaging and dynamics simulations. We have studied the reaction F(-) + CH3Cl and compared it to F(-) + CH3I. For the two leaving groups, Cl and I, we find very similar structures and energetics, but the dynamics show qualitatively different features. Simple scaling of the leaving group mass does not explain these differences. Instead, the relevant impact parameters for the reaction mechanisms are found to be crucial and the differences are attributed to the relative orientation of the approaching reactants. This effect occurs on short timescales and may also prevail in solution-phase conditions.

Theoretical study on the identity ion pair SN2 reactions of LiX with CH3SX (X=Cl, Br, and I): structure, mechanism, and potential energy surface.

PubMed

Ren, Yi; Gai, Jing-Gang; Xiong, Yan; Lee, Kuo-Hsing; Chu, San-Yan

2007-07-26

Three archetypal ion pair nucleophilic substitution reactions at the methylsulfenyl sulfur atom LiX+CH3SX-->XSCH3+LiX (X=Cl, Br, and I) are investigated by the modified Gaussian-2 theory. Including lithium cation in the anionic models makes the ion pair reactions proceed along an SN2 mechanism, contrary to the addition-elimination pathway occurring in the corresponding anionic nucleophilic substitution reactions X-+CH3SX-->XSCH3+X-. Two reaction pathways for the ion pair SN2 reactions at sulfur, inversion and retention, are proposed. Results indicate the inversion pathway is favorable for all the halogens. Comparison of the transition structures and energetics for the ion pair SN2 at sulfur with the potential competition ion pair SN2 reactions at carbon LiX+CH3SX-->XCH3+LiXS shows that the SN2 reactions at carbon are not favorable from the viewpoints of kinetics and thermodynamics.

The Experimental Evidence in Support of Glycosylation Mechanisms at the SN1-SN2 Interface.

PubMed

Adero, Philip Ouma; Amarasekara, Harsha; Wen, Peng; Bohé, Luis; Crich, David

2018-05-30

A critical review of the state-of-the-art evidence in support of the mechanisms of glycosylation reactions is provided. Factors affecting the stability of putative oxocarbenium ions as intermediates at the S N 1 end of the mechanistic continuum are first surveyed before the evidence, spectroscopic and indirect, for the existence of such species on the time scale of glycosylation reactions is presented. Current models for diastereoselectivity in nucleophilic attack on oxocarbenium ions are then described. Evidence in support of the intermediacy of activated covalent glycosyl donors is reviewed, before the influences of the structure of the nucleophile, of the solvent, of temperature, and of donor-acceptor hydrogen bonding on the mechanism of glycosylation reactions are surveyed. Studies on the kinetics of glycosylation reactions and the use of kinetic isotope effects for the determination of transition-state structure are presented, before computational models are finally surveyed. The review concludes with a critical appraisal of the state of the art.

Steric Effects of Solvent Molecules on SN2 Substitution Dynamics.

PubMed

Liu, Xu; Xie, Jing; Zhang, Jiaxu; Yang, Li; Hase, William L

2017-04-20

Influences of solvent molecules on S N 2 reaction dynamics of microsolvated F - (H 2 O) n with CH 3 I, for n = 0-3, are uncovered by direct chemical dynamics simulations. The direct substitution mechanism, which is important without microsolvation, is quenched dramatically upon increasing hydration. The water molecules tend to force reactive encounters to proceed through the prereaction collision complex leading to indirect reaction. In contrast to F - (H 2 O), reaction with higher hydrated ions shows a strong propensity for ion desolvation in the entrance channel, diminishing steric hindrance for nucleophilic attack. Thus, nucleophilic substitution avoids the potential energy barrier with all of the solvent molecules intact and instead occurs through the less solvated barrier, which is energetically unexpected because the former barrier has a lower energy. The work presented here reveals a trade-off between reaction energetics and steric effects, with the latter found to be crucial in understanding how hydration influences microsolvated S N 2 dynamics.

Enzymatic Addition of Alcohols to Terpenes by Squalene Hopene Cyclase Variants.

PubMed

Kühnel, Lisa C; Nestl, Bettina M; Hauer, Bernhard

2017-11-16

Squalene-hopene cyclases (SHCs) catalyze the polycyclization of squalene into a mixture of hopene and hopanol. Recently, amino-acid residues lining the catalytic cavity of the SHC from Alicyclobacillus acidocaldarius were replaced by small and large hydrophobic amino acids. The alteration of leucine 607 to phenylalanine resulted in increased enzymatic activity towards the formation of an intermolecular farnesyl-farnesyl ether product from farnesol. Furthermore, the addition of small-chain alcohols acting as nucleophiles led to the formation of non-natural ether-linked terpenoids and, thus, to significant alteration of the product pattern relative to that obtained with the wild type. It is proposed that the mutation of leucine at position 607 may facilitate premature quenching of the intermediate by small alcohol nucleophiles. This mutagenesis-based study opens the field for further intermolecular bond-forming reactions and the generation of non-natural products. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

An Active Site Water Network in the Plasminogen Activator Pla from Yersinia pestis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eren, Elif; Murphy, Megan; Goguen, Jon

2010-08-13

The plasminogen activator Pla from Yersinia pestis is an outer membrane protease (omptin) that is important for the virulence of plague. Here, we present the high-resolution crystal structure of wild-type, enzymatically active Pla at 1.9 {angstrom}. The structure shows a water molecule located between active site residues D84 and H208, which likely corresponds to the nucleophilic water. A number of other water molecules are present in the active site, linking residues important for enzymatic activity. The R211 sidechain in loop L4 is close to the nucleophilic water and possibly involved in the stabilization of the oxyanion intermediate. Subtle conformational changesmore » of H208 result from the binding of lipopolysaccharide to the outside of the barrel, explaining the unusual dependence of omptins on lipopolysaccharide for activity. The Pla structure suggests a model for the interaction with plasminogen substrate and provides a more detailed understanding of the catalytic mechanism of omptin proteases.« less

Global profiling of lysine reactivity and ligandability in the human proteome.

PubMed

Hacker, Stephan M; Backus, Keriann M; Lazear, Michael R; Forli, Stefano; Correia, Bruno E; Cravatt, Benjamin F

2017-12-01

Nucleophilic amino acids make important contributions to protein function, including performing key roles in catalysis and serving as sites for post-translational modification. Electrophilic groups that target amino-acid nucleophiles have been used to create covalent ligands and drugs, but have, so far, been mainly limited to cysteine and serine. Here, we report a chemical proteomic platform for the global and quantitative analysis of lysine residues in native biological systems. We have quantified, in total, more than 9,000 lysines in human cell proteomes and have identified several hundred residues with heightened reactivity that are enriched at protein functional sites and can frequently be targeted by electrophilic small molecules. We have also discovered lysine-reactive fragment electrophiles that inhibit enzymes by active site and allosteric mechanisms, as well as disrupt protein-protein interactions in transcriptional regulatory complexes, emphasizing the broad potential and diverse functional consequences of liganding lysine residues throughout the human proteome.

What Happens when Representations Fail to Represent? Graduate Students' Mental Models of Organic Chemistry Diagrams

ERIC Educational Resources Information Center

Strickland, Amanda M.; Kraft, Adam; Bhattacharyya, Gautam

2010-01-01

As part of our investigations into the development of representational competence, we report results from a study in which we elicited sixteen graduate students' expressed mental models of commonly-used terms for describing organic reactions--functional group, nucleophile/electrophile, acid/base--and for diagrams of transformations and their…

The Chemistry of Photographic Color Dye Formation

ERIC Educational Resources Information Center

Kahn, Bruce E.

2004-01-01

A laboratory activity that can be used at a number of levels from high school to college is discussed. This activity can be used to teach chemical concepts such as oxidation and reduction, stoichiometry, acids and bases, pH, nucleophilic reactions, conjugation, leaving groups, complexation, solubility, and reversibility.

The Preparation and Reaction of Phenyl-Substituted Pyrylium and Pyridinium Salts.

ERIC Educational Resources Information Center

Awartani, Radi; And Others

1986-01-01

Describes this reaction sequence involving reactivity and synthesis of heterocycles: (1) synthesis of 2,4,6-triphenylpyrylium tetrafluoroborate, II; (2) its reaction with nucleophiles; (3) reaction of pyrylium salt II with a primary amine (benzylamine, p-methoxybenzylamine, and furfurylamine) to form the N-substituted-2,4,6-triphenylpyridinium…

Organocatalyzed enantioselective desymmetrization of aziridines and epoxides

PubMed Central

2013-01-01

Summary Enantioselective desymmetrization of meso-aziridines and meso-epoxides with various nucleophiles by organocatalysis has emerged as a cutting-edge approach in recent years. This review summarizes the origin and recent developments of enantioselective desymmetrization of meso-aziridines and meso-epoxides in the presence of organocatalysts. PMID:24062828

Reactivity II: A Second Foundation-Level Course in Integrated Organic, Inorganic, and Biochemistry

ERIC Educational Resources Information Center

Schaller, Chris P.; Graham, Kate J.; McIntee, Edward J.; Jones, T. Nicholas; Johnson, Brian J.

2016-01-01

A foundation-level course is described that integrates material related to reactivity in organic, inorganic, and biochemistry. Designed for second-year students, the course serves majors in chemistry, biochemistry, and biology, as well as prehealth-professions students. Building on an earlier course that developed concepts of nucleophiles and…

Electrostatic Potential Maps and Natural Bond Orbital Analysis: Visualization and Conceptualization of Reactivity in Sanger's Reagent

ERIC Educational Resources Information Center

Mottishaw, Jeffery D.; Erck, Adam R.; Kramer, Jordan H.; Sun, Haoran; Koppang, Miles

2015-01-01

Frederick Sanger's early work on protein sequencing through the use of colorimetric labeling combined with liquid chromatography involves an important nucleophilic aromatic substitution (S[subscript N]Ar) reaction in which the N-terminus of a protein is tagged with Sanger's reagent. Understanding the inherent differences between this S[subscript…

Preparation of pyrrolizinone derivatives via sequential transformations of cyclic allyl imides: synthesis of quinolactacide and marinamide.

PubMed

Simic, Milena; Tasic, Gordana; Jovanovic, Predrag; Petkovic, Milos; Savic, Vladimir

2018-03-28

A facile synthetic route has been developed for the preparation of pyrrolizinone derivatives employing N-allyl imides as starting materials. The nucleophilic addition of a vinyl Grignard reagent/RCM/elimination sequence afforded pyrrolizinones in good yields and has been applied for the preparation of naturally occurring quinolactacide and marinamide.

Traceless splicing enabled by substrate-induced activation of the Nostoc punctiforme Npu DnaE intein after mutation of a catalytic cysteine to serine.

PubMed

Cheriyan, Manoj; Chan, Siu-Hong; Perler, Francine

2014-12-12

Inteins self-catalytically cleave out of precursor proteins while ligating the surrounding extein fragments with a native peptide bond. Much attention has been lavished on these molecular marvels with the hope of understanding and harnessing their chemistry for novel biochemical transformations including coupling peptides from synthetic or biological origins and controlling protein function. Despite an abundance of powerful applications, the use of inteins is still hampered by limitations in our understanding of their specificity (defined as flanking sequences that permit splicing) and the challenge of inserting inteins into target proteins. We examined the frequently used Nostoc punctiforme Npu DnaE intein after the C-extein cysteine nucleophile (Cys+1) was mutated to serine or threonine. Previous studies demonstrated reduced rates and/or splicing yields with the Npu DnaE intein after mutation of Cys+1 to Ser+1. In this study, genetic selection identified extein sequences with Ser+1 that enabled the Npu DnaE intein to splice with only a 5-fold reduction in rate compared to the wild-type Cys+1 intein and without mutation of the intein itself to activate Ser+1 as a nucleophile. Three different proteins spliced efficiently after insertion of the intein flanked by the selected sequences. We then used this selected specificity to achieve traceless splicing in a targeted enzyme at a location predicted by primary sequence similarity to only the selected C-extein sequence. This study highlights the latent catalytic potential of the Npu DnaE intein to splice with an alternative nucleophile and enables broader intein utility by increasing insertion site choices. Copyright © 2014. Published by Elsevier Ltd.

Origins of the different metal preferences of Escherichia coli peptide deformylase and Bacillus thermoproteolyticus thermolysin: a comparative quantum mechanical/molecular mechanical study.

PubMed

Dong, Minghui; Liu, Haiyan

2008-08-21

The Escherichia coli peptide deformylase (PDF) and Bacillus thermoproteolyticus thermolysin (TLN) are two representative metal-requiring peptidases having remarkably similar active centers but distinctively different metal preferences. Zinc is a competent catalytic cofactor for TLN but not for PDF. Reaction pathways and the associated energetics for both enzymes were determined using combined semiempirical and ab initio quantum mechanical/molecular mechanical modeling, without presuming reaction coordinates. The results confirmed that both enzymes catalyze via the same chemical steps, and reproduced their different preferences for zinc or iron as competent cofactors. Further analyses indicated that different feasibility of the nucleophilic attack step leads to different metal preferences of the two enzymes. In TLN, the substrate is strongly activated and can serve as the fifth coordination ligand of zinc prior to the chemical steps. In PDF, the substrate carbonyl is activated by the chemical step itself, and becomes the fifth coordination partner of zinc only in a later stage of the nucleophilic attack. These leads to a much more difficult nucleophilic attack in PDF than in TLN. Different from some earlier suggestions, zinc has no difficulty in accepting an activated substrate as the fifth ligand to switch from tetra- to penta-coordination in either PDF or TLN. When iron replaces zinc, its stronger interaction with the hydroxide ligand may lead to higher activation barrier in TLN. In PDF, the stronger interactions of iron with ligands allow iron-substrate coordination to take place either before or at a very early stage of the chemical step, leading to effective catalysis. Our calculations also show combined semiempirical and ab initio quantum mechanical modeling can be efficient approaches to explore complicated reaction pathways in enzyme systems.

Determinants of reactivity and selectivity in soluble epoxide hydrolase from quantum mechanics/molecular mechanics modeling.

PubMed

Lonsdale, Richard; Hoyle, Simon; Grey, Daniel T; Ridder, Lars; Mulholland, Adrian J

2012-02-28

Soluble epoxide hydrolase (sEH) is an enzyme involved in drug metabolism that catalyzes the hydrolysis of epoxides to form their corresponding diols. sEH has a broad substrate range and shows high regio- and enantioselectivity for nucleophilic ring opening by Asp333. Epoxide hydrolases therefore have potential synthetic applications. We have used combined quantum mechanics/molecular mechanics (QM/MM) umbrella sampling molecular dynamics (MD) simulations (at the AM1/CHARMM22 level) and high-level ab initio (SCS-MP2) QM/MM calculations to analyze the reactions, and determinants of selectivity, for two substrates: trans-stilbene oxide (t-SO) and trans-diphenylpropene oxide (t-DPPO). The calculated free energy barriers from the QM/MM (AM1/CHARMM22) umbrella sampling MD simulations show a lower barrier for phenyl attack in t-DPPO, compared with that for benzylic attack, in agreement with experiment. Activation barriers in agreement with experimental rate constants are obtained only with the highest level of QM theory (SCS-MP2) used. Our results show that the selectivity of the ring-opening reaction is influenced by several factors, including proximity to the nucleophile, electronic stabilization of the transition state, and hydrogen bonding to two active site tyrosine residues. The protonation state of His523 during nucleophilic attack has also been investigated, and our results show that the protonated form is most consistent with experimental findings. The work presented here illustrates how determinants of selectivity can be identified from QM/MM simulations. These insights may also provide useful information for the design of novel catalysts for use in the synthesis of enantiopure compounds.

Crystal structure of glycoside hydrolase family 127 β-L-arabinofuranosidase from Bifidobacterium longum

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ito, Tasuku; Saikawa, Kyo; Kim, Seonah

2014-04-25

Graphical abstract: - Highlights: • HypBA1 β-L-arabinofuranosidase belongs to glycoside hydrolase family 127. • Crystal structure of HypBA1 was determined. • HypBA1 consists of a catalytic barrel and two additional β-sandwich domains. • The active site contains a Zn{sup 2+} coordinated by glutamate and three cysteines. • A possible reaction mechanism involving cysteine as the nucleophile is proposed. - Abstract: Enzymes acting on β-linked arabinofuranosides have been unknown until recently, in spite of wide distribution of β-L-arabinofuranosyl oligosaccharides in plant cells. Recently, a β-L-arabinofuranosidase from the glycoside hydrolase family 127 (HypBA1) was discovered in the newly characterized degradation system ofmore » hydroxyproline-linked β-L-arabinooligosaccharides in the bacterium Bifidobacterium longum. Here, we report the crystal structure of HypBA1 in the ligand-free and β-L-arabinofuranose complex forms. The structure of HypBA1 consists of a catalytic barrel domain and two additional β-sandwich domains, with one β-sandwich domain involved in the formation of a dimer. Interestingly, there is an unprecedented metal-binding motif with Zn{sup 2+} coordinated by glutamate and three cysteines in the active site. The glutamate residue is located far from the anomeric carbon of the β-L-arabinofuranose ligand, but one cysteine residue is appropriately located for nucleophilic attack for glycosidic bond cleavage. The residues around the active site are highly conserved among GH127 members. Based on biochemical experiments and quantum mechanical calculations, a possible reaction mechanism involving cysteine as the nucleophile is proposed.« less

Re-engineering specificity in 1,3-1, 4-β-glucanase to accept branched xyloglucan substrates.

PubMed

Addington, Trevor; Calisto, Barbara; Alfonso-Prieto, Mercedes; Rovira, Carme; Fita, Ignasi; Planas, Antoni

2011-02-01

Family 16 carbohydrate active enzyme members Bacillus licheniformis 1,3-1,4-β-glucanase and Populus tremula x tremuloides xyloglucan endotransglycosylase (XET16-34) are highly structurally related but display different substrate specificities. Although the first binds linear gluco-oligosaccharides, the second binds branched xylogluco-oligosaccharides. Prior engineered nucleophile mutants of both enzymes are glycosynthases that catalyze the condensation between a glycosyl fluoride donor and a glycoside acceptor. With the aim of expanding the glycosynthase technology to produce designer oligosaccharides consisting of hybrids between branched xylogluco- and linear gluco-oligosaccharides, enzyme engineering on the negative subsites of 1,3-1,4-β-glucanase to accept branched substrates has been undertaken. Removal of the 1,3-1,4-β-glucanase major loop and replacement with that of XET16-34 to open the binding cleft resulted in a folded protein, which still maintained some β-glucan hydrolase activity, but the corresponding nucleophile mutant did not display glycosynthase activity with either linear or branched glycosyl donors. Next, point mutations of the 1,3-1,4-β-glucanase β-sheets forming the binding site cleft were mutated to resemble XET16-34 residues. The final chimeric protein acquired binding affinity for xyloglucan and did not bind β-glucan. Therefore, binding specificity has been re-engineered, but affinity was low and the nucleophile mutant of the chimeric enzyme did not show glycosynthase activity to produce the target hybrid oligosaccharides. Structural analysis by X-ray crystallography explains these results in terms of changes in the protein structure and highlights further engineering approaches toward introducing the desired activity. © 2010 Wiley-Liss, Inc.

The Study of Substitution and Elimination Reactions Using Gas Chromatography: An Examination of the Effects of Alkane and Base Structure on Product Distributions

ERIC Educational Resources Information Center

Wharry, Donald L.

2011-01-01

An experiment that compares product distribution obtained by either substitution or elimination utilizing alkyl bromides and methoxide, ethoxide, or t-butoxide as the base (or nucleophile) is described. The change in product distribution caused by steric effects of the base and substrate are readily apparent. Prior work on this experiment focused…