Density Functional Study for Chemical Reaction between Cr and Fe with Sodium Diethyldithiocarbamate (NaDDC)

NASA Astrophysics Data System (ADS)

Setiyanto, Henry; Muhida, Rifki; Kishi, Tomoya; Rahman, Md. Mahmudur; Dipojono, Hermawan K.; Diño, Wilson A.; Matsumoto, Shigeno; Kasai, Hideaki

Analytical chemistry in the perspective of ab initio molecular orbital calculation is introduced by investigating the chemical reaction between transition metals Cr and Fe with sodium diethyldithiocarbamate (NaDDC), a complexing agent to detect and extract Cr in human blood sample. Using density functional theory—based calculations, we determine the stable structure of the Cr-DDC and Fe-DDC complexes and obtain its dissociation energies. We found dissociation energy values of -3.24 and -2.67 eV for Cr and Fe complexes, respectively; and hence the formation of the former complex is more favorable than the formation of the latter.

Thermodynamic and kinetic data for adduct formation, cis-trans isomerization and redox reactions of ML4 complexes: a case study with rhodium- and iridium-tropp complexes in d8, d9 and d10 valence electron configurations (tropp=dibenzotropylidene phosphanes).

PubMed

Breher, Frank; Rüegger, Heinz; Mlakar, Marina; Rudolph, Manfred; Deblon, Stephan; Schönberg, Hartmut; Boulmaâz, Souad; Thomaier, Jörg; Grützmacher, Hansjörg

2004-02-06

The formation of adducts of the square-planar 16-electron complexes trans-[M(tropp(ph))(2)](+) and cis-[M(tropp(ph))(2)](+) (M=Rh, Ir; tropp(Ph)=5-diphenylphosphanyldibenzo[a,d]cycloheptene) with acetonitrile (acn) and Cl(-), and the redox chemistry of these complexes was investigated by various physical methods (NMR and UV-visible spectroscopy, square-wave voltammetry), in order to obtain some fundamental thermodynamic and kinetic data for these systems. A trans/cis isomerization cannot be detected for [M(tropp(ph))(2)](+) in non-coordinating solvents. However, both isomers are connected through equilibria of the type trans-[M(tropp(ph))(2)](+)+L<==>[ML(tropp(ph))(2)](n)<==>cis-[M(tropp(ph))(2)](+)+L, involving five-coordinate intermediates [ML(tropp(ph))(2)](n) (L=acn, n=+1; L=Cl(-), n=0). Values for K(d) (K(f)), that is, the dissociation (formation) equilibrium constant, and k(d) (k(f)), that is, the dissociation (formation) rate constant, were obtained. The formation reactions are fast, especially with the trans isomers (k(f)>1x10(5) m(-1) s(-1)). The reaction with the sterically more hindered cis isomers is at least one order of magnitude slower. The stability of the five-coordinate complexes [ML(tropp(ph))(2)](n) increases with Ir>Rh and Cl(-)>acn. The dissociation reaction has a pronounced influence on the square-wave (SW) voltammograms of trans/cis-[Ir(tropp(ph))(2)](+). With the help of the thermodynamic and kinetic data independently determined by other physical means, these reactions could be simulated and allowed the setting up of a reaction sequence. Examination of the data obtained showed that the trans/cis isomerization is a process with a low activation barrier for the four-coordinate 17-electron complexes [M(tropp(ph))(2)](0) and especially that a disproportionation reaction 2 trans/cis-[M(tropp(ph))(2)](0)-->[M(tropp(ph))(2)](+)+[M(tropp(ph))(2)](-) may be sufficiently fast to mask the true reactivity of the paramagnetic species, which are probably less reactive than their diamagnetic equilibrium partners.

Photochemistry and reactivity of the phenyl radical-water system: a matrix isolation and computational study.

PubMed

Mardyukov, Artur; Crespo-Otero, Rachel; Sanchez-Garcia, Elsa; Sander, Wolfram

2010-08-02

The reaction of the phenyl radical 1 with water has been investigated by using matrix isolation spectroscopy and quantum chemical calculations. The primary thermal product of the reaction between 1 and water is a weakly bound complex stabilized by an OH...pi interaction. This complex is photolabile, and visible-light irradiation (lambda>420 nm) results in hydrogen atom transfer from water to radical 1 and the formation of a highly labile complex between benzene and the OH radical. This complex is stable under the conditions of matrix isolation, however, continuous irradiation with lambda>420 nm light results in the complete destruction of the aromatic system and formation of an acylic unsaturated ketene. The mechanisms of all reaction steps are discussed in the light of ab initio and DFT calculations.

Dependence of the enthalpies of formation of glycylglycinate complexes of nickel(II) on the composition of a mixed water-dimethylsulfoxide solvent

NASA Astrophysics Data System (ADS)

Naumov, V. V.; Kovaleva, Yu. A.; Isaeva, V. A.; Usacheva, T. R.; Sharnin, V. A.

2014-06-01

The heat effects of the complexation reactions of nickel(II) with a glycylglycinate ion in a water-dimethylsulfoxide solvent in a range of compositions of 0.00-0.60 molar parts of dimethylsulfoxide (DMSO) (an ionic strength of 0.1 was maintained using sodium perchlorate) were determined by means of calorimetry at 298.15 K. It is established that the exothermicity of complexation reactions rises by the first two steps and falls upon the addition of a third glycylglycinate anion with an increase in the concentration of DMSO. It is shown that the formation of mono- and bis-glycylglycinate complexes of nickel(II) in a water-DMSO solvent is determined mostly by the enthalpic contribution. It is concluded that the formation of tris-ligand complexes is more associated with the entropic contribution.

Why can a gold salt react as a base?

PubMed

Anania, Mariarosa; Jašíková, Lucie; Jašík, Juraj; Roithová, Jana

2017-09-26

This study shows that gold salts [(L)AuX] (L = PMe 3 , PPh 3 , JohnPhos, IPr; X = SbF 6 , PF 6 , BF 4 , TfO, Tf 2 N) act as bases in aqueous solutions and can transform acetone to digold acetonyl complexes [(L) 2 Au 2 (CH 2 COCH 3 )] + without any additional base present in solution. The key step is the formation of digold hydroxide complexes [(L) 2 Au 2 (OH)] + . The kinetics of the formation of the digold complexes and their mutual transformation is studied by electrospray ionization mass spectrometry and the delayed reactant labelling method. We show that the formation of digold hydroxide is the essential first step towards the formation of the digold acetonyl complex, the reaction is favoured by more polar solvents, and the effect of counter ions is negligible. DFT calculations suggest that digold hydroxide and digold acetonyl complexes can exist in solution only due to the stabilization by the interaction with two gold atoms. The reaction between the digold hydroxide and acetone proceeds towards the dimer {[(L)Au(OH)]·[(L)Au(CH 3 COCH 3 )] + }. The monomeric units interact at the gold atoms in the perpendicular arrangement typical of the gold clusters bound by the aurophilic interaction. The hydrogen is transferred within the dimer and the reaction continues towards the digold acetonyl complex and water.

Glycoconjugate Oxime Formation Catalyzed at Neutral pH: Mechanistic Insights and Applications of 1,4-Diaminobenzene as a Superior Catalyst for Complex Carbohydrates.

PubMed

Østergaard, Mads; Christensen, Niels Johan; Hjuler, Christian T; Jensen, Knud J; Thygesen, Mikkel B

2018-04-18

The reaction of unprotected carbohydrates with aminooxy reagents to provide oximes is a key method for the construction of glycoconjugates. Aniline and derivatives serve as organocatalysts for the formation of oximes from simple aldehydes, and we have previously reported that aniline also catalyzes the formation of oximes from the more complex aldehydes, carbohydrates. Here, we present a comprehensive study of the effect of aniline analogues on the formation of carbohydrate oximes and related glycoconjugates depending on organocatalyst structure, pH, nucleophile, and carbohydrate, covering more than 150 different reaction conditions. The observed superiority of the 1,4-diaminobenzene (PDA) catalyst at neutral pH is rationalized by NMR analyses and DFT studies of reaction intermediates. Carbohydrate oxime formation at pH 7 is demonstrated by the formation of a bioactive glycoconjugate from a labile, decorated octasaccharide originating from exopolysaccharides of the soil bacterium Mesorhizobium loti. This study of glycoconjugate formation includes the first direct comparison of aniline-catalyzed reaction rates and equilibrium constants for different classes of nucleophiles, including primary oxyamines, secondary N-alkyl oxyamines, as well as aryl and arylsulfonyl hydrazides. We identified 1,4-diaminobenzene as a superior catalyst for the construction of oxime-linked glycoconjugates under mild conditions.

Kinetics of Mn3+-oxalate formation and decay in reactions catalyzed by manganese peroxidase of Ceriporiopsis subvermispora

Treesearch

Ulises Urzua; Philip J. Kersten; Rafael Vicuna

1998-01-01

The kinetics of Mn3+- oxalate formation and decay were investigated in reactions catalyzed by manganese peroxidase (MnP) from the basiomycete Ceriporiopsis subvermispora in the absence of externally added hydrogen peroxide. A characteristic lag observed in the formation of this complex was shortened by glyoxylate or catalytic amounts of Mn3+ or hydrogen peroxide. MnP...

Characterization of the complex between native and reduced bovine serum albumin with aquacobalamin and evidence of dual tetrapyrrole binding.

PubMed

Dereven'kov, Ilia A; Hannibal, Luciana; Makarov, Sergei V; Makarova, Anna S; Molodtsov, Pavel A; Koifman, Oskar I

2018-05-02

Serum albumin binds to a variety of endogenous ligands and drugs. Human serum albumin (HSA) binds to heme via hydrophobic interactions and axial coordination of the iron center by protein residue Tyr161. Human serum albumin binds to another tetrapyrrole, cobalamin (Cbl), but the structural and functional properties of this complex are poorly understood. Herein, we investigate the reaction between aquacobalamin (H 2 OCbl) and bovine serum albumin (BSA, the bovine counterpart of HSA) using Ultraviolet-Visible and fluorescent spectroscopy, and electron paramagnetic resonance. The reaction between H 2 OCbl and BSA led to the formation of a BSA-Cbl(III) complex consistent with N-axial ligation (amino). Prior to the formation of this complex, the reactants participate in an additional binding event that has been examined by fluorescence spectroscopy. Binding of BSA to Cbl(III) reduced complex formation between the bound cobalamin and free cyanide to form cyanocobalamin (CNCbl), suggesting that the β-axial position of the cobalamin may be occupied by an amino acid residue from the protein. Reaction of BSA containing reduced disulfide bonds with H 2 OCbl produces cob(II)alamin and disulfide with intermediate formation of thiolate Cbl(III)-BSA complex and its decomposition. Finally, in vitro studies showed that cobalamin binds to BSA only in the presence of an excess of protein, which is in contrast to heme binding to BSA that involves a 1:1 stoichiometry. In vitro formation of BSA-Cbl(III) complex does not preclude subsequent heme binding, which occurs without displacement of H 2 OCbl bound to BSA. These data suggest that the two tetrapyrroles interact with BSA in different binding pockets.

Reaction mechanism of Ru(II) piano-stool complexes: umbrella sampling QM/MM MD study.

PubMed

Futera, Zdeněk; Burda, Jaroslav V

2014-07-15

Biologically relevant interactions of piano-stool ruthenium(II) complexes with ds-DNA are studied in this article by hybrid quantum mechanics-molecular mechanics (QM/MM) computational technique. The whole reaction mechanism is divided into three phases: (i) hydration of the [Ru(II) (η(6) -benzene)(en)Cl](+) complex, (ii) monoadduct formation between the resulting aqua-Ru(II) complex and N7 position of one of the guanines in the ds-DNA oligomer, and (iii) formation of the intrastrand Ru(II) bridge (cross-link) between two adjacent guanines. Free energy profiles of all the reactions are explored by QM/MM MD umbrella sampling approach where the Ru(II) complex and two guanines represent a quantum core, which is described by density functional theory methods. The combined QM/MM scheme is realized by our own software, which was developed to couple several quantum chemical programs (in this study Gaussian 09) and Amber 11 package. Calculated free energy barriers of the both ruthenium hydration and Ru(II)-N7(G) DNA binding process are in good agreement with experimentally measured rate constants. Then, this method was used to study the possibility of cross-link formation. One feasible pathway leading to Ru(II) guanine-guanine cross-link with synchronous releasing of the benzene ligand is predicted. The cross-linking is an exergonic process with the energy barrier lower than for the monoadduct reaction of Ru(II) complex with ds-DNA. Copyright © 2014 Wiley Periodicals, Inc.

Mössbauer and NMR study of novel Tin(IV)-lactames

NASA Astrophysics Data System (ADS)

Kuzmann, Erno; Szalay, Roland; Homonnay, Zoltan; Nagy, Sandor

2012-03-01

N-tributylstannylated 2-pyrrolidinone was reacted with tributyltin triflate in different molar ratios and the complex formation monitored using 1H-NMR, 13C-NMR and 119Sn Mössbauer spectroscopy. Comparing the carbon NMR and tin Mössbauer results, a reaction scheme is suggested for the complexation which assumes the formation of a simultaneously O- and N-tributylstannylated pyrrolidinone cation. The formation of the only O-stannylated pyrrolidinone is also assumed to account for the non-constant Mössbauer parameters of the two tin environments in the distannylated pyrrolidinone cation when the ratio of tributyltin triflate is increased in the reaction.

Transfer hydrogenation catalysis in cells as a new approach to anticancer drug design

PubMed Central

Soldevila-Barreda, Joan J.; Romero-Canelón, Isolda; Habtemariam, Abraha; Sadler, Peter J.

2015-01-01

Organometallic complexes are effective hydrogenation catalysts for organic reactions. For example, Noyori-type ruthenium complexes catalyse reduction of ketones by transfer of hydride from formate. Here we show that such catalytic reactions can be achieved in cancer cells, offering a new strategy for the design of safe metal-based anticancer drugs. The activity of ruthenium(II) sulfonamido ethyleneamine complexes towards human ovarian cancer cells is enhanced by up to 50 × in the presence of low non-toxic doses of formate. The extent of conversion of coenzyme NAD+ to NADH in cells is dependent on formate concentration. This novel reductive stress mechanism of cell death does not involve apoptosis or perturbation of mitochondrial membrane potentials. In contrast, iridium cyclopentadienyl catalysts cause cancer cell death by oxidative stress. Organometallic complexes therefore have an extraordinary ability to modulate the redox status of cancer cells. PMID:25791197

Nickel-catalyzed coupling reaction of alkyl halides with aryl Grignard reagents in the presence of 1,3-butadiene: mechanistic studies of four-component coupling and competing cross-coupling reactions† †Electronic supplementary information (ESI) available: Detailed experimental and computational results, procedures, characterization data, copies of NMR charts, and crystallographic data. CCDC 1572238. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7sc04675h

PubMed Central

Fukuoka, Asuka; Yokoyama, Wataru; Min, Xin; Hisaki, Ichiro; Kuniyasu, Hitoshi

2018-01-01

We describe the mechanism, substituent effects, and origins of the selectivity of the nickel-catalyzed four-component coupling reactions of alkyl fluorides, aryl Grignard reagents, and two molecules of 1,3-butadiene that affords a 1,6-octadiene carbon framework bearing alkyl and aryl groups at the 3- and 8-positions, respectively, and the competing cross-coupling reaction. Both the four-component coupling reaction and the cross-coupling reaction are triggered by the formation of anionic nickel complexes, which are generated by the oxidative dimerization of two molecules of 1,3-butadiene on Ni(0) and the subsequent complexation with the aryl Grignard reagents. The C–C bond formation of the alkyl fluorides with the γ-carbon of the anionic nickel complexes leads to the four-component coupling product, whereas the cross-coupling product is yielded via nucleophilic attack of the Ni center toward the alkyl fluorides. These steps are found to be the rate-determining and selectivity-determining steps of the whole catalytic cycle, in which the C–F bond of the alkyl fluorides is activated by the Mg cation rather than a Li or Zn cation. ortho-Substituents of the aryl Grignard reagents suppressed the cross-coupling reaction leading to the selective formation of the four-component products. Such steric effects of the ortho-substituents were clearly demonstrated by crystal structure characterizations of ate complexes and DFT calculations. The electronic effects of the para-substituent of the aryl Grignard reagents on both the selectivity and reaction rates are thoroughly discussed. The present mechanistic study offers new insight into anionic complexes, which are proposed as the key intermediates in catalytic transformations even though detailed mechanisms are not established in many cases, and demonstrates their synthetic utility as promising intermediates for C–C bond forming reactions, providing useful information for developing efficient and straightforward multicomponent reactions. PMID:29719693

Scope and Mechanistic Investigations on the Solvent-Controlled Regio- and Stereoselective Formation of Enol Esters from the Ruthenium-Catalyzed Coupling Reaction of Terminal Alkynes and Carboxylic Acids

PubMed Central

Yi, Chae S.; Gao, Ruili

2009-01-01

The ruthenium-hydride complex (PCy3)2(CO)RuHCl was found to be a highly effective catalyst for the alkyne-to-carboxylic acid coupling reaction to give synthetically useful enol ester products. Strong solvent effect was observed for the ruthenium catalyst in modulating the activity and selectivity; the coupling reaction in CH2Cl2 led to the regioselective formation of gem-enol ester products, while the stereoselective formation of (Z)-enol esters was obtained in THF. The coupling reaction was found to be strongly inhibited by PCy3. The coupling reaction of both PhCO2H/PhC≡CD and PhCO2D/PhC≡CH led to the extensive deuterium incorporation on the vinyl positions of the enol ester products. An opposite Hammett value was observed when the correlation of a series of para-substituted p-X-C6H4CO2H (X = OMe, CH3, H, CF3, CN) with phenylacetylene was examined in CDCl3 (ρ = +0.30) and THF (ρ = −0.68). Catalytically relevant Ru-carboxylate and –vinylidene-carboxylate complexes, (PCy3)2(CO)(Cl)Ru(κ2-O2CC6H4-p-OMe) and (PCy3)2(CO)(Cl)RuC(=CHPh)O2CC6H4-p-OMe, were isolated, and the structure of both complexes was completely established by X-ray crystallography. A detailed mechanism of the coupling reaction involving a rate-limiting C-O bond formation step was proposed on the basis of these kinetic and structural studies. The regioselective formation of the gem-enol ester products in CH2Cl2 was rationalized by a direct migratory insertion of the terminal alkyne via a Ru-carboxylate species, whereas the stereoselective formation of (Z)-enol ester products in THF was explained by invoking a Ru-vinylidene species. PMID:20161379

Metal-assisted in situ formation of a tridentate acetylacetone ligand for complexation of fac-Re(CO)3+ for radiopharmaceutical applications.

PubMed

Benny, Paul D; Fugate, Glenn A; Barden, Adam O; Morley, Jennifer E; Silva-Lopez, Elsa; Twamley, Brendan

2008-04-07

Reaction of [NEt4]2[ReBr3(CO)3] with 2,4-pentanedione (acac) yields a complex of the type fac-Re(acac)(OH2)(CO)3 (1) under aqueous conditions. 1 was further reacted with a monodentate ligand (pyridine) to yield a fac-Re(acac)(pyridine)(CO)3 complex (2). Complex 1 was found to react with primary amines to generate a Schiff base (imine) in aqueous solutions. When a mixed-nitrogen donor bidentate ligand, 2-(2-aminoethyl)pyridine, that has different coordination affinities for fac-Re(acac)(OH2)(CO)3 was utilized, a unique tridentate ligand was formed in situ utilizing a metal-assisted Schiff base formation to yield a complex fac-Re(CO)3(3[(2-phenylethyl)imino]-2-pentanone) (3). Tridentate ligand formation was found to occur only with the Re-coordinated acac ligand. Reactions of acac with fac-Re(CO)3Br(2-(2-aminoethyl)pyridine) (4) or a mixture of [NEt4]2[ReBr3(CO)3], acac, and 2-(2-aminoethyl)pyridine did not yield the formation of complex 3 in water.

Simulations of photochemical smog formation in complex urban areas

NASA Astrophysics Data System (ADS)

Muilwijk, C.; Schrijvers, P. J. C.; Wuerz, S.; Kenjereš, S.

2016-12-01

In the present study we numerically investigated the dispersion of photochemical reactive pollutants in complex urban areas by applying an integrated Computational Fluid Dynamics (CFD) and Computational Reaction Dynamics (CRD) approach. To model chemical reactions involved in smog generation, the Generic Reaction Set (GRS) approach is used. The GRS model was selected since it does not require detailed modeling of a large set of reactive components. Smog formation is modeled first in the case of an intensive traffic emission, subjected to low to moderate wind conditions in an idealized two-dimensional street canyon with a building aspect ratio (height/width) of one. It is found that Reactive Organic Components (ROC) play an important role in the chemistry of smog formation. In contrast to the NOx/O3 photochemical steady state model that predicts a depletion of the (ground level) ozone, the GRS model predicts generation of ozone. Secondly, the effect of direct sunlight and shadow within the street canyon on the chemical reaction dynamics is investigated for three characteristic solar angles (morning, midday and afternoon). Large differences of up to one order of magnitude are found in the ozone production for different solar angles. As a proof of concept for real urban areas, the integrated CFD/CRD approach is applied for a real scale (1 × 1 km2) complex urban area (a district of the city of Rotterdam, The Netherlands) with high traffic emissions. The predicted pollutant concentration levels give realistic values that correspond to moderate to heavy smog. It is concluded that the integrated CFD/CRD method with the GRS model of chemical reactions is both accurate and numerically robust, and can be used for modeling of smog formation in complex urban areas.

Formation of multi-stereogenic centers using a catalytic diastereoselective Henry reaction.

PubMed

Arai, Takayoshi; Taneda, Yoshinori; Endo, Yoko

2010-11-14

A diastereoselective Henry reaction of chiral aldehydes with nitroalkanes was developed using a chiral sulfonyldiamine (L1)-CuCl complex. The reaction of (R)-2-phenylpropanal and nitromethane was smoothly catalyzed by the (S,S,S)-L1-CuCl complex to give the adduct with 99/1 syn/anti selectivity in 99% ee. In the reaction of (S)-2-phenylpropanal and nitroethane, the (R,R,R)-L1-CuCl catalyst yielded the expected three contiguous stereogenic centers in a highly syn-selective Henry reaction.

Reactions of guanine with methyl chloride and methyl bromide: O6-methylation versus charge transfer complex formation

NASA Astrophysics Data System (ADS)

Shukla, P. K.; Mishra, P. C.; Suhai, S.

Density functional theory (DFT) at the B3LYP/6-31+G* and B3LYP/AUG-cc-pVDZ levels was employed to study O6-methylation of guanine due to its reactions with methyl chloride and methyl bromide and to obtain explanation as to why the methyl halides cause genotoxicity and possess mutagenic and carcinogenic properties. Geometries of the various isolated species involved in the reactions, reactant complexes (RCs), and product complexes (PCs) were optimized in gas phase. Transition states connecting the reactant complexes with the product complexes were also optimized in gas phase at the same levels of theory. The reactant complexes, product complexes, and transition states were solvated in aqueous media using the polarizable continuum model (PCM) of the self-consistent reaction field theory. Zero-point energy (ZPE) correction to total energy and the corresponding thermal energy correction to enthalpy were made in each case. The reactant complexes of the keto form of guanine with methyl chloride and methyl bromide in water are appreciably more stable than the corresponding complexes involving the enol form of guanine. The nature of binding in the product complexes was found to be of the charge transfer type (O6mG+ · X-, X dbond Cl, Br). Binding of HCl, HBr, and H2O molecules to the PCs obtained with the keto form of guanine did not alter the positions of the halide anions in the PCs, and the charge transfer character of the PCs was also not modified due to this binding. Further, the complexes obtained due to the binding of HCl, HBr, and H2O molecules to the PCs had greater stability than the isolated PCs. The reaction barriers involved in the formation of PCs were found to be quite high (?50 kcal/mol). Mechanisms of genotoxicity, mutagenesis and carcinogenesis caused by the methyl halides appear to involve charge transfer-type complex formation. Thus the mechanisms of these processes involving the methyl halides appear to be quite different from those that involve the other strongly carcinogenic methylating agents.

Completion of biosynthetic pathways for bacteriochlorophyll g in Heliobacterium modesticaldum: The C8-ethylidene group formation.

PubMed

Tsukatani, Yusuke; Yamamoto, Haruki; Mizoguchi, Tadashi; Fujita, Yuichi; Tamiaki, Hitoshi

2013-10-01

Heliobacteria have the simplest photosynthetic apparatus, i.e., a type-I reaction center lacking a peripheral light-harvesting complex. Bacteriochlorophyll (BChl) g molecules are bound to the reaction center complex and work both as special-pair and antenna pigments. The C8-ethylidene group formation for BChl g is the last missing link in biosynthetic pathways for bacterial special-pair pigments, which include BChls a and b as well. Here, we report that chlorophyllide a oxidoreductase (COR) of Heliobacterium modesticaldum catalyzes the C8-ethylidene formation from 8-vinyl-chlorophyllide a, producing bacteriochlorophyllide g, the direct precursor for BChl g without the farnesyl tail. The finding led to plausible biosynthetic pathways for 8(1)-hydroxy-chlorophyll a, a primary electron acceptor from the special pair in heliobacterial reaction centers. Proposed catalytic mechanisms on hydrogenation reaction of the ethylidene synthase-type CORs are also discussed. Copyright © 2013 Elsevier B.V. All rights reserved.

Dianionic Carbon-Bridged Scandium-Copper/Silver Heterobimetallic Complexes: Synthesis, Bonding, and Reactivity.

PubMed

Wang, Chen; Xiang, Li; Yang, Yan; Fang, Jian; Maron, Laurent; Leng, Xuebing; Chen, Yaofeng

2018-04-11

Alkylidene-bridged scandium-copper/silver heterobimetallic complexes were synthesized and structurally characterized. The complexes contain different Sc-C and M-C (M=Cu I , Ag I ) bonds. The reactivity of the scandium-copper heterobimetallic complex was also studied, which reveals that the heterobimetallic complex is a reaction intermediate for the transmetalation of akylidene group from Sc III to Cu I . The scandium-copper heterobimetallic complex also undergoes an addition reaction with CO, resulting in the formation of a new C=C double bond. DFT calculations were used to study the bonding and the subsequent reactivity with CO of the scandium-copper heterobimetallic complex. It clearly demonstrates a cooperative effect between the two metal centers through the formation of a direct Sc⋅⋅⋅Cu interaction that drives the reactivity with CO. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Reactions in 1,1,1-trifluoroacetone triggered by low energy electrons (0-10 eV): from simple bond cleavages to complex unimolecular reactions.

PubMed

Illenberger, Eugen; Meinke, Martina C

2014-08-21

The impact of low energy electrons (0-10 eV) to 1,1,1-trifluoroacetone yields a variety of fragment anions which are formed via dissociative electron attachment (DEA) through three pronounced resonances located at 0.8 eV, near 4 eV, and in the energy range 8-9 eV. The fragment ions arise from different reactions ranging from the direct cleavage of one single or double bond (formation of F(-), CF3(-), O(-), (M-H)(-), and M-F)(-)) to remarkably complex unimolecular reactions associated with substantial geometric and electronic rearrangement in the transitory intermediate (formation of OH(-), FHF(-), (M-HF)(-), CCH(-), and HCCO(-). The ion CCH(-), for example, is formed by an excision of unit from the target molecule through the concerted cleavage of four bonds and recombination to H2O within the neutral component of the reaction.

Cu-free 1,3-dipolar cycloaddition click reactions to form isoxazole linkers in chelating ligands for fac-[M(I)(CO)3]+ centers (M = Re, 99mTc).

PubMed

Bottorff, Shalina C; Kasten, Benjamin B; Stojakovic, Jelena; Moore, Adam L; MacGillivray, Leonard R; Benny, Paul D

2014-02-17

Isoxazole ring formation was examined as a potential Cu-free alternative click reaction to Cu(I)-catalyzed alkyne/azide cycloaddition. The isoxazole reaction was explored at macroscopic and radiotracer concentrations with the fac-[M(I)(CO)3](+) (M = Re, (99m)Tc) core for use as a noncoordinating linker strategy between covalently linked molecules. Two click assembly methods (click, then chelate and chelate, then click) were examined to determine the feasibility of isoxazole ring formation with either alkyne-functionalized tridentate chelates or their respective fac-[M(I)(CO)3](+) complexes with a model nitrile oxide generator. Macroscale experiments, alkyne-functionalized chelates, or Re complexes indicate facile formation of the isoxazole ring. (99m)Tc experiments demonstrate efficient radiolabeling with click, then chelate; however, the chelate, then click approach led to faster product formation, but lower yields compared to the Re analogues.

Reversing the stereoselectivity of the intermolecular Pauson-Khand reaction: formation of endo-fused norbornadiene adducts.

PubMed

Rios, Ramon; Pericàs, Miquel A; Moyano, Albert; Maestro, Miguel A; Mahía, José

2002-04-04

[reaction: see text] An unprecedented endo-selective and regioselective intermolecular Pauson-Khand reaction takes place when heterobimetallic (Mo-Co) complexes derived from N-(2-alkynoyl)oxazolidinones or sultams are heated in the presence of norbornadiene.

Carbon-sulfur bond formation by reductive elimination of gold(iii) thiolates.

PubMed

Currie, Lucy; Rocchigiani, Luca; Hughes, David L; Bochmann, Manfred

2018-05-08

Whereas the reaction of the gold(iii) pincer complex (C^N^C)AuCl with 1-adamantyl thiol (AdSH) in the presence of base affords (C^N^C)AuSAd, the same reaction in the absence of base leads to formation of aryl thioethers as the products of reductive elimination of the Au-C and Au-S ligands (C^N^C = dianion of 2-6-diphenylpyridine or 2-6-diphenylpyrazine). Although high chemical stability is usually taken as a characteristic of pincer complexes, results show that thiols are capable of cleaving one of the pincer Au-C bonds. This reaction is not simply a function of S-H acidity, since no cleavage takes place with other more acidic X-H compounds, such as carbazole, amides, phenols and malonates. The reductive C-S elimination follows a second-order rate law, -d[1a]/dt = k[1a][AdSH]. Reductive elimination is enabled by displacement of the N-donor by thiol; this provides the conformational flexibility necessary for C-S bond formation to occur. Alternatively, reductive C-S bond formation can be induced by reaction of pre-formed thiolates (C^N^C)AuSR with a strong Brønsted acid, followed by addition of SMe2 as base. On the other hand, treatment of (C^N^C)AuR (R = Me, aryl, alkynyl) with thiols under similar conditions leads to selective C-C rather than C-S bond formation. The reaction of (C^N^C)AuSAd with H+ in the absence of a donor ligand affords the thiolato-bridged complex [{(C^N-CH)Au(μ-SAd)}2]2+ which was crystallographically characterised.

Catalytic effects of histidine enantiomers and glycine on the formation of dileucine and dimethionine in the salt-induced peptide formation reaction.

PubMed

Li, Feng; Fitz, Daniel; Fraser, Donald G; Rode, Bernd M

2010-01-01

The salt-induced peptide formation (SIPF) reaction takes place readily under mild reaction conditions and proceeds via a copper complex. Its ease of reaction and the universality for prebiotic scenarios add weights to the arguments in favour of the importance of peptide and proteins in the tug of war with the RNA world hypothesis. In addition, the SIPF reaction has a preference for L-form amino acids in dipeptide formation, casting light on the puzzle of biohomochirality, especially for the amino acids with aliphatic side chains. A detailed investigation on the behaviour of aliphatic leucine in the SIPF reaction is presented in this paper, including the catalytic effects of glycine, L- and D-histidine as well as the stereoselectivity under all the reaction conditions above. The results show a relatively low reactivity and stereoselectivity of leucine in the SIPF reaction, while both glycine and histidine enantiomers remarkably increase the yields of dileucine by factors up to 40. Moreover, a comparative study of the effectiveness of L- and D-histidine in catalysing the formation of dimethionine was also carried out and extends the scope of mutual catalysis by amino acid enantiomers in the SIPF reaction.

Preparation and spectroscopic studies on charge-transfer complexes of 2,2'-bipyridine with picric and chloranilic acids

NASA Astrophysics Data System (ADS)

Teleb, Said M.; Gaballa, Akmal S.

2005-11-01

Charge-transfer (CT) complexes formed on the reaction of 2,2'-bipyridine with some acceptors such as picric acid (HPA) and chloranilic acid (H 2CA) have been studied in CHCl 3 and MeOH at room temperature. Based on elemental analysis and IR spectra of the solid CT complexes along with the photometric titration curves for the reactions, the data obtained indicate the formation of 1:1 charge-transfer complexes [(bpyH)(PA)] and [(bpyH 2)(CA)], respectively. The infrared and 1H NMR spectroscopic data indicate a charge-transfer interaction associated with a proton migration from the acceptor to the donor followed by intramolecular hydrogen bonding. The formation constants ( KC) for the complexes were shown to be dependent on the structure of the electron acceptors used.

Preparation and spectroscopic studies on charge-transfer complexes of 2,2'-bipyridine with picric and chloranilic acids.

PubMed

Teleb, Said M; Gaballa, Akmal S

2005-11-01

Charge-transfer (CT) complexes formed on the reaction of 2,2'-bipyridine with some acceptors such as picric acid (HPA) and chloranilic acid (H(2)CA) have been studied in CHCl(3) and MeOH at room temperature. Based on elemental analysis and IR spectra of the solid CT complexes along with the photometric titration curves for the reactions, the data obtained indicate the formation of 1:1 charge-transfer complexes [(bpyH)(PA)] and [(bpyH(2))(CA)], respectively. The infrared and (1)H NMR spectroscopic data indicate a charge-transfer interaction associated with a proton migration from the acceptor to the donor followed by intramolecular hydrogen bonding. The formation constants (K(C)) for the complexes were shown to be dependent on the structure of the electron acceptors used.

Reactions of a Chromium(III)-Superoxo Complex and Nitric Oxide That Lead to the Formation of Chromium(IV)-Oxo and Chromium(III)-Nitrito Complexes

PubMed Central

Yokoyama, Atsutoshi; Cho, Kyung-Bin

2013-01-01

The reaction of an end-on Cr(III)-superoxo complex bearing a 14-membered tetraazamacrocyclic TMC ligand, [CrIII(14-TMC)(O2)(Cl)]+, with nitric oxide (NO) resulted in the generation of a stable Cr(IV)-oxo species, [CrIV(14-TMC)(O)(Cl)]+, via the formation of a Cr(III)-peroxynitrite intermediate and homolytic O-O bond cleavage of the peroxynitrite ligand. Evidence for the latter comes from EPR spectroscopy, computational chemistry, and the observation of phenol nitration chemistry. The Cr(IV)-oxo complex does not react with nitrogen dioxide (NO2), but reacts with NO to afford a Cr(III)-nitrito complex, [CrIII(14-TMC)(NO2)(Cl)]+. The Cr(IV)-oxo and Cr(III)-nitrito complexes were also characterized spectroscopically and/or structurally. PMID:24066924

Formation of singlet oxygen by decomposition of protein hydroperoxide in photosystem II.

PubMed

Pathak, Vinay; Prasad, Ankush; Pospíšil, Pavel

2017-01-01

Singlet oxygen (1O2) is formed by triplet-triplet energy transfer from triplet chlorophyll to O2 via Type II photosensitization reaction in photosystem II (PSII). Formation of triplet chlorophyll is associated with the change in spin state of the excited electron and recombination of triplet radical pair in the PSII antenna complex and reaction center, respectively. Here, we have provided evidence for the formation of 1O2 by decomposition of protein hydroperoxide in PSII membranes deprived of Mn4O5Ca complex. Protein hydroperoxide is formed by protein oxidation initiated by highly oxidizing chlorophyll cation radical and hydroxyl radical formed by Type I photosensitization reaction. Under highly oxidizing conditions, protein hydroperoxide is oxidized to protein peroxyl radical which either cyclizes to dioxetane or recombines with another protein peroxyl radical to tetroxide. These highly unstable intermediates decompose to triplet carbonyls which transfer energy to O2 forming 1O2. Data presented in this study show for the first time that 1O2 is formed by decomposition of protein hydroperoxide in PSII membranes deprived of Mn4O5Ca complex.

Formation of singlet oxygen by decomposition of protein hydroperoxide in photosystem II

PubMed Central

Pathak, Vinay; Prasad, Ankush

2017-01-01

Singlet oxygen (1O2) is formed by triplet-triplet energy transfer from triplet chlorophyll to O2 via Type II photosensitization reaction in photosystem II (PSII). Formation of triplet chlorophyll is associated with the change in spin state of the excited electron and recombination of triplet radical pair in the PSII antenna complex and reaction center, respectively. Here, we have provided evidence for the formation of 1O2 by decomposition of protein hydroperoxide in PSII membranes deprived of Mn4O5Ca complex. Protein hydroperoxide is formed by protein oxidation initiated by highly oxidizing chlorophyll cation radical and hydroxyl radical formed by Type I photosensitization reaction. Under highly oxidizing conditions, protein hydroperoxide is oxidized to protein peroxyl radical which either cyclizes to dioxetane or recombines with another protein peroxyl radical to tetroxide. These highly unstable intermediates decompose to triplet carbonyls which transfer energy to O2 forming 1O2. Data presented in this study show for the first time that 1O2 is formed by decomposition of protein hydroperoxide in PSII membranes deprived of Mn4O5Ca complex. PMID:28732060

Preparation, characterization, and thermal stability of β-cyclodextrin/soybean lecithin inclusion complex.

PubMed

Wang, Xinge; Luo, Zhigang; Xiao, Zhigang

2014-01-30

β-Cyclodextrin (β-CD), which is widely used to increase the stability, solubility, and bioavailability of guests, can form host-guest inclusion complexes with a wide variety of organic molecules. In this study the β-CD/soybean lecithin inclusion complex was prepared. The effect of reaction parameters such as reaction temperature, reaction time and the molar ratio of β-CD/soybean lecithin on inclusion ratio were studied. The inclusion ratio of the product prepared under the optimal conditions of β-CD/soybean lecithin molar ratio 2:1, reaction temperature 60°C reaction time 2h was 40.2%. The results of UV-vis, DSC, XRD and FT-IR spectrum indicated the formation of inclusion complex. The thermal stability experiment indicated that the thermal stability of soybean lecithin in inclusion complex was significantly improved compared with free soybean lecithin. Copyright © 2013 Elsevier Ltd. All rights reserved.

Formation of hydroxyl radicals and Co3+ in the reaction of Co(2+)-EDTA with hydrogen peroxide. Catalytic effect of Fe3+.

PubMed

Eberhardt, M K; Santos, C; Soto, M A

1993-05-07

Co2+ ions (Co(NO3)2.6H2O) react with H2O2 only in presence of EDTA to yield OH radicals and Co3+. This reaction was carried out in unbuffered aqueous solutions (pH = 2.6). The formation of Co3+ was confirmed by spectroscopy. The Co(3+)-EDTA complex shows two typical absorptions at 382 nm and 532 nm. The Co(3+)-EDTA complex can be prepared by a number of oxidizing agents, like Fe3+, Fe(3+)-EDTA, Ag+, Ag2+, Ce4+, and hydroxyl radicals. Since Fe3+ oxidizes Co(2+)-EDTA to Co(3+)-EDTA and Fe2+ we initiate a chain reaction for .OH formation. Our results show that there are two modes for H2O2 decomposition: (1) One electron transfer to give OH radicals and (2) Decomposition of H2O2 to H2O and O2 without intermediate .OH formation. This reaction depends strongly on the pH of the buffer. The H2O2 decomposition increases with increasing pH and increasing Co2+ concentration.

Electron transfer reactions of excited dyes with metal complexes. Progress report, May 1, 1976--January 31, 1977. [Fe(III)--thionine reaction

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

Lichtin, N.N.

1977-02-01

A study was initiated of the factors which determine quantum efficiency of transfer of reducing equivalents between excited dye molecules and metal complexes in their ground state and composition and dynamics of formation and decay of related photostationary states. A ruby laser capable of delivering a 3.6 J, 19 nsec flash was acquired and assembly of an apparatus for laser flash photolysis begun. At the same time, conventional flash photolysis was used to pursue investigation of the dependence upon solvent, anions, pH, and ionic strength of the kinetics of the spontaneous dark reaction of Fe(H/sub 2/O)/sup 3 +//sub 6/ withmore » leucothionine and with semithionine, reactions which contribute to the composition and dynamics of formation and decay of the photostationary state of the iron-thionine photoredox reaction. Results are consistent with formation of an intermediate complex between leucothionine and Fe(III), K/sub A/ = 380 M/sup -1/ and k(elec. transfer) = 0.88 s/sup -1/ at approximately 22/sup 0/ in water solution at pH2, with sulfate as anion and ..mu.. = .05 - .1 M. Under similar conditions in 50 v/v percent aqueous CH/sub 3/CN, K/sub A/ = 780 M/sup -1/, k(elec. transfer) = 0.55 s/sup -1/. In both solvents, sulfate produces a large positive salt effect. Intermediacy of a complex was not established for the faster reaction of Fe(III) with semithionine under similar conditions: K/sub A/ . k(elec. transfer) approximately 3.5 x 10/sup 5/ M/sup -1/s/sup -1/ in H/sub 2/O, approximately 1.0 x 10/sup 4/ in 50 v/v percent aqueous CH/sub 3/CN.« less

Influence of the composition of aqueous dimethylsulfoxide solvent on thermodynamics of complexing between 18-crown-6-ether and D,L-alanine

NASA Astrophysics Data System (ADS)

Usacheva, T. R.; Kuzmina, I. A.; Sharnin, V. A.; Chernov, I. V.; Matteoli, E.

2012-07-01

Standard thermodynamic parameters (log K o, Δr H o, TΔr S o) of complexing 18-crown-6 ether (18C6) with D,L-alanine (Ala) in mixed water-dimethysulfoxide (H2O-DMSO) solvents are calculated on the basis of calorimetric titration results. A rise in the DMSO concentration in mixed solvent is found to increase stability and increase the exothermicity of the formation of [Ala-18C6] molecular complex. Changes in the reaction energetic are shown to be determined by changes in the solvation state of 18C6 that is the characteristic of the reactions of molecular complex formation between 18C6 and D,L-alanine or glycine in water-organic solvents.

The Determination of Molecular Quantities from Measurements on Macroscopic Systems.V. Existence and Properties of 1:1 and 2:1-Electron-Donor-Acceptor Complexes of Hexamethylbenzene with Tetracyanoethylene

NASA Astrophysics Data System (ADS)

Liptay, Wolfgang; Rehm, Torsten; Wehning, Detlev; Schanne, Lothar; Baumann, Wolfram; Lang, Werner

1982-12-01

The formation of electron-donor-acceptor complexes of hexamethylbenzene (HMB) with tetracyanoethylene (TCNE) was investigated by measurements of the optical absorptions, the densities, the permittivities and the electro-optical absorptions of solutions in CCl4. The careful evaluation of data based on some previously reported models, has shown that the assumption of the formation of the 1: 1 and the 2 : 1 complex agrees with all experimental data, but that the assumption of the formation of only the 1: 1 complex is contradictory to experimental facts even if the activity effects on the equilibrium constant and of the solvent dependences of observed molar quantities are taken into account. The evaluation leads to the molar optical absorption coefficients and the molar volumes of both complexes and to their electric dipole moments in the electronic ground state and the considered excited state. According to these results the complexes are of the sandwich type HMB-TCNE and HMB-TCNE-HMB. In spite of the fact that the 2: 1 complex owns a center of symmetry, at least approximately, there is a rather large electric dipole moment in its excited state. Furthermore, values for the equilibrium constants and for the standard reaction enthalpies of both complex formation reactions are estimated from experimental data.

Hydrogen-bond formation between isoindolo[2,1-a]indol-6-one and aliphatic alcohols in n-hexane.

PubMed

Demeter, Attila; Bérces, Tibor

2005-03-17

The spectroscopic, kinetic, and equilibrium properties of isoindolo[2,1-a]indol-6-one (I) were studied in n-hexane in the presence and absence of alcohols (X). Hydrogen-bonded-complex formation was found to occur between the alcohol and the ground state as well as the excited state of the I molecule. The spectra of I and its singly complexed derivative (IX) are similar; however, that of IX is red shifted. The extent of red shift increases with the hydrogen-bonding ability of the alcohol. Equilibrium constant measurements were made to determine the hydrogen-bond basicity (beta(2)(H)) for I and the singlet excited (1)I. The beta(2)(H) value for (1)I is found to be about twice that of the ground-state I. Time-resolved fluorescence decay measurements indicate that the reaction of singlet excited I with fluorinated alcohols is diffusion controlled, while the rate of complexation with nonfluorinated (weaker hydrogen bonding) aliphatic alcohols depends on the Gibbs energy change in the complexation reaction. The quantitative correlation between the rate coefficient of complexation of (1)I with alcohols and the Gibbs energy change in the complexation process allowed us to estimate the rate coefficient for the complexation of the ground-state I with alcohols. The formation of the singlet excited hydrogen-bonded complex is irreversible; (1)IX disappears in a first order and an alcohol induced second order reaction. The first order decay is predominantly due to internal conversion to the ground state, the rate of which depends on the ionization energy of the complexing alcohol.

Sunlight assisted direct amide formation via a charge-transfer complex.

PubMed

Cohen, Irit; Mishra, Abhaya K; Parvari, Galit; Edrei, Rachel; Dantus, Mauricio; Eichen, Yoav; Szpilman, Alex M

2017-09-12

We report on the use of charge-transfer complexes between amines and carbon tetrachloride, as a novel way to activate the amine for photochemical reactions. This principle is demonstrated in a mild, transition metal free, visible light assisted, dealkylative amide formation from feedstock carboxylic acids and amines. The low absorption coefficient of the complex allows deep light penetration and thus scale up to a gram scale.

Efficient surface formation route of interstellar hydroxylamine through NO hydrogenation. II. The multilayer regime in interstellar relevant ices

NASA Astrophysics Data System (ADS)

Fedoseev, G.; Ioppolo, S.; Lamberts, T.; Zhen, J. F.; Cuppen, H. M.; Linnartz, H.

2012-08-01

Hydroxylamine (NH2OH) is one of the potential precursors of complex pre-biotic species in space. Here, we present a detailed experimental study of hydroxylamine formation through nitric oxide (NO) surface hydrogenation for astronomically relevant conditions. The aim of this work is to investigate hydroxylamine formation efficiencies in polar (water-rich) and non-polar (carbon monoxide-rich) interstellar ice analogues. A complex reaction network involving both final (N2O, NH2OH) and intermediate (HNO, NH2O., etc.) products is discussed. The main conclusion is that hydroxyl-amine formation takes place via a fast and barrierless mechanism and it is found to be even more abundantly formed in a water-rich environment at lower temperatures. In parallel, we experimentally verify the non-formation of hydroxylamine upon UV photolysis of NO ice at cryogenic temperatures as well as the non-detection of NC- and NCO-bond bearing species after UV processing of NO in carbon monoxide-rich ices. Our results are implemented into an astrochemical reaction model, which shows that NH2OH is abundant in the solid phase under dark molecular cloud conditions. Once NH2OH desorbs from the ice grains, it becomes available to form more complex species (e.g., glycine and β-alanine) in gas phase reaction schemes.

Coordination properties of tridentate (N,O,O) heterocyclic alcohol (PDC) with Cu(II). Mixed ligand complex formation reactions of Cu(II) with PDC and some bio-relevant ligands.

PubMed

El-Sherif, Ahmed A; Shoukry, Mohamed M

2007-03-01

The formation equilibria of copper(II) complexes and the ternary complexes Cu(PDC)L (PDC=2,6-bis-(hydroxymethyl)-pyridine, HL=amino acid, amides or DNA constituents) have been investigated. Ternary complexes are formed by a simultaneous mechanism. The results showed the formation of Cu(PDC)L, Cu(PDC, H(-1))(L) and Cu(PDC, H(-2))(L) complexes. The concentration distribution of the complexes in solution is evaluated as a function of pH. The effect of dioxane as a solvent on the protonation constant of PDC and the formation constants of Cu(II) complexes are discussed. The thermodynamic parameters DeltaH degrees and DeltaS degrees calculated from the temperature dependence of the equilibrium constants are investigated.

Antibody-mediated cofactor-driven reactions

DOEpatents

Schultz, Peter G.

1993-01-01

Chemical reactions capable of being rate-enhanced by auxiliary species which interact with the reactants but do not become chemically bound to them in the formation of the final product are performed in the presence of antibodies which promote the reactions. The antibodies contain regions within their antigen binding sites which recognize the auxiliary species in a conformation which promotes the reaction. The antigen binding site frequently recognizes a particular transition state complex or other high energy complex along the reaction coordinate, thereby promoting the progress of the reaction along the desired route as opposed to other less favorable routes. Various classes of reaction together with appropriate antigen binding site specificities tailored for each are disclosed.

Monitoring chemical reactions by low-field benchtop NMR at 45 MHz: pros and cons.

PubMed

Silva Elipe, Maria Victoria; Milburn, Robert R

2016-06-01

Monitoring chemical reactions is the key to controlling chemical processes where NMR can provide support. High-field NMR gives detailed structural information on chemical compounds and reactions; however, it is expensive and complex to operate. Conversely, low-field NMR instruments are simple and relatively inexpensive alternatives. While low-field NMR does not provide the detailed information as the high-field instruments as a result of their smaller chemical shift dispersion and the complex secondary coupling, it remains of practical value as a process analytical technology (PAT) tool and is complimentary to other established methods, such as ReactIR and Raman spectroscopy. We have tested a picoSpin-45 (currently under ThermoFisher Scientific) benchtop NMR instrument to monitor three types of reactions by 1D (1) H NMR: a Fischer esterification, a Suzuki cross-coupling, and the formation of an oxime. The Fischer esterification is a relatively simple reaction run at high concentration and served as proof of concept. The Suzuki coupling is an example of a more complex, commonly used reaction involving overlapping signals. Finally, the oxime formation involved a reaction in two phases that cannot be monitored by other PAT tools. Here, we discuss the pros and cons of monitoring these reactions at a low-field of 45 MHz by 1D (1) H NMR. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Selective Conversion of CO2 into Isocyanate by Low-Coordinate Iron Complexes.

PubMed

Broere, Daniël L J; Mercado, Brandon Q; Holland, Patrick L

2018-04-06

Discovery of the mechanisms for selective transformations of CO 2 into organic compounds is a challenge. Herein, we describe the reaction of low-coordinate Fe silylamide complexes with CO 2 to give trimethylsilyl isocyanate and the corresponding Fe siloxide complex. Kinetic studies show that this is a two-stage reaction, and the presence of a single equivalent of THF influences the rates of both steps. Isolation of a thermally unstable intermediate provides mechanistic insight that explains both the effect of THF in this reaction, and the way in which the reaction achieves high selectivity for isocyanate formation. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Thermodynamics of formation for the 18-crown-6-triglycine molecular complex in water-dimethylsulfoxide solvents

NASA Astrophysics Data System (ADS)

Usacheva, T. R.; Lan, Pham Thi; Sharnin, V. A.

2014-06-01

The effect of a water-dimethylsulfoxide (DMSO) solvent on the formation of a molecular complex of 18-crown-6 (18C6) with triglycine (diglycylglycine, 3Gly) is studied via calorimetric titration. It is found that switching from water to an H2O-DMSO mixture with DMSO mole fraction of 0.30 is accompanied by a monotonic increase in the stability of [3Gly18C6] complex, from log K ∘ = 1.10 to log K ∘ = 2.44, and an increase in the exothermicity of the reaction of its formation, from -5.9 to -16.9 kJ/mol. It is shown that the [3Gly18C6] complex exhibits enthalpy stabilization with negative values of enthalpy and entropy over the investigated range of H2O-DMSO solvents. Analysis of the reagents' solvation characteristics reveals that the increase in the reaction's exothermicity of transfer is due to differences in the solvation of [3Gly18C6] and 18C6 with a small solvation contribution from 3Gly. It is concluded that the change in the Gibbs energy of the reaction 3Glysolv + 18C6solv ↔ [3Gly18C6]solv is due to differences in the change in the solvation state of the complex and the peptide (Δtr G ∘([3Gly18C6])-Δtr G ∘(3Gly)).

Determination of equilibrium and rate constants for complex formation by fluorescence correlation spectroscopy supplemented by dynamic light scattering and Taylor dispersion analysis.

PubMed

Zhang, Xuzhu; Poniewierski, Andrzej; Jelińska, Aldona; Zagożdżon, Anna; Wisniewska, Agnieszka; Hou, Sen; Hołyst, Robert

2016-10-04

The equilibrium and rate constants of molecular complex formation are of great interest both in the field of chemistry and biology. Here, we use fluorescence correlation spectroscopy (FCS), supplemented by dynamic light scattering (DLS) and Taylor dispersion analysis (TDA), to study the complex formation in model systems of dye-micelle interactions. In our case, dyes rhodamine 110 and ATTO-488 interact with three differently charged surfactant micelles: octaethylene glycol monododecyl ether C 12 E 8 (neutral), cetyltrimethylammonium chloride CTAC (positive) and sodium dodecyl sulfate SDS (negative). To determine the rate constants for the dye-micelle complex formation we fit the experimental data obtained by FCS with a new form of the autocorrelation function, derived in the accompanying paper. Our results show that the association rate constants for the model systems are roughly two orders of magnitude smaller than those in the case of the diffusion-controlled limit. Because the complex stability is determined by the dissociation rate constant, a two-step reaction mechanism, including the diffusion-controlled and reaction-controlled rates, is used to explain the dye-micelle interaction. In the limit of fast reaction, we apply FCS to determine the equilibrium constant from the effective diffusion coefficient of the fluorescent components. Depending on the value of the equilibrium constant, we distinguish three types of interaction in the studied systems: weak, intermediate and strong. The values of the equilibrium constant obtained from the FCS and TDA experiments are very close to each other, which supports the theoretical model used to interpret the FCS data.

O2-Promoted Allylic Acetoxylation of Alkenes: Assessment of "Push" vs. "Pull" Mechanisms and Comparison between O2 and Benzoquinone.

PubMed

Diao, Tianning; Stahl, Shannon S

2014-12-14

Palladium-catalyzed acetoxylation of allylic C-H bonds has been the subject of extensive study. These reactions proceed via allyl-palladium(II) intermediates that react with acetate to afford the allyl acetate product. Benzoquinone and molecular oxygen are two common oxidants for these reactions. Benzoquinone has been shown to promote allyl acetate formation from well-defined π-allyl palladium(II) complexes. Here, we assess the ability of O 2 to promote similar reactions with a series of "unligated" π-allyl palladium(II) complexes (i.e., in the absence of ancillary phosphorus, nitrogen or related donor ligands). Stoichiometric and catalytic allyl acetate formation is observed under aerobic conditions with several different alkenes. Mechanistic studies are most consistent with a "pull" mechanism in which O 2 traps the Pd 0 intermediate following reversible C-O bond-formation from an allyl-palladium(II) species. A "push" mechanism, involving oxidatively induced C-O bond formation, does not appear to participate. These results and conclusions are compared with benzoquinone-promoted allylic acetoxylation, in which a "push" mechanism seems to be operative.

Synthesis, spectral and thermal studies of the newly hydrogen bonded charge transfer complex of o-phenylenediamine with π acceptor picric acid

NASA Astrophysics Data System (ADS)

Khan, Ishaat M.; Ahmad, Afaq

2010-10-01

Newly proton or charge transfer complex [(OPDH) +(PA) -] was synthesized by the reaction of the donor, o-phenylenediamine (OPD) with acceptor, 2,4,6-trinitrophenol (PAH). The chemical reaction has occurred via strong hydrogen bonding followed by migration of proton from acceptor to donor. UV-vis, 1H NMR and FTIR spectra, in addition to the thermal and elemental analysis were used to confirm the proposed occurrence of the chemical reaction and to investigate the newly synthesized solid CT complex. The stoichiometry of the CT complex was found to be 1:1. The formation constant and molar extinction coefficient of the CT complex were evaluated by the Benesi-Hildebrand equation.

A study on an unusual SN2 mechanism in the methylation of benzyne through nickel-complexation.

PubMed

Hatakeyama, Makoto; Sakamoto, Yuki; Ogata, Koji; Sumida, Yuto; Sumida, Tomoe; Hosoya, Takamitsu; Nakamura, Shinichiro

2017-10-11

In this study, three reaction mechanisms of a benzyne-nickel (Ni) complex ([Ni(C 6 H 4 )(dcpe)]) with iodomethane during the methylation process were investigated, namely (a) S N 2 reaction of the benzyne-Ni complex with iodomethane, (b) concerted σ-bond metathesis during the bond breaking/forming processes, and (c) oxidative addition of iodomethane to the Ni-center and the subsequent reductive elimination process. DFT calculations revealed that the reaction barrier of the S N 2 reaction is slightly lower than those of the other mechanisms. The results of orbital analyses suggest that [Ni(C 6 H 4 )(dcpe)] forms a metallacycle structure between benzyne and the Ni II (3d 8 ) center instead of the η 2 -structure with the Ni 0 (3d 10 ) center. The metallacycle structures became inappropriate as the intermediates of oxidative addition in the formation of the Ni II -Me bond, avoiding further oxidation to the high-valent Ni IV . The high free energy along σ-bond metathesis was generated from the steric hindrance, thus invoking methylation and Ni-I bond formation concertedly.

Unfolding and Targeting Thermodynamics of a DNA Intramolecular Complex with Joined Triplex-Duplex Domains.

PubMed

Johnson, Sarah E; Reiling-Steffensmeier, Calliste; Lee, Hui-Ting; Marky, Luis A

2018-01-25

Our laboratory is interested in developing methods that can be used for the control of gene expression. In this work, we are investigating the reaction of an intramolecular complex containing a triplex-duplex junction with partially complementary strands. We used a combination of isothermal titration calorimetry (ITC), differential scanning calorimetry (DSC), and spectroscopy techniques to determine standard thermodynamic profiles for these targeting reactions. Specifically, we have designed single strands to target one loop (CTTTC) or two loops (CTTTC and GCAA) of this complex. Both reactions yielded exothermic enthalpies of -66.3 and -82.8 kcal/mol by ITC, in excellent agreement with the reaction enthalpies of -72.7 and -88.7 kcal/mol, respectively, obtained from DSC Hess cycles. The favorable heat contributions result from the formation of base-pair stacks involving mainly the unpaired bases of the loops. This shows that each complementary strand is able to invade and disrupt the secondary structure. The simultaneous targeting of two loops yielded a more favorable reaction free energy, by approximately -8 kcal/mol, which corresponds to the formation of roughly four base-pair stacks involving the unpaired bases of the 5'-GCAA loop. The main conclusion is that the targeting of loops with a large number of unpaired bases results in a more favorable reaction free energy.

A new metalation complex for organic synthesis and polymerization reactions

NASA Technical Reports Server (NTRS)

Hirshfield, S. M.

1971-01-01

Organometallic complex of N,N,N',N' tetramethyl ethylene diamine /TMEDA/ and lithium acts as metalation intermediate for controlled systhesis of aromatic organic compounds and polymer formation. Complex of TMEDA and lithium aids in preparation of various organic lithium compounds.

Structure and stability of hexa-aqua V(III) cations in vanadium redox flow battery electrolytes.

PubMed

Vijayakumar, M; Li, Liyu; Nie, Zimin; Yang, Zhenguo; Hu, JianZhi

2012-08-07

The vanadium(III) cation structure in mixed acid based electrolyte solution from vanadium redox flow batteries is studied by (17)O and (35/37)Cl nuclear magnetic resonance (NMR) spectroscopy, electronic spectroscopy and density functional theory (DFT) based computational modelling. Both computational and experimental results reveal that the V(III) species can complex with counter anions (sulfate/chlorine) depending on the composition of its solvation sphere. By analyzing the powder precipitate it was found that the formation of sulfate complexed V(III) species is the crucial process in the precipitation reaction. The precipitation occurs through nucleation of neutral species formed through deprotonation and ion-pair formation process. However, the powder precipitate shows a multiphase nature which warrants multiple reaction pathways for precipitation reaction.

An unexpected semi-hydrogenation of a ligand in the complexation of 2,7-bispyridinyl-1,8-naphthyridine with Ru3(CO)12.

PubMed

Liao, Bei-Sih; Liu, Yi-Hung; Peng, Shie-Ming; Reddy, K Rajender; Liu, Shin-Hung; Chou, Pi-Tai; Liu, Shiuh-Tzung

2014-03-07

Thermal reaction of 2,7-bis(2-pyridinyl)-l,8-naphthyridine () with Ru3(CO)12 in the presence of moisture resulted in the formation of a formate-bridged diruthenium complex [(-H3)Ru2(μ-HCOO)(CO)4] (), in which the ligand was partially hydrogenated. Complex was fully characterized by spectroscopic analyses and X-ray single crystal determination. Regarding the partially reduced ligand in , it occurs through a water-gas shift type reduction. The bridging formate ligand can be substituted by other carboxylate ligands. Physical and chemical properties of the newly prepared complexes were investigated.

Detection of Maillard reaction products by a coupled HPLC-Fraction collector technique and FTIR characterization of Cu(II)-complexation with the isolated species

NASA Astrophysics Data System (ADS)

Ioannou, Aristos; Daskalakis, Vangelis; Varotsis, Constantinos

2017-08-01

The isolation of reaction products of asparagine with reducing sugars at alkaline pH and high temperature has been probed by a combination of high performance liquid chromatography (HPLC) coupled with a Fraction Collector. The UV-vis and FTIR spectra of the isolated Maillard reaction products showed structure-sensitive changes as depicted by deamination events and formation of asparagine-saccharide conjugates. The initial reaction species of the Asn-Gluc reaction were also characterized by Density Functional Theory (DFT) methods. Evidence for Cu (II) metal ion complexation with the Maillard reaction products is supported by UV-vis and FTIR spectroscopy.

Equilibrium Thermodynamics, Formation, and Dissociation Kinetics of Trivalent Iron and Gallium Complexes of Triazacyclononane-Triphosphinate (TRAP) Chelators: Unraveling the Foundations of Highly Selective Ga-68 Labeling.

PubMed

Vágner, Adrienn; Forgács, Attila; Brücher, Ernő; Tóth, Imre; Maiocchi, Alessandro; Wurzer, Alexander; Wester, Hans-Jürgen; Notni, Johannes; Baranyai, Zsolt

2018-01-01

In order to rationalize the influence of Fe III contamination on labeling with the 68 Ga eluted from 68 Ge/ 68 Ga- g enerator, a detailed investigation was carried out on the equilibrium properties, formation and dissociation kinetics of Ga III - and Fe III -complexes of 1,4,7-triazacyclononane-1,4,7-tris(methylene[2-carboxyethylphosphinic acid]) (H 6 TRAP). The stability and protonation constants of the [Fe(TRAP)] 3- complex were determined by pH-potentiometry and spectrophotometry by following the competition reaction between the TRAP ligand and benzhydroxamic acid (0.15 M NaNO 3 , 25°C). The formation rates of [Fe(TRAP)] and [Ga(TRAP)] complexes were determined by spectrophotometry and 31 P-NMR spectroscopy in the pH range 4.5-6.5 in the presence of 5-40 fold H x TRAP (x-6) excess (x = 1 and 2, 0.15 M NaNO 3 , 25°C). The kinetic inertness of [Fe(TRAP)] 3- and [Ga(TRAP)] 3- was examined by the trans-chelation reactions with 10 to 20-fold excess of H x HBED (x-4) ligand by spectrophotometry at 25°C in 0.15 M NaCl (x = 0,1 and 2). The stability constant of [Fe(TRAP)] 3- (log K FeL = 26.7) is very similar to that of [Ga(TRAP)] 3- (log K GaL = 26.2). The rates of ligand exchange reaction of [Fe(TRAP)] 3- and [Ga(TRAP)] 3- with H x HBED (x-4) are similar. The reactions take place quite slowly via spontaneous dissociation of [M(TRAP)] 3- , [M(TRAP)OH] 4- and [M(TRAP)(OH) 2 ] 5- species. Dissociation half-lives ( t 1/2 ) of [Fe(TRAP)] 3- and [Ga(TRAP)] 3- complexes are 1.1 × 10 5 and 1.4 × 10 5 h at pH = 7.4 and 25°C. The formation reactions of [Fe(TRAP)] 3- and [Ga(TRAP)] 3- are also slow due to the formation of the unusually stable monoprotonated [ * M(HTRAP)] 2- intermediates [ * log K Ga(HL) = 10.4 and * log K Fe(HL) = 9.9], which are much more stable than the [ * Ga(HNOTA)] + intermediate [ * log K Ga(HL) = 4.2]. Deprotonation and transformation of the monoprotonated [ * M(HTRAP)] 2- intermediates into the final complex occur via OH - -assisted reactions. Rate constants ( k OH ) characterizing the OH - -driven deprotonation and transformation of [ * Ga(HTRAP)] 2- and [ * Fe(HTRAP)] 2- intermediates are 1.4 × 10 5 M -1 s -1 and 3.4 × 10 4 M -1 s -1 , respectively. In conclusion, the equilibrium and kinetic properties of [Fe(TRAP)] and [Ga(TRAP)] complexes are remarkably similar due to the close physico-chemical properties of Fe III and Ga III -ions. However, a slightly faster formation of [Ga(TRAP)] over [Fe(TRAP)] provides a rationale for a previously observed, selective complexation of 68 Ga III in presence of excess Fe III .

Equilibrium Thermodynamics, Formation, and Dissociation Kinetics of Trivalent Iron and Gallium Complexes of Triazacyclononane-Triphosphinate (TRAP) Chelators: Unraveling the Foundations of Highly Selective Ga-68 Labeling

PubMed Central

Vágner, Adrienn; Forgács, Attila; Brücher, Ernő; Tóth, Imre; Maiocchi, Alessandro; Wurzer, Alexander; Wester, Hans-Jürgen; Notni, Johannes; Baranyai, Zsolt

2018-01-01

In order to rationalize the influence of FeIII contamination on labeling with the 68Ga eluted from 68Ge/68Ga-generator, a detailed investigation was carried out on the equilibrium properties, formation and dissociation kinetics of GaIII- and FeIII-complexes of 1,4,7-triazacyclononane-1,4,7-tris(methylene[2-carboxyethylphosphinic acid]) (H6TRAP). The stability and protonation constants of the [Fe(TRAP)]3− complex were determined by pH-potentiometry and spectrophotometry by following the competition reaction between the TRAP ligand and benzhydroxamic acid (0.15 M NaNO3, 25°C). The formation rates of [Fe(TRAP)] and [Ga(TRAP)] complexes were determined by spectrophotometry and 31P-NMR spectroscopy in the pH range 4.5–6.5 in the presence of 5–40 fold HxTRAP(x−6) excess (x = 1 and 2, 0.15 M NaNO3, 25°C). The kinetic inertness of [Fe(TRAP)]3− and [Ga(TRAP)]3− was examined by the trans-chelation reactions with 10 to 20-fold excess of HxHBED(x−4) ligand by spectrophotometry at 25°C in 0.15 M NaCl (x = 0,1 and 2). The stability constant of [Fe(TRAP)]3− (logKFeL = 26.7) is very similar to that of [Ga(TRAP)]3− (logKGaL = 26.2). The rates of ligand exchange reaction of [Fe(TRAP)]3− and [Ga(TRAP)]3− with HxHBED(x−4) are similar. The reactions take place quite slowly via spontaneous dissociation of [M(TRAP)]3−, [M(TRAP)OH]4− and [M(TRAP)(OH)2]5− species. Dissociation half-lives (t1/2) of [Fe(TRAP)]3− and [Ga(TRAP)]3− complexes are 1.1 × 105 and 1.4 × 105 h at pH = 7.4 and 25°C. The formation reactions of [Fe(TRAP)]3− and [Ga(TRAP)]3− are also slow due to the formation of the unusually stable monoprotonated [*M(HTRAP)]2− intermediates [*logKGa(HL) = 10.4 and *logKFe(HL) = 9.9], which are much more stable than the [*Ga(HNOTA)]+ intermediate [*logKGa(HL) = 4.2]. Deprotonation and transformation of the monoprotonated [*M(HTRAP)]2− intermediates into the final complex occur via OH−-assisted reactions. Rate constants (kOH) characterizing the OH−-driven deprotonation and transformation of [* Ga(HTRAP)]2− and [*Fe(HTRAP)]2− intermediates are 1.4 × 105 M−1s−1 and 3.4 × 104 M−1s−1, respectively. In conclusion, the equilibrium and kinetic properties of [Fe(TRAP)] and [Ga(TRAP)] complexes are remarkably similar due to the close physico-chemical properties of FeIII and GaIII-ions. However, a slightly faster formation of [Ga(TRAP)] over [Fe(TRAP)] provides a rationale for a previously observed, selective complexation of 68GaIII in presence of excess FeIII. PMID:29876344

Spectrophotometric Determination of Iron(III)-Glycine Formation Constant in Aqueous Medium Using Competitive Ligand Binding

ERIC Educational Resources Information Center

Prasad, Rajendra; Prasad, Surendra

2009-01-01

The formation constant of iron(III) complex with glycine (Gly) ligand in aqueous acidic medium (0.2 M HNO[subscript 3], I = 0.2 M at 28 plus or minus 1 degree C) was determined spectrophotometrically in which a competing color reaction between Fe(III) and SCN[superscript -] was used as an indicator reaction. Under the specified conditions Fe(III)…

Formation of complex organic molecules in cold objects: the role of gas-phase reactions

NASA Astrophysics Data System (ADS)

Balucani, Nadia; Ceccarelli, Cecilia; Taquet, Vianney

2015-04-01

While astrochemical models are successful in reproducing many of the observed interstellar species, they have been struggling to explain the observed abundances of complex organic molecules. Current models tend to privilege grain surface over gas-phase chemistry in their formation. One key assumption of those models is that radicals trapped in the grain mantles gain mobility and react on lukewarm ( ≳ 30 K) dust grains. Thus, the recent detections of methyl formate (MF) and dimethyl ether (DME) in cold objects represent a challenge and may clarify the respective role of grain-surface and gas-phase chemistry. We propose here a new model to form DME and MF with gas-phase reactions in cold environments, where DME is the precursor of MF via an efficient reaction overlooked by previous models. Furthermore, methoxy, a precursor of DME, is also synthesized in the gas phase from methanol, which is desorbed by a non-thermal process from the ices. Our new model reproduces fairly well the observations towards L1544. It also explains, in a natural way, the observed correlation between DME and MF. We conclude that gas-phase reactions are major actors in the formation of MF, DME and methoxy in cold gas. This challenges the exclusive role of grain-surface chemistry and favours a combined grain-gas chemistry.

Students' Understanding of Acid, Base and Salt Reactions in Qualitative Analysis.

ERIC Educational Resources Information Center

Tan, Kim-Chwee Daniel; Goh, Ngoh-Khang; Chia, Lian-Sai; Treagust, David F.

2003-01-01

Uses a two-tier, multiple-choice diagnostic instrument to determine (n=915) grade 10 students' understanding of the acid, base, and salt reactions involved in basic qualitative analysis. Reports that many students did not understand the formation of precipitates and the complex salts, acid/salt-base reactions, and thermal decomposition involved in…

Thermochemistry of Alane Complexes for Hydrogen Storage: A Theoretical and Experimental Investigation

PubMed Central

2011-01-01

Knowledge of the relative stabilities of alane (AlH3) complexes with electron donors is essential for identifying hydrogen storage materials for vehicular applications that can be regenerated by off-board methods; however, almost no thermodynamic data are available to make this assessment. To fill this gap, we employed the G4(MP2) method to determine heats of formation, entropies, and Gibbs free energies of formation for 38 alane complexes with NH3−nRn (R = Me, Et; n = 0−3), pyridine, pyrazine, triethylenediamine (TEDA), quinuclidine, OH2−nRn (R = Me, Et; n = 0−2), dioxane, and tetrahydrofuran (THF). Monomer, bis, and selected dimer complex geometries were considered. Using these data, we computed the thermodynamics of the key formation and dehydrogenation reactions that would occur during hydrogen delivery and alane regeneration, from which trends in complex stability were identified. These predictions were tested by synthesizing six amine−alane complexes involving trimethylamine, triethylamine, dimethylethylamine, TEDA, quinuclidine, and hexamine and obtaining upper limits of ΔG° for their formation from metallic aluminum. Combining these computational and experimental results, we establish a criterion for complex stability relevant to hydrogen storage that can be used to assess potential ligands prior to attempting synthesis of the alane complex. On the basis of this, we conclude that only a subset of the tertiary amine complexes considered and none of the ether complexes can be successfully formed by direct reaction with aluminum and regenerated in an alane-based hydrogen storage system. PMID:22962624

The reaction of formic acid with RaneyTM copper

NASA Astrophysics Data System (ADS)

Callear, Samantha K.; Silverwood, Ian P.; Chutia, Arunabhiram; Catlow, C. Richard A.; Parker, Stewart F.

2016-04-01

The interaction of formic acid with RaneyTM Cu proves to be complex. Rather than the expected generation of a monolayer of bidentate formate, we find the formation of a Cu(II) compound. This process occurs by direct reaction of copper and formic acid; in contrast, previous methods are by solution reaction. This is a rare example of formic acid acting as an oxidant rather than, as more commonly found, a reductant. The combination of diffraction, spectroscopic and computational methods has allowed this unexpected process to be characterized.

Comparison of group transfer, inner sphere and outer sphere electron transfer mechanisms for organometallic complexes

NASA Astrophysics Data System (ADS)

Our studies of reactions of metal carbonyl cations and anions have shown that metal carbonyl cations can catalyze CO exchange reactions on metal carbonyl anions. This result provides further evidence for a mechanism involving attack of the metal carbonyl anion on a carbon of the metal carbonyl cation in CO(exp 2+) transfer reactions. Reaction of metal carbonyl anions with metal carbonyl halides is a common approach to formation of metal-metal bonds. We have begun to use kinetic data and product analysis to understand the formation of homobimetallic versus heterobimetallic products in such reactions. Initial data indicate a nucleophilic attack, possibly through a ring-slippage mechanism.

Synthesis, characterization and catalytic activity of nanosized Ni complexed aminoclay

NASA Astrophysics Data System (ADS)

Ranchani, A. Amala Jeya; Parthasarathy, V.; Devi, A. Anitha; Meenarathi, B.; Anbarasan, R.

2017-11-01

A novel Ni complexed aminoclay (AC) catalyst was prepared by complexation method followed by reduction reaction. Various analytical techniques such as FTIR spectroscopy, UV-visible spectroscopy, DSC, TGA, SEM, HRTEM, EDX, XPS and WCA measurement are used to characterize the synthesized material. The AC-Ni catalyst system exhibited improved thermal stability and fiber-like morphology. The XPS results declared the formation of Ni nanoparticles. Thus, synthesized catalyst was tested towards the Schiff base formation reaction between various bio-medical polymers and aniline under air atmosphere at 85 °C for 24 h. The catalytic activity of the catalyst was studied by varying the % weight loading of the AC-Ni system towards the Schiff base formation. The Schiff base formation was quantitatively calculated by the 1H-NMR spectroscopy. While increasing the % weight loading of the AC-Ni catalyst, the % yield of Schiff base was also increased. The k app and Ti values were determined for the reduction of indole and α-terpineol in the presence of AC-Ni catalyst system. The experimental results were compared with the literature report.

Kinetics and thermochemistry of 2,5-dimethyltetrahydrofuran and related oxolanes: next next-generation biofuels.

PubMed

Simmie, John M

2012-05-10

The enthalpies of formation, entropies, specific heats at constant pressure, enthalpy functions, and all carbon-hydrogen and carbon-methyl bond dissociation energies have been computed using high-level methods for the cyclic ethers (oxolanes) tetrahydrofuran, 2-methyltetrahydrofuran, and 2,5-dimethyltetrahydrofuran. Barrier heights for hydrogen-abstraction reactions by hydrogen atoms and the methyl radical are also computed and shown to correlate with reaction energy change. The results show a pleasing consistency and considerably expands the available data for these important compounds. Abstraction by ȮH is accompanied by formation of both pre- and postreaction weakly bound complexes. The resulting radicals formed after abstraction undergo ring-opening reactions leading to readily recognizable intermediates, while competitive H-elimination reactions result in formation of dihydrofurans. Formation enthalpies of all 2,3- and 2,5-dihydrofurans and associated radicals are also reported. It is probable that the compounds at the center of this study will be relatively clean-burning biofuels, although formation of intermediate aldehydes might be problematic.

Energy conservation by oxidation of formate to carbon dioxide and hydrogen via a sodium ion current in a hyperthermophilic archaeon

PubMed Central

Lim, Jae Kyu; Mayer, Florian; Kang, Sung Gyun; Müller, Volker

2014-01-01

Thermococcus onnurineus NA1 is known to grow by the anaerobic oxidation of formate to CO2 and H2, a reaction that operates near thermodynamic equilibrium. Here we demonstrate that this reaction is coupled to ATP synthesis by a transmembrane ion current. Formate oxidation leads to H+ translocation across the cytoplasmic membrane that then drives Na+ translocation. The ion-translocating electron transfer system is rather simple, consisting of only a formate dehydrogenase module, a membrane-bound hydrogenase module, and a multisubunit Na+/H+ antiporter module. The electrochemical Na+ gradient established then drives ATP synthesis. These data give a mechanistic explanation for chemiosmotic energy conservation coupled to formate oxidation to CO2 and H2. Because it is discussed that the membrane-bound hydrogenase with the Na+/H+ antiporter module are ancestors of complex I of mitochondrial and bacterial electron transport these data also shed light on the evolution of ion transport in complex I-like electron transport chains. PMID:25049407

Energy conservation by oxidation of formate to carbon dioxide and hydrogen via a sodium ion current in a hyperthermophilic archaeon.

PubMed

Lim, Jae Kyu; Mayer, Florian; Kang, Sung Gyun; Müller, Volker

2014-08-05

Thermococcus onnurineus NA1 is known to grow by the anaerobic oxidation of formate to CO2 and H2, a reaction that operates near thermodynamic equilibrium. Here we demonstrate that this reaction is coupled to ATP synthesis by a transmembrane ion current. Formate oxidation leads to H(+) translocation across the cytoplasmic membrane that then drives Na(+) translocation. The ion-translocating electron transfer system is rather simple, consisting of only a formate dehydrogenase module, a membrane-bound hydrogenase module, and a multisubunit Na(+)/H(+) antiporter module. The electrochemical Na(+) gradient established then drives ATP synthesis. These data give a mechanistic explanation for chemiosmotic energy conservation coupled to formate oxidation to CO2 and H2. Because it is discussed that the membrane-bound hydrogenase with the Na(+)/H(+) antiporter module are ancestors of complex I of mitochondrial and bacterial electron transport these data also shed light on the evolution of ion transport in complex I-like electron transport chains.

Gas Phase Reactions of Ions Derived from Anionic Uranyl Formate and Uranyl Acetate Complexes.

PubMed

Perez, Evan; Hanley, Cassandra; Koehler, Stephen; Pestok, Jordan; Polonsky, Nevo; Van Stipdonk, Michael

2016-12-01

The speciation and reactivity of uranium are topics of sustained interest because of their importance to the development of nuclear fuel processing methods, and a more complete understanding of the factors that govern the mobility and fate of the element in the environment. Tandem mass spectrometry can be used to examine the intrinsic reactivity (i.e., free from influence of solvent and other condensed phase effects) of a wide range of metal ion complexes in a species-specific fashion. Here, electrospray ionization, collision-induced dissociation, and gas-phase ion-molecule reactions were used to create and characterize ions derived from precursors composed of uranyl cation (U VI O 2 2+ ) coordinated by formate or acetate ligands. Anionic complexes containing U VI O 2 2+ and formate ligands fragment by decarboxylation and elimination of CH 2 =O, ultimately to produce an oxo-hydride species [U VI O 2 (O)(H)] - . Cationic species ultimately dissociate to make [U VI O 2 (OH)] + . Anionic complexes containing acetate ligands exhibit an initial loss of acetyloxyl radical, CH 3 CO 2 •, with associated reduction of uranyl to U V O 2 + . Subsequent CID steps cause elimination of CO 2 and CH 4 , ultimately to produce [U V O 2 (O)] - . Loss of CH 4 occurs by an intra-complex H + transfer process that leaves U V O 2 + coordinated by acetate and acetate enolate ligands. A subsequent dissociation step causes elimination of CH 2 =C=O to leave [U V O 2 (O)] - . Elimination of CH 4 is also observed as a result of hydrolysis caused by ion-molecule reaction with H 2 O. The reactions of other anionic species with gas-phase H 2 O create hydroxyl products, presumably through the elimination of H 2 . Graphical Abstract ᅟ.

Gas Phase Reactions of Ions Derived from Anionic Uranyl Formate and Uranyl Acetate Complexes

NASA Astrophysics Data System (ADS)

Perez, Evan; Hanley, Cassandra; Koehler, Stephen; Pestok, Jordan; Polonsky, Nevo; Van Stipdonk, Michael

2016-12-01

The speciation and reactivity of uranium are topics of sustained interest because of their importance to the development of nuclear fuel processing methods, and a more complete understanding of the factors that govern the mobility and fate of the element in the environment. Tandem mass spectrometry can be used to examine the intrinsic reactivity (i.e., free from influence of solvent and other condensed phase effects) of a wide range of metal ion complexes in a species-specific fashion. Here, electrospray ionization, collision-induced dissociation, and gas-phase ion-molecule reactions were used to create and characterize ions derived from precursors composed of uranyl cation (UVIO2 2+) coordinated by formate or acetate ligands. Anionic complexes containing UVIO2 2+ and formate ligands fragment by decarboxylation and elimination of CH2=O, ultimately to produce an oxo-hydride species [UVIO2(O)(H)]-. Cationic species ultimately dissociate to make [UVIO2(OH)]+. Anionic complexes containing acetate ligands exhibit an initial loss of acetyloxyl radical, CH3CO2•, with associated reduction of uranyl to UVO2 +. Subsequent CID steps cause elimination of CO2 and CH4, ultimately to produce [UVO2(O)]-. Loss of CH4 occurs by an intra-complex H+ transfer process that leaves UVO2 + coordinated by acetate and acetate enolate ligands. A subsequent dissociation step causes elimination of CH2=C=O to leave [UVO2(O)]-. Elimination of CH4 is also observed as a result of hydrolysis caused by ion-molecule reaction with H2O. The reactions of other anionic species with gas-phase H2O create hydroxyl products, presumably through the elimination of H2.

Selective formation of 2-imidazolines and 2-substituted oxazoles by using a three-component reaction.

PubMed

Elders, Niels; Ruijter, Eelco; de Kanter, Frans J J; Groen, Marinus B; Orru, Romano V A

2008-01-01

Selective formation of 2H-2-imidazolines and 2-substituted oxazoles by using a multicomponent reaction of amines, either aldehydes or ketones, and alpha-acidic isocyano amides or esters is described. By selecting the appropriate solvent, Ag(I) or Cu(I) catalyst, or by employing a weak Brønsted acid, the product formation can be fully controlled and directed quantitatively to the desired heterocyclic scaffold. The described experimental procedures not only significantly increase the scope of compatible inputs for this complexity-generating three-component reaction, but also allow for considerable chemical diversity: At least four diversity points in two distinct scaffolds can be exploited in this way.

Synthesis, spectral and thermal studies of the newly hydrogen bonded charge transfer complex of o-phenylenediamine with pi acceptor picric acid.

PubMed

Khan, Ishaat M; Ahmad, Afaq

2010-10-01

Newly proton or charge transfer complex [(OPDH)(+)(PA)(-)] was synthesized by the reaction of the donor, o-phenylenediamine (OPD) with acceptor, 2,4,6-trinitrophenol (PAH). The chemical reaction has occurred via strong hydrogen bonding followed by migration of proton from acceptor to donor. UV-vis, (1)H NMR and FTIR spectra, in addition to the thermal and elemental analysis were used to confirm the proposed occurrence of the chemical reaction and to investigate the newly synthesized solid CT complex. The stoichiometry of the CT complex was found to be 1:1. The formation constant and molar extinction coefficient of the CT complex were evaluated by the Benesi-Hildebrand equation. Copyright 2010 Elsevier B.V. All rights reserved.

Glycine and diglycine as possible catalytic factors in the prebiotic evolution of peptides.

PubMed

Plankensteiner, Kristof; Righi, Alessandro; Rode, Bernd M

2002-06-01

Mutual catalytic effects within the Salt-Induced Peptide Formation (SIPF) Reaction might be one little puzzle piece in the complicated process of the formation of complex peptidic systems and their chemical evolution on the prebiotic earth. The catalytic effects of glycine and diglycine on the formation of dipeptides from mixed amino acid systems in the SIPF Reaction was investigated for systems with leucine, proline, valine and aspartic acid and showed to result in a significant increase of the yield of the majority of the produced dipeptides. The results of the experiments strongly confirm previous theories on the catalytic mechanism and show the ability of the SIPF Reaction to produce a very diverse set of peptide products with relevance to the formation of a biosphere.

Glycine and Diglycine as Possible Catalytic Factors in the Prebiotic Evolution of Peptides

NASA Astrophysics Data System (ADS)

Plankensteiner, Kristof; Righi, Alessandro; Rode, Bernd M.

2002-06-01

Mutual catalytic effects within the Salt-Induced Peptide Formation (SIPF) Reaction might be one little puzzle piece in the complicated process of the formation of complex peptidic systems and their chemical evolution on the prebiotic earth. The catalytic effects of glycine and diglycine on the formation of dipeptides from mixed amino acid systems in the SIPF Reaction was investigated for systems with leucine, proline, valine and aspartic acid and showed to result in a significant increase of the yield of the majority of the produced dipeptides. The results of the experiments strongly confirm previous theories on the catalytic mechanism and show the ability of the SIPF Reaction to produce a very diverse set of peptide products with relevance to the formation of a biosphere.

Chemical dynamics simulations of the monohydrated OH-(H2O) + CH3I reaction. Atomic-level mechanisms and comparison with experiment

NASA Astrophysics Data System (ADS)

Xie, Jing; Otto, Rico; Wester, Roland; Hase, William L.

2015-06-01

Direct dynamics simulations, with B97-1/ECP/d theory, were performed to study the role of microsolvation for the OH-(H2O) + CH3I reaction. The SN2 reaction dominates at all reactant collision energies, but at higher collision energies proton transfer to form CH2I-, and to a lesser extent CH2I- (H2O), becomes important. The SN2 reaction occurs by direct rebound and stripping mechanisms, and 28 different indirect atomistic mechanisms, with the latter dominating. Important components of the indirect mechanisms are the roundabout and formation of SN2 and proton transfer pre-reaction complexes and intermediates, including [CH3--I--OH]-. In contrast, for the unsolvated OH- + CH3I SN2 reaction, there are only seven indirect atomistic mechanisms and the direct mechanisms dominate. Overall, the simulation results for the OH-(H2O) + CH3IߙSN2 reaction are in good agreement with experiment with respect to reaction rate constant, product branching ratio, etc. Differences between simulation and experiment are present for the SN2 velocity scattering angle at high collision energies and the proton transfer probability at low collision energies. Equilibrium solvation by the H2O molecule is unimportant. The SN2 reaction is dominated by events in which H2O leaves the reactive system as CH3OH is formed or before CH3OH formation. Formation of solvated products is unimportant and participation of the (H2O)CH3OH---I- post-reaction complex for the SN2 reaction is negligible.

Reaction of Pb(II) and Zn(II) with Ethyl Linoleate To Form Structured Hybrid Inorganic–Organic Complexes: A Model for Degradation in Historic Paint Films

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

MacDonald, Margaret G.; Palmer, Michael R.; Suchomel, Matthew R.

To investigate soap formation in drying oils in historic paints, the reaction between metal acetates (K +, Zn 2+, Pb 2+) and ethyl linoleate (EL) was studied using optical microscopy, X-ray powder diffraction, and electron microscopy. Pb(II) and Zn(II) react rapidly with EL to form highly structured, spherulitic, luminescent crystallites that aggregate. Evidence from Fourier transform infrared (FTIR) and scanning electron microscopy/energy dispersive X-ray analysis and high-resolution synchrotron powder X-ray diffraction indicates that these are organic-inorganic hybrid complexes or coordination polymers. FTIR absorbance peaks at ca. 1540 cm -1 for Pb(II) and ca. 1580 cm -1 for Zn(II) are consistentmore » with the formation of carboxylate complexes. The complexes formed offer insight into the degradation processes observed in oil paint films, suggesting that soap formation is rapid when metal ions are solubilized and can occur with unsaturated fatty acids that are present in fresh oils. Finally, these complexes may account for the atypical luminescence observed in lead-containing cured oil paint films.« less

Reaction of Pb(II) and Zn(II) with Ethyl Linoleate To Form Structured Hybrid Inorganic–Organic Complexes: A Model for Degradation in Historic Paint Films

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

MacDonald, Margaret G.; Palmer, Michael R.; Suchomel, Matthew R.

To investigate soap formation in drying oils in historic paints, the reaction between metal acetates (K +, Zn 2+, Pb 2+) and ethyl linoleate (EL) was studied using optical microscopy, X-ray powder diffraction, and electron microscopy. Pb(II) and Zn(II) react rapidly with EL to form highly structured, spherulitic, luminescent crystallites that aggregate. Evidence from Fourier transform infrared (FTIR) and scanning electron microscopy/energy dispersive X-ray analysis and high-resolution synchrotron powder X-ray diffraction indicates that these are organic–inorganic hybrid complexes or coordination polymers. FTIR absorbance peaks at ca. 1540 cm –1 for Pb(II) and ca. 1580 cm –1 for Zn(II) are consistentmore » with the formation of carboxylate complexes. The complexes formed offer insight into the degradation processes observed in oil paint films, suggesting that soap formation is rapid when metal ions are solubilized and can occur with unsaturated fatty acids that are present in fresh oils. These complexes may account for the atypical luminescence observed in lead-containing cured oil paint films.« less

Reaction of Pb(II) and Zn(II) with Ethyl Linoleate To Form Structured Hybrid Inorganic–Organic Complexes: A Model for Degradation in Historic Paint Films

DOE PAGES

MacDonald, Margaret G.; Palmer, Michael R.; Suchomel, Matthew R.; ...

2016-09-07

To investigate soap formation in drying oils in historic paints, the reaction between metal acetates (K +, Zn 2+, Pb 2+) and ethyl linoleate (EL) was studied using optical microscopy, X-ray powder diffraction, and electron microscopy. Pb(II) and Zn(II) react rapidly with EL to form highly structured, spherulitic, luminescent crystallites that aggregate. Evidence from Fourier transform infrared (FTIR) and scanning electron microscopy/energy dispersive X-ray analysis and high-resolution synchrotron powder X-ray diffraction indicates that these are organic-inorganic hybrid complexes or coordination polymers. FTIR absorbance peaks at ca. 1540 cm -1 for Pb(II) and ca. 1580 cm -1 for Zn(II) are consistentmore » with the formation of carboxylate complexes. The complexes formed offer insight into the degradation processes observed in oil paint films, suggesting that soap formation is rapid when metal ions are solubilized and can occur with unsaturated fatty acids that are present in fresh oils. Finally, these complexes may account for the atypical luminescence observed in lead-containing cured oil paint films.« less

Aerobic oxidations catalyzed by chromium corroles.

PubMed

Mahammed, Atif; Gray, Harry B; Meier-Callahan, Alexandre E; Gross, Zeev

2003-02-05

Oxochromium(V) complexes of 5,10,15-tris(pentafluorophenyl)corrole and brominated derivatives oxygenate substrates (triphenylphosphine and norbornene) with concomitant production of chromium(III). Regeneration of CrVO by reaction of dioxygen with CrIII completes an aerobic catalytic cycle, with very large solvent effects; in acetonitrile, rapid initial turnovers observed initially are shut down by formation of CrIVO, while in toluene, THF, and methanol, relatively slow reactions are further inhibited by product formation.

Two-center three-electron bonding in ClNH 3 revealed via helium droplet infrared laser Stark spectroscopy: Entrance channel complex along the Cl + NH 3 → ClNH 2 + H reaction

DOE PAGES

Moradi, Christopher P.; Xie, Changjian; Kaufmann, Matin; ...

2016-04-22

Pyrolytic dissociation of Cl 2 is employed to dope helium droplets with single Cl atoms. Sequential addition of NH 3 to Cl-doped droplets leads to the formation of a complex residing in the entry valley to the substitution reaction Cl + NH 3 → ClNH 2 + H. Infrared Stark spectroscopy in the NH stretching region reveals symmetric and antisymmetric vibrations of a C 3v symmetric top. Frequency shifts from NH 3 and dipole moment measurements are consistent with a ClNH 3 complex containing a relatively strong two-center three-electron (2c–3e) bond. The nature of the 2c–3e bonding in ClNH 3more » is explored computationally and found to be consistent with the complexation-induced blue shifts observed experimentally. As a result, computations of interconversion pathways reveal nearly barrierless routes to the formation of this complex, consistent with the absence in experimental spectra of two other complexes, NH 3Cl and Cl–HNH 2, which are predicted in the entry valley to the hydrogen abstraction reaction Cl + NH 3 → HCl + NH 2.« less

Two-center three-electron bonding in ClNH{sub 3} revealed via helium droplet infrared laser Stark spectroscopy: Entrance channel complex along the Cl + NH{sub 3} → ClNH{sub 2} + H reaction

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

Moradi, Christopher P.; Douberly, Gary E., E-mail: douberly@uga.edu; Xie, Changjian

2016-04-28

Pyrolytic dissociation of Cl{sub 2} is employed to dope helium droplets with single Cl atoms. Sequential addition of NH{sub 3} to Cl-doped droplets leads to the formation of a complex residing in the entry valley to the substitution reaction Cl + NH{sub 3} → ClNH{sub 2} + H. Infrared Stark spectroscopy in the NH stretching region reveals symmetric and antisymmetric vibrations of a C{sub 3v} symmetric top. Frequency shifts from NH{sub 3} and dipole moment measurements are consistent with a ClNH{sub 3} complex containing a relatively strong two-center three-electron (2c–3e) bond. The nature of the 2c–3e bonding in ClNH{sub 3}more » is explored computationally and found to be consistent with the complexation-induced blue shifts observed experimentally. Computations of interconversion pathways reveal nearly barrierless routes to the formation of this complex, consistent with the absence in experimental spectra of two other complexes, NH{sub 3}Cl and Cl–HNH{sub 2}, which are predicted in the entry valley to the hydrogen abstraction reaction Cl + NH{sub 3} → HCl + NH{sub 2}.« less

Determination of Reaction Stoichiometries by Flow Injection Analysis.

ERIC Educational Resources Information Center

Rios, Angel; And Others

1986-01-01

Describes a method of flow injection analysis intended for calculation of complex-formation and redox reaction stoichiometries based on a closed-loop configuration. The technique is suitable for use in undergraduate laboratories. Information is provided for equipment, materials, procedures, and sample results. (JM)

New reactions involving the oxidative O-, N-, and C-phosphorylation of organic compounds by phosphorus and phosphides in the presence of metal complexes

NASA Astrophysics Data System (ADS)

Dorfman, Ya A.; Aleshkova, M. M.; Polimbetova, G. S.; Levina, L. V.; Petrova, T. V.; Abdreimova, R. R.; Doroshkevich, D. M.

1993-09-01

The mechanisms of new catalytic reactions leading to the formation of di-, and tri-alkyl phosphates, di- and tri-alkyl phosphites, phosphoramidites, phosphazenes, phosphines, and phosphine oxides from hydrogen, copper, and zinc phosphides and white and red phosphorus are analysed. The mechanisms of the activation of the reactants by metal complexes and of the reactions involving the oxidative P-O, P-N, and P-C coupling of organic compounds to phosphorus and phosphides are considered. The bibliography includes 124 references.

Formation of polycyclic lactones through a ruthenium-catalyzed ring-closing metathesis/hetero-Pauson-Khand reaction sequence.

PubMed

Finnegan, David F; Snapper, Marc L

2011-05-20

Processes that form multiple carbon-carbon bonds in one operation can generate molecular complexity quickly and therefore be used to shorten syntheses of desirable molecules. We selected the hetero-Pauson-Khand (HPK) cycloaddition and ring-closing metathesis (RCM) as two unique carbon-carbon bond-forming reactions that could be united in a tandem ruthenium-catalyzed process. In doing so, complex polycyclic products can be obtained in one reaction vessel from acyclic precursors using a single ruthenium additive that can catalyze sequentially two mechanistically distinct transformations.

Kinetics of oxidation of bilirubin and its protein complex by hydrogen peroxide in aqueous solutions

NASA Astrophysics Data System (ADS)

Solomonov, A. V.; Rumyantsev, E. V.; Antina, E. V.

2010-12-01

A comparative study of oxidation reactions of bilirubin and its complex with albumin was carried out in aqueous solutions under the action of hydrogen peroxide and molecular oxygen at different pH values. Free radical oxidation of the pigment in both free and bound forms at pH 7.4 was shown not to lead to the formation of biliverdin, but to be associated with the decomposition of the tetrapyrrole chromophore into monopyrrolic products. The effective and true rate constants of the reactions under study were determined. It was assumed that one possible mechanism of the oxidation reaction is associated with the interaction of peroxyl radicals and protons of the NH groups of bilirubin molecules at the limiting stage with the formation of a highly reactive radical intermediate. The binding of bilirubin with albumin was found to result in a considerable reduction in the rate of the oxidation reaction associated with the kinetic manifestation of the protein protection effect. It was found that the autoxidation of bilirubin by molecular oxygen with the formation of biliverdin at the intermediate stage can be observed with an increase in the pH of solutions.

Spectrophotometric study on the proton transfer reaction between 2-amino-4-methylpyridine with 2,6-dichloro-4-nitrophenol in methanol, acetonitrile and the binary mixture 50% methanol + 50% acetonitrile

NASA Astrophysics Data System (ADS)

Al-Ahmary, Khairia M.; Habeeb, Moustafa M.; Al-Obidan, Areej H.

2016-02-01

Proton transfer reaction between 2-amino-4-methylpyridine (2AMP) as the proton acceptor with 2,6-dichloro-4-nitrophenol (DCNP) as the proton donor has been investigated spectrophotometrically in methanol (MeOH), acetonitrile (AN) and a binary mixture composed of 50% MeOH and 50% AN (AN-Me). The composition of the complex has been investigated utilizing Job's and photometric titration methods to be 1:1. Minimum-maximum absorbance equation has been applied to estimate the formation constant of the proton transfer reaction (KPT) where it reached high values in the investigated solvent confirming its high stability. The formation constant recorded higher value in AN compared with MeOH and mixture of AN-Me. Based on the formation of stable proton transfer complex, a sensitive spectrophotometric method was suggested for quantitative determination of 2AMP. The Lambert-Beer's law was obeyed in the concentration range 0.5-8 μg mL- 1 with small values of limits of detection and quantification. The solid complex between 2AMP with DCNP has been synthesized and characterized by elemental analysis to be 1:1 in concordant with the molecular stoichiometry in solution. Further analysis of the solid complex was carried out using infrared and 1H NMR spectroscopy.

Reaction mechanism of molybdoenzyme formate dehydrogenase.

PubMed

Leopoldini, Monica; Chiodo, Sandro G; Toscano, Marirosa; Russo, Nino

2008-01-01

Formate dehydrogenase is a molybdoenzyme of the anaerobic formate hydrogen lyase complex of the Escherichia coli microorganism that catalyzes the oxidation of formate to carbon dioxide. The two proposed mechanisms of reaction, which differ in the occurrence of a direct coordination or not of a SeCys residue to the molybdenum metal during catalysis were analyzed at the density functional level in both vacuum and protein environments. Some DF functionals, in addition to the very popular B3LYP one, were employed to compute barrier heights. Results revealed the role played by the SeCys residue in performing the abstraction of the proton from the formate substrate. The computation of the energetic profiles for both mechanisms indicated that the reaction barriers are higher when the selenium is directly coordinated to the metal, whereas less energy is required when SeCys is not a ligand at the molybdenum site.

Preparation, spectroscopic and structural studies on charge-transfer complexes of 2,9-dimethyl-1,10-phenanthroline with some electron acceptors

NASA Astrophysics Data System (ADS)

Gaballa, Akmal S.; Wagner, Christoph; Teleb, Said M.; Nour, El-Metwally; Elmosallamy, M. A. F.; Kaluđerović, Goran N.; Schmidt, Harry; Steinborn, Dirk

2008-03-01

Charge-transfer (CT) complexes formed in the reactions of 2,9-dimethyl-1,10-phenanthroline (Me 2phen) with some acceptors such as chloranil (Chl), picric acid (HPA) and chloranilic acid (H 2CA) have been studied in the defined solvent at room temperature. Based on elemental analysis and infrared spectra of the solid CT-complexes along with the photometric titration curves for the reactions, obtained data indicate the formation of 1:1 charge-transfer complexes [(Me 2phen)(Chl)] ( 1), [(Me 2phenH)(PA)] ( 2) and [(Me 2phenH)(HCA)] ( 3), respectively, was proposed. In the three complexes, infrared and 1H NMR spectroscopic data indicate a charge-transfer interaction and as far as complexes 2 and 3 are concerned this interaction is associated with a hydrogen bonding. The formation constants for the complexes ( KC) were shown to be dependent upon the nature of the electron acceptors used. The X-ray structure of complex 3 indicate the formation of dimeric units [Me 2phenH] 2[(HCA) 2] in which the two anions (HCA) - are connected by two O-H⋯O hydrogen bonds whereas the cations and anions are joined together by strong three-center (bifurcated) N-H⋯O hydrogen bonds. Furthermore, the cations are arranged in a π-π stacking.

Recent advances in the chemistry of Rh carbenoids: multicomponent reactions of diazocarbonyl compounds

NASA Astrophysics Data System (ADS)

Medvedev, J. J.; Nikolaev, V. A.

2015-07-01

Multicomponent reactions of diazo compounds catalyzed by RhII complexes become a powerful tool for organic synthesis. They enable three- or four-step processes to be carried out as one-pot procedures (actually as one step) with high stereoselectivity to give complex organic molecules, including biologically active compounds. This review addresses recent results in the chemistry of Rh-catalyzed multicomponent reactions of diazocarbonyl compounds with the intermediate formation of N-, O- and C=O-ylides. The diastereo- and enantioselectivity of these reactions and the possibility of using various co-catalysts to increase the efficiency of the processes under consideration are discussed. The bibliography includes 120 references.

O2-Promoted Allylic Acetoxylation of Alkenes: Assessment of “Push” vs. “Pull” Mechanisms and Comparison between O2 and Benzoquinone

PubMed Central

Diao, Tianning

2014-01-01

Palladium-catalyzed acetoxylation of allylic C–H bonds has been the subject of extensive study. These reactions proceed via allyl-palladium(II) intermediates that react with acetate to afford the allyl acetate product. Benzoquinone and molecular oxygen are two common oxidants for these reactions. Benzoquinone has been shown to promote allyl acetate formation from well-defined π-allyl palladium(II) complexes. Here, we assess the ability of O2 to promote similar reactions with a series of “unligated” π-allyl palladium(II) complexes (i.e., in the absence of ancillary phosphorus, nitrogen or related donor ligands). Stoichiometric and catalytic allyl acetate formation is observed under aerobic conditions with several different alkenes. Mechanistic studies are most consistent with a “pull” mechanism in which O2 traps the Pd0 intermediate following reversible C–O bond-formation from an allyl-palladium(II) species. A “push” mechanism, involving oxidatively induced C–O bond formation, does not appear to participate. These results and conclusions are compared with benzoquinone-promoted allylic acetoxylation, in which a “push” mechanism seems to be operative. PMID:25435646

Insight into Temperature Dependence of GTPase Activity in Human Guanylate Binding Protein-1

PubMed Central

Rahman, Safikur; Deep, Shashank; Sau, Apurba Kumar

2012-01-01

Interferon-γ induced human guanylate binding protein-1(hGBP1) belongs to a family of dynamin related large GTPases. Unlike all other GTPases, hGBP1 hydrolyzes GTP to a mixture of GDP and GMP with GMP being the major product at 37°C but GDP became significant when the hydrolysis reaction was carried out at 15°C. The hydrolysis reaction in hGBP1 is believed to involve with a number of catalytic steps. To investigate the effect of temperature in the product formation and on the different catalytic complexes of hGBP1, we carried out temperature dependent GTPase assays, mutational analysis, chemical and thermal denaturation studies. The Arrhenius plot for both GDP and GMP interestingly showed nonlinear behaviour, suggesting that the product formation from the GTP-bound enzyme complex is associated with at least more than one step. The negative activation energy for GDP formation and GTPase assay with external GDP together indicate that GDP formation occurs through the reversible dissociation of GDP-bound enzyme dimer to monomer, which further reversibly dissociates to give the product. Denaturation studies of different catalytic complexes show that unlike other complexes the free energy of GDP-bound hGBP1 decreases significantly at lower temperature. GDP formation is found to be dependent on the free energy of the GDP-bound enzyme complex. The decrease in the free energy of this complex at low temperature compared to at high is the reason for higher GDP formation at low temperature. Thermal denaturation studies also suggest that the difference in the free energy of the GTP-bound enzyme dimer compared to its monomer plays a crucial role in the product formation; higher stability favours GMP but lower favours GDP. Thus, this study provides the first thermodynamic insight into the effect of temperature in the product formation of hGBP1. PMID:22859948

Spectroscopic diagnostics of organic chemistry in the protostellar environment

NASA Technical Reports Server (NTRS)

Charnley, S. B.; Ehrenfreund, P.; Kuan, Y. J.

2001-01-01

A combination of astronomical observations, laboratory studies, and theoretical modelling is necessary to determine the organic chemistry of dense molecular clouds. We present spectroscopic evidence for the composition and evolution of organic molecules in protostellar environments. The principal reaction pathways to complex molecule formation by catalysis on dust grains and by reactions in the interstellar gas are described. Protostellar cores, where warming of dust has induced evaporation of icy grain mantles, are excellent sites in which to study the interaction between gas phase and grain-surface chemistries. We investigate the link between organics that are observed as direct products of grain surface reactions and those which are formed by secondary gas phase reactions of evaporated surface products. Theory predicts observable correlations between specific interstellar molecules, and also which new organics are viable for detection. We discuss recent infrared observations obtained with the Infrared Space Observatory, laboratory studies of organic molecules, theories of molecule formation, and summarise recent radioastronomical searches for various complex molecules such as ethers, azaheterocyclic compounds, and amino acids.

Frataxin Accelerates [2Fe-2S] Cluster Formation on the Human Fe–S Assembly Complex

PubMed Central

Fox, Nicholas G.; Das, Deepika; Chakrabarti, Mrinmoy; Lindahl, Paul A.; Barondeau, David P.

2015-01-01

Iron–sulfur (Fe–S) clusters function as protein cofactors for a wide variety of critical cellular reactions. In human mitochondria, a core Fe–S assembly complex [called SDUF and composed of NFS1, ISD11, ISCU2, and frataxin (FXN) proteins] synthesizes Fe–S clusters from iron, cysteine sulfur, and reducing equivalents and then transfers these intact clusters to target proteins. In vitro assays have relied on reducing the complexity of this complicated Fe–S assembly process by using surrogate electron donor molecules and monitoring simplified reactions. Recent studies have concluded that FXN promotes the synthesis of [4Fe-4S] clusters on the mammalian Fe–S assembly complex. Here the kinetics of Fe–S synthesis reactions were determined using different electron donation systems and by monitoring the products with circular dichroism and absorbance spectroscopies. We discovered that common surrogate electron donor molecules intercepted Fe–S cluster intermediates and formed high-molecular weight species (HMWS). The HMWS are associated with iron, sulfide, and thiol-containing proteins and have properties of a heterogeneous solubilized mineral with spectroscopic properties remarkably reminiscent of those of [4Fe-4S] clusters. In contrast, reactions using physiological reagents revealed that FXN accelerates the formation of [2Fe-2S] clusters rather than [4Fe-4S] clusters as previously reported. In the preceding paper [Fox, N. G., et al. (2015) Biochemistry 54, DOI: 10.1021/bi5014485], [2Fe-2S] intermediates on the SDUF complex were shown to readily transfer to uncomplexed ISCU2 or apo acceptor proteins, depending on the reaction conditions. Our results indicate that FXN accelerates a rate-limiting sulfur transfer step in the synthesis of [2Fe-2S] clusters on the human Fe–S assembly complex. PMID:26016518

Frataxin Accelerates [2Fe-2S] Cluster Formation on the Human Fe-S Assembly Complex.

PubMed

Fox, Nicholas G; Das, Deepika; Chakrabarti, Mrinmoy; Lindahl, Paul A; Barondeau, David P

2015-06-30

Iron-sulfur (Fe-S) clusters function as protein cofactors for a wide variety of critical cellular reactions. In human mitochondria, a core Fe-S assembly complex [called SDUF and composed of NFS1, ISD11, ISCU2, and frataxin (FXN) proteins] synthesizes Fe-S clusters from iron, cysteine sulfur, and reducing equivalents and then transfers these intact clusters to target proteins. In vitro assays have relied on reducing the complexity of this complicated Fe-S assembly process by using surrogate electron donor molecules and monitoring simplified reactions. Recent studies have concluded that FXN promotes the synthesis of [4Fe-4S] clusters on the mammalian Fe-S assembly complex. Here the kinetics of Fe-S synthesis reactions were determined using different electron donation systems and by monitoring the products with circular dichroism and absorbance spectroscopies. We discovered that common surrogate electron donor molecules intercepted Fe-S cluster intermediates and formed high-molecular weight species (HMWS). The HMWS are associated with iron, sulfide, and thiol-containing proteins and have properties of a heterogeneous solubilized mineral with spectroscopic properties remarkably reminiscent of those of [4Fe-4S] clusters. In contrast, reactions using physiological reagents revealed that FXN accelerates the formation of [2Fe-2S] clusters rather than [4Fe-4S] clusters as previously reported. In the preceding paper [Fox, N. G., et al. (2015) Biochemistry 54, DOI: 10.1021/bi5014485], [2Fe-2S] intermediates on the SDUF complex were shown to readily transfer to uncomplexed ISCU2 or apo acceptor proteins, depending on the reaction conditions. Our results indicate that FXN accelerates a rate-limiting sulfur transfer step in the synthesis of [2Fe-2S] clusters on the human Fe-S assembly complex.

Validated spectrophotometric methods for determination of sodium valproate based on charge transfer complexation reactions.

PubMed

Belal, Tarek S; El-Kafrawy, Dina S; Mahrous, Mohamed S; Abdel-Khalek, Magdi M; Abo-Gharam, Amira H

2016-02-15

This work presents the development, validation and application of four simple and direct spectrophotometric methods for determination of sodium valproate (VP) through charge transfer complexation reactions. The first method is based on the reaction of the drug with p-chloranilic acid (p-CA) in acetone to give a purple colored product with maximum absorbance at 524nm. The second method depends on the reaction of VP with dichlone (DC) in dimethylformamide forming a reddish orange product measured at 490nm. The third method is based upon the interaction of VP and picric acid (PA) in chloroform resulting in the formation of a yellow complex measured at 415nm. The fourth method involves the formation of a yellow complex peaking at 361nm upon the reaction of the drug with iodine in chloroform. Experimental conditions affecting the color development were studied and optimized. Stoichiometry of the reactions was determined. The proposed spectrophotometric procedures were effectively validated with respect to linearity, ranges, precision, accuracy, specificity, robustness, detection and quantification limits. Calibration curves of the formed color products with p-CA, DC, PA and iodine showed good linear relationships over the concentration ranges 24-144, 40-200, 2-20 and 1-8μg/mL respectively. The proposed methods were successfully applied to the assay of sodium valproate in tablets and oral solution dosage forms with good accuracy and precision. Assay results were statistically compared to a reference pharmacopoeial HPLC method where no significant differences were observed between the proposed methods and reference method. Copyright © 2015 Elsevier B.V. All rights reserved.

Validated spectrophotometric methods for determination of sodium valproate based on charge transfer complexation reactions

NASA Astrophysics Data System (ADS)

Belal, Tarek S.; El-Kafrawy, Dina S.; Mahrous, Mohamed S.; Abdel-Khalek, Magdi M.; Abo-Gharam, Amira H.

2016-02-01

This work presents the development, validation and application of four simple and direct spectrophotometric methods for determination of sodium valproate (VP) through charge transfer complexation reactions. The first method is based on the reaction of the drug with p-chloranilic acid (p-CA) in acetone to give a purple colored product with maximum absorbance at 524 nm. The second method depends on the reaction of VP with dichlone (DC) in dimethylformamide forming a reddish orange product measured at 490 nm. The third method is based upon the interaction of VP and picric acid (PA) in chloroform resulting in the formation of a yellow complex measured at 415 nm. The fourth method involves the formation of a yellow complex peaking at 361 nm upon the reaction of the drug with iodine in chloroform. Experimental conditions affecting the color development were studied and optimized. Stoichiometry of the reactions was determined. The proposed spectrophotometric procedures were effectively validated with respect to linearity, ranges, precision, accuracy, specificity, robustness, detection and quantification limits. Calibration curves of the formed color products with p-CA, DC, PA and iodine showed good linear relationships over the concentration ranges 24-144, 40-200, 2-20 and 1-8 μg/mL respectively. The proposed methods were successfully applied to the assay of sodium valproate in tablets and oral solution dosage forms with good accuracy and precision. Assay results were statistically compared to a reference pharmacopoeial HPLC method where no significant differences were observed between the proposed methods and reference method.

Mechanisms of formation of 8-oxoguanine due to reactions of one and two OH* radicals and the H2O2 molecule with guanine: A quantum computational study.

PubMed

Jena, N R; Mishra, P C

2005-07-28

Mechanisms of formation of the mutagenic product 8-oxoguanine (8OG) due to reactions of guanine with two separate OH* radicals and with H2O2 were investigated at the B3LYP/6-31G, B3LYP/6-311++G, and B3LYP/AUG-cc-pVDZ levels of theory. Single point energy calculations were carried out with the MP2/AUG-cc-pVDZ method employing the optimized geometries at the B3LYP/AUG-cc-pVDZ level. Solvent effect was treated using the PCM and IEF-PCM models. Reactions of two separate OH* radicals and H2O2 with the C2 position of 5-methylimidazole (5MI) were investigated taking 5MI as a model to study reactions at the C8 position of guanine. The addition reaction of an OH* radical at the C8 position of guanine is found to be nearly barrierless while the corresponding adduct is quite stable. The reaction of a second OH* radical at the C8 position of guanine leading to the formation of 8OG complexed with a water molecule can take place according to two different mechanisms, involving two steps each. According to one mechanism, at the first step, 8-hydroxyguanine (8OHG) complexed with a water molecule is formed ,while at the second step, 8OHG is tautomerized to 8OG. In the other mechanism, at the first step, an intermediate complexed (IC) with a water molecule is formed, the five-membered ring of which is open, while at the second step, the five-membered ring is closed and a hydrogen bonded complex of 8OG with a water molecule is formed. The reaction of H2O2 with guanine leading to the formation of 8OG complexed with a water molecule can also take place in accordance with two different mechanisms having two steps each. At the first step of one mechanism, H2O2 is dissociated into two OH* groups that react with guanine to form the same IC as that formed in the reaction with two separate OH* radicals, and the subsequent step of this mechanism is also the same as that of the reaction of guanine with two separate OH* radicals. At the first step of the other mechanism of the reaction of guanine with H2O2, the latter molecule is dissociated into a hydrogen atom and an OOH* group which become bonded to the N7 and C8 atoms of guanine, respectively. At the second step of this mechanism, the OOH* group is dissociated into an oxygen atom and an OH* group, the former becomes bonded to the C8 atom of guanine while the latter abstracts the H8 atom bonded to C8, thus producing 8OG complexed with a water molecule. Solvent effects of the aqueous medium on certain reaction barriers and released energies are appreciable. 5MI works as a satisfactory model for a qualitative study of the reactions of two separate OH* radicals or H2O2 occurring at the C8 position of guanine.

Stereoselective Synthesis of Tetrahydroindolizines through the Catalytic Formation of Pyridinium Ylides from Diazo Compounds.

PubMed

Day, Jonathan; McKeever-Abbas, Ben; Dowden, James

2016-05-04

Commercially available iron(III) and copper(I) complexes catalyzed multicomponent cycloaddition reactions between diazo compounds, pyridines, and electrophilic alkenes to give alkaloid-inspired tetrahydroindolizidines in high yield with high diastereoselectivity. Hitherto, the catalytic formation of versatile pyridinium ylides from metal carbenes has been poorly developed; the broad utility demonstrated herein sets the stage for the invention of further multicomponent reactions in future. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Decarboxylative aldol reactions of allyl beta-keto esters via heterobimetallic catalysis.

PubMed

Lou, Sha; Westbrook, John A; Schaus, Scott E

2004-09-22

Mild and selective heterobimetallic-catalyzed decarboxylative aldol reactions involving allyl beta-keto esters have been developed. The reaction is promoted by Pd(0)- and Yb(III)-DIOP complexes at room temperature and involves the in situ formation of a ketone enolate from allyl beta-keto esters followed by addition of the enolate to aldehydes. The reaction is a new example of heterobimetallic catalysis in which the optimized reaction conditions require the addition of both metals.

Spectro- and electrochemical studies of some ruthenium and osmium complexes of 2-(2'-pyridyl)benzimidazole; complexes with intra-molecular charge transfer.

PubMed

Khalil, M M; Ali, S A; Ramadan, R M

2001-04-01

Reaction of Ru3(CO)12, with 2-(2'-pyridyl)benzimidazole (HPBI) resulted in the formation of Ru(CO)3(HPBI) (I) complex. In presence of pyridine or dipyridine, the two derivatives [Ru(CO)3(HPBI)].Py (II) and [Ru(CO)3(HPBI)].dpy (III) were isolated. The corresponding reactions of Os3(CO)12 yielded only one single product; Os(CO)2(HPBI)2 (IV). Spectroscopic studies of these complexes revealed intramolecular metal to ligand CT interactions. Reactions of RuCl3 with HPBI gave three distinct products; [Ru(HPBI)2Cl2]Cl (V), [Ru(HPBI)(dipy)Cl2]C1 (VI) and [Ru(PBI)2(py)2]Cl (VII). The UV-vis studies indicated the presence of intramolecular ligand to metal CT interactions. Electrochemical investigation of the complexes showed some irreversible, reversible and quasi-reversible redox reactions due to tautomeric interconversions through electron transfer.

Formation Mechanism of Spherical TiC in Ni-Ti-C System during Combustion Synthesis.

PubMed

Zhu, Guoliang; Wang, Wei; Wang, Rui; Zhao, Chuanbao; Pan, Weitao; Huang, Haijun; Du, Dafan; Wang, Donghong; Shu, Da; Dong, Anping; Sun, Baode; Jiang, Sheng; Pu, Yilong

2017-08-29

The formation mechanism of TiC particles in a Ni-Ti-C system were revealed by using differential thermal analysis (DTA), XRD, and SEM to identify the reaction products in different temperature ranges. The results indicated that the synthesis mechanism of TiC in Ni-Ti-C system was complex; several reactions were involved in the combustion synthesis of TiC-Ni composite. The Ni-Ti intermediate phases play important roles during the formation of TiC. Moreover, the influence of heating rate on the size range of TiC was also discussed.

Formation Mechanism of Spherical TiC in Ni-Ti-C System during Combustion Synthesis

PubMed Central

Zhu, Guoliang; Wang, Wei; Wang, Rui; Zhao, Chuanbao; Pan, Weitao; Huang, Haijun; Du, Dafan; Wang, Donghong; Shu, Da; Dong, Anping; Sun, Baode; Jiang, Sheng; Pu, Yilong

2017-01-01

The formation mechanism of TiC particles in a Ni-Ti-C system were revealed by using differential thermal analysis (DTA), XRD, and SEM to identify the reaction products in different temperature ranges. The results indicated that the synthesis mechanism of TiC in Ni-Ti-C system was complex; several reactions were involved in the combustion synthesis of TiC-Ni composite. The Ni-Ti intermediate phases play important roles during the formation of TiC. Moreover, the influence of heating rate on the size range of TiC was also discussed. PMID:28850088

About the Barriers to Reaction of CCl4 with HFeOH and FeCl2

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

Ginovska-Pangovska, Bojana; Camaioni, Donald M.; Dupuis, Michel

2011-08-11

The reactivity of iron nanoparticles in aqueous environments has received considerable attention due to their potential utilization in environmental remediation technologies. As part of a broader program aiming at an improved understanding of the mechanisms involved in the degradation of harmful chlorocarbons, joint experimental and computational studies of model systems were initiated. We previously reported on the reaction of one and two Fe atoms reactions with carbon tetrachloride (CCl4) in direct mimic of “atom-dropping” experiments, with insights into the formation of novel iron-carbon-chlorine complexes, their structures and possible reaction mechanisms. Increasing the level of complexity, we report here on themore » modeling of the reaction of HFeOH and CCl4 as companion research of recent ultra high vacuum experiments of the reaction of Fe with water and CCl4. HFeOH is a stable molecular species formed in the reaction of Fe with H2O. Experimentally the (Fe, H2O, CCl4) system showed no reactivity up to the desorption temperature of CCl4. Electron correlated CCSD(T) calculations (at DFT(B3LYP) optimized structures) indicated an energy barrier to reactivity of 24.5 kcal/mol following the formation of a stable ( 7.5 kcal/mol) long-range precursor complex. This finding is consistent with the lack of experimentally detected reaction products. This work was supported by the US Department of Energy Basic Energy Sciences' Chemical Sciences, Geosciences & Biosciences Division. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.« less

Aqueous photochemical reactions of chloride, bromide, and iodide ions in a diode-array spectrophotometer. Autoinhibition in the photolysis of iodide ions.

PubMed

Kalmár, József; Dóka, Éva; Lente, Gábor; Fábián, István

2014-03-28

The aqueous photoreactions of three halide ions (chloride, bromide and iodide) were studied using a diode array spectrophotometer to drive and detect the process at the same time. The concentration and pH dependences of the halogen formation rates were studied in detail. The experimental data were interpreted by improving earlier models where the cage complex of a halogen atom and an electron has a central role. The triiodide ion was shown to exert a strong inhibiting effect on the reaction sequence leading to its own formation. An assumed chemical reaction between the triiodide ion and the cage complex interpreted the strong autoinhibition effect. It is shown that there is a real danger of unwanted interference from the photoreactions of halide ions when halide salts are used as supporting electrolytes in spectrophotometric experiments using a relatively high intensity UV light source.

Spatial Heterogeneity and Imperfect Mixing in Chemical Reactions: Visualization of Density-Driven Pattern Formation

DOE PAGES

Sobel, Sabrina G.; Hastings, Harold M.; Testa, Matthew

2009-01-01

Imore » mperfect mixing is a concern in industrial processes, everyday processes (mixing paint, bread machines), and in understanding salt water-fresh water mixing in ecosystems. The effects of imperfect mixing become evident in the unstirred ferroin-catalyzed Belousov-Zhabotinsky reaction, the prototype for chemical pattern formation. Over time, waves of oxidation (high ferriin concentration, blue) propagate into a background of low ferriin concentration (red); their structure reflects in part the history of mixing in the reaction vessel. However, it may be difficult to separate mixing effects from reaction effects. We describe a simpler model system for visualizing density-driven pattern formation in an essentially unmixed chemical system: the reaction of pale yellow Fe 3 + with colorless SCN − to form the blood-red Fe ( SCN ) 2 + complex ion in aqueous solution. Careful addition of one drop of Fe ( NO 3 ) 3 to KSCN yields striped patterns after several minutes. The patterns appear reminiscent of Rayleigh-Taylor instabilities and convection rolls, arguing that pattern formation is caused by density-driven mixing.« less

Spatial Heterogeneity and Imperfect Mixing in Chemical Reactions: Visualization of Density-Driven Pattern Formation

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

Sobel, Sabrina G.; Hastings, Harold M.; Testa, Matthew

Imore » mperfect mixing is a concern in industrial processes, everyday processes (mixing paint, bread machines), and in understanding salt water-fresh water mixing in ecosystems. The effects of imperfect mixing become evident in the unstirred ferroin-catalyzed Belousov-Zhabotinsky reaction, the prototype for chemical pattern formation. Over time, waves of oxidation (high ferriin concentration, blue) propagate into a background of low ferriin concentration (red); their structure reflects in part the history of mixing in the reaction vessel. However, it may be difficult to separate mixing effects from reaction effects. We describe a simpler model system for visualizing density-driven pattern formation in an essentially unmixed chemical system: the reaction of pale yellow Fe 3 + with colorless SCN − to form the blood-red Fe ( SCN ) 2 + complex ion in aqueous solution. Careful addition of one drop of Fe ( NO 3 ) 3 to KSCN yields striped patterns after several minutes. The patterns appear reminiscent of Rayleigh-Taylor instabilities and convection rolls, arguing that pattern formation is caused by density-driven mixing.« less

Siderophores in Cloud Waters and Potential Impact on Atmospheric Chemistry: Photoreactivity of Iron Complexes under Sun-Simulated Conditions.

PubMed

Passananti, Monica; Vinatier, Virginie; Delort, Anne-Marie; Mailhot, Gilles; Brigante, Marcello

2016-09-06

In the present work, the photoreactivity of a mixture of iron(III)–pyoverdin (Fe(III)–Pyo) complexes was investigated under simulated cloud conditions. Pyoverdins are expected to complex ferric ions naturally present in cloudwater, thus modifying their availability and photoreactivity. The spectroscopic properties and photoreactivity of Fe(III)-Pyo were investigated, with particular attention to their fate under solar irradiation, also studied through simulations. The photolysis of the Fe(III)–Pyo complex leads to the generation of Fe(II), with rates of formation (RFe(II)f) of 6.98 and 3.96 × 10–9 M s–1 at pH 4.0 and 6.0, respectively. Interestingly, acetate formation was observed during the iron-complex photolysis, suggesting that fragmentation can occur after the ligand-to-metal charge transfer (LMCT) via a complex reaction mechanism. Moreover, photogenerated Fe(II) represent an important source of hydroxyl radical via the Fenton reaction in cloudwater. This reactivity might be relevant for the estimation of the rates of formation and steady-state concentrations of the hydroxyl radical by cloud chemistry models and for organic matter speciation in the cloud aqueous phase. In fact, the conventional models, which describe the iron photoreactivity in terms of iron–aqua and oxalate complexes, are not in accordance with our results.

Mechanism of Pd(NHC)-catalyzed transfer hydrogenation of alkynes.

PubMed

Hauwert, Peter; Boerleider, Romilda; Warsink, Stefan; Weigand, Jan J; Elsevier, Cornelis J

2010-12-01

The transfer semihydrogenation of alkynes to (Z)-alkenes shows excellent chemo- and stereoselectivity when using a zerovalent palladium(NHC)(maleic anhydride)-complex as precatalyst and triethylammonium formate as hydrogen donor. Studies on the kinetics under reaction conditions showed a broken positive order in substrate and first order in catalyst and hydrogen donor. Deuterium-labeling studies on the hydrogen donor showed that both hydrogens of formic acid display a primary kinetic isotope effect, indicating that proton and hydride transfers are separate rate-determining steps. By monitoring the reaction with NMR, we observed the presence of a coordinated formate anion and found that part of the maleic anhydride remains coordinated during the reaction. From these observations, we propose a mechanism in which hydrogen transfer from coordinated formate anion to zerovalent palladium(NHC)(MA)(alkyne)-complex is followed by migratory insertion of hydride, after which the product alkene is liberated by proton transfer from the triethylammonium cation. The explanation for the high selectivity observed lies in the competition between strongly coordinating solvent and alkyne for a Pd(alkene)-intermediate.

[Parametabolism as Non-Specific Modifier of Supramolecular Interactions in Living Systems].

PubMed

Kozlov, V A; Sapozhnikov, S P; Sheptuhina, A I; Golenkov, A V

2015-01-01

As it became known recently, in addition to the enzyme (enzymes and/or ribozymes) in living organisms occur a large number of ordinary chemical reactions without the participation of biological catalysts. These reactions are distinguished by low speed and, as a rule, the irreversibility. For example, along with diabetes mellitus, glycation and fructosilation of proteins are observed resulted in posttranslational modification with the low- or nonfunctioning protein formation which is poorly exposed to enzymatic proteolysis and therefore accumulates in the body. In addition, the known processes such as the nonenzymatic carbomoylation, pyridoxylation and thiamiation proteins. There is a reasonable basis to believe that alcoholic injury also realized through parametabolic secondary metabolites synthesis such as acetaldehyde. At the same time, the progress in supramolecular chemistry proves that in biological objects there is another large group ofparametabolic reactions caused by the formation of supramolecular complexes. Obviously, known parameterizes interactions can modify the formation of supramolecular complexes in living objects. These processes are of considerable interest for fundamental biology and fundamental and practical medicine, but they remain unexplored due to a lack of awareness of a wide range of researchers.

[Study on the interaction of hemoglobin and Cu(II)-ARS complex].

PubMed

Wu, Xiao-Hua; Miao, Ji-Gen; Miao, Yu-Qing; Chen, Jian-Rong

2007-06-01

The reaction of hemoglobin (Hb) with copper(II)-Alizarin red S (ARS) complex was studied in H3PO4-KH2PO4 buffer solution (pH 4. 2) by ultraviolet-visible spectrophotometry. The results show that the interaction of Hb and Cu(II)-ARS complex produces red ionic association complex with its maximum absorption peak at 537 nm. At the maximum absorption, the composition of the complex was determined to be n(Hb) : n(Cu(II)) : n(ARS) =1 : 4 : 8, and the apparent molar absorptivity was 1.52 x 10(5) L x mol(-1) x cm(-1). The concentration of Hb is linear with the absorbency in the range of 1.0 x 10(-7)-2.0 x 10(-6) mol x L(-1) and the regression equation was established as A = 0.026 9 + 151 675c (mol x L(-1)) with the coefficient r = 0.997 2. The effects of solution acidity, reagent amount, reaction time, temperature, ionic strength and the added surfactant were examined on the formation of the Hb-Cu(II)-ARS complex. A preliminary investigation was carried out to elucidate the reaction mechanism, and it could be concluded that the Hb and Cu(II)-ARS complex are combined mainly by electrostatic attraction. Further investigation was also undertaken to find out the effects of common amino acids and metallic ions on the formation of Hb-Cu(II)-ARS complex.

H-atom addition and abstraction reactions in mixed CO, H2CO and CH3OH ices - an extended view on complex organic molecule formation

NASA Astrophysics Data System (ADS)

Chuang, K.-J.; Fedoseev, G.; Ioppolo, S.; van Dishoeck, E. F.; Linnartz, H.

2016-01-01

Complex organic molecules (COMs) have been observed not only in the hot cores surrounding low- and high-mass protostars, but also in cold dark clouds. Therefore, it is interesting to understand how such species can be formed without the presence of embedded energy sources. We present new laboratory experiments on the low-temperature solid state formation of three complex molecules - methyl formate (HC(O)OCH3), glycolaldehyde (HC(O)CH2OH) and ethylene glycol (H2C(OH)CH2OH) - through recombination of free radicals formed via H-atom addition and abstraction reactions at different stages in the CO→H2CO→CH3OH hydrogenation network at 15 K. The experiments extend previous CO hydrogenation studies and aim at resembling the physical-chemical conditions typical of the CO freeze-out stage in dark molecular clouds, when H2CO and CH3OH form by recombination of accreting CO molecules and H-atoms on ice grains. We confirm that H2CO, once formed through CO hydrogenation, not only yields CH3OH through ongoing H-atom addition reactions, but is also subject to H-atom-induced abstraction reactions, yielding CO again. In a similar way, H2CO is also formed in abstraction reactions involving CH3OH. The dominant methanol H-atom abstraction product is expected to be CH2OH, while H-atom additions to H2CO should at least partially proceed through CH3O intermediate radicals. The occurrence of H-atom abstraction reactions in ice mantles leads to more reactive intermediates (HCO, CH3O and CH2OH) than previously thought, when assuming sequential H-atom addition reactions only. This enhances the probability to form COMs through radical-radical recombination without the need of UV photolysis or cosmic rays as external triggers.

Probing surface sites of TiO2: reactions with [HRe(CO)5] and [CH3Re(CO)5].

PubMed

Lobo-Lapidus, Rodrigo J; Gates, Bruce C

2010-10-04

Two carbonyl complexes of rhenium, [HRe(CO)(5)] and [CH(3)Re(CO)(5)], were used to probe surface sites of TiO(2) (anatase). These complexes were adsorbed from the gas phase onto anatase powder that had been treated in flowing O(2) or under vacuum to vary the density of surface OH sites. Infrared (IR) spectra demonstrate the variation in the number of sites, including Ti(+3)-OH and Ti(+4)-OH. IR and extended X-ray absorption fine structure (EXAFS) spectra show that chemisorption of the rhenium complexes led to their decarbonylation, with formation of surface-bound rhenium tricarbonyls, when [HRe(CO)(5)] was adsorbed, or rhenium tetracarbonyls, when [CH(3)Re(CO)(5)] was adsorbed. These reactions were accompanied by the formation of water and surface carbonates and removal of terminal hydroxyl groups associated with Ti(+3) and Ti(+4) ions on the anatase. Data characterizing the samples after adsorption of [HRe(CO)(5)] or [CH(3)Re(CO)(5)] determined a ranking of the reactivity of the surface OH sites, with the Ti(+3)-OH groups being the more reactive towards the rhenium complexes but the less likely to be dehydroxylated. The two rhenium pentacarbonyl probes provided complementary information, suggesting that the carbonate species originate from carbonyl ligands initially bonded to the rhenium and from hydroxyl groups of the titania surface, with the reaction leading to the formation of water and bridging hydroxyl groups on the titania. The results illustrate the value of using a family of organometallic complexes as probes of oxide surface sites.

Squarylium-based chromogenic anion sensors

NASA Astrophysics Data System (ADS)

Lee, Eun-Mi; Gwon, Seon-Yeong; Son, Young-A.; Kim, Sung-Hoon

2012-09-01

A squarylium (SQ) dye was synthesized by the reaction between squaric acid and 2,3,3-trimethylindolenine and its anion sensing properties were investigated using absorption and emission spectroscopy. This chemosensor exhibited high selectivity for CN- as compared with F-, CHCO2-, Br-, HPO4-, Cl-, and NO3- in acetonitrile, which was attributed to the formation of a 1:1 squarylium:CN- coordination complex, the formation of which was supported by the calculated geometry of the complex.

Spectrophotometric Determination of 6-Propyl-2-Thiouracil in Pharmaceutical Formulations Based on Prussian Blue Complex Formation: An Undergraduate Instrumental Analysis Laboratory Experiment

ERIC Educational Resources Information Center

Zakrzewski, Robert; Skowron, Monika; Ciesielski, Witold; Rembisz, Zaneta

2016-01-01

The laboratory experiment challenges students to determine 6-propyl-2-thiouracil (PTU) based on Prussian blue complex formation. Prussian blue is formed by ferricyanide and Fe(II) ions which are generated in situ from Fe(III) ions reduced by PTU. The absorbance of this product was measured at a wavelength of 840 nm, after a reaction time of 30…

Preparation, spectroscopic and antibacterial studies on charge-transfer complexes of 2-hydroxypyridine with picric acid and 7,7‧,8,8‧-tetracyano-p-quinodimethane

NASA Astrophysics Data System (ADS)

Gaballa, Akmal S.; Amin, Alaa S.

2015-06-01

The reactions of electron acceptors such as picric acid (HPA) and 7,7‧,8,8‧-tetracyano-p-quinodimethane (TCNQ) with 2-hydroxypyridine (HPyO) have been investigated in EtOH at room temperature. Based on elemental analysis and IR spectra of the solid CT-complexes along with the photometric titration curves for the reactions, the data obtained indicate the formation of 1:1 charge transfer complexes [(H2PyO)(PA)] and [(PyO)(HTCNQ)], respectively. The infrared and 1H NMR spectroscopic data indicate a charge transfer interaction associated with a proton migration from the acceptor to the donor followed by intramolecular hydrogen bonding in [(H2PyO)(PA)] complex. Another charge transfer interaction was observed in [(PyO)(HTCNQ)] complex. The formation constants (KCT) for the CT-complexes are shown to be strongly dependent on the type and structure of the electron acceptors. Factors affecting the CT-processes and the kinetics of thermal decomposition of the complexes have been studied. The CT complexes were screened for their antibacterial activities against selected bacterial strains.

Preparation, spectroscopic and antibacterial studies on charge-transfer complexes of 2-hydroxypyridine with picric acid and 7,7',8,8'-tetracyano-p-quinodimethane.

PubMed

Gaballa, Akmal S; Amin, Alaa S

2015-06-15

The reactions of electron acceptors such as picric acid (HPA) and 7,7',8,8'-tetracyano-p-quinodimethane (TCNQ) with 2-hydroxypyridine (HPyO) have been investigated in EtOH at room temperature. Based on elemental analysis and IR spectra of the solid CT-complexes along with the photometric titration curves for the reactions, the data obtained indicate the formation of 1:1 charge transfer complexes [(H2PyO)(PA)] and [(PyO)(HTCNQ)], respectively. The infrared and (1)H NMR spectroscopic data indicate a charge transfer interaction associated with a proton migration from the acceptor to the donor followed by intramolecular hydrogen bonding in [(H2PyO)(PA)] complex. Another charge transfer interaction was observed in [(PyO)(HTCNQ)] complex. The formation constants (KCT) for the CT-complexes are shown to be strongly dependent on the type and structure of the electron acceptors. Factors affecting the CT-processes and the kinetics of thermal decomposition of the complexes have been studied. The CT complexes were screened for their antibacterial activities against selected bacterial strains. Copyright © 2015 Elsevier B.V. All rights reserved.

Formation of Glycerol through Hydrogenation of CO Ice under Prestellar Core Conditions

NASA Astrophysics Data System (ADS)

Fedoseev, G.; Chuang, K.-J.; Ioppolo, S.; Qasim, D.; van Dishoeck, E. F.; Linnartz, H.

2017-06-01

Observational studies reveal that complex organic molecules (COMs) can be found in various objects associated with different star formation stages. The identification of COMs in prestellar cores, I.e., cold environments in which thermally induced chemistry can be excluded and radiolysis is limited by cosmic rays and cosmic-ray-induced UV photons, is particularly important as this stage sets up the initial chemical composition from which ultimately stars and planets evolve. Recent laboratory results demonstrate that molecules as complex as glycolaldehyde and ethylene glycol are efficiently formed on icy dust grains via nonenergetic atom addition reactions between accreting H atoms and CO molecules, a process that dominates surface chemistry during the “CO freeze-out stage” in dense cores. In the present study we demonstrate that a similar mechanism results in the formation of the biologically relevant molecule glycerol—HOCH2CH(OH)CH2OH—a three-carbon-bearing sugar alcohol necessary for the formation of membranes of modern living cells and organelles. Our experimental results are fully consistent with a suggested reaction scheme in which glycerol is formed along a chain of radical-radical and radical-molecule interactions between various reactive intermediates produced upon hydrogenation of CO ice or its hydrogenation products. The tentative identification of the chemically related simple sugar glyceraldehyde—HOCH2CH(OH)CHO—is discussed as well. These new laboratory findings indicate that the proposed reaction mechanism holds much potential to form even more complex sugar alcohols and simple sugars.

Reduction of pertechnetate by acetohydroxamic acid: Formation of [TcNO(AHA)2(H2O)]+ and implications for the UREX process.

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

1Harry Reid Center for Environmental Studies, Nuclear Science and Technology Division, University of Nevada, Las Vegas, Las Vegas, NV, 89154-4006; Gong, Cynthia-May S; Poineau, Frederic

2008-02-26

Reductive nitrosylation and complexation of ammonium pertechnetate by acetohydroxamic acid has been achieved in aqueous nitric and perchloric acid solutions. The kinetics of the reaction depend on the relative concentrations of the reaction components and are accelerated at higher temperatures. The reaction does not occur unless conditions are acidic. Analysis of the x-ray absorption fine structure spectroscopic data is consistent with a pseudo-octahedral geometry with the linear Tc-N-O bond typical of technetium nitrosyl compounds, and electron spin resonance spectroscopy is consistent with a the d{sup 5} Tc(II) nitrosyl complex. The nitrosyl source is generally AHA, but may be augmented bymore » products of reaction with nitric acid. The resulting low-valency trans-aquonitrosyl(diacetohydroxamic)-technetium(II) complex (1) is highly soluble in water, extremely hydrophilic, and is not extracted by tri-n-butylphosphate in a dodecane diluent. Its extraction properties are not pH-dependent; titration studies indicate a single species from pH 4.5 down to -0.6 (calculated). This molecule is resistant to oxidation by H{sub 2}O{sub 2}, even at high pH, and can undergo substitution to form other technetium nitrosyl complexes. The formation of 1 may strongly impact the fate of technetium in the nuclear fuel cycle.« less

Cobalt(II) and Cobalt(III) Coordination Compounds.

ERIC Educational Resources Information Center

Thomas, Nicholas C.; And Others

1989-01-01

Presents a laboratory experiment which illustrates the formation of tris(phenanthroline)cobalt complexes in the 2+ and 3+ oxidation states, the effect of coordination on reactions of the ligand, and the use of a ligand displacement reaction in recovering the transformed ligand. Uses IR, UV-VIS, conductivity, and NMR. (MVL)

Complex Organic Molecules Formation in Space Through Gas Phase Reactions: A Theoretical Approach

NASA Astrophysics Data System (ADS)

Redondo, Pilar; Barrientos, Carmen; Largo, Antonio

2017-02-01

Chemistry in the interstellar medium (ISM) is capable of producing complex organic molecules (COMs) of great importance to astrobiology. Gas phase and grain surface chemistry almost certainly both contribute to COM formation. Amino acids as building blocks of proteins are some of the most interesting COMs. The simplest one, glycine, has been characterized in meteorites and comets and, its conclusive detection in the ISM seems to be highly plausible. In this work, we analyze the gas phase reaction of glycine and {{{CH}}5}+ to establish the role of this process in the formation of alanine or other COMs in the ISM. Formation of protonated α- and β-alanine in spite of being exothermic processes is not viable under interstellar conditions because the different paths leading to these isomers present net activation energies. Nevertheless, glycine can evolve to protonated 1-imide-2, 2-propanediol, protonated amino acetone, protonated hydroxyacetone, and protonated propionic acid. However, formation of acetic acid and protonated methylamine is also a favorable process and therefore will be a competitive channel with the evolution of glycine to COMs.

Formation kinetics and mechanism of metastable vacancy-dioxygen complex in neutron irradiated Czochralski silicon

NASA Astrophysics Data System (ADS)

Dong, Peng; Wang, Rong; Yu, Xuegong; Chen, Lin; Ma, Xiangyang; Yang, Deren

2017-07-01

We have quantitatively investigated the formation kinetics of metastable vacancy-dioxygen (VO2) complex in a structure of [VO + Oi], where a VO complex is trapped in a next-neighbor position to an interstitial oxygen atom (Oi). It is found that the VO annihilation is accompanied by the generation of metastable [VO + Oi] complex during annealing in the temperature range of 220-250 °C. The activation energy for [VO + Oi] generation appears at around 0.48 eV, which is much lower than the counterpart of stable VO2 complex. This indicates that the formation of [VO + Oi] complex originates from the reaction between VO and Oi. The ab initio calculations show that the formation energy of [VO + Oi] complex is larger than that of VO2 complex, which means that [VO + Oi] complex is thermodynamically unfavorable as compared to VO2 complex. However, the binding energy of [VO + Oi] complex is positive, indicating that [VO + Oi] complex is stable against decomposition of VO and Oi in silicon. It is believed that [VO + Oi] complex serves as the intermediate for VO to VO2 conversion.

Reaction with cyanide of hydroxylamine oxidoreductase of Nitrosomonas europaea.

PubMed

Logan, M S; Balny, C; Hooper, A B

1995-07-18

Hydroxylamine oxidoreductase (HAO) catalyzes the reaction NH2OH+H2O-->HNO2+4e- + 4H+, a step in the energy-generating oxidation of ammonia to nitrite by the bacterium Nitrosomonas europaea. Each subunit of HAO contains 7 c-hemes and 1 heme P460. The latter, c-heme cross-linked from a methylene carbon to the ring of a protein tyrosine, forms part of the active site. The iron of heme P460 is probably linked by a bridging ligand to the iron of a c-heme. Here, the reaction of cyanide with ferric HAO was studied by optical, transient, and steady state kinetic techniques. The molecules, F-, Cl-, Br-, N3-, SCN-, and OCN- did not react with HAO. A single molecule of cyanide bound with high affinity to heme P460 of HAO. The optical and kinetic characteristics of formation of the monocyano complex of HAO resembled those of cyanide derivatives of other heme proteins. Cyanide, in the monocyano complex, was a noncompetitive inhibitor and remained bound during turnover. HAO was found in two forms. The most common form, HAO-A, formed only the monocyano derivative of heme P460, whereas the other, HAO-B, formed a mono- and dicyano complex. The optical properties and kinetics of formation of the mono- and dicyano complexes were different enough to easily allow independent analysis. The optical and kinetic characteristics of formation of the monocyano complex of heme P460 of HAO A and B were very similar. The dicyano complex of HAO-B appeared to result from the addition of a second molecule of cyanide to heme P460. The rate of conversion of the monocyano to the dicyano complex was stimulated 100-fold by the binding of substrate. Formation of the monoheme complex inhibited enzyme activity. The kinetic constants for the first-order formation of the monocyano derivative and the inhibition of substrate oxidation (under either transient or steady-state conditions) were different. The apparent discrepancy could be resolved by the hypothesis that HAO is functionally a dimer in which electrons rapidly equilibrate between the c-hemes of each subunit but not between oligomers. The results form the basis for the use of cyanide as a probe of the active site of HAO.

A Design Principle for an Autonomous Post-translational Pattern Formation.

PubMed

Sugai, Shuhei S; Ode, Koji L; Ueda, Hiroki R

2017-04-25

Previous autonomous pattern-formation models often assumed complex molecular and cellular networks. This theoretical study, however, shows that a system composed of one substrate with multisite phosphorylation and a pair of kinase and phosphatase can generate autonomous spatial information, including complex stripe patterns. All (de-)phosphorylation reactions are described with a generic Michaelis-Menten scheme, and all species freely diffuse without pre-existing gradients. Computational simulation upon >23,000,000 randomly generated parameter sets revealed the design motifs of cyclic reaction and enzyme sequestration by slow-diffusing substrates. These motifs constitute short-range positive and long-range negative feedback loops to induce Turing instability. The width and height of spatial patterns can be controlled independently by distinct reaction-diffusion processes. Therefore, multisite reversible post-translational modification can be a ubiquitous source for various patterns without requiring other complex regulations such as autocatalytic regulation of enzymes and is applicable to molecular mechanisms for inducing subcellular localization of proteins driven by post-translational modifications. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

The anaerobic digestion process

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

Rivard, C.J.; Boone, D.R.

1996-01-01

The microbial process of converting organic matter into methane and carbon dioxide is so complex that anaerobic digesters have long been treated as {open_quotes}black boxes.{close_quotes} Research into this process during the past few decades has gradually unraveled this complexity, but many questions remain. The major biochemical reactions for forming methane by methanogens are largely understood, and evolutionary studies indicate that these microbes are as different from bacteria as they are from plants and animals. In anaerobic digesters, methanogens are at the terminus of a metabolic web, in which the reactions of myriads of other microbes produce a very limited rangemore » of compounds - mainly acetate, hydrogen, and formate - on which the methanogens grow and from which they form methane. {open_quotes}Interspecies hydrogen-transfer{close_quotes} and {open_quotes}interspecies formate-transfer{close_quotes} are major mechanisms by which methanogens obtain their substrates and by which volatile fatty acids are degraded. Present understanding of these reactions and other complex interactions among the bacteria involved in anaerobic digestion is only now to the point where anaerobic digesters need no longer be treated as black boxes.« less

Formation Mechanism of Oxide-Sulfide Complex Inclusions in High-Sulfur-Containing Steel Melts

NASA Astrophysics Data System (ADS)

Shin, Jae Hong; Park, Joo Hyun

2018-02-01

The [S] content in resulfurized steel is controlled in the range of 200 to 800 ppm to ensure good machinability and workability. It is well known that "MgAl2O4(spinel)+CaS" complex inclusions are formed in molten steel during the ladle refining process, and these cause nozzle clogging during continuous casting. Thus, in the present study, the "Refractory-Slag-Metal-Inclusions (ReSMI)" multiphase reaction model was employed in conjunction with experiments to investigate the influence of slag composition and [S] content in the steel on the formation of oxide-sulfide complex inclusions. The critical [S] and [Al] contents necessary for the precipitation of CaS in the CaO-Al2O3-MgO-SiO2 (CAMS) oxide inclusions were predicted from the composition of the liquid inclusions, as observed by scanning electron microscopy-electron dispersive spectrometry (SEM-EDS) and calculated using the ReSMI multiphase reaction model. The critical [S] content increases with increasing content of SiO2 in the slag at a given [Al] content. Formation mechanisms for spinel+CaS and spinel+MnS complex inclusions were also proposed.

The Kinetic Mechanism of Phenylalanine Hydroxylase: Intrinsic Binding and Rate Constants from Single Turnover Experiments†

PubMed Central

Roberts, Kenneth M.; Pavon, Jorge Alex; Fitzpatrick, Paul F.

2013-01-01

Phenylalanine hydroxylase (PheH) catalyzes the key step in the catabolism of dietary phenylalanine, its hydroxylation to tyrosine using tetrahydrobiopterin (BH4) and O2. A complete kinetic mechanism for PheH was determined by global analysis of single turnover data in the reaction of PheHΔ117, a truncated form of the enzyme lacking the N-terminal regulatory domain. Formation of the productive PheHΔ117-BH4-phenylalanine complex begins with the rapid binding of BH4 (Kd = 65 µM). Subsequent addition of phenylalanine to the binary complex to form the productive ternary complex (Kd = 130 µM) is approximately ten-fold slower. Both substrates can also bind to the free enzyme to form inhibitory binary complexes. O2 rapidly binds to the productive ternary complex; this is followed by formation of an unidentified intermediate, detectable as a decrease in absorbance at 340 nm, with a rate constant of 140 s−1. Formation of the 4a-hydroxypterin and Fe(IV)O intermediates is ten-fold slower and is followed by the rapid hydroxylation of the amino acid. Product release is the rate-determining step and largely determines kcat. Similar reactions using 6-methyltetrahydropterin indicate a preference for the physiological pterin during hydroxylation. PMID:23327364

Synthesis, crystal growth, structural and physicochemical studies of novel binary organic complex: 4-chloroaniline-3-hydroxy-4-methoxybenzaldehyde

NASA Astrophysics Data System (ADS)

Sharma, K. P.; Reddi, R. S. B.; Bhattacharya, S.; Rai, R. N.

2012-06-01

The solid-state reaction, which is solvent free and green synthesis, has been adopted to explore the novel compound. The phase diagram of 4-chloroaniline (CA) and 3-hydroxy-4-methoxybenzaldehyde (HMB) system shows the formation of a novel 1:1 molecular complex, and two eutectics on either sides of complex. Thermochemical studies of complex and eutectics have been carried out for various properties such as heat of fusion, entropy of fusion, Jackson's parameters, interfacial energy and excess thermodynamic functions. The formation of molecular complex was also studied by IR, NMR, elemental analysis and UV-Vis absorption spectra. The single crystal of molecular complex was grown and its XRD study confirms the formation of complex and identifies the crystal structure and atomic packing of crystal of complex. Transmission spectra of grown crystal of the complex show 70% transmittance efficiency with cut off wavelength 412 nm. The band gap and refractive index of the crystal of complex have also been studied.

Rapid-mix and chemical quench studies of ferredoxin-reduced stearoyl-acyl carrier protein desaturase.

PubMed

Lyle, Karen S; Haas, Jeffrey A; Fox, Brian G

2003-05-20

Stearoyl-ACP Delta9 desaturase (Delta9D) catalyzes the NADPH- and O(2)-dependent insertion of a cis double bond between the C9 and C10 positions of stearoyl-ACP (18:0-ACP) to produce oleoyl-ACP (18:1-ACP). This work revealed the ability of reduced [2Fe-2S] ferredoxin (Fd) to act as a catalytically competent electron donor during the rapid conversion of 18:0-ACP into 18:1-ACP. Experiments on the order of addition for substrate and reduced Fd showed high conversion of 18:0-ACP to 18:1-ACP (approximately 95% per Delta9D active site in a single turnover) when 18:0-ACP was added prior to reduced Fd. Reactions of the prereduced enzyme-substrate complex with O(2) and the oxidized enzyme-substrate complex with reduced Fd were studied by rapid-mix and chemical quench methods. For reaction of the prereduced enzyme-substrate complex, an exponential burst phase (k(burst) = 95 s(-1)) of product formation accounted for approximately 90% of the turnover expected for one subunit in the dimeric protein. This rapid phase was followed by a slower phase (k(linear) = 4.0 s(-1)) of product formation corresponding to the turnover expected from the second subunit. For reaction of the oxidized enzyme-substrate complex with excess reduced Fd, a slower, linear rate (k(obsd) = 3.4 s(-1)) of product formation was observed over approximately 1.5 turnovers per Delta9D active site potentially corresponding to a third phase of reaction. An analysis of the deuterium isotope effect on the two rapid-mix reaction sequences revealed only a modest effect on k(burst) ((D)k(burst) approximately 1.5) and k(linear) (D)k(linear) approximately 1.4), indicating C-H bond cleavage does not contribute significantly to the rate-limiting steps of pre-steady-state catalysis. These results were used to assemble and evaluate a minimal kinetic model for Delta9D catalysis.

Complex supramolecular interfacial tessellation through convergent multi-step reaction of a dissymmetric simple organic precursor

NASA Astrophysics Data System (ADS)

Zhang, Yi-Qi; Paszkiewicz, Mateusz; Du, Ping; Zhang, Liding; Lin, Tao; Chen, Zhi; Klyatskaya, Svetlana; Ruben, Mario; Seitsonen, Ari P.; Barth, Johannes V.; Klappenberger, Florian

2018-03-01

Interfacial supramolecular self-assembly represents a powerful tool for constructing regular and quasicrystalline materials. In particular, complex two-dimensional molecular tessellations, such as semi-regular Archimedean tilings with regular polygons, promise unique properties related to their nontrivial structures. However, their formation is challenging, because current methods are largely limited to the direct assembly of precursors, that is, where structure formation relies on molecular interactions without using chemical transformations. Here, we have chosen ethynyl-iodophenanthrene (which features dissymmetry in both geometry and reactivity) as a single starting precursor to generate the rare semi-regular (3.4.6.4) Archimedean tiling with long-range order on an atomically flat substrate through a multi-step reaction. Intriguingly, the individual chemical transformations converge to form a symmetric alkynyl-Ag-alkynyl complex as the new tecton in high yields. Using a combination of microscopy and X-ray spectroscopy tools, as well as computational modelling, we show that in situ generated catalytic Ag complexes mediate the tecton conversion.

Chemical composition of donor-acceptor complexes of hydroxyoxo(5,10,15,20-tetraphenylporphinato)molybdenum(V) with 3,5-dimethylpyrazole and equilibrium constants for their formation

NASA Astrophysics Data System (ADS)

Motorina, E. V.; Lomova, T. N.

2017-11-01

The results from a quantitative study of reactions between hydroxyoxo(5,10,15,20-tetraphenylporphinato)molybdenum(V) (O=Mo(OH)TPP) and 3,5-dimethylpyrazole, a biologically active base, in toluene are presented. The chemical structure and key parameters of intermediates and reaction products are determined by spectral means. The equilibrium constant ( K = 51.3 L/mol) is calculated and a full kinetic description of simple reactions that occur in this system during complex transformation is obtained. The prospect of using a mixed porphyrin-containing complex as a receptor for 3,5-dimethylpyrazole, a building block for alkaloids and pharmaceutical preparations, is substantiated.

Formation and Recondensation of Complex Organic Molecules During Protostellar Luminosity Outbursts

NASA Technical Reports Server (NTRS)

Taquet, Vianney; Wirstrom, Eva S.; Charnley, Steven B.

2016-01-01

During the formation of stars, the accretion of surrounding material toward the central object is thought to undergo strong luminosity outbursts followed by long periods of relative quiescence, even at the early stages of star formation when the protostar is still embedded in a large envelope. We investigated the gas-phase formation and recondensation of the complex organic molecules (COMs) di-methyl ether and methyl formate, induced by sudden ice evaporation processes occurring during luminosity outbursts of different amplitudes in protostellar envelopes. For this purpose, we updated a gas-phase chemical network forming COMs in which ammonia plays a key role. The model calculations presented here demonstrate that ion-molecule reactions alone could account for the observed presence of di-methyl ether and methyl formate in a large fraction of protostellar cores without recourse to grain-surface chemistry, although they depend on uncertain ice abundances and gas-phase reaction branching ratios. In spite of the short outburst timescales of about 100 years, abundance ratios of the considered species higher than 10% with respect to methanol are predicted during outbursts due to their low binding energies relative to water and methanol which delay their recondensation during cooling. Although the current luminosity of most embedded protostars would be too low to produce complex organics in the hot-core regions that are observable with current sub-millimetric interferometers, previous luminosity outburst events would induce the formation of COMs in extended regions of protostellar envelopes with sizes increasing by up to one order of magnitude.

Formation and Recondensation of Complex Organic Molecules during Protostellar Luminosity Outbursts

NASA Astrophysics Data System (ADS)

Taquet, Vianney; Wirström, Eva S.; Charnley, Steven B.

2016-04-01

During the formation of stars, the accretion of surrounding material toward the central object is thought to undergo strong luminosity outbursts followed by long periods of relative quiescence, even at the early stages of star formation when the protostar is still embedded in a large envelope. We investigated the gas-phase formation and recondensation of the complex organic molecules (COMs) di-methyl ether and methyl formate, induced by sudden ice evaporation processes occurring during luminosity outbursts of different amplitudes in protostellar envelopes. For this purpose, we updated a gas-phase chemical network forming COMs in which ammonia plays a key role. The model calculations presented here demonstrate that ion-molecule reactions alone could account for the observed presence of di-methyl ether and methyl formate in a large fraction of protostellar cores without recourse to grain-surface chemistry, although they depend on uncertain ice abundances and gas-phase reaction branching ratios. In spite of the short outburst timescales of about 100 years, abundance ratios of the considered species higher than 10% with respect to methanol are predicted during outbursts due to their low binding energies relative to water and methanol which delay their recondensation during cooling. Although the current luminosity of most embedded protostars would be too low to produce complex organics in the hot-core regions that are observable with current sub-millimetric interferometers, previous luminosity outburst events would induce the formation of COMs in extended regions of protostellar envelopes with sizes increasing by up to one order of magnitude.

Metal-Free Oxidative C-C Bond Formation through C-H Bond Functionalization.

PubMed

Narayan, Rishikesh; Matcha, Kiran; Antonchick, Andrey P

2015-10-12

The formation of C-C bonds embodies the core of organic chemistry because of its fundamental application in generation of molecular diversity and complexity. C-C bond-forming reactions are well-known challenges. To achieve this goal through direct functionalization of C-H bonds in both of the coupling partners represents the state-of-the-art in organic synthesis. Oxidative C-C bond formation obviates the need for prefunctionalization of both substrates. This Minireview is dedicated to the field of C-C bond-forming reactions through direct C-H bond functionalization under completely metal-free oxidative conditions. Selected important developments in this area have been summarized with representative examples and discussions on their reaction mechanisms. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Study on reaction mechanism by analysis of kinetic energy spectra of light particles and formation of final products

NASA Astrophysics Data System (ADS)

Giardina, G.; Mandaglio, G.; Nasirov, A. K.; Anastasi, A.; Curciarello, F.; Fazio, G.

2018-05-01

The sensitivity of reaction mechanism in the formation of compound nucleus (CN) by the analysis of kinetic energy spectra of light particles and of reaction products are shown. The dependence of the P CN fusion probability of reactants and W sur survival probability of CN against fission at its deexcitation on the mass and charge symmetries in the entrance channel of heavy-ion collisions, as well as on the neutron numbers is discussed. The possibility of conducting a complex program of investigations of the complete fusion by reliable ways depends on the detailed and refined methods of experimental and theoretical analyses.

Formate as a CO surrogate for cascade processes: Rh-catalyzed cooperative decarbonylation and asymmetric Pauson-Khand-type cyclization reactions.

PubMed

Lee, Hang Wai; Chan, Albert S C; Kwong, Fuk Yee

2007-07-07

A rhodium-(S)-xyl-BINAP complex-catalyzed tandem formate decarbonylation and [2 + 2 + 1] carbonylative cyclization is described; this cooperative process utilizes formate as a condensed CO source, and the newly developed cascade protocol can be extended to its enantioselective version, providing up to 94% ee of the cyclopentenone adducts.

Transient removal of proflavine inhibition of bovine beta-trypsin by the bovine basic pancreatic trypsin inhibitor (Kunitz). A case for "chronosteric effects".

PubMed

Antonini, E; Ascenzi, P; Bolognesi, M; Menegatti, E; Guarneri, M

1983-04-25

The formation of the bovine beta-trypsin-bovine basic pancreatic trypsin inhibitor (Kunitz) (BPTI) complex was monitored, making use of three different signals: proflavine displacement, optical density changes in the ultraviolet region, and the loss of the catalytic activity. The rates of the reactions indicated by the three different signals were similar at neutral pH, but diverged at low pH. At pH 3.50, proflavine displacement precedes the optical density changes in the ultraviolet and the loss of enzyme activity by several orders of magnitude in time (Antonini, E., Ascenzi, P., Menegatti, E., and Guarneri, M. (1983) Biopolymers 22, 363-375). These data indicated that the bovine beta-trypsin-BPTI complex formation is a multistage process and led to the prediction that, at pH 3.50, BPTI addition to the bovine beta-trypsin-proflavine complex would remove proflavine inhibition and the enzyme would recover transiently its catalytic activity before being irreversibly inhibited by completion of BPTI binding. The kinetic evidences, by completion of BPTI binding. The kinetic evidences, here shown, verified this prediction, indicating that during the bovine beta-trypsin-BPTI complex formation one transient intermediate occurs, which is not able to bind proflavine but may bind and hydrolyze the substrate. Thus, the observed peculiar catalytic behavior is in line with the proposed reaction mechanism for the bovine beta-trypsin-BPTI complex formation, which postulates a sequence of distinct polar and apolar interactions at the contact area.

A study of [Co2(alkyne)(binap)(CO)4] complexes (BINAP=(1,1'-binaphthalene)-2,2'-diylbis(diphenylphosphine)).

PubMed

Gibson, Susan E; Kaufmann, Karina A C; Loch, Jennifer A; Steed, Jonathan W; White, Andrew J P

2005-04-08

Understanding the interaction of chiral ligands, alkynes, and alkenes with cobaltcarbonyl sources is critical to learning more about the mechanism of the catalytic, asymmetric Pauson-Khand reaction. We have successfully characterized complexes of the type [Co2(alkyne)(binap)(CO)4] (BINAP=(1,1'-binaphthalene)-2,2'-diylbis(diphenylphosphine)) and shown that diastereomer interconversion occurs under Pauson-Khand reaction conditions when alkyne=HC[triple bond]CCO2Me. Attempts to isolate [Co2(alkyne)(binap)(CO)x] complexes with coordinated alkenes led to the formation of cobaltacyclopentadiene species.

Exit channel dynamics in a micro-hydrated SN2 reaction of the hydroxyl anion.

PubMed

Otto, R; Brox, J; Trippel, S; Stei, M; Best, T; Wester, R

2013-08-29

We report on the reaction dynamics of the monosolvated SN2 reaction of cold OH(-)(H2O) with CH3I that have been studied using crossed beam ion imaging. Two SN2 reaction channels are possible for this reaction: Formation of unsolvated I(-) and of solvated I(-)(H2O) products. We find a strong preference for the formation of unsolvated I(-) reaction products with respect to the energetically favored reaction toward solvated I(-)(H2O). Angle differential cross section measurements reveal similar velocity and angular distributions for all solvated and parts of the unsolvated reaction products. We furthermore find that the contribution of these two products to the total product flux can be described by the same collision energy dependence. We interpret our findings in terms of a joint reaction mechanism in which a CH3OH(H2O)···I(-) complex is formed that decays into either solvated or unsolvated products. Quantum chemical calculation are used to support this assumption.

A Molecular Copper Catalyst for Hydrogenation of CO­2 to Formate

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

Zall, Christopher M.; Linehan, John C.; Appel, Aaron M.

2015-09-04

There is widespread interest in the hydrogenation of CO2 to energy-rich products such as formate. However, first-row transition metal complexes that catalyze the hydrogenation of CO2 to formate remain rare. Copper phosphine complexes are widely used in the reduction of organic substrates but have not previously been used as catalysts for the conversion of H2 and CO2 to formate. Here we demonstrate that the triphosphine-ligated copper(I) complex LCu(MeCN)PF6 is an active catalyst for CO2 hydrogenation in the presence of a suitable base. Screening of bases and studies of catalytic reactions by in operando spectroscopy revealed important and unusual roles formore » the base in promoting H2 activation and turnover.« less

PEaCH4 v.2.0: A modelling platform to predict early diagenetic processes in marine sediments with a focus on biogenic methane - Case study: Offshore Namibia

NASA Astrophysics Data System (ADS)

Arning, Esther T.; Häußler, Steffen; van Berk, Wolfgang; Schulz, Hans-Martin

2016-07-01

The modelling of early diagenetic processes in marine sediments is of interest in marine science, and in the oil and gas industry, here, especially with respect to methane occurrence and gas hydrate formation as resources. Early diagenesis in marine sediments evolves from a complex web of intertwining (bio)geochemical reactions. It comprises microbially catalysed reactions and inorganic mineral-water-gas interactions. A model that will describe and consider all of these reactions has to be complex. However, it should be user-friendly, as well as to be applicable for a broad community and not only for experts in the field of marine chemistry. The presented modelling platform PeaCH4 v.2.0 combines both aspects, and is Microsoft Excel©-based. The modelling tool is PHREEQC (version 2), a computer programme for speciation, batch-reaction, one-dimensional transport, and inverse geochemical calculations. The conceptual PEaCH4 model is based on the conversion of sediment-bound degradable organic matter. PEaCH4 v.2.0 was developed to quantify and predict early diagenetic processes in marine sediments with the focus on biogenic methane formation and its phase behaviour, and allows carbon mass balancing. In regard to the irreversible degradation of organic matter, it comprises a "reaction model" and a "kinetic model" to predict methane formation. Both approaches differ in their calculations and outputs as the "kinetic model" considers the modelling time to integrate temperature dependent biogenic methane formation in its calculations, whereas the "reaction model" simply relies on default organic matter degradation. With regard to the inorganic mineral-water-gas interactions, which are triggered by irreversible degradation of organic matter, PEaCH4 v.2.0 is based on chemical equilibrium thermodynamics, appropriate mass-action laws, and their temperature dependent equilibrium constants. The programme is exemplarily presented with the example of upwelling sediments off Namibia, ODP Leg 175, Site 1082. The application demonstrates that the modelling platform PEaCH4 v.2.0 provides a user-friendly, but complex scientific tool that delivers retraceable information about early diagenetic processes and products in marine sediments.

Reagent Anions for Charge Inversion of Polypeptide/Protein Cations in the Gas Phase

PubMed Central

He, Min; Emory, Joshua F.; McLuckey, Scott A.

2005-01-01

Various reagent anions capable of converting polypeptide cations to anions via ion/ion reactions have been investigated. The major charge inversion reaction channels include multiple proton transfer and adduct formation. Dianions composed of sulfonate groups as the negative charge carriers show essentially exclusive adduct formation in converting protonated peptides and proteins to anions. Dianions composed of carboxylate groups, on the other hand, show far more charge inversion via multiple proton transfer, with the degree of adduct formation dependent upon both the size of the polypeptide and the spacings between carboxylate groups in the dianion. More highly charged carboxylate-containing anions, such as those derived from carboxylate-terminated polyamidoamine half-generation dendrimers show charge inversion to give anion charges as high in magnitude as −4, with the degree of adduct formation being inversely related to dendrimer generation. All observations can be interpreted on the basis of charge inversion taking place via a long-lived chemical complex. The lifetime of this complex is related to the strengths and numbers of the interactions of the reactants in the complex. Calculations with model systems are fully consistent with sulfonate groups giving rise to more stable complexes. The kinetic stability of the complex can also be affected by the presence of electrostatic repulsion if it is multiply charged. In general, this situation destabilizes the complex and reduces the likelihood for observation of adducts. The findings highlight the characteristics of multiply charged anions that play roles in determining the nature of charge inversion products associated with protonated peptides and proteins. PMID:15889906

Understanding the Reaction Chemistry of 2,2':5',2''-Terthiophene Films with Vapor-Deposited Ag, Al, and Ca

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

Sang, Lingzi; Matz, Dallas L.; Pemberton, Jeanne E.

The reaction chemistry of vapor-deposited 2,2':5',2''-terthiophene (α-3T) solid-state thin films with postdeposited Ag, Al, and Ca is investigated in ultrahigh vacuum using Raman spectroscopy. Vapor-deposited Ag forms nanoparticles on these films and induces considerable surface enhanced Raman scattering (SERS) along with a change in molecular symmetry of adjacent α-3T and formation of Ag–S bonds; no other reaction chemistry is observed. Vapor-deposited Al and Ca undergo chemical reaction with α-3T initiated by metal-to-α-3T electron transfer. For Al, the resulting product is predominantly amorphous carbon through initial radical formation and subsequent decomposition reactions. For Ca, the spectral evidence suggests two pathways: onemore » leading to α-3T polymerization and the other resulting in thiophene ring opening, both initiated by radical formation through Ca-to-α-3T electron transfer. These interfacial reactions reflect the complex chemistry that can occur between low work function metals and thiophene-based oligomers. This reactivity is strongly correlated with metal work function.« less

Understanding the Reaction Chemistry of 2,2':5',2"-Terthiophene Films with Vapor-Deposited Ag, Al, and Ca

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

Sang, Lingzi; Matz, Dallas L.; Pemberton, Jeanne E.

The reaction chemistry of vapor-deposited 2,2':5',2''-terthiophene (α-3T) solid-state thin films with postdeposited Ag, Al, and Ca is investigated in ultrahigh vacuum using Raman spectroscopy. Vapor-deposited Ag forms nanoparticles on these films and induces considerable surface enhanced Raman scattering (SERS) along with a change in molecular symmetry of adjacent α-3T and formation of Ag–S bonds; no other reaction chemistry is observed. Vapor-deposited Al and Ca undergo chemical reaction with α-3T initiated by metal-to-α-3T electron transfer. For Al, the resulting product is predominantly amorphous carbon through initial radical formation and subsequent decomposition reactions. For Ca, the spectral evidence suggests two pathways: onemore » leading to α-3T polymerization and the other resulting in thiophene ring opening, both initiated by radical formation through Ca-to-α-3T electron transfer. These interfacial reactions reflect the complex chemistry that can occur between low work function metals and thiophene-based oligomers. This reactivity is strongly correlated with metal work function.« less

Hydrogen transfer reactions of interstellar Complex Organic Molecules

NASA Astrophysics Data System (ADS)

Álvarez-Barcia, S.; Russ, P.; Kästner, J.; Lamberts, T.

2018-06-01

Radical recombination has been proposed to lead to the formation of complex organic molecules (COMs) in CO-rich ices in the early stages of star formation. These COMs can then undergo hydrogen addition and abstraction reactions leading to a higher or lower degree of saturation. Here, we have studied 14 hydrogen transfer reactions for the molecules glyoxal, glycoaldehyde, ethylene glycol, and methylformate and an additional three reactions where CHnO fragments are involved. Over-the-barrier reactions are possible only if tunneling is invoked in the description at low temperature. Therefore the rate constants for the studied reactions are calculated using instanton theory that takes quantum effects into account inherently. The reactions were characterized in the gas phase, but this is expected to yield meaningful results for CO-rich ices due to the minimal alteration of reaction landscapes by the CO molecules. We found that rate constants should not be extrapolated based on the height of the barrier alone, since the shape of the barrier plays an increasingly larger role at decreasing temperature. It is neither possible to predict rate constants based only on considering the type of reaction, the specific reactants and functional groups play a crucial role. Within a single molecule, though, hydrogen abstraction from an aldehyde group seems to be always faster than hydrogen addition to the same carbon atom. Reactions that involve heavy-atom tunneling, e.g., breaking or forming a C-C or C-O bond, have rate constants that are much lower than those where H transfer is involved.

Chemical dynamics simulations of the monohydrated OH{sup −}(H{sub 2}O) + CH{sub 3}I reaction. Atomic-level mechanisms and comparison with experiment

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

Xie, Jing; Hase, William L., E-mail: bill.hase@ttu.edu; Otto, Rico

2015-06-28

Direct dynamics simulations, with B97-1/ECP/d theory, were performed to study the role of microsolvation for the OH{sup −}(H{sub 2}O) + CH{sub 3}I reaction. The S{sub N}2 reaction dominates at all reactant collision energies, but at higher collision energies proton transfer to form CH{sub 2}I{sup −}, and to a lesser extent CH{sub 2}I{sup −} (H{sub 2}O), becomes important. The S{sub N}2 reaction occurs by direct rebound and stripping mechanisms, and 28 different indirect atomistic mechanisms, with the latter dominating. Important components of the indirect mechanisms are the roundabout and formation of S{sub N}2 and proton transfer pre-reaction complexes and intermediates, includingmore » [CH{sub 3}--I--OH]{sup −}. In contrast, for the unsolvated OH{sup −} + CH{sub 3}I S{sub N}2 reaction, there are only seven indirect atomistic mechanisms and the direct mechanisms dominate. Overall, the simulation results for the OH{sup −}(H{sub 2}O) + CH{sub 3}I S{sub N}2 reaction are in good agreement with experiment with respect to reaction rate constant, product branching ratio, etc. Differences between simulation and experiment are present for the S{sub N}2 velocity scattering angle at high collision energies and the proton transfer probability at low collision energies. Equilibrium solvation by the H{sub 2}O molecule is unimportant. The S{sub N}2 reaction is dominated by events in which H{sub 2}O leaves the reactive system as CH{sub 3}OH is formed or before CH{sub 3}OH formation. Formation of solvated products is unimportant and participation of the (H{sub 2}O)CH{sub 3}OH---I{sup −} post-reaction complex for the S{sub N}2 reaction is negligible.« less

Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation

PubMed Central

Serganov, Alexander; Keiper, Sonja; Malinina, Lucy; Tereshko, Valentina; Skripkin, Eugene; Höbartner, Claudia; Polonskaia, Anna; Phan, Anh Tuân; Wombacher, Richard; Micura, Ronald; Dauter, Zbigniew; Jäschke, Andres; Patel, Dinshaw J

2015-01-01

The majority of structural efforts addressing RNA’s catalytic function have focused on natural ribozymes, which catalyze phosphodiester transfer reactions. By contrast, little is known about how RNA catalyzes other types of chemical reactions. We report here the crystal structures of a ribozyme that catalyzes enantioselective carbon-carbon bond formation by the Diels-Alder reaction in the unbound state and in complex with a reaction product. The RNA adopts a λ-shaped nested pseudoknot architecture whose preformed hydrophobic pocket is precisely complementary in shape to the reaction product. RNA folding and product binding are dictated by extensive stacking and hydrogen bonding, whereas stereoselection is governed by the shape of the catalytic pocket. Catalysis is apparently achieved by a combination of proximity, complementarity and electronic effects. We observe structural parallels in the independently evolved catalytic pocket architectures for ribozyme- and antibody-catalyzed Diels-Alder carbon-carbon bond-forming reactions. PMID:15723077

Reductive Elimination from Phosphine-Ligated Alkylpalladium(II) Amido Complexes To Form sp3 Carbon-Nitrogen Bonds.

PubMed

Peacock, D Matthew; Jiang, Quan; Hanley, Patrick S; Cundari, Thomas R; Hartwig, John F

2018-04-11

We report the formation of phosphine-ligated alkylpalladium(II) amido complexes that undergo reductive elimination to form alkyl-nitrogen bonds and a combined experimental and computational investigation of the factors controlling the rates of these reactions. The free-energy barriers to reductive elimination from t-Bu 3 P-ligated complexes were significantly lower (ca. 3 kcal/mol) than those previously reported from NHC-ligated complexes. The rates of reactions from complexes containing a series of electronically and sterically varied anilido ligands showed that the reductive elimination is slower from complexes of less electron-rich or more sterically hindered anilido ligands than from those containing more electron-rich and less hindered anilido ligands. Reductive elimination of alkylamines also occurred from complexes bearing bidentate P,O ligands. The rates of reactions of these four-coordinate complexes were slower than those for reactions of the three-coordinate, t-Bu 3 P-ligated complexes. The calculated pathway for reductive elimination from rigid, 2-methoxyarylphosphine-ligated complexes does not involve initial dissociation of the oxygen. Instead, reductive elimination is calculated to occur directly from the four-coordinate complex in concert with a lengthening of the Pd-O bond. To investigate this effect experimentally, a four-coordinate Pd(II) anilido complex containing a flexible, aliphatic linker between the P and O atoms was synthesized. Reductive elimination from this complex was faster than that from the analogous complex containing the more rigid, aryl linker. The flexible linker enables full dissociation of the ether ligand during reductive elimination, leading to the faster reaction of this complex.

Synthesis, characterization and solid-state properties of [Zn(Hdmmthiol)2]\\cdot2H2O complex

NASA Astrophysics Data System (ADS)

Dagdelen, Fethi; Aydogdu, Yildirim; Dey, Kamalendu; Biswas, Susobhan

2016-05-01

The zinc(II) complex with tridentate thiohydrazone ligand have been prepared by metal template reaction. The metal template reaction was used to prepare the zinc (II) complex with tridentate thiohydrazone ligand. The reaction of diacetylmonoxime and, morpholine N-thiohydrazidewith Zn(OAc)2 \\cdot2H2O under reflux yielded the formation of the [Zn(Hdmmthiol )2]\\cdot2H2O complex. The complex was characterized by a combination of protocols including elemental analysis, UV+vis, FT-IR, TG and PXRD. The temperature dependence of the electrical conductivity and the optical property of the [Zn(Hdmmthiol )2] \\cdot2H2O complex is called H2dammthiol was studied. Powder X-ray diffraction (PXRD) method was used to investigate the crystal structure of the sample. The zinc complex was shown to be a member of the triclinic system. The zinc complex was determined to have n-type conductivity as demonstrated in the hot probe measurements. The complex was determined to display direct optical transition with band gaps of 2.52eV as determined by the optical absorption analysis.

Reaction-diffusion controlled growth of complex structures

NASA Astrophysics Data System (ADS)

Noorduin, Willem; Mahadevan, L.; Aizenberg, Joanna

2013-03-01

Understanding how the emergence of complex forms and shapes in biominerals came about is both of fundamental and practical interest. Although biomineralization processes and organization strategies to give higher order architectures have been studied extensively, synthetic approaches to mimic these self-assembled structures are highly complex and have been difficult to emulate, let alone replicate. The emergence of solution patterns has been found in reaction-diffusion systems such as Turing patterns and the BZ reaction. Intrigued by this spontaneous formation of complexity we explored if similar processes can lead to patterns in the solid state. We here identify a reaction-diffusion system in which the shape of the solidified products is a direct readout of the environmental conditions. Based on insights in the underlying mechanism, we developed a toolbox of engineering strategies to deterministically sculpt patterns and shapes, and combine different morphologies to create a landscape of hierarchical multi scale-complex tectonic architectures with unprecedented levels of complexity. These findings may hold profound implications for understanding, mimicking and ultimately expanding upon nature's morphogenesis strategies, allowing the synthesis of advanced highly complex microscale materials and devices. WLN acknowledges the Netherlands Organization for Scientific Research for financial support

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

Mugridge, Jeffrey; Fiedler, Dorothea; Raymond, Kenneth

A ferrocene-based biscatecholamide ligand was prepared and investigated for the formation of metal-ligand supramolecular assemblies with different metals. Reaction with Ge(IV) resulted in the formation of a variety of Ge{sub n}L{sub m} coordination complexes, including [Ge{sub 2}L{sub 3}]{sup 4-} and [Ge{sub 2}L{sub 2}({mu}-OMe){sub 2}]{sup 2-}. The ligand's ability to swivel about the ferrocenyl linker and adopt different conformations accounts for formation of many different Ge{sub n}L{sub m} species. This study demonstrates why conformational ligand rigidity is essential in the rational design and directed self-assembly of supramolecular complexes.

Protective role of quercetin against copper(II)-induced oxidative stress: A spectroscopic, theoretical and DNA damage study.

PubMed

Jomova, Klaudia; Lawson, Michael; Drostinova, Lenka; Lauro, Peter; Poprac, Patrik; Brezova, Vlasta; Michalik, Martin; Lukes, Vladimir; Valko, Marian

2017-12-01

The radical scavenging and metal chelating properties of flavonoids indicate that they may play a protective role in diseases with perturbed metal homeostasis such as Alzheimer's disease. In this work we investigated the effect of the coordination of quercetin to copper(II) in view of the formation of ROS in Cu-catalyzed Fenton reaction. ABTS and DPPH assays confirmed that the copper(II)-quercetin complex exhibits a stronger radical scavenging activity than does quercetin alone. EPR spin trapping experiments have shown that chelation of quercetin to copper significantly suppressed the formation of hydroxyl radicals in the Cu(II)-Fenton reaction. DNA damage experiments revealed a protective effect for quercetin, but only at higher stoichiometric ratios of quercetin relative to copper. DNA protective effect of quercetin against ROS attack was described by two mechanisms. The first mechanism lies in suppressed formation of ROS due to the decreased catalytic action of copper in the Fenton reaction, as a consequence of its chelation and direct scavenging of ROS by free quercetin. Since the Cu-quercetin complex intercalates into DNA, the second mechanism was attributed to a suppressed intercalating ability of the Cu-quercetin complex due to the mildly intercalating free quercetin into DNA, thus creating a protective wall against stronger intercalators. Copyright © 2017 Elsevier Ltd. All rights reserved.

Spectrophotometric investigation on the kinetics of oxidation of adrenaline by dioxygen of μ-dioxytetrakis(histidinato)-dicobalt(II) complex

NASA Astrophysics Data System (ADS)

Rafiquee, M. Z. A.; Siddiqui, Masoom R.; Ali, Mohd. Sajid; Al-Lohedan, Hamad A.

The cobalt(II)histidine complex binds molecular oxygen reversibly to form an oxygen adduct complex, μ-dioxytetrakis-(histidinato)dicobalt(II). The molecular oxygen can be released from the oxygenated complex by heating it or by passing N2, He or Ar gas through its solution. μ-Dioxytetrakis-(histidinato)dicobalt(II) complex oxidizes adrenaline into leucoadrenochrome at 25 °C while at higher temperature (>40 °C) adrenochrome with λmax at 490 nm is formed. The rate of formation of leucoadrenochrome was found to be independent of [bis(histidinato)cobalt(II)]. The rate of reaction for the formation of leucoadrenochrome and adrenochrome increased with the increase in [adrenaline] at its lower concentration but become independent at higher concentration. Similarly, the rate of formation of both leucoadrenochrome and adrenochrome was linearly dependent upon [NaOH]. The values of activation parameters i.e. ΔEa, ΔH‡ and ΔS‡ for the formation of leucoadrenochrome are reported.

A peroxynitrite complex of copper: formation from a copper-nitrosyl complex, transformation to nitrite and exogenous phenol oxidative coupling or nitration.

PubMed

Park, Ga Young; Deepalatha, Subramanian; Puiu, Simona C; Lee, Dong-Heon; Mondal, Biplab; Narducci Sarjeant, Amy A; del Rio, Diego; Pau, Monita Y M; Solomon, Edward I; Karlin, Kenneth D

2009-11-01

Reaction of nitrogen monoxide with a copper(I) complex possessing a tridentate alkylamine ligand gives a Cu(I)-(*NO) adduct, which when exposed to dioxygen generates a peroxynitrite (O=NOO(-))-Cu(II) species. This undergoes thermal transformation to produce a copper(II) nitrito (NO(2) (-)) complex and 0.5 mol equiv O(2). In the presence of a substituted phenol, the peroxynitrite complex effects oxidative coupling, whereas addition of chloride ion to dissociate the peroxynitrite moiety instead leads to phenol ortho nitration. Discussions include the structures (including electronic description) of the copper-nitrosyl and copper-peroxynitrite complexes and the formation of the latter, based on density functional theory calculations and accompanying spectroscopic data.

Gas-Phase Formation Rates of Nitric Acid and Its Isomers Under Urban Conditions

NASA Technical Reports Server (NTRS)

Okumura, M.; Mollner, A. K.; Fry, J. L.; Feng, L.

2005-01-01

Ozone formation in urban smog is controlled by a complex set of reactions which includes radical production from photochemical processes, catalytic cycles which convert NO to NO2, and termination steps that tie up reactive intermediates in long-lived reservoirs. The reaction OH + NO2 + M -4 HONO2 + M (la) is a key termination step because it transforms two short-lived reactive intermediates, OH and NO2, into relatively long-lived nitric acid. Under certain conditions (low VOC/NOx), ozone production in polluted urban airsheds can be highly sensitive to this reaction, but the rate parameters are not well constrained. This report summarizes the results of new laboratory studies of the OH + NO2 + M reaction including direct determination of the overall rate constant and branching ratio for the two reaction channels under atmospherically relevant conditions.

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

Martinez, Jorge L.; Lin, Hsiu-Jung; Lee, Wei-Tsung

The new iron(IV) nitride complex PhB( iPr 2Im) 3Fe≡N reacts with two equivalents of bis(diisopropylamino)cyclopropenylidene (BAC) to provide PhB( iPr 2Im) 3Fe(CN)(N 2)(BAC). This unusual example of a four-electron reaction involves carbon atom transfer from BAC to create a cyanide ligand along with the alkyne iPr 2N-C≡C-N iPr 2. The iron complex is in equilibrium with an N 2- free species. Further reaction with CO leads to formation of a CO analogue, which can be independently prepared using NaCN as the cyanide source, while reaction with B(C 6F 5) 3 provides the cyanoborane derivative.

Formation of E-cyanomethamine in a nitrile rich environment

NASA Astrophysics Data System (ADS)

Shivani; Misra, Alka; Tandon, Poonam

2017-01-01

Recently a new molecule, cyanomethamine, has been detected towards Sagittarius B2(N) (Sgr B2(N)). Studying the formation mechanisms of complex interstellar molecules is difficult. Hence, a theoretical quantum chemical approach for analyzing the reaction mechanism describing the formation of interstellar cyanomethamine through detected interstellar molecules and radicals (NCCN+H) is discussed in the present work. Calculations are performed by using quantum chemical techniques, such as Density Functional Theory (DFT) and Møller-Plesset perturbation (MP2) theory with a 6-311G(d,p) basis set, both in the gas phase and in icy grains. The proposed reaction path (NCCN+H+H) has exothermicity with no barrier which indicates the possibility of cyanomethamine formation in the interstellar medium.

Aromatic sulfonation with sulfur trioxide: mechanism and kinetic model.

PubMed

Moors, Samuel L C; Deraet, Xavier; Van Assche, Guy; Geerlings, Paul; De Proft, Frank

2017-01-01

Electrophilic aromatic sulfonation of benzene with sulfur trioxide is studied with ab initio molecular dynamics simulations in gas phase, and in explicit noncomplexing (CCl 3 F) and complexing (CH 3 NO 2 ) solvent models. We investigate different possible reaction pathways, the number of SO 3 molecules participating in the reaction, and the influence of the solvent. Our simulations confirm the existence of a low-energy concerted pathway with formation of a cyclic transition state with two SO 3 molecules. Based on the simulation results, we propose a sequence of elementary reaction steps and a kinetic model compatible with experimental data. Furthermore, a new alternative reaction pathway is proposed in complexing solvent, involving two SO 3 and one CH 3 NO 2 .

Exhaustive oxidation of a nickel dithiolate complex: some mechanistic insights en route to sulfate formation.

PubMed

Hosler, Erik R; Herbst, Robert W; Maroney, Michael J; Chohan, Balwant S

2012-01-21

A study of the step-wise oxidation of a Ni(II) diaminodithiolate complex through the formation of sulfate, the ultimate sulfur oxygenate, is reported. Controlled oxygenations or peroxidations of a neutral, planar, tetracoordinate, low-spin Ni(II) complex of a N(2)S(2)-donor ligand, (N,N'-dimethyl-N-N'-bis(2-mecaptoethyl)-1,3-propanediaminato) nickel(ii) (1), led to a series of sulfur oxygenates that have been isolated and characterized by ESI-MS and single-crystal X-ray diffraction. A monosulfenate complex (2) was detected by ESI-MS as a product of oxidation with one equivalent of H(2)O(2). However, this complex proved too unstable to isolate. Reaction of the dithiolate (1) with two equivalents of H(2)O(2) or one O(2) molecule leads to the formation of a monosulfinate complex (3), which was isolated and fully characterized by crystallography. The oxidation product of the monosulfinate (3) produced with either O(2) or H(2)O(2) is an interesting dimeric complex containing both sulfonate and thiolate ligands (4), this complex was fully characterized by crystallography, details of which were reported earlier by us. A disulfonate complex (7) is produced by reaction of 1 in the presence of O(2) or by reaction with exactly six equivalents of H(2)O(2). This complex was isolated and also fully characterized by crystallography. Possible intermediates in the conversion of the monosulfinate complex (3) to the disulfonate complex (7) include complexes with mixed sulfonate/sulfenate (5) or sulfonate/sulfinate (6) ligands. Complex 5, a four-oxygen adduct of 1, was not detected, but the sulfonate/sulfinate complex (6) was isolated and characterized. The oxidation chemistry of 1 is very different from that reported for other planar cis-N(2)S(2) Ni(ii) complexes including N,N'-dimethyl-N-N'-bis(2-mecaptoethyl)-1,3-ethylenediaminato) nickel(II), (8), and N,N'-bis(mercaptoethyl)-1,5-diazacyclooctane nickel(II). To address the structural aspects of the reactivity differences, the crystal structure of 8 was also determined. A comparison of the structures of planar Ni(II) complexes containing cis-dithiolate ligands, strongly suggests that the differences in reactivity are determined in part by the degree of flexibility that is allowed by the NN' chelate ring.

Observing the real time formation of phosphine-ligated gold clusters by electrospray ionization mass spectrometry

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

Ligare, Marshall R.; Johnson, Grant E.; Laskin, Julia

Early stages of the reduction and nucleation of solution-phase gold clusters are largely unknown. This is due, in part, to the high reaction rates and the complexity of the cluster synthesis process. Through the addition of a diphosphine ligand, 1-4,Bis(diphenylphosphino)butane (L4) to the gold precursor, chloro(triphenylphosphine) gold(I) (Au(PPh3)Cl), in methanol organometallic complexes of the type, [Au(L4)x(L4O)y(PPh3)z]+, are formed. These complexes lower the rate of reduction so that the reaction can be directly monitored from 1 min to over an hour using on-line electrospray ionization mass spectrometry (ESI-MS). Our results indicate that the formation of Au8(L4)42+, Au9(L4)4H2+ and Au10(L4)52+ cationic clustersmore » occurs through different reaction pathways that may be kinetically controlled either through the reducing agent concentration or the extent of oxidation of L4. Through comparison of selected ion chronograms our results indicate that Au2(L4)2H+ may be an intermediate in the formation of Au8(L4)42+and Au10(L4)52+ while a variety of chlorinated clusters are involved in the formation of Au9(L4)4H2+. Additionally, high-resolution mass spectrometry was employed to identify 53 gold containing species produced under highly oxidative conditions. New intermediate species are identified which help understand how different gold cluster nuclearities can be stabilized during the growth process.« less

Formation of Glycerol through Hydrogenation of CO Ice under Prestellar Core Conditions

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

Fedoseev, G.; Chuang, K.-J.; Qasim, D.

Observational studies reveal that complex organic molecules (COMs) can be found in various objects associated with different star formation stages. The identification of COMs in prestellar cores, i.e., cold environments in which thermally induced chemistry can be excluded and radiolysis is limited by cosmic rays and cosmic-ray-induced UV photons, is particularly important as this stage sets up the initial chemical composition from which ultimately stars and planets evolve. Recent laboratory results demonstrate that molecules as complex as glycolaldehyde and ethylene glycol are efficiently formed on icy dust grains via nonenergetic atom addition reactions between accreting H atoms and CO molecules,more » a process that dominates surface chemistry during the “CO freeze-out stage” in dense cores. In the present study we demonstrate that a similar mechanism results in the formation of the biologically relevant molecule glycerol—HOCH{sub 2}CH(OH)CH{sub 2}OH—a three-carbon-bearing sugar alcohol necessary for the formation of membranes of modern living cells and organelles. Our experimental results are fully consistent with a suggested reaction scheme in which glycerol is formed along a chain of radical–radical and radical–molecule interactions between various reactive intermediates produced upon hydrogenation of CO ice or its hydrogenation products. The tentative identification of the chemically related simple sugar glyceraldehyde—HOCH{sub 2}CH(OH)CHO—is discussed as well. These new laboratory findings indicate that the proposed reaction mechanism holds much potential to form even more complex sugar alcohols and simple sugars.« less

Cisplatin carbonato complexes. Implications for uptake, antitumor properties, and toxicity.

PubMed

Centerwall, Corey R; Goodisman, Jerry; Kerwood, Deborah J; Dabrowiak, James C

2005-09-21

The reaction of aquated cisplatin with carbonate which is present in culture media and blood is described. The first formed complex is a monochloro monocarbonato species, which upon continued exposure to carbonate slowly forms a biscarbonato complex. The formation of carbonato species under conditions that simulate therapy may have important implications for uptake, antitumor properties, and toxicity of cisplatin.

Reduction of Pertechnetate By Acetohydroxamic Acid: Formation of [tc**II(NO)(AHA)(2)(H(2)O)]**+ And Implications for the UREX Process

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

Gong, C.-M.S.; Lukens, W.W.; Poineau, F.

2009-05-18

Reductive nitrosylation and complexation of ammonium pertechnetate by acetohydroxamic acid has been achieved in aqueous nitric and perchloric acid solutions. The kinetics of the reaction depend on the relative concentrations of the reaction components and are accelerated at higher temperatures. The reaction does not occur unless conditions are acidic. Analysis of the X-ray absorption fine structure spectroscopic data is consistent with a pseudo-octahedral geometry and the linear Tc-N-O bond typical of technetium nitrosyl compounds, and electron spin resonance spectroscopy is consistent with a d{sup 5} Tc(II) nitrosyl complex. The nitrosyl source is generally AHA, but it may be augmented bymore » some products of the reaction with nitric acid. The resulting low-valency trans-aquonitrosyl(diacetohydroxamic)-technetium(II) complex ([Tc{sup II}(NO)(AHA){sub 2}H{sub 2}O]{sup +}, 1) is highly soluble in water, extremely hydrophilic, and is not extracted by tri-n-butylphosphate in a dodecane diluent. Its extraction properties are not pH-dependent: potentiometric-spectrophotometric titration studies indicate a single species from pH 4 down to -0.6 (calculated). This molecule is resistant to oxidation by H{sub 2}O{sub 2}, even at high pH, and can undergo substitution to form other technetium nitrosyl complexes. The potential formation of 1 during reprocessing may strongly impact the fate of technetium in the nuclear fuel cycle.« less

The prokaryotic enhancer binding protein NTRC has an ATPase activity which is phosphorylation and DNA dependent.

PubMed Central

Austin, S; Dixon, R

1992-01-01

The prokaryotic activator protein NTRC binds to enhancer-like elements and activates transcription in response to nitrogen limitation by catalysing open complex formation by sigma 54 RNA polymerase holoenzyme. Formation of open complexes requires the phosphorylated form of NTRC and the reaction is ATP dependent. We find that NTRC has an ATPase activity which is activated by phosphorylation and is strongly stimulated by the presence of DNA containing specific NTRC binding sites. Images PMID:1534752

Steric and Electronic Effects of Bidentate Phosphine Ligands on Ruthenium(II)-Catalyzed Hydrogenation of Carbon Dioxide.

PubMed

Zhang, Pan; Ni, Shao-Fei; Dang, Li

2016-09-20

The reactivity difference between the hydrogenation of CO2 catalyzed by various ruthenium bidentate phosphine complexes was explored by DFT. In addition to the ligand dmpe (Me2 PCH2 CH2 PMe2 ), which was studied experimentally previously, a more bulky diphosphine ligand, dmpp (Me2 PCH2 CH2 CH2 PMe2 ), together with a more electron-withdrawing diphosphine ligand, PN(Me) P (Me2 PCH2 N(Me) CH2 PMe2 ), have been studied theoretically to analyze the steric and electronic effects on these catalyzed reactions. Results show that all of the most favorable pathways for the hydrogenation of CO2 catalyzed by bidentate phosphine ruthenium dihydride complexes undergo three major steps: cis-trans isomerization of ruthenium dihydride complex, CO2 insertion into the Ru-H bond, and H2 insertion into the ruthenium formate ion. Of these steps, CO2 insertion into the Ru-H bond has the lowest barrier compared with the other two steps in each preferred pathway. For the hydrogenation of CO2 catalyzed by ruthenium complexes of dmpe and dmpp, cis-trans isomerization of ruthenium dihydride complex has a similar barrier to that of H2 insertion into the ruthenium formate ion. However, in the reaction catalyzed by the PN(Me) PRu complex, cis-trans isomerization of the ruthenium dihydride complex has a lower barrier than H2 insertion into the ruthenium formate ion. These results suggest that the steric effect caused by the change of the outer sphere of the diphosphine ligand on the reaction is not clear, although the electronic effect is significant to cis-trans isomerization and H2 insertion. This finding refreshes understanding of the mechanism and provides necessary insights for ligand design in transition-metal-catalyzed CO2 transformation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Hair dye-incorporated poly-γ-glutamic acid/glycol chitosan nanoparticles based on ion-complex formation.

PubMed

Lee, Hye-Young; Jeong, Young-Il; Choi, Ki-Choon

2011-01-01

p-Phenylenediamine (PDA) or its related chemicals are used more extensively than oxidative hair dyes. However, permanent hair dyes such as PDA are known to have potent contact allergy reactions in humans, and severe allergic reactions are problematic. PDA-incorporated nanoparticles were prepared based on ion-complex formation between the cationic groups of PDA and the anionic groups of poly(γ-glutamic acid) (PGA). To reinforce PDA/PGA ion complexes, glycol chitosan (GC) was added. PDA-incorporated nanoparticles were characterized using field-emission scanning electron microscopy, Fourier- transform infrared (FT-IR) spectroscopy, dynamic light scattering, and powder X-ray diffractometry (XRD). Nanoparticles were formed by ion-complex formation between the amine groups of PDA and the carboxyl groups of PGA. PDA-incorporated nanoparticles are small in size (<100 nm), and morphological observations showed spherical shapes. FT-IR spectra results showed that the carboxylic acid peak of PGA decreased with increasing PDA content, indicating that the ion complexes were formed between the carboxyl groups of PGA and the amine groups of PDA. Furthermore, the intrinsic peak of the carboxyl groups of PGA was also decreased by the addition of GC. Intrinsic crystalline peaks of PDA were observed by XRD. This crystalline peak of PDA was completely nonexistent when nanoparticles were formed by ion complex between PDA, PGA, and GC, indicating that PDA was complexed with PGA and no free drug existed in the formulation. During the drug-release experiment, an initial burst release of PDA was observed, and then PDA was continuously released over 1 week. Cytotoxicity testing against HaCaT human skin keratinocyte cells showed PDA-incorporated nanoparticles had lower toxicity than PDA itself. Furthermore, PDA-incorporated nanoparticles showed reduced apoptosis and necrosis reaction at HaCaT cells. The authors suggest that these microparticles are ideal candidates for a vehicle for decreasing side effects of hair dye.

RNA–protein binding kinetics in an automated microfluidic reactor

PubMed Central

Ridgeway, William K.; Seitaridou, Effrosyni; Phillips, Rob; Williamson, James R.

2009-01-01

Microfluidic chips can automate biochemical assays on the nanoliter scale, which is of considerable utility for RNA–protein binding reactions that would otherwise require large quantities of proteins. Unfortunately, complex reactions involving multiple reactants cannot be prepared in current microfluidic mixer designs, nor is investigation of long-time scale reactions possible. Here, a microfluidic ‘Riboreactor’ has been designed and constructed to facilitate the study of kinetics of RNA–protein complex formation over long time scales. With computer automation, the reactor can prepare binding reactions from any combination of eight reagents, and is optimized to monitor long reaction times. By integrating a two-photon microscope into the microfluidic platform, 5-nl reactions can be observed for longer than 1000 s with single-molecule sensitivity and negligible photobleaching. Using the Riboreactor, RNA–protein binding reactions with a fragment of the bacterial 30S ribosome were prepared in a fully automated fashion and binding rates were consistent with rates obtained from conventional assays. The microfluidic chip successfully combines automation, low sample consumption, ultra-sensitive fluorescence detection and a high degree of reproducibility. The chip should be able to probe complex reaction networks describing the assembly of large multicomponent RNPs such as the ribosome. PMID:19759214

Clostridium acidurici electron-bifurcating formate dehydrogenase.

PubMed

Wang, Shuning; Huang, Haiyan; Kahnt, Jörg; Thauer, Rudolf K

2013-10-01

Cell extracts of uric acid-grown Clostridium acidurici catalyzed the coupled reduction of NAD(+) and ferredoxin with formate at a specific activity of 1.3 U/mg. The enzyme complex catalyzing the electron-bifurcating reaction was purified 130-fold and found to be composed of four subunits encoded by the gene cluster hylCBA-fdhF2.

Kinetic and mechanisms of methanimine reactions with singlet and triplet molecular oxygen: Substituent and catalyst effects

NASA Astrophysics Data System (ADS)

Asgharzadeh, Somaie; Vahedpour, Morteza

2018-06-01

Methanimine reaction with O2 on singlet and triplet potential energy surfaces are investigated using B3PW91, M06-2X, MP2 and CCSD(T) methods. Thermodynamic and kinetic parameters are calculated at M06-2X method. The most favorable channel involves H-abstraction of CH2NH+O2 to the formation of HCN + H2O2 products via low level energy barrier. The catalytic effect of water molecule on HCN + H2O2 products pathway are investigated. Result shows that contribution of water molecule using complex formation with methanimine can decreases barrier energy of transition state and the reaction rate increases. Also, substituent effect of fluorine atom as deactivating group are investigated on the main reaction pathway.

Metathesis of a UV imido complex: a route to a terminal UV sulfide† †Electronic supplementary information (ESI) available: Full computational and experimental details, NMR spectra, and detailed X-ray crystallographic data in CIF format. CCDC 1535285–1535289. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7sc01111c Click here for additional data file. Click here for additional data file.

PubMed Central

Kelly, Rory P.; Falcone, Marta; Lamsfus, Carlos Alvarez; Scopelliti, Rosario; Maron, Laurent; Meyer, Karsten

2017-01-01

Herein, we report the synthesis and characterisation of the first terminal uranium(v) sulfide and a related UV trithiocarbonate complex supported by sterically demanding tris(tert-butoxy)siloxide ligands. The reaction of the potassium-bound UV imido complex, [U(NAd){OSi(OtBu)3}4K] (4), with CS2 led to the isolation of perthiodicarbonate [K(18c6)]2[C2S6] (6), with concomitant formation of the UIV complex, [U{OSi(OtBu)3}4], and S 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 CNAd. In contrast, the reaction of the UV imido complex, [K(2.2.2-cryptand)][U(NAd){OSi(OtBu)3}4] (5), with one or two equivalents of CS2 afforded the trithiocarbonate complex, [K(2.2.2-cryptand)][U(CS3){OSi(OtBu)3}4] (7), which was isolated in 57% yield, with concomitant elimination of the admantyl thiocyanate product, SCNAd. Complex 7 is likely formed by fast nucleophilic addition of a UV terminal sulfide intermediate, resulting from the slow metathesis reaction of the imido complex with CS2, to a second CS2 molecule. The addition of a solution of H2S in thf (1.3 eq.) to 4 afforded the first isolable UV terminal sulfide complex, [K(2.2.2-cryptand)][US{OSi(OtBu)3}4] (8), in 41% yield. Based on DFT calculations, triple-bond character with a strong covalent interaction is suggested for the U–S bond in complex 7. PMID:28970911

A quantum informational approach for dissecting chemical reactions

NASA Astrophysics Data System (ADS)

Duperrouzel, Corinne; Tecmer, Paweł; Boguslawski, Katharina; Barcza, Gergely; Legeza, Örs; Ayers, Paul W.

2015-02-01

We present a conceptionally different approach to dissect bond-formation processes in metal-driven catalysis using concepts from quantum information theory. Our method uses the entanglement and correlation among molecular orbitals to analyze changes in electronic structure that accompany chemical processes. As a proof-of-principle example, the evolution of nickel-ethene bond-formation is dissected, which allows us to monitor the interplay of back-bonding and π-donation along the reaction coordinate. Furthermore, the reaction pathway of nickel-ethene complexation is analyzed using quantum chemistry methods, revealing the presence of a transition state. Our study supports the crucial role of metal-to-ligand back-donation in the bond-forming process of nickel-ethene.

Catalysis of a 1,3-dipolar reaction by distorted DNA incorporating a heterobimetallic platinum(ii) and copper(ii) complex.

PubMed

Rivilla, Iván; de Cózar, Abel; Schäfer, Thomas; Hernandez, Frank J; Bittner, Alexander M; Eleta-Lopez, Aitziber; Aboudzadeh, Ali; Santos, José I; Miranda, José I; Cossío, Fernando P

2017-10-01

A novel catalytic system based on covalently modified DNA is described. This catalyst promotes 1,3-dipolar reactions between azomethine ylides and maleimides. The catalytic system is based on the distortion of the double helix of DNA by means of the formation of Pt(ii) adducts with guanine units. This distortion, similar to that generated in the interaction of DNA with platinum chemotherapeutic drugs, generates active sites that can accommodate N -metallated azomethine ylides. The proposed reaction mechanism, based on QM(DFT)/MM calculations, is compatible with thermally allowed concerted (but asynchronous) [π4s + π2s] mechanisms leading to the exclusive formation of racemic endo -cycloadducts.

FORMATION AND RECONDENSATION OF COMPLEX ORGANIC MOLECULES DURING PROTOSTELLAR LUMINOSITY OUTBURSTS

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

Taquet, Vianney; Wirström, Eva S.; Charnley, Steven B.

2016-04-10

During the formation of stars, the accretion of surrounding material toward the central object is thought to undergo strong luminosity outbursts followed by long periods of relative quiescence, even at the early stages of star formation when the protostar is still embedded in a large envelope. We investigated the gas-phase formation and recondensation of the complex organic molecules (COMs) di-methyl ether and methyl formate, induced by sudden ice evaporation processes occurring during luminosity outbursts of different amplitudes in protostellar envelopes. For this purpose, we updated a gas-phase chemical network forming COMs in which ammonia plays a key role. The modelmore » calculations presented here demonstrate that ion–molecule reactions alone could account for the observed presence of di-methyl ether and methyl formate in a large fraction of protostellar cores without recourse to grain-surface chemistry, although they depend on uncertain ice abundances and gas-phase reaction branching ratios. In spite of the short outburst timescales of about 100 years, abundance ratios of the considered species higher than 10% with respect to methanol are predicted during outbursts due to their low binding energies relative to water and methanol which delay their recondensation during cooling. Although the current luminosity of most embedded protostars would be too low to produce complex organics in the hot-core regions that are observable with current sub-millimetric interferometers, previous luminosity outburst events would induce the formation of COMs in extended regions of protostellar envelopes with sizes increasing by up to one order of magnitude.« less

Bridge-bonded formate: active intermediate or spectator species in formic acid oxidation on a Pt film electrode?

PubMed

Chen, Y-X; Heinen, M; Jusys, Z; Behm, R J

2006-12-05

We present and discuss the results of an in situ IR study on the mechanism and kinetics of formic acid oxidation on a Pt film/Si electrode, performed in an attenuated total reflection (ATR) flow cell configuration under controlled mass transport conditions, which specifically aimed at elucidating the role of the adsorbed bridge-bonded formates in this reaction. Potentiodynamic measurements show a complex interplay between formation and desorption/oxidation of COad and formate species and the total Faradaic current. The notably faster increase of the Faradaic current compared to the coverage of bridge-bonded formate in transient measurements at constant potential, but with different formic acid concentrations, reveals that adsorbed formate decomposition is not rate-limiting in the dominant reaction pathway. If being reactive intermediate at all, the contribution of formate adsorption/decomposition to the reaction current decreases with increasing formic acid concentration, accounting for at most 15% for 0.2 M DCOOH at 0.7 VRHE. The rapid build-up/removal of the formate adlayer and its similarity with acetate or (bi-)sulfate adsorption/desorption indicate that the formate adlayer coverage is dominated by a fast dynamic adsorption-desorption equilibrium with the electrolyte, and that formate desorption is much faster than its decomposition. The results corroborate the proposal of a triple pathway reaction mechanism including an indirect pathway, a formate pathway, and a dominant direct pathway, as presented previously (Chen, Y. X.; et al. Angew. Chem. Int. Ed. 2006, 45, 981), in which adsorbed formates act as a site-blocking spectator in the dominant pathway rather than as an active intermediate.

The role of NaCl in flame chemistry, in the deposition process, and in its reactions with protective oxides as related to hot corrosion

NASA Technical Reports Server (NTRS)

Kohl, F. J.; Stearns, C. A.

1979-01-01

Sodium chloride is believed to be the primary source of turbine engine contamination that contributes to hot corrosion. The behavior of NaCl-containing aerosols ingested with turbine intake air is very complex; some of the NaCl may vaporize during combustion while some may remain as particulates. The NaCl can lead to Na2SO4 formation by several possible routes or it can contribute to corrosion directly. Hydrogen or oxygen atom reaction with NaCl(c) was shown to result in the release of Na(g). Gaseous NaCl in flames can be partially converted to gaseous Na2SO4 by homogeneous reactions. The remaining gaseous NaCl and other Na-containing molecules can act as sodium carriers for condensate deposition of Na2SO4 on cool surfaces. A frozen boundary layer theory was developed to predict the rates of deposition. The condensed phase NaCl can be converted directly to condensed Na2SO4 by reaction with sulfur oxides and O2. Reaction of gaseous NaCl with Cr2O3 results in the vapor phase transport of chromium by the formation of complex Cr-containing gaseous molecules. Similar gaseous complexes are formed with molybdenum. The presence of gaseous NaCl was shown to affect the oxidation kinetics of Ni-Cr alloys. It also causes changes in the surface morphology of Al2O3 scales formed on Al-containing alloys.

Coordination Chemistry of Cyclic Disilylated Germylenes and Stannylenes with Group 11 Metals

PubMed Central

2014-01-01

Reactions of Et3P adducts of bissilylated germylenes and stannylenes with gold, silver, and copper cyanides led to cyanogermyl or -stannyl complexes of the respective metals. In the course of the reaction the phosphine moved to the metal, while the cyanide migrated to the low-coordinate group 14 element. The respective gold complexes were found to be monomeric, whereas the silver and copper complexes exhibited a tendency to dimerize in the solid state. Attempts to abstract the phosphine ligand with B(C6F5)3 led only to the formation of adducts with the borane coordinating to the cyanide nitrogen atom. PMID:25550678

Involvement of Lipocalin-like CghA in Decalin-Forming Stereoselective Intramolecular [4+2] Cycloaddition

PubMed Central

Sato, Michio; Yagishita, Fumitoshi; Mino, Takashi; Uchiyama, Nahoko; Patel, Ashay; Chooi, Yit-Heng; Goda, Yukihiro; Xu, Wei; Noguchi, Hiroshi; Yamamoto, Tsuyoshi; Hotta, Kinya; Houk, Kendall N.; Tang, Yi

2016-01-01

Understanding enzymatic Diels—Alder (DA) reactions that can form complex natural product scaffold is of considerable interest. Sch 210972 1, a potential anti-HIV fungal natural product, contains a decalin core that is proposed to form via a DA reaction. We identified the gene cluster responsible for the biosynthesis of 1 and heterologously reconstituted the biosynthetic pathway in Aspergillus nidulans to characterize the enzymes involved. Most notably, deletion of cghA resulted in a loss of stereoselective decalin core formation, yielding both an endo 1 and a diastereomeric exo adducts of the proposed DA reaction. Complementation with cghA restored the sole formation of 1. Density functional theory computation of the proposed DA reaction provided a plausible explanation of the observed pattern of product formation. Based on our study, we propose that lipocalin-like CghA is responsible for the stereoselective intramolecular [4+2] cycloaddition that forms the decalin core of 1. PMID:26360642

What is the mechanism of the OSO ring formation in sulfur tetroxide (SO4(C2v)) molecule?

NASA Astrophysics Data System (ADS)

Goodarzi, Moein; Vahedpour, Morteza; Solimannejad, Mohammad

2012-06-01

The mechanism of SO2 + O2 and O + SO3(D3h) reactions have been investigated at the MP2/6-31 + G(d) and CCSD(T)/cc-pV(Q + d)Z//MP2 levels on the triplet and singlet PESs. Although, no stable collision complexes have been found for the SO2 + O2(3∑g-), O(3P) + SO3(D3h) and O(1D) + SO3(D3h) reactions, 1IN(O2S-O2) has been considered on the singlet PES for the SO2 + O2(1Δg) reaction. The results show that there are no favorable paths for the OSO ring formation of SO4(C2v) in the atmospheric reactions of the SO2 + O2(3∑g-), SO2 + O2(1Δg) and O(3P) + SO3(D3h) while, the O(1D) + SO3(D3h) reaction can be suitable for the SO4(C2v) formation on the singlet PES.

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

Krasnokutski, Serge A., E-mail: skrasnokutskiy@yahoo.com; Huisken, Friedrich, E-mail: friedrich.huisken@uni-jena.de

The reaction of carbon atoms with benzene has been investigated in liquid helium droplets at T = 0.37 K. We found an addition of the carbon atom to form an initial intermediate complex followed by a ring opening and the formation of a seven-membered ring. In contrast to a previous gas phase study, the reaction is frozen after these steps and the loss of hydrogen does not occur. A calorimetric technique was applied to monitor the energy balance of the reaction. It was found that more than 267 kJ mol{sup −1} were released in this reaction. This estimation is inmore » line with quantum chemical calculations of the formation energy of a seven-membered carbon ring. It is suggested that reactions of this kind could be responsible for the low abundance of small polycyclic aromatic hydrocarbon molecules in the interstellar medium. We also found the formation of weakly bonded water-carbon adducts, in which the carbon atom is linked to the oxygen atom of the water molecule with a binding energy of about 33.4 kJ mol{sup −1}.« less

Spin trapping combined with quantitative mass spectrometry defines free radical redistribution within the oxidized hemoglobin:haptoglobin complex.

PubMed

Vallelian, Florence; Garcia-Rubio, Ines; Puglia, Michele; Kahraman, Abdullah; Deuel, Jeremy W; Engelsberger, Wolfgang R; Mason, Ronald P; Buehler, Paul W; Schaer, Dominik J

2015-08-01

Extracellular or free hemoglobin (Hb) accumulates during hemolysis, tissue damage, and inflammation. Heme-triggered oxidative reactions can lead to diverse structural modifications of lipids and proteins, which contribute to the propagation of tissue damage. One important target of Hb׳s peroxidase reactivity is its own globin structure. Amino acid oxidation and crosslinking events destabilize the protein and ultimately cause accumulation of proinflammatory and cytotoxic Hb degradation products. The Hb scavenger haptoglobin (Hp) attenuates oxidation-induced Hb degradation. In this study we show that in the presence of hydrogen peroxide (H2O2), Hb and the Hb:Hp complex share comparable peroxidative reactivity and free radical generation. While oxidation of both free Hb and Hb:Hp complex generates a common tyrosine-based free radical, the spin-trapping reaction with 5,5-dimethyl-1-pyrroline N-oxide (DMPO) yields dissimilar paramagnetic products in Hb and Hb:Hp, suggesting that radicals are differently redistributed within the complex before reacting with the spin trap. With LC-MS(2) mass spectrometry we assigned multiple known and novel DMPO adduct sites. Quantification of these adducts suggested that the Hb:Hp complex formation causes extensive delocalization of accessible free radicals with drastic reduction of the major tryptophan and cysteine modifications in the β-globin chain of the Hb:Hp complex, including decreased βCys93 DMPO adduction. In contrast, the quantitative changes in DMPO adduct formation on Hb:Hp complex formation were less pronounced in the Hb α-globin chain. In contrast to earlier speculations, we found no evidence that free Hb radicals are delocalized to the Hp chain of the complex. The observation that Hb:Hp complex formation alters free radical distribution in Hb may help to better understand the structural basis for Hp as an antioxidant protein. Copyright © 2015 Elsevier Inc. All rights reserved.

Complexation reactions in pyridine and 2,6-dimethylpyridine-water system: The quantum-chemical description and the path to liquid phase separation.

PubMed

Chernia, Zelig; Tsori, Yoav

2018-03-14

Phase separation in substituted pyridines in water is usually described as an interplay between temperature-driven breakage of hydrogen bonds and the associating interaction of the van der Waals force. In previous quantum-chemical studies, the strength of hydrogen bonding between one water and one pyridine molecules (the 1:1 complex) was assigned a pivotal role. It was accepted that the disassembly of the 1:1 complex at a critical temperature leads to phase separation and formation of the miscibility gap. Yet, for over two decades, notable empirical data and theoretical arguments were presented against that view, thus revealing the need in a revised quantum-mechanical description. In the present study, pyridine-water and 2,6-dimethylpyridine-water systems at different complexation stages are calculated using high level Kohn-Sham theory. The hydrophobic-hydrophilic properties are accounted for by the polarizable continuum solvation model. Inclusion of solvation in free energy of formation calculations reveals that 1:1 complexes are abundant in the organically rich solvents but higher level oligomers (i.e., 2:1 dimers with two pyridines and one water molecule) are the only feasible stable products in the more polar media. At the critical temperature, the dissolution of the external hydrogen bonds between the 2:1 dimer and the surrounding water molecules induces the demixing process. The 1:1 complex acts as a precursor in the formation of the dimers but is not directly involved in the demixing mechanism. The existence of the miscibility gap in one pyridine-water system and the lack of it in another is explained by the ability of the former to maintain stable dimerization. Free energy of formation of several reaction paths producing the 2:1 dimers is calculated and critically analyzed.

Complexation reactions in pyridine and 2,6-dimethylpyridine-water system: The quantum-chemical description and the path to liquid phase separation

NASA Astrophysics Data System (ADS)

Chernia, Zelig; Tsori, Yoav

2018-03-01

Phase separation in substituted pyridines in water is usually described as an interplay between temperature-driven breakage of hydrogen bonds and the associating interaction of the van der Waals force. In previous quantum-chemical studies, the strength of hydrogen bonding between one water and one pyridine molecules (the 1:1 complex) was assigned a pivotal role. It was accepted that the disassembly of the 1:1 complex at a critical temperature leads to phase separation and formation of the miscibility gap. Yet, for over two decades, notable empirical data and theoretical arguments were presented against that view, thus revealing the need in a revised quantum-mechanical description. In the present study, pyridine-water and 2,6-dimethylpyridine-water systems at different complexation stages are calculated using high level Kohn-Sham theory. The hydrophobic-hydrophilic properties are accounted for by the polarizable continuum solvation model. Inclusion of solvation in free energy of formation calculations reveals that 1:1 complexes are abundant in the organically rich solvents but higher level oligomers (i.e., 2:1 dimers with two pyridines and one water molecule) are the only feasible stable products in the more polar media. At the critical temperature, the dissolution of the external hydrogen bonds between the 2:1 dimer and the surrounding water molecules induces the demixing process. The 1:1 complex acts as a precursor in the formation of the dimers but is not directly involved in the demixing mechanism. The existence of the miscibility gap in one pyridine-water system and the lack of it in another is explained by the ability of the former to maintain stable dimerization. Free energy of formation of several reaction paths producing the 2:1 dimers is calculated and critically analyzed.

The reaction of indole with the aminoacrylate intermediate of Salmonella typhimurium tryptophan synthase: observation of a primary kinetic isotope effect with 3-[(2)H]indole.

PubMed

Cash, Michael T; Miles, Edith W; Phillips, Robert S

2004-12-15

The bacterial tryptophan synthase alpha(2)beta(2) complex catalyzes the final reactions in the biosynthesis of L-tryptophan. Indole is produced at the active site of the alpha-subunit and is transferred through a 25-30 A tunnel to the beta-active site, where it reacts with an aminoacrylate intermediate. Lane and Kirschner proposed a two-step nucleophilic addition-tautomerization mechanism for the reaction of indole with the aminoacrylate intermediate, based on the absence of an observed kinetic isotope effect (KIE) when 3-[(2)H]indole reacts with the aminoacrylate intermediate. We have now observed a KIE of 1.4-2.0 in the reaction of 3-[(2)H]indole with the aminoacrylate intermediate in the presence of monovalent cations, but not when an alpha-subunit ligand, disodium alpha-glycerophosphate (Na(2)GP), is present. Rapid-scanning stopped flow kinetic studies were performed of the reaction of indole and 3-[(2)H]indole with tryptophan synthase preincubated with L-serine, following the decay of the aminoacrylate intermediate at 350 nm, the formation of the quinonoid intermediate at 476 nm, and the formation of the L-Trp external aldimine at 423 nm. The addition of Na(2)GP dramatically slows the rate of reaction of indole with the alpha-aminoacrylate intermediate. A primary KIE is not observed in the reaction of 3-[(2)H]indole with the aminoacrylate complex of tryptophan synthase in the presence of Na(2)GP, suggesting binding of indole with tryptophan synthase is rate limiting under these conditions. The reaction of 2-methylindole does not show a KIE, either in the presence of Na(+) or Na(2)GP. These results support the previously proposed mechanism for the beta-reaction of tryptophan synthase, but suggest that the rate limiting step in quinonoid intermediate formation from indole and the aminoacrylate intermediate is deprotonation.

Influence of a reaction medium on the oxidation of aromatic nitrogen-containing compounds by peroxyacids

NASA Astrophysics Data System (ADS)

Dutka, V. S.; Matsyuk, N. V.; Dutka, Yu. V.

2011-01-01

The influence of different solvents on the oxidation reaction rate of pyridine (Py), quinoline (QN), acridine (AN), α-oxyquinoline (OQN) and α-picolinic acid (APA) by peroxydecanoic acid (PDA) was studied. It was found that the oxidation rate grows in the series Py < QN < AN, and the rate of the oxidation reaction of compounds containing a substituent in the α position from a reactive center is significantly lower than for unsubstituted analogues. The effective energies of activation of the oxidation reaction were found. It was shown that in the first stage, the reaction mechanism includes the rapid formation of an intermediate complex nitrogen-containing compound, peroxyacid, which forms products upon decomposing in the second stage. A kinetic equation that describes the studied process is offered. The constants of equilibrium of the intermediate complex formation ( K eq) and its decomposition constant ( k 2) in acetone and benzene were calculated. It was shown that the nature of the solvent influences the numerical values of both K p and k 2. It was established that introduction of acetic acid (which is able to form compounds with Py) into the reaction medium slows the rate of the oxidation process drastically. Correlation equations linking the polarity, polarizability, electrophilicity, and basicity of solvents with the constant of the PDA oxidation reaction rate for Py were found. It was concluded that the basicity and polarity of the solvent have a decisive influence on the oxidation reaction rate, while the polarizability and electrophilicity of the reaction medium do not influence the oxidation reaction rate.

Ab initio study on the formation of triiodide CT complex from the reaction of iodine with 2,3-diaminopyridine.

PubMed

Al-Hashimi, Nessreen A; Hussein, Yasser H A

2010-01-01

The charge transfer (CT) interaction between iodine and 2,3-diaminopyridine (DAPY) has been thoroughly investigated via theoretical calculations. A Hartree-Fock, 3-21G level of theory was used to optimize and calculate the Mullican charge distribution scheme as well as the vibrational frequencies of DAPY alone and both its CT complexes with one and two iodine molecules. A very good agreement was found between experiment and theory. New illustrations were concluded with a deep analysis and description for the vibrational frequencies of the formed CT complexes. The two-step CT complex formation mechanism published earlier was supported. Copyright 2009 Elsevier B.V. All rights reserved.

Reactions of a Ruthenium Complex with Substituted N-Propargyl Pyrroles.

PubMed

Chia, Pi-Yeh; Huang, Shou-Ling; Liu, Yi-Hong; Lin, Ying-Chih

2016-04-05

In an investigation into the chemical reactions of N-propargyl pyrroles 1 a-c, containing aldehyde, keto, and ester groups on the pyrrole ring, with [Ru]-Cl ([Ru]=Cp(PPh3 )2 Ru; Cp=C5 H5 ), an aldehyde group in the pyrrole ring is found to play a crucial role in stimulating the cyclization reaction. The reaction of 1 a, containing an aldehyde group, with [Ru]-Cl in the presence of NH4 PF6 yields the vinylidene complex 2 a, which further reacts with allyl amine to give the carbene complex 6 a with a pyrrolizine group. However, if 1 a is first reacted with allyl amine to yield the iminenyne 8 a, then the reaction of 8 a with [Ru]-Cl in the presence of NH4 PF6 yields the ruthenium complex 9 a, containing a cationic pyrrolopyrazinium group, which has been fully characterized by XRD analysis. These results can be adequately explained by coordination of the triple bond of the propargyl group to the ruthenium metal center first, followed by two processes, that is, formation of a vinylidene intermediate or direct nucleophilic attack. Additionally, the deprotonation of 2 a by R4 NOH yields the neutral acetylide complex 3 a. In the presence of NH4 PF6 , the attempted alkylation of 3 a resulted in the formation the Fischer-type amino-carbene complex 5 a as a result of the presence of NH3, which served as a nucleophile. With KPF6, the alkylation of 3 a with ethyl and benzyl bromoacetates afforded the disubstituted vinylidene complexes 10 a and 11 a, containing ester groups, which underwent deprotonation reactions to give the furyl complexes 12 a and 13 a, respectively. For 13 a, containing an O-benzyl group, subsequent 1,3-migration of the benzyl group was observed to yield product 14 a with a lactone unit. Similar reactivity was not observed for the corresponding N-propargyl pyrroles 1 b and 1 c, which contained keto and ester groups, respectively, on the pyrrole ring. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Carbinolamine Formation and Dehydration in a DNA Repair Enzyme Active Site

PubMed Central

Dodson, M. L.; Walker, Ross C.; Lloyd, R. Stephen

2012-01-01

In order to suggest detailed mechanistic hypotheses for the formation and dehydration of a key carbinolamine intermediate in the T4 pyrimidine dimer glycosylase (T4PDG) reaction, we have investigated these reactions using steered molecular dynamics with a coupled quantum mechanics–molecular mechanics potential (QM/MM). We carried out simulations of DNA abasic site carbinolamine formation with and without a water molecule restrained to remain within the active site quantum region. We recovered potentials of mean force (PMF) from thirty replicate reaction trajectories using Jarzynski averaging. We demonstrated feasible pathways involving water, as well as those independent of water participation. The water–independent enzyme–catalyzed reaction had a bias–corrected Jarzynski–average barrier height of approximately for the carbinolamine formation reaction and ) for the reverse reaction at this level of representation. When the proton transfer was facilitated with an intrinsic quantum water, the barrier height was approximately in the forward (formation) reaction and for the reverse. In addition, two modes of unsteered (free dynamics) carbinolamine dehydration were observed: in one, the quantum water participated as an intermediate proton transfer species, and in the other, the active site protonated glutamate hydrogen was directly transferred to the carbinolamine oxygen. Water–independent unforced proton transfer from the protonated active site glutamate carboxyl to the unprotonated N–terminal amine was also observed. In summary, complex proton transfer events, some involving water intermediates, were studied in QM/MM simulations of T4PDG bound to a DNA abasic site. Imine carbinolamine formation was characterized using steered QM/MM molecular dynamics. Dehydration of the carbinolamine intermediate to form the final imine product was observed in free, unsteered, QM/MM dynamics simulations, as was unforced acid-base transfer between the active site carboxylate and the N–terminal amine. PMID:22384015

Unified Microscopic-Macroscopic Monte Carlo Simulations of Complex Organic Molecule Chemistry in Cold Cores

NASA Astrophysics Data System (ADS)

Chang, Qiang; Herbst, Eric

2016-03-01

The recent discovery of methyl formate and dimethyl ether in the gas phase of cold cores with temperatures as cold as 10 K challenges our previous astrochemical models concerning the formation of complex organic molecules (COMs). The strong correlation between the abundances and distributions of methyl formate and dimethyl ether further shows that current astrochemical models may be missing important chemical processes in cold astronomical sources. We investigate a scenario in which COMs and the methoxy radical can be formed on dust grains via a so-called chain reaction mechanism, in a similar manner to CO2. A unified gas-grain microscopic-macroscopic Monte Carlo approach with both normal and interstitial sites for icy grain mantles is used to perform the chemical simulations. Reactive desorption with varying degrees of efficiency is included to enhance the nonthermal desorption of species formed on cold dust grains. In addition, varying degrees of efficiency for the surface formation of methoxy are also included. The observed abundances of a variety of organic molecules in cold cores can be reproduced in our models. The strong correlation between the abundances of methyl formate and dimethyl ether in cold cores can also be explained. Nondiffusive chemical reactions on dust grain surfaces may play a key role in the formation of some COMs.

Reactive Desorption and Radiative Association as Possible Drivers of Complex Molecule Formation in the Cold Interstellar Medium

NASA Astrophysics Data System (ADS)

Vasyunin, A. I.; Herbst, Eric

2013-05-01

The recent discovery of terrestrial-type organic species such as methyl formate and dimethyl ether in the cold interstellar gas has proved that the formation of organic matter in the Galaxy begins at a much earlier stage of star formation than was previously thought. This discovery represents a challenge for astrochemical modelers. The abundances of these molecules cannot be explained by the previously developed "warm-up" scenario, in which organic molecules are formed via diffusive chemistry on surfaces of interstellar grains starting at 30 K, and then released to the gas at higher temperatures during later stages of star formation. In this article, we investigate an alternative scenario in which complex organic species are formed via a sequence of gas-phase reactions between precursor species formed on grain surfaces and then ejected into the gas via efficient reactive desorption, a process in which non-thermal desorption occurs as a result of conversion of the exothermicity of chemical reactions into the ejection of products from the surface. The proposed scenario leads to reasonable if somewhat mixed results at temperatures as low as 10 K and may be considered as a step toward the explanation of abundances of terrestrial-like organic species observed during the earliest stages of star formation.

Experimental and theoretical studies of the products of reaction between Ln(hfa) 3 and Cu(acac) 2 (Ln = La, Y; acac = acetylacetonate, hfa = hexafluoroacetylacetonate)

NASA Astrophysics Data System (ADS)

Rogachev, Andrey Yu.; Mironov, Andrey V.; Nemukhin, Alexander V.

2007-04-01

The new unusual heterobimetallic complex [La(hfa) 3Cu(acac) 2(H 2O)] ( I) was obtained in the reaction La(hfa) 3·2H 2O with Cu(acac) 2 in CHCl 3. This is the first example of such type of heterobimetallic complexes based on the Cu(acac) 2 species. According to the X-ray single crystal analysis, complex I crystallizes in the monoclinic space group P2 1/c, with a = 12.516(3) Å, b = 17.757(4) Å, c = 17.446(4) Å, β = 93.90(3)° and Z = 4. The structure consists of isolated heterobinuclear molecules with the coordination number of La being 9. The molecules are further assembled into dimers via hydrogen bonds. The theoretical modeling of the structure and the properties of parent monometallic complexes Ln(hfa) 3 (Ln = La, Y) and Cu(acac) 2 is described. The comparative theoretical study of lanthanide complexes indicates relations in formation of a heterobimetallic complex to the Lewis acidity of original monometallic complexes. In particular, the Lewis acidity and charge of the central metal ion in Ln(hfa) 3 are the key parameters accounting for the formation of [Ln(hfa) 3Cu(acac) 2].

Ionization dynamics of the water trimer: A direct ab initio MD study

NASA Astrophysics Data System (ADS)

Tachikawa, Hiroto; Takada, Tomoya

2013-03-01

Ionization dynamics of the cyclic water trimer (H2O)3 have been investigated by means of direct ab initio molecular dynamics (AIMD) method. Two reaction channels, complex formation and OH dissociation, were found following the ionization of (H2O)3. In both channels, first, a proton was rapidly transferred from H2O+ to H2O (time scale is ˜15 fs after the ionization). In complex channel, an ion-radical contact pair (H3O+-OH) solvated by the third water molecule was formed as a long-lived H3O+(OH)H2O complex. In OH dissociation channel, the second proton transfer further takes place from H3O+(OH) to H2O (time scale is 50-100 fs) and the OH radical is separated from the H3O+. At the same time, the OH dissociation takes place when the excess energy is efficiently transferred into the kinetic energy of OH radical. The OH dissociation channel is significantly minor, and almost all product channels were the complex formation. The reaction mechanism was discussed on the basis of theoretical results.

Brief ultrasonication improves detection of biofilm-formative bacteria around a metal implant.

PubMed

Kobayashi, Naomi; Bauer, Thomas W; Tuohy, Marion J; Fujishiro, Takaaki; Procop, Gary W

2007-04-01

Biofilms are complex microenvironments produced by microorganisms on surfaces. Ultrasonication disrupts biofilms and may make the microorganism or its DNA available for detection. We determined whether ultrasonication could affect our ability to detect bacteria adherent to a metal substrate. A biofilm-formative Staphylococcus aureus strain was used for an in vitro implant infection model (biofilm-formative condition). We used quantitative culture and real time-polymerase chain reaction to determine the influence of different durations of ultrasound on bacterial adherence and viability. Sonication for 1 minute increased the yield of bacteria. Sonication longer than 5 minutes led to fewer bacterial colonies by conventional culture but not by polymerase chain reaction. This suggests short periods of sonication help release bacteria from the metal substrate by disrupting the biofilm, but longer periods of sonication lyse bacteria prohibiting their detection in microbiologic cultures. A relatively short duration of sonication may be desirable for maximizing detection of biofilm-formative bacteria around implants by culture or polymerase chain reaction.

Comparing 2-nt 3' overhangs against blunt-ended siRNAs: a systems biology based study.

PubMed

Ghosh, Preetam; Dullea, Robert; Fischer, James E; Turi, Tom G; Sarver, Ronald W; Zhang, Chaoyang; Basu, Kalyan; Das, Sajal K; Poland, Bradley W

2009-07-07

In this study, we formulate a computational reaction model following a chemical kinetic theory approach to predict the binding rate constant for the siRNA-RISC complex formation reaction. The model allowed us to study the potency difference between 2-nt 3' overhangs against blunt-ended siRNA molecules in an RNA interference (RNAi) system. The rate constant predicted by this model was fed into a stochastic simulation of the RNAi system (using the Gillespie stochastic simulator) to study the overall potency effect. We observed that the stochasticity in the transcription/translation machinery has no observable effects in the RNAi pathway. Sustained gene silencing using siRNAs can be achieved only if there is a way to replenish the dsRNA molecules in the cell. Initial findings show about 1.5 times more blunt-ended molecules will be required to keep the mRNA at the same reduced level compared to the 2-nt overhang siRNAs. However, the mRNA levels jump back to saturation after a longer time when blunt-ended siRNAs are used. We found that the siRNA-RISC complex formation reaction rate was 2 times slower when blunt-ended molecules were used pointing to the fact that the presence of the 2-nt overhangs has a greater effect on the reaction in which the bound RISC complex cleaves the mRNA.

Comparing 2-nt 3' overhangs against blunt-ended siRNAs: a systems biology based study

PubMed Central

Ghosh, Preetam; Dullea, Robert; Fischer, James E; Turi, Tom G; Sarver, Ronald W; Zhang, Chaoyang; Basu, Kalyan; Das, Sajal K; Poland, Bradley W

2009-01-01

In this study, we formulate a computational reaction model following a chemical kinetic theory approach to predict the binding rate constant for the siRNA-RISC complex formation reaction. The model allowed us to study the potency difference between 2-nt 3' overhangs against blunt-ended siRNA molecules in an RNA interference (RNAi) system. The rate constant predicted by this model was fed into a stochastic simulation of the RNAi system (using the Gillespie stochastic simulator) to study the overall potency effect. We observed that the stochasticity in the transcription/translation machinery has no observable effects in the RNAi pathway. Sustained gene silencing using siRNAs can be achieved only if there is a way to replenish the dsRNA molecules in the cell. Initial findings show about 1.5 times more blunt-ended molecules will be required to keep the mRNA at the same reduced level compared to the 2-nt overhang siRNAs. However, the mRNA levels jump back to saturation after a longer time when blunt-ended siRNAs are used. We found that the siRNA-RISC complex formation reaction rate was 2 times slower when blunt-ended molecules were used pointing to the fact that the presence of the 2-nt overhangs has a greater effect on the reaction in which the bound RISC complex cleaves the mRNA. PMID:19594876

Controlling First-Row Catalysts: Amination of Aryl and Heteroaryl Chlorides and Bromides with Primary Aliphatic Amines Catalyzed by a BINAP-Ligated Single-Component Ni(0) Complex

PubMed Central

2015-01-01

First-row metal complexes often undergo undesirable one-electron redox processes during two-electron steps of catalytic cycles. We report the amination of aryl chlorides and bromides with primary aliphatic amines catalyzed by a well-defined, single-component nickel precursor (BINAP)Ni(η2-NC-Ph) (BINAP = 2,2′-bis(biphenylphosphino)-1,1′-binaphthalene) that minimizes the formation of Ni(I) species and (BINAP)2Ni. The scope of the reaction encompasses electronically varied aryl chlorides and nitrogen-containing heteroaryl chlorides, including pyridine, quinoline, and isoquinoline derivatives. Mechanistic studies support the catalytic cycle involving a Ni(0)/Ni(II) couple for this nickel-catalyzed amination and are inconsistent with a Ni(I) halide intermediate. Monitoring the reaction mixture by 31P NMR spectroscopy identified (BINAP)Ni(η2-NC-Ph) as the resting state of the catalyst in the amination of both aryl chlorides and bromides. Kinetic studies showed that the amination of aryl chlorides and bromides is first order in both catalyst and aryl halide and zero order in base and amine. The reaction of a representative aryl chloride is inverse first order in PhCN, but the reaction of a representative aryl bromide is zero order in PhCN. This difference in the order of the reaction in PhCN indicates that the aryl chloride reacts with (BINAP)Ni(0), formed by dissociation PhCN from (BINAP)Ni(η2-NC-Ph), but the aryl bromide directly reacts with (BINAP)Ni(η2-NC-Ph). The overall kinetic behavior is consistent with turnover-limiting oxidative addition of the aryl halide to Ni(0). Several pathways for catalyst decomposition were identified, such as the formation of the catalytically inactive bis(amine)-ligated arylnickel(II) chloride, (BINAP)2Ni(0), and the Ni(I) species [(BINAP)Ni(μ-Cl)]2. By using a well-defined nickel complex as catalyst, the formation of (BINAP)2Ni(0) is avoided and the formation of the Ni(I) species [(BINAP)Ni(μ-Cl)]2 is minimized. PMID:24397570

Bromamine Decomposition Revisited: A Holistic Approach for Analyzing Acid and Base Catalysis Kinetics.

PubMed

Wahman, David G; Speitel, Gerald E; Katz, Lynn E

2017-11-21

Chloramine chemistry is complex, with a variety of reactions occurring in series and parallel and many that are acid or base catalyzed, resulting in numerous rate constants. Bromide presence increases system complexity even further with possible bromamine and bromochloramine formation. Therefore, techniques for parameter estimation must address this complexity through thoughtful experimental design and robust data analysis approaches. The current research outlines a rational basis for constrained data fitting using Brønsted theory, application of the microscopic reversibility principle to reversible acid or base catalyzed reactions, and characterization of the relative significance of parallel reactions using fictive product tracking. This holistic approach was used on a comprehensive and well-documented data set for bromamine decomposition, allowing new interpretations of existing data by revealing that a previously published reaction scheme was not robust; it was not able to describe monobromamine or dibromamine decay outside of the conditions for which it was calibrated. The current research's simplified model (3 reactions, 17 constants) represented the experimental data better than the previously published model (4 reactions, 28 constants). A final model evaluation was conducted based on representative drinking water conditions to determine a minimal model (3 reactions, 8 constants) applicable for drinking water conditions.

Catecholase activity of dicopper(II)-bispidine complexes: stabilities and structures of intermediates, kinetics and reaction mechanism.

PubMed

Born, Karin; Comba, Peter; Daubinet, André; Fuchs, Alexander; Wadepohl, Hubert

2007-01-01

A mechanism for the oxidation of 3,5-di-tert-butylcatechol (dtbc) with dioxygen to the corresponding quinone (dtbq), catalyzed by bispidine-dicopper complexes (bispidines are various mono- and dinucleating derivatives of 3,7-diazabicyclo[3.3.1]nonane with bis-tertiary-amine-bispyridyl or bis-tertiary-amine-trispyridyl donor sets), is proposed on the basis of (1) the stoichiometry of the reaction as well as the stabilities and structures [X-ray, density functional theory (B3LYP, TZV)] of the bispidine-dicopper(II)-3,4,5,6-tetrachlorcatechol intermediates, (2) formation kinetics and structures (molecular mechanics, MOMEC) of the end-on peroxo-dicopper(II) complexes and (3) kinetics of the stoichiometric (anaerobic) and catalytic (aerobic) copper-complex-assisted oxidation of dtbc. This involves (1) the oxidation of the dicopper(I) complexes with dioxygen to the corresponding end-on peroxo-dicopper(II) complexes, (2) coordination of dtbc as a bridging ligand upon liberation of H(2)O(2) and (3) intramolecular electron transfer to produce dtbq, which is liberated, and the dicopper(I) catalyst. Although the bispidine complexes have reactivities comparable to those of recently published catalysts with macrocyclic ligands, which seem to reproduce the enzyme-catalyzed process in various reaction sequences, a strikingly different oxidation mechanism is derived from the bispidine-dicopper-catalyzed reaction.

COBRA: A Computational Brewing Application for Predicting the Molecular Composition of Organic Aerosols

PubMed Central

Fooshee, David R.; Nguyen, Tran B.; Nizkorodov, Sergey A.; Laskin, Julia; Laskin, Alexander; Baldi, Pierre

2012-01-01

Atmospheric organic aerosols (OA) represent a significant fraction of airborne particulate matter and can impact climate, visibility, and human health. These mixtures are difficult to characterize experimentally due to their complex and dynamic chemical composition. We introduce a novel Computational Brewing Application (COBRA) and apply it to modeling oligomerization chemistry stemming from condensation and addition reactions in OA formed by photooxidation of isoprene. COBRA uses two lists as input: a list of chemical structures comprising the molecular starting pool, and a list of rules defining potential reactions between molecules. Reactions are performed iteratively, with products of all previous iterations serving as reactants for the next. The simulation generated thousands of structures in the mass range of 120–500 Da, and correctly predicted ~70% of the individual OA constituents observed by high-resolution mass spectrometry. Select predicted structures were confirmed with tandem mass spectrometry. Esterification was shown to play the most significant role in oligomer formation, with hemiacetal formation less important, and aldol condensation insignificant. COBRA is not limited to atmospheric aerosol chemistry; it should be applicable to the prediction of reaction products in other complex mixtures for which reasonable reaction mechanisms and seed molecules can be supplied by experimental or theoretical methods. PMID:22568707

Single-Molecule Spectroscopy and Imaging Studies of Protein Dynamics

NASA Astrophysics Data System (ADS)

Lu, H. Peter

2012-04-01

Enzymatic reactions and protein-protein interactions are traditionally studied at the ensemble level, despite significant static and dynamic inhomogeneities. Subtle conformational changes play a crucial role in protein functions, and these protein conformations are highly dynamic rather than being static. We applied AFM-enhanced single-molecule spectroscopy to study the mechanisms and dynamics of enzymatic reactions involved with kinase and lysozyme proteins. Enzymatic reaction turnovers and the associated structure changes of individual protein molecules were observed simultaneously in real-time by single-molecule FRET detections. Our single-molecule spectroscopy measurements of T4 lysozyme and HPPK enzymatic conformational dynamics have revealed time bunching effect and intermittent coherence in conformational state change dynamics involving in enzymatic reaction cycles. The coherent conformational state dynamics suggests that the enzymatic catalysis involves a multi-step conformational motion along the coordinates of substrate-enzyme complex formation and product releasing, presenting as an extreme dynamic behavior intrinsically related to the time bunching effect that we have reported previously. Our results of HPPK interaction with substrate support a multiple-conformational state model, being consistent with a complementary conformation selection and induced-fit enzymatic loop-gated conformational change mechanism in substrate-enzyme active complex formation. Our new approach is applicable to a wide range of single-molecule FRET measurements for protein conformational changes under enzymatic reactions.

The reactions of SO3 with HO2 radical and H2O...HO2 radical complex. Theoretical study on the atmospheric formation of HSO5 and H2SO4.

PubMed

Gonzalez, Javier; Torrent-Sucarrat, Miquel; Anglada, Josep M

2010-03-07

The influence of a single water molecule on the gas-phase reactivity of the HO(2) radical has been investigated by studying the reactions of SO(3) with the HO(2) radical and with the H(2)O...HO(2) radical complex. The naked reaction leads to the formation of the HSO(5) radical, with a computed binding energy of 13.81 kcal mol(-1). The reaction with the H(2)O...HO(2) radical complex can give two different products, namely (a) HSO(5) + H(2)O, which has a binding energy that is computed to be 4.76 kcal mol(-1) more stable than the SO(3) + H(2)O...HO(2) reactants (Delta(E + ZPE) at 0K) and an estimated branching ratio of about 34% at 298K and (b) sulfuric acid and the hydroperoxyl radical, which is computed to be 10.51 kcal mol(-1) below the energy of the reactants (Delta(E + ZPE) at 0K), with an estimated branching ratio of about 66% at 298K. The fact that one of the products is H(2)SO(4) may have relevance in the chemistry of the atmosphere. Interestingly, the water molecule acts as a catalyst, [as it occurs in (a)] or as a reactant [as it occurs in (b)]. For a sake of completeness we have also calculated the anharmonic vibrational frequencies for HO(2), HSO(5), the HSO(5)...H(2)O hydrogen bonded complex, H(2)SO(4), and two H(2)SO(4)...H(2)O complexes, in order to help with the possible experimental identification of some of these species.

Clostridium acidurici Electron-Bifurcating Formate Dehydrogenase

PubMed Central

Wang, Shuning; Huang, Haiyan; Kahnt, Jörg

2013-01-01

Cell extracts of uric acid-grown Clostridium acidurici catalyzed the coupled reduction of NAD+ and ferredoxin with formate at a specific activity of 1.3 U/mg. The enzyme complex catalyzing the electron-bifurcating reaction was purified 130-fold and found to be composed of four subunits encoded by the gene cluster hylCBA-fdhF2. PMID:23872566

NO ICE HYDROGENATION: A SOLID PATHWAY TO NH{sub 2}OH FORMATION IN SPACE

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

Congiu, Emanuele; Dulieu, Francois; Chaabouni, Henda

2012-05-01

Icy dust grains in space act as catalytic surfaces onto which complex molecules form. These molecules are synthesized through exothermic reactions from precursor radicals and, mostly, hydrogen atom additions. Among the resulting products are species of biological relevance, such as hydroxylamine-NH{sub 2}OH-a precursor molecule in the formation of amino acids. In this Letter, laboratory experiments are described that demonstrate NH{sub 2}OH formation in interstellar ice analogs for astronomically relevant temperatures via successive hydrogenation reactions of solid nitric oxide (NO). Inclusion of the experimental results in an astrochemical gas-grain model proves the importance of a solid-state NO+H reaction channel as amore » starting point for prebiotic species in dark interstellar clouds and adds a new perspective to the way molecules of biological importance may form in space.« less

An ab initio molecular dynamics and density functional theory study of the formation of phosphate chains from metathiophosphates.

PubMed

Mosey, Nicholas J; Woo, Tom K

2006-09-04

The reactions that occur between metathiophosphate (MTP) molecules are identified and examined through ab initio molecular dynamics simulations and static quantum chemical calculations at the density functional level of theory. The simulations show that certain types of MTPs can react to yield phosphate chains, while others only dimerize. These differences are rationalized in terms of reaction energies and the electronic structures of these molecules. In the reaction leading to the formation of phosphate chains, the reactive center, a tri-coordinate phosphorus atom, is continually regenerated. A polymerization mechanism linking MTPs to phosphate chains is developed on the basis of these results. This information sheds light on the underlying processes that may be responsible for the formation of phosphates under high-temperature conditions and may prove useful in the development of protocols for the rational synthesis of complex phosphate structures.

A mathematical model for foreign body reactions in 2D.

PubMed

Su, Jianzhong; Gonzales, Humberto Perez; Todorov, Michail; Kojouharov, Hristo; Tang, Liping

2011-02-01

The foreign body reactions are commonly referred to the network of immune and inflammatory reactions of human or animals to foreign objects placed in tissues. They are basic biological processes, and are also highly relevant to bioengineering applications in implants, as fibrotic tissue formations surrounding medical implants have been found to substantially reduce the effectiveness of devices. Despite of intensive research on determining the mechanisms governing such complex responses, few mechanistic mathematical models have been developed to study such foreign body reactions. This study focuses on a kinetics-based predictive tool in order to analyze outcomes of multiple interactive complex reactions of various cells/proteins and biochemical processes and to understand transient behavior during the entire period (up to several months). A computational model in two spatial dimensions is constructed to investigate the time dynamics as well as spatial variation of foreign body reaction kinetics. The simulation results have been consistent with experimental data and the model can facilitate quantitative insights for study of foreign body reaction process in general.

Hydrogen bonding effects on the reorganization energy for photoinduced charge separation reaction between porphyrin and quinone studied by nanosecond laser flash photolysis.

PubMed

Yago, Tomoaki; Gohdo, Masao; Wakasa, Masanobu

2010-02-25

Alcohol concentration dependences of photoinduced charge separation (CS) reaction of zinc tetraphenyl-porphyrin (ZnTPP) and duroquinone (DQ) were investigated in benzonitrile by a nanosecond laser flash photolysis technique. The photoinduced CS reaction was accelerated by the addition of alcohols, whereas the addition of acetonitrile caused little effect on the CS reactions. The simple theory was developed to calculate an increase in reorganization energies induced by the hydrogen bonding interactions between DQ and alcohols using the chemical equilibrium constants for the hydrogen bonding complexes through the concerted pathway and the stepwise one. The experimental results were analyzed by using the Marcus equation where we took into account the hydrogen bonding effects on the reorganization energy and the reaction free energy for the CS reaction. The observed alcohol concentration dependence of the CS reaction rates was well explained by the formation of the hydrogen bonding complexes through the concerted pathway, demonstrating the increase in the reorganization energy by the hydrogen bonding interactions.

The role of amine ligands in governing film morphology and electrical properties of copper films derived from copper formate-based molecular inks.

PubMed

Paquet, Chantal; Lacelle, Thomas; Liu, Xiangyang; Deore, Bhavana; Kell, Arnold J; Lafrenière, Sylvie; Malenfant, Patrick R L

2018-04-19

Copper formate complexes with various primary amines, secondary amines and pyridines were prepared, and their decomposition into conductive films was characterized. A comparison of the various complexes reveals that the temperature of thermolysis depends on the number of hydrogen bonds that can be formed between the amine and formate ligands. The particle size resulting from sintering of the copper complexes is shown to depend on the fraction of amine ligand released during the thermolysis reaction. The particle size in turn is shown to govern the electrical properties of the copper films. Correlations between the properties of the amines, such as boiling point and coordination strength, with the morphology and electrical performance of the copper films were established and provide a basis for the molecular design of copper formate molecular inks.

Formate-induced inhibition of the water-oxidizing complex of photosystem II studied by EPR.

PubMed

Feyziev, Y M; Yoneda, D; Yoshii, T; Katsuta, N; Kawamori, A; Watanabe, Y

2000-04-04

The effects of various formate concentrations on both the donor and the acceptor sides in oxygen-evolving PS II membranes (BBY particles) were examined. EPR, oxygen evolution and variable chlorophyll fluorescence have been observed. It was found that formate inhibits the formation of the S(2) state multiline signal concomitant with stimulation of the Q(A)(-)Fe(2+) signal at g = 1.82. The decrease and the increase in intensities of the multiline and Q(A)(-)Fe(2+) signals, respectively, had a linear relation for formate concentrations between 5 and 500 mM. The g = 4.1 signal formation measured in the absence of methanol was not inhibited by formate up to 250 mM in the buffer. In the presence of 3% methanol the g = 4.1 signal evolved as formate concentration increased. The evolved signal could be ascribed to the inhibited centers. Oxygen evolution measured in the presence of an electron acceptor, phenyl-p-benzoquinone, was also inhibited by formate proportionally to the decrease in the multiline signal intensity. The inhibition seemed to be due to a retarded electron transfer from the water-oxidizing complex to Y(Z)(+), which was observed in the decay kinetics of the Y(Z)(+) signal induced by illumination above 250 K. These results show that formate induces inhibition of water oxidation reactions as well as electron transfer on the PS II acceptor side. The inhibition effects of formate in PS II were found to be reversible, indicating no destructive effect on the reaction center induced by formate.

Infrared spectra of SF6-.HCOOH.Arn (n=0-2): Infrared triggered reaction and Ar-induced reactive inhibition

NASA Astrophysics Data System (ADS)

Schneider, Holger; Takahashi, Kaito; Skodje, Rex T.; Weber, J. Mathias

2009-05-01

We present the infrared spectra of SF6-ṡHCOOHṡArm (m =0-2) complexes. We find that the binding motif involves a single hydrogen bond between the SF6- anion and the OH group of the formic acid, with the CH group weakly tethered to a neighboring F atom. Similar to the case of hydrated SF6-, the SF bond involved in the (OH-F) bond is significantly stretched and weakened by the attachment of the HCOOH ligand. The bare complex undergoes reaction upon infrared absorption in the CH/OH stretching region of the formic acid moiety, leading predominantly to the formation of SF4-+2HF+CO2. The reaction can be inhibited by attachment of two Ar atoms. We discuss a likely reaction mechanism in the framework of ab initio calculations, suggesting that reaction proceeds via tunneling through the potential barrier.

On the positronium spin conversion reactions caused by some macrocyclic Co II complexes

NASA Astrophysics Data System (ADS)

Fantola-Lazzarini, Anna L.; Lazzarini, Ennio

2002-08-01

The rate constants, kCR, of ortho- into para-positronium ( o-Ps→ p-Ps) spin conversion reactions, CR, caused by the high-spin [Co IIsep] 2+, [Co IIdinosar] 2+ and [Co IIdiamsar] 2+ macrocyclic complexes and also by high-spin [Co II sen] 2+ tripod complex were measured at several temperatures. The delocalizations, β, of Co II unpaired electrons, promoted by the mentioned ligands, were determined by using the previously established correlations between kCR and the electron delocalization β of unpaired metal electrons. β is given by the ratio between the Racah inter-electronic repulsion parameters of complexes, B, and that of the free ions, B0. The β values are compared with those of the Co II complexes with en (1,2-ethanediamine), pn (1,2 propanediamine) and dien (2,2' diamino diethylamine) ligands. The kCR rate constants are also compared with those of the Ps oxidation reactions, OR, promoted by the corresponding Co III complexes. It is concluded that, unlike OR's, the CR's do not occur by formation of hepta-coordinate adducts with Ps atoms.

Formation mechanism of complex pattern on fishes' skin

NASA Astrophysics Data System (ADS)

Li, Xia; Liu, Shuhua

2009-10-01

In this paper, the formation mechanism of the complex patterns observed on the skin of fishes has been investigated by a two-coupled reaction diffusion model. The effects of coupling strength between two layers play an important role in the pattern-forming process. It is found that only the epidermis layer can produce complicated patterns that have structures on more than one length scale. These complicated patterns including super-stripe pattern, mixture of spots and stripe, and white-eye pattern are similar to the pigmentation patterns on fishes' skin.

Squarylium-based chromogenic anion sensors.

PubMed

Lee, Eun-Mi; Gwon, Seon-Yeong; Son, Young-A; Kim, Sung-Hoon

2012-09-01

A squarylium (SQ) dye was synthesized by the reaction between squaric acid and 2,3,3-trimethylindolenine and its anion sensing properties were investigated using absorption and emission spectroscopy. This chemosensor exhibited high selectivity for CN(-) as compared with F(-), CH(3)CO(2)(-), Br(-), H(2)PO(4)(-), Cl(-), and NO(3)(-) in acetonitrile, which was attributed to the formation of a 1:1 squarylium:CN(-) coordination complex, the formation of which was supported by the calculated geometry of the complex. Copyright © 2012 Elsevier B.V. All rights reserved.

Dual gold catalysis: σ,π-propyne acetylide and hydroxyl-bridged digold complexes as easy-to-prepare and easy-to-handle precatalysts.

PubMed

Hashmi, A Stephen K; Lauterbach, Tobias; Nösel, Pascal; Vilhelmsen, Mie Højer; Rudolph, Matthias; Rominger, Frank

2013-01-14

A series of dinuclear gold σ,π-propyne acetylide complexes were prepared and tested for their catalytic ability in dual gold catalysis that was based on the reaction of an electrophilic π-complex of gold with a gold acetylide. The air-stable and storable catalysts can be isolated as silver-free catalysts in their activated form. These dual catalysts allow a fast initiation phase for the dual catalytic cycles without the need for additional additives for acetylide formation. Because propyne serves as a throw-away ligand, no traces of the precatalyst are generated. Based on the fast initiation process, side products are minimized and reaction rates are higher for these catalysts. A series of test reactions were used to demonstrate the general applicability of these catalysts. Lower catalyst loadings, faster reaction rates, and better selectivity, combined with the practicability of these catalysts, make them ideal catalysts for dual gold catalysis. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chlorodifluoromethane-triggered formation of difluoromethylated arenes catalysed by palladium

NASA Astrophysics Data System (ADS)

Feng, Zhang; Min, Qiao-Qiao; Fu, Xia-Ping; An, Lun; Zhang, Xingang

2017-09-01

Difluoromethylated aromatic compounds are of increasing importance in pharmaceuticals, agrochemicals and materials. Chlorodifluoromethane (ClCF2H), an inexpensive, abundant and widely used industrial raw material, represents the ideal and most straightforward difluoromethylating reagent, but introduction of the difluoromethyl group (CF2H) from ClCF2H into aromatics has not been reported. Here, we describe a direct palladium-catalysed difluoromethylation method for coupling ClCF2H with arylboronic acids and esters to generate difluoromethylated arenes with high efficiency. The reaction exhibits a remarkably broad substrate scope, including heteroarylboronic acids, and was used for difluoromethylation of a range of pharmaceuticals and biologically active compounds. Preliminary mechanistic studies revealed that a palladium difluorocarbene intermediate is involved in the reaction. Although numerous metal-difluorocarbene complexes have been prepared, the catalytic synthesis of difluoromethylated or difluoromethylenated compounds involving metal-difluorocarbene complexes has not received much attention. This new reaction therefore also opens the door to understand metal-difluorocarbene complex catalysed reactions.

Photocatalytic CO2 reduction with high turnover frequency and selectivity of formic acid formation using Ru(II) multinuclear complexes.

PubMed

Tamaki, Yusuke; Morimoto, Tatsuki; Koike, Kazuhide; Ishitani, Osamu

2012-09-25

Previously undescribed supramolecules constructed with various ratios of two kinds of Ru(II) complexes-a photosensitizer and a catalyst-were synthesized. These complexes can photocatalyze the reduction of CO(2) to formic acid with high selectivity and durability using a wide range of wavelengths of visible light and NADH model compounds as electron donors in a mixed solution of dimethylformamide-triethanolamine. Using a higher ratio of the photosensitizer unit to the catalyst unit led to a higher yield of formic acid. In particular, of the reported photocatalysts, a trinuclear complex with two photosensitizer units and one catalyst unit photocatalyzed CO(2) reduction (Φ(HCOOH) = 0.061, TON(HCOOH) = 671) with the fastest reaction rate (TOF(HCOOH) = 11.6 min(-1)). On the other hand, photocatalyses of a mixed system containing two kinds of model mononuclear Ru(II) complexes, and supramolecules with a higher ratio of the catalyst unit were much less efficient, and black oligomers and polymers were produced from the Ru complexes during photocatalytic reactions, which reduced the yield of formic acid. The photocatalytic formation of formic acid using the supramolecules described herein proceeds via two sequential processes: the photochemical reduction of the photosensitizer unit by NADH model compounds and intramolecular electron transfer to the catalyst unit.

Theoretical study of the kinetics of chlorine atom abstraction from chloromethanes by atomic chlorine.

PubMed

Brudnik, Katarzyna; Twarda, Maria; Sarzyński, Dariusz; Jodkowski, Jerzy T

2013-10-01

Ab initio calculations at the G3 level were used in a theoretical description of the kinetics and mechanism of the chlorine abstraction reactions from mono-, di-, tri- and tetra-chloromethane by chlorine atoms. The calculated profiles of the potential energy surface of the reaction systems show that the mechanism of the studied reactions is complex and the Cl-abstraction proceeds via the formation of intermediate complexes. The multi-step reaction mechanism consists of two elementary steps in the case of CCl4 + Cl, and three for the other reactions. Rate constants were calculated using the theoretical method based on the RRKM theory and the simplified version of the statistical adiabatic channel model. The temperature dependencies of the calculated rate constants can be expressed, in temperature range of 200-3,000 K as [Formula: see text]. The rate constants for the reverse reactions CH3/CH2Cl/CHCl2/CCl3 + Cl2 were calculated via the equilibrium constants derived theoretically. The kinetic equations [Formula: see text] allow a very good description of the reaction kinetics. The derived expressions are a substantial supplement to the kinetic data necessary to describe and model the complex gas-phase reactions of importance in combustion and atmospheric chemistry.

Chiral Nickel(II) Complex Catalyzed Enantioselective Doyle-Kirmse Reaction of α-Diazo Pyrazoleamides.

PubMed

Lin, Xiaobin; Tang, Yu; Yang, Wei; Tan, Fei; Lin, Lili; Liu, Xiaohua; Feng, Xiaoming

2018-03-07

Although high enantioselectivity of [2,3]-sigmatropic rearrangement of sulfonium ylides (Doyle-Kirmse reaction) has proven surprisingly elusive using classic chiral Rh(II) and Cu(I) catalysts, in principle it is due to the difficulty in fine discrimination of the heterotopic lone pairs of sulfur and chirality inversion at sulfur of sulfonium ylides. Here, we show that the synergistic merger of new α-diazo pyrazoleamides and a chiral N, N'-dioxide-nickel(II) complex catalyst enables a highly enantioselective Doyle-Kirmse reaction. The pyrazoleamide substituent serves as both an activating and a directing group for the ready formation of a metal-carbene- and Lewis-acid-bonded ylide intermediate in the assistance of a dual-tasking nickel(II) complex. An alternative chiral Lewis-acid-bonded ylide pathway greatly improves the product enantiopurity even for the reaction of a symmetric diallylsulfane. The majority of transformations over a series of aryl- or vinyl-substituted α-diazo pyrazoleamindes and sulfides proceed rapidly (within 5-20 min in most cases) with excellent results (up to 99% yield and 96% ee), providing a breakthrough in enantioselective Doyle-Kirmse reaction.

Kinetics of DSB rejoining and formation of simple chromosome exchange aberrations

NASA Technical Reports Server (NTRS)

Cucinotta, F. A.; Nikjoo, H.; O'Neill, P.; Goodhead, D. T.

2000-01-01

PURPOSE: To investigate the role of kinetics in the processing of DNA double strand breaks (DSB), and the formation of simple chromosome exchange aberrations following X-ray exposures to mammalian cells based on an enzymatic approach. METHODS: Using computer simulations based on a biochemical approach, rate-equations that describe the processing of DSB through the formation of a DNA-enzyme complex were formulated. A second model that allows for competition between two processing pathways was also formulated. The formation of simple exchange aberrations was modelled as misrepair during the recombination of single DSB with undamaged DNA. Non-linear coupled differential equations corresponding to biochemical pathways were solved numerically by fitting to experimental data. RESULTS: When mediated by a DSB repair enzyme complex, the processing of single DSB showed a complex behaviour that gives the appearance of fast and slow components of rejoining. This is due to the time-delay caused by the action time of enzymes in biomolecular reactions. It is shown that the kinetic- and dose-responses of simple chromosome exchange aberrations are well described by a recombination model of DSB interacting with undamaged DNA when aberration formation increases with linear dose-dependence. Competition between two or more recombination processes is shown to lead to the formation of simple exchange aberrations with a dose-dependence similar to that of a linear quadratic model. CONCLUSIONS: Using a minimal number of assumptions, the kinetics and dose response observed experimentally for DSB rejoining and the formation of simple chromosome exchange aberrations are shown to be consistent with kinetic models based on enzymatic reaction approaches. A non-linear dose response for simple exchange aberrations is possible in a model of recombination of DNA containing a DSB with undamaged DNA when two or more pathways compete for DSB repair.

STEPS: Modeling and Simulating Complex Reaction-Diffusion Systems with Python

PubMed Central

Wils, Stefan; Schutter, Erik De

2008-01-01

We describe how the use of the Python language improved the user interface of the program STEPS. STEPS is a simulation platform for modeling and stochastic simulation of coupled reaction-diffusion systems with complex 3-dimensional boundary conditions. Setting up such models is a complicated process that consists of many phases. Initial versions of STEPS relied on a static input format that did not cleanly separate these phases, limiting modelers in how they could control the simulation and becoming increasingly complex as new features and new simulation algorithms were added. We solved all of these problems by tightly integrating STEPS with Python, using SWIG to expose our existing simulation code. PMID:19623245

Synthesis of Stereoisomeric - Metal Complexes Using Phase-Transfer Catalysis and Photochemical Transforms.

DTIC Science & Technology

1984-05-25

bonded arrangement (2) as depicted in Figure 1-1. Fe Fe.’. % V3 1 2 Figure I-1 Proposed Structures of Ferrocene In order to understand clearly the... phosphines (PR3) or methanol (CH3OH) results in the formation nf o-alkylmetal complexes (Scheme Ill-1, 1). If stable, further reaction of these

Chemical-Biological Properties of Zinc Sensors TSQ and Zinquin: Formation of Sensor-Zn-Protein Adducts versus Zn(Sensor)2 Complexes.

PubMed

Nowakowski, Andrew B; Meeusen, Jeffrey W; Menden, Heather; Tomasiewicz, Henry; Petering, David H

2015-12-21

Fluorescent zinc sensors are the most commonly used tool to study the intracellular mobile zinc status within cellular systems. Previously, we have shown that the quinoline-based sensors Zinquin and 6-methoxy-8-p-toluenesulfonamido-quinoline (TSQ) predominantly form ternary adducts with members of the Zn-proteome. Here, the chemistries of these sensors are further characterized, including how Zn(sensor)2 complexes may react in an intracellular environment. We demonstrate that these sensors are typically used in higher concentrations than needed to obtain maximum signal. Exposing cells to either Zn(Zinquin)2 or Zn(TSQ)2 resulted in efficient cellular uptake and the formation of sensor-Zn-protein adducts as evidenced by both a fluorescence spectral shift toward that of ternary adducts and the localization of the fluorescence signal within the proteome after gel filtration of cellular lysates. Likewise, reacting Zn(sensor)2 with the Zn-proteome from LLC-PK1 cells resulted in the formation of sensor-Zn-protein ternary adducts that could be inhibited by first saturating the Zn- proteome with excess sensor. Further, a native SDS-PAGE analysis of the Zn-proteome reacted with either the sensor or the Zn(sensor)2 complex revealed that both reactions result in the formation of a similar set of sensor-Zn-protein fluorescent products. The results of this experiment also demonstrated that TSQ and Zinquin react with different members of the Zn-proteome. Reactions with the model apo-Zn-protein bovine serum albumin showed that both Zn(TSQ)2 and Zn(Zinquin)2 reacted to form ternary adducts with its apo-Zn-binding site. Moreover, incubating Zn(sensor)2 complexes with non-zinc binding proteins failed to elicit a spectral shift in the fluorescence spectrum, supporting the premise that blue-shifted emission spectra are due to sensor-Zn-protein ternary adducts. It was concluded that Zn(sensors)2 species do not play a significant role in the overall reaction between these sensors and intact cells. In turn, this study further supports the formation of sensor-Zn-protein adducts as the principal observed fluorescent product during experiments employing these two sensors.

First Evidence of Vibrationally Driven Bimolecular Reactions in Solution: Reactions of Br Atoms with Dimethylsulfoxide and Methanol.

PubMed

Shin, Jae Yoon; Shaloski, Michael A; Crim, F Fleming; Case, Amanda S

2017-03-23

We present evidence for vibrational enhancement of the rate of bimolecular reactions of Br atoms with dimethylsulfoxide (DMSO) and methanol (CH 3 OH) in the condensed phase. The abstraction of a hydrogen atom from either of these solvents by a Br atom is highly endoergic: 3269 cm -1 for DMSO and 1416 or 4414 cm -1 for CH 3 OH, depending on the hydrogen atom abstracted. Thus, there is no thermal abstraction reaction at room temperature. Broadband electronic transient absorption shows that following photolysis of bromine precursors Br atoms form van der Waals complexes with the solvent molecules in about 5 ps and this Br • -solvent complex undergoes recombination. To explore the influence of vibrational energy on the abstraction reactions, we introduce a near-infrared (NIR) pump pulse following the photolysis pulse to excite the first overtone of the C-H (or O-H) stretch of the solvent molecules. Using single-wavelength detection, we observe a loss of the Br • -solvent complex that requires the presence of both photolysis and NIR pump pulses. Moreover, the magnitude of this loss depends on the NIR wavelength. Although this loss of reactive Br supports the notion of vibrationally driven chemistry, it is not concrete evidence of the hydrogen-abstraction reaction. To verify that the loss of reactive Br results from the vibrationally driven bimolecular reaction, we examine the pH dependence of the solution (as a measure of the formation of the HBr product) following long-time irradiation of the sample with both photolysis and NIR pump beams. We observe that when the NIR beam is on-resonance, the hydronium ion concentration increases fourfold as compared to that when it is off-resonance, suggesting the formation of HBr via a vibrationally driven hydrogen-abstraction reaction in solution.

Charge-Transfer Complexes and Photochemistry of Ozone with Ferrocene and n-Butylferrocene: A UV-vis Matrix-Isolation Study.

PubMed

Pinelo, Laura F; Kugel, Roger W; Ault, Bruce S

2015-10-15

The reactions of ozone with ferrocene (cp2Fe) and with n-butylferrocene (n-butyl cp2Fe) were studied using matrix isolation, UV-vis spectroscopy, and theoretical calculations. The codeposition of cp2Fe with O3 and of n-butyl cp2Fe with O3 into an argon matrix led to the production of 1:1 charge-transfer complexes with absorptions at 765 and 815 nm, respectively. These absorptions contribute to the green matrix color observed upon initial deposition. The charge-transfer complexes underwent photochemical reactions upon irradiation with red light (λ ≥ 600 nm). Theoretical UV-vis spectra of the charge-transfer complexes and photochemical products were calculated using TD-DFT at the B3LYP/6-311G++(d,2p) level of theory. The calculated UV-vis spectra were in good agreement with the experimental results. MO analysis of these long-wavelength transitions showed them to be n→ π* on the ozone subunit in the complex and indicated that the formation of the charge-transfer complex between ozone and cp2Fe or n-butyl cp2Fe affects how readily the π* orbital on O3 is populated when red light (λ ≥ 600 nm) is absorbed. 1:1 complexes of cp2Fe and n-butyl cp2Fe with O2 were also observed experimentally and calculated theoretically. These results support and enhance previous infrared studies of the mechanism of photooxidation of ferrocene by ozone, a reaction that has considerable significance for the formation of iron oxide thin films for a range of applications.

Response to the Comment on Paper 'Water vapor Enhancement of Rates of Peroxy Radical Reactions', Int. J. Chem. Kinetics, 47, 395, 2015

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

Kumbhani, Sambhav R.; Cline, Taylor S.; Killian, Marie C.

Comments provided here aid in understanding the effect of water vapor on the rate of the self-reaction of HOCH2CH2O2 recently reported by Kumbhani et al. [1] Kumbhani et al. asserts that water vapor increases the rate of the HOCH2CH2O2 self-reaction by formation of an HOCH2CH2O2-H2O complex.

Phosphinosilylenes as a novel ligand system for heterobimetallic complexes.

PubMed

Breit, Nora C; Eisenhut, Carsten; Inoue, Shigeyoshi

2016-04-25

A dihydrophosphinosilylene iron complex [LSi{Fe(CO)4}PH2] has been prepared and utilized in the synthesis of novel heterobimetallic complexes. The phosphine moiety in this phosphinosilylene complex allows coordination towards tungsten leading to the iron-tungsten heterobimetallic complex [LSi{Fe(CO)4}PH2{W(CO)5}]. In contrast, the reaction of [LSi{Fe(CO)4}PH2] with ethylenebis(triphenylphosphine)platinum(0) results in the formation of the iron-platinum heterobimetallic complex [LSi{Fe(CO)4}PH{PtH(PPh3)2}] via oxidative addition.

Dehydrogenation, disproportionation and transfer hydrogenation reactions of formic acid catalyzed by molybdenum hydride compounds.

PubMed

Neary, Michelle C; Parkin, Gerard

2015-03-01

The cyclopentadienyl molybdenum hydride compounds, Cp R Mo(PMe 3 ) 3- x (CO) x H (Cp R = Cp, Cp*; x = 0, 1, 2 or 3), are catalysts for the dehydrogenation of formic acid, with the most active catalysts having the composition Cp R Mo(PMe 3 ) 2 (CO)H. The mechanism of the catalytic cycle is proposed to involve (i) protonation of the molybdenum hydride complex, (ii) elimination of H 2 and coordination of formate, and (iii) decarboxylation of the formate ligand to regenerate the hydride species. NMR spectroscopy indicates that the nature of the resting state depends on the composition of the catalyst. For example, (i) the resting states for the CpMo(CO) 3 H and CpMo(PMe 3 )(CO) 2 H systems are the hydride complexes themselves, (ii) the resting state for the CpMo(PMe 3 ) 3 H system is the protonated species [CpMo(PMe 3 ) 3 H 2 ] + , and (iii) the resting state for the CpMo(PMe 3 ) 2 (CO)H system is the formate complex, CpMo(PMe 3 ) 2 (CO)(κ 1 -O 2 CH), in the presence of a high concentration of formic acid, but CpMo(PMe 3 ) 2 (CO)H when the concentration of acid is low. While CO 2 and H 2 are the principal products of the catalytic reaction induced by Cp R Mo(PMe 3 ) 3- x (CO) x H, methanol and methyl formate are also observed. The generation of methanol is a consequence of disproportionation of formic acid, while methyl formate is a product of subsequent esterification. The disproportionation of formic acid is a manifestation of a transfer hydrogenation reaction, which may also be applied to the reduction of aldehydes and ketones. Thus, CpMo(CO) 3 H also catalyzes the reduction of a variety of ketones and aldehydes to alcohols by formic acid, via a mechanism that involves ionic hydrogenation.

Anti-fibrillogenic properties of phthalocyanines: effect of the out-of-plane ligands.

PubMed

Kovalska, V; Cherepanov, V; Losytskyy, M; Chernii, S; Senenko, A; Chernii, V; Tretyakova, I; Yarmoluk, S; Volkov, S

2014-12-15

The axially-coordinated phthalocyanines were previously reported as agents possessing strong anti-fibrillogenic properties. In the presented study we used the atomic force microscopy to investigate the intermediates and the products of insulin aggregation reaction formed in the presence of Zr and Hf phthalocyanine complexes that contain out-of-plane ligands of different size and nature. It is shown that while phthalocyanine-free insulin generated mostly amyloid fibrils with a diameter of 2-8nm and a length of up to 5μm, the presence of phthalocyanines with spatial bulky ligands (PcZrDbm2) leads to the redirection of the fibrillization reaction to the formation of the spherical oligomer aggregates with a diameter of 4-12nm. At the same time the phthalocyanine complex PcHfCl2 having the small-volume ligands induces the formation of large size insulin aggregates with a height of about 100nm that are supposed to be amorphous species. The study of the aggregation intermediates showed the certain similarity of the reaction passing for phthalocyanine-free insulin and insulin in the presence of PcZrDbm2. The large-size amorphous species were observed at the beginning of reaction, later they dissociated, leading to the formation and growth of the smaller size particles. The amyloid-sensitive cyanine dye 7519 demonstrates the strong fluorescent response both in the presence of fibrils and spherical oligomers, while it is non-sensitive to amorphous aggregates. Copyright © 2014 Elsevier Ltd. All rights reserved.

The effect of caffeine on the reactions of the excited singlet state of pyrene in micellar sodium lauryl sulfate

NASA Astrophysics Data System (ADS)

Hashimoto, Shuichi; Thomas, J. Kerry

1984-08-01

The effect of caffeine on a few photo-induced reactions of pyrene in micellar sodium lauryl sulfate (NaLS) has been studied. In these systems caffeine complexes with the pyrene (K asso = 85 ± 10 M -1 and also with the other reactants, e.g. Cu 2+ or TI +. The efficiencies of reactions which involve contact, i.e. pyrene excimer formation, and quenching by TI + ions to give the triplet state of pyrene, are significantly reduced in the presence of caffeine, due to geometric inhibitions formed by the complexation processes. The kinetics of photo-induced electron transfer, e.g. between excited pyrene and Cu 2+, are not affected. However, the subsequent reactions of the products are modified and the yield of ionic products is markedly increased.

Half-sandwich rhodium(III) transfer hydrogenation catalysts: Reduction of NAD(+) and pyruvate, and antiproliferative activity.

PubMed

Soldevila-Barreda, Joan J; Habtemariam, Abraha; Romero-Canelón, Isolda; Sadler, Peter J

2015-12-01

Organometallic complexes have the potential to behave as catalytic drugs. We investigate here Rh(III) complexes of general formula [(Cp(x))Rh(N,N')(Cl)], where N,N' is ethylenediamine (en), 2,2'-bipyridine (bpy), 1,10-phenanthroline (phen) or N-(2-aminoethyl)-4-(trifluoromethyl)benzenesulfonamide (TfEn), and Cp(x) is pentamethylcyclopentadienyl (Cp*), 1-phenyl-2,3,4,5-tetramethylcyclopentadienyl (Cp(xPh)) or 1-biphenyl-2,3,4,5-tetramethyl cyclopentadienyl (Cp(xPhPh)). These complexes can reduce NAD(+) to NADH using formate as a hydride source under biologically-relevant conditions. The catalytic activity decreased in the order of N,N-chelated ligand bpy > phen > en with Cp* as the η(5)-donor. The en complexes (1-3) became more active with extension to the Cp(X) ring, whereas the activity of the phen (7-9) and bpy (4-6) compounds decreased. [Cp*Rh(bpy)Cl](+) (4) showed the highest catalytic activity, with a TOF of 37.4±2h(-1). Fast hydrolysis of the chlorido complexes 1-10 was observed by (1)H NMR (<10min at 310K). The pKa* values for the aqua adducts were determined to be ca. 8-10. Complexes 1-9 also catalysed the reduction of pyruvate to lactate using formate as the hydride donor. The efficiency of the transfer hydrogenation reactions was highly dependent on the nature of the chelating ligand and the Cp(x) ring. Competition reactions between NAD(+) and pyruvate for reduction by formate catalysed by 4 showed a preference for reduction of NAD(+). The antiproliferative activity of complex 3 towards A2780 human ovarian cancer cells increased by up to 50% when administered in combination with non-toxic doses of formate, suggesting that transfer hydrogenation can induce reductive stress in cancer cells. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Just Click It: Undergraduate Procedures for the Copper(I)-Catalyzed Formation of 1,2,3-Triazoles from Azides and Terminal Acetylenes

ERIC Educational Resources Information Center

Sharpless, William D.; Peng Wu; Hansen, Trond Vidar; Lindberg, James G.

2005-01-01

The click chemistry uses only the most reliable reactions to build complex molecules from olefins, electrophiles and heteroatom linkers. A variation on Huisgen's azide-alkyne 1,2,3-triazole synthesis, the addition of the copper (I), the premium example of the click reaction, catalyst strongly activates terminal acetylenes towards the 1,3-dipole in…

Single and double C-Cl-activation of methylene chloride by P,N-ligand coordinated rhodium complexes.

PubMed

Blank, Benoît; Glatz, Germund; Kempe, Rhett

2009-02-02

Two in one: The simultaneous formation of bimetallic mu-methylene bridged Rh(III) complexes as well as dimeric Rh(III) complexes with terminal chloromethyl groups is observed for P,N-ligand stabilized Rh(I) complexes by C-Cl bond activation of methylene chloride. A mechanistic proposal for the formation of both activation products is also discussed. The synthesis of Rh(I) complexes with P-functionalized aminopyridine ligands is reported as well as the first simultaneous observation of a single and double activation of C-Cl bonds of methylene chloride affording both a dimeric Rh(III) complex bearing terminal CH(2)Cl groups in addition to a binuclear Rh(III) complex with a bridging mu-CH(2) group. The structures of the oxidative addition products were obtained by X-ray diffraction studies and NMR experiments were performed to elucidate some aspects of the reaction pathway.

Mechanisms and kinetics of alkaline hydrolysis of the energetic nitroaromatic compounds 2,4,6-trinitrotoluene (TNT) and 2,4-dinitroanisole (DNAN).

PubMed

Salter-Blanc, Alexandra J; Bylaska, Eric J; Ritchie, Julia J; Tratnyek, Paul G

2013-07-02

The environmental impacts of energetic compounds can be minimized through the design and selection of new energetic materials with favorable fate properties. Building predictive models to inform this process, however, is difficult because of uncertainties and complexities in some major fate-determining transformation reactions such as the alkaline hydrolysis of energetic nitroaromatic compounds (NACs). Prior work on the mechanisms of the reaction between NACs and OH(-) has yielded inconsistent results. In this study, the alkaline hydrolysis of 2,4,6-trinitrotoluene (TNT) and 2,4-dinitroanisole (DNAN) was investigated with coordinated experimental kinetic measurements and molecular modeling calculations. For TNT, the results suggest reversible formation of an initial product, which is likely either a Meisenheimer complex or a TNT anion formed by abstraction of a methyl proton by OH(-). For DNAN, the results suggest that a Meisenheimer complex is an intermediate in the formation of 2,4-dinitrophenolate. Despite these advances, the remaining uncertainties in the mechanisms of these reactions-and potential variability between the hydrolysis mechanisms for different NACs-mean that it is not yet possible to generalize the results into predictive models (e.g., quantitative structure-activity relationships, QSARs) for hydrolysis of other NACs.

Catalysis for Fluorination and Trifluoromethylation

PubMed Central

Furuya, Takeru; Kamlet, Adam S.; Ritter, Tobias

2011-01-01

Preface Recent advances in catalysis have made the incorporation of fluorine into complex organic molecules easier than ever before, but selective, general, and practical fluorination reactions remain sought after. Fluorination of molecules often imparts desirable properties such as metabolic and thermal stability, and fluorinated molecules are therefore frequently used as pharmaceuticals or materials. Even with the latest advances in chemistry, carbon–fluorine bond formation in complex molecules is still a significant challenge. Within the last few years, new reactions to make organofluorides have emerged and exemplify how to overcome some of the intricate challenges associated with fluorination. PMID:21614074

Unusual Complex Formation and Chemical Reaction of Haloacetate Anion on the Exterior Surface of Cucurbit[6]uril in the Gas Phase

NASA Astrophysics Data System (ADS)

Choi, Tae Su; Ko, Jae Yoon; Heo, Sung Woo; Ko, Young Ho; Kim, Kimoon; Kim, Hugh I.

2012-10-01

Noncovalent interactions of cucurbit[6]uril (CB[6]) with haloacetate and halide anions are investigated in the gas phase using electrospray ionization ion mobility mass spectrometry. Strong noncovalent interactions of monoiodoacetate, monobromoacetate, monochloroacetate, dichloroacetate, and trichloroacetate on the exterior surface of CB[6] are observed in the negative mode electrospray ionization mass spectra. The strong binding energy of the complex allows intramolecular SN2 reaction of haloacetate, which yields externally bound CB[6]-halide complex, by collisional activation. Utilizing ion mobility technique, structures of exteriorly bound CB[6] complexes of haloacetate and halide anions are confirmed. Theoretically determined low energy structures using density functional theory (DFT) further support results from ion mobility studies. The DFT calculation reveals that the binding energy and conformation of haloacetate on the CB[6] surface affect the efficiency of the intramolecular SN2 reaction of haloacetate, which correlate well with the experimental observation.

Definitions of Complexity are Notoriously Difficult

NASA Astrophysics Data System (ADS)

Schuster, Peter

Definitions of complexity are notoriously difficult if not impossible at all. A good working hypothesis might be: Everything is complex that is not simple. This is precisely the way in which we define nonlinear behavior. Things appear complex for different reasons: i) Complexity may result from lack of insight, ii) complexity may result from lack of methods, and (iii) complexity may be inherent to the system. The best known example for i) is celestial mechanics: The highly complex Pythagorean epicycles become obsolete by the introduction of Newton's law of universal gravitation. To give an example for ii), pattern formation and deterministic chaos became not really understandable before extensive computer simulations became possible. Cellular metabolism may serve as an example for iii) and is caused by the enormous complexity of biochemical reaction networks with up to one hundred individual reaction fluxes. Nevertheless, only few fluxes are dominant in the sense that using Pareto optimal values for them provides near optimal values for all the others...

Modular "Click" Preparation of Bifunctional Polymeric Heterometallic Catalysts.

PubMed

Wang, Wenlong; Zhao, Liyuan; Lv, Hui; Zhang, Guodong; Xia, Chungu; Hahn, F Ekkehardt; Li, Fuwei

2016-06-27

Heterobimetallic molecular complexes or strictly alternating metallated polymers are obtained by a click reaction between mononuclear metal complexes (secondary building units, SBUs) bearing NHCs functionalized with either p-azidophenyl or p-ethynylphenyl wingtips. With a copper-NHC complex as SBU the formation of molecular or polymeric compounds did not require any additives as the copper complex catalyzes the click reaction. Transmetallation from heterobimetallic Cu/Ag derivatives to Cu/Pd derivatives was achieved. The linker between the SBUs (flexible or rigid) influences the catalytic activity of the heterobimetallic compounds. The polymer with alternating copper-NHC and silver-NHC units and a flexible methylene-triazole bridge between them shows the highest activity in the catalytic alkynylation of trifluoromethyl ketones to give fluorinated propargylic alcohols. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cyanide Ligand Assembly by Carbon Atom Transfer to an Iron Nitride

DOE PAGES

Martinez, Jorge L.; Lin, Hsiu-Jung; Lee, Wei-Tsung; ...

2017-09-21

The new iron(IV) nitride complex PhB( iPr 2Im) 3Fe≡N reacts with two equivalents of bis(diisopropylamino)cyclopropenylidene (BAC) to provide PhB( iPr 2Im) 3Fe(CN)(N 2)(BAC). This unusual example of a four-electron reaction involves carbon atom transfer from BAC to create a cyanide ligand along with the alkyne iPr 2N-C≡C-N iPr 2. The iron complex is in equilibrium with an N 2- free species. Further reaction with CO leads to formation of a CO analogue, which can be independently prepared using NaCN as the cyanide source, while reaction with B(C 6F 5) 3 provides the cyanoborane derivative.

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

Schoendorff, George E.; De Jong, Wibe A.; Gordon, Mark S.

The formation of uranyl dicationic complexes containing water and nitrile (acetonitrile, propionitrile, and benzonitrile) ligands, [UO2(H2O)n(RCN)m]2+, has been studied using density functional theory (DFT) with a relativistic effective core potential (RECP) to account for scalar relativistic effects on uranium. It is shown that nitrile addition is favored over the addition of water ligands. Decomposition of these complexes to [UO2OH(H2O)n(RCN)m]+ by the loss of either H3O+ or (RCN+H)+ is also examined. It is found that this reaction occurs when the coordination sphere of uranyl is unsaturated. Additionally, this reaction is influenced by the size of the nitrile ligand with reactions involvingmore » acetonitrile being the most prevalent.« less

Study of holmium (III) and yttrium(III) with DOTA complexes as candidates for radiopharmaceutical use

NASA Astrophysics Data System (ADS)

Ernestová, M.; Jedináková-Křížová, V.

2003-01-01

Reaction conditions for complexation of radionuclides with DOTA were studied using thinlayer chromatography (TLC), paper chromatography (PC) and potentiometry. It was found that all of the studied complexes can reach very high radiochemical yield about 95%. Optimal conditions for obtaining such high radiochemical yields are as follows: pH higher than 4 and the excess of chelating agent must be minimally 3∶1. Potentiometric study showed that the formation of complexes is characterised by very slow kinetics.

Kinetic competence of the cADP-ribose-CD38 complex as an intermediate in the CD38/NAD+ glycohydrolase-catalysed reactions: implication for CD38 signalling.

PubMed Central

Cakir-Kiefer, C; Muller-Steffner, H; Oppenheimer, N; Schuber, F

2001-01-01

CD38/NAD(+) glycohydrolase is a type II transmembrane glycoprotein widely used to study T- and B-cell activation and differentiation. CD38 is endowed with two different activities: it is a signal transduction molecule and an ectoenzyme that converts NAD(+) into ADP-ribose (NAD(+) glycohydrolase activity) and small proportions of cADP-ribose (cADPR; ADP-ribosyl cyclase activity), a calcium-mobilizing metabolite, which, ultimately, can also be hydrolysed (cADPR hydrolase activity). The relationship between these two properties, and strikingly the requirement for signalling in the formation of free or enzyme-complexed cADPR, is still ill-defined. In the present study we wanted to test whether the CD38-cADPR complex is kinetically competent in the conversion of NAD(+) into the reaction product ADP-ribose. In principle, such a complex could be invoked for cross-talk, via conformational changes, with neighbouring partner(s) of CD38 thus triggering the signalling phenomena. Analysis of the kinetic parameters measured for the CD38/NAD(+) glycohydrolase-catalysed hydrolysis of 2'-deoxy-2'-aminoribo-NAD(+) and ADP-cyclo[N1,C1']-2'-deoxy-2'-aminoribose (slowly hydrolysable analogues of NAD(+) and cADPR respectively) ruled out that the CD38-cADPR complex can accumulate under steady-state conditions. This was borne out by simulation of the prevalent kinetic mechanism of CD38, which involve the partitioning of a common E.ADP-ribosyl intermediate in the formation of the enzyme-catalysed reaction products. Using this mechanism, microscopic rate conditions were found which transform a NAD(+) glycohydrolase into an ADP-ribosyl cyclase. Altogether, the present work shows that if the cross-talk with a partner depends on a conformational change of CD38, this is most probably not attributable to the formation of the CD38-cADPR complex. In line with recent results on the conformational change triggered by CD38 ligands [Berthelier, Laboureau, Boulla, Schuber and Deterre (2000) Eur. J. Biochem. 267, 3056-3064], we believe that the Michaelis CD38-NAD(+) complex could play such a role instead. PMID:11513738

The C( 3P) + NH 3 reaction in interstellar chemistry. I. Investigation of the product formation channels

DOE PAGES

Bourgalais, Jeremy; Capron, Michael; Kailasanathan, Ranjith Kumar Abhinavam; ...

2015-10-13

The product formation channels of ground state carbon atoms, C( 3P), reacting with ammonia, NH3, have been investigated using two complementary experiments and electronic structure calculations. Reaction products are detected in a gas flow tube experiment (330 K, 4 Torr) using tunable vacuum-ultraviolet (VUV) photoionization coupled with time of flight mass spectrometry. Temporal profiles of the species formed and photoionization spectra are used to identify primary products of the C + NH 3 reaction. In addition, H-atom formation is monitored by VUV laser induced fluorescence (LIF) from room temperature to 50 K in a supersonic gas flow generated by themore » Laval nozzle technique. Electronic structure calculations are performed to derive intermediates, transition states, and complexes formed along the reaction coordinate. The combination of photoionization and LIF experiments supported by theoretical calculations indicate that in the temperature and pressure range investigated, the H + H 2CN production channel represents 100% of the product yield for this reaction. As a result, kinetics measurements of the title reaction down to 50 K and the effect of the new rate constants on interstellar nitrogen hydride abundances using a model of dense interstellar clouds are reported in Paper II.« less

Protonation at the aromatic ring vs at the carbonyl group of lanthanide-diaryl ketone dianion species by aryl alcohols. Formation, structural characterization, and reactivity of lanthanide aryloxide, mixed aryloxide/alkoxide, and aryloxide/enolate complexes

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

Yoshimura, Takashi; Hou, Z.; Wakatsuki, Yasua

1995-11-01

Reaction of the ytterbium-benzophenone dianion complex (1), which was formed by reaction of Yb metal with benzophenone in THF/HMPA, with 2,6-di-tert-butyl-4-methylphenol, yielded the ytterbium(II) aryloxide complex Yb(OAr){sub 2}(HMPA){sub 2} (2, Ar= C{sub 6}H{sub 2} -{sup t}Bu{sub 2}-2,6-Me-4) as a major product (80%) and the ytterbium(III) enolate complex (3) as a minor one (ca. 5% yield). The mechanisms of these reactions are discussed. X-ray crystallographic studies reveal that 3, 4a, and 7b are isostructural, and so are 5a and 6. The central metal ions in these complexes are all five-coordinated in a trigonal bipyramid form (highly distorted in the case ofmore » 5a and 6) with two HMPA ligands at the apical and three anionic oxygen ligands at the equatorial positions. 25 refs., 7 figs., 7 tabs.« less

Quantum Chemical Study of CH3 + O2 Combustion Reaction System: Catalytic Effects of Additional CO2 Molecule.

PubMed

Masunov, Artëm E; Wait, Elizabeth; Vasu, Subith S

2017-08-03

The supercritical carbon dioxide diluent is used to control the temperature and to increase the efficiency in oxycombustion fossil fuel energy technology. It may affect the rates of combustion by altering mechanisms of chemical reactions, compared to the ones at low CO 2 concentrations. Here, we investigate potential energy surfaces of the four elementary reactions in the CH 3 + O 2 reactive system in the presence of one CO 2 molecule. In the case of reaction CH 3 + O 2 → CH 2 O + OH (R1 channel), van der Waals (vdW) complex formation stabilizes the transition state and reduces the activation barrier by ∼2.2 kcal/mol. Alternatively, covalently bonded CO 2 may form a six-membered ring transition state and reduce the activation barrier by ∼0.6 kcal/mol. In case of reaction CH 3 + O 2 → CH 3 O + O (R2 channel), covalent participation of CO 2 lowers the barrier for the rate limiting step by 3.9 kcal/mol. This is expected to accelerate the R2 process, important for the branching step of the radical chain reaction mechanism. For the reaction CH 3 + O 2 → CHO + H 2 O (R3 channel) with covalent participation of CO 2 , the activation barrier is lowered by 0.5 kcal/mol. The reaction CH 2 O + OH → CHO + H 2 O (R4 channel) involves hydrogen abstraction from formaldehyde by OH radical. Its barrier is reduced from 7.1 to 0.8 kcal/mol by formation of vdW complex with spectator CO 2 . These new findings are expected to improve the kinetic reaction mechanism describing combustion processes in supercritical CO 2 medium.

Chemical dynamics of triacetylene formation and implications to the synthesis of polyynes in Titan's atmosphere

PubMed Central

Gu, X.; Kim, Y. S.; Kaiser, R. I.; Mebel, A. M.; Liang, M. C.; Yung, Y. L.

2009-01-01

For the last four decades, the role of polyynes such as diacetylene (HCCCCH) and triacetylene (HCCCCCCH) in the chemical evolution of the atmosphere of Saturn's moon Titan has been a subject of vigorous research. These polyacetylenes are thought to serve as an UV radiation shield in planetary environments; thus, acting as prebiotic ozone, and are considered as important constituents of the visible haze layers on Titan. However, the underlying chemical processes that initiate the formation and control the growth of polyynes have been the least understood to date. Here, we present a combined experimental, theoretical, and modeling study on the synthesis of the polyyne triacetylene (HCCCCCCH) via the bimolecular gas phase reaction of the ethynyl radical (CCH) with diacetylene (HCCCCH). This elementary reaction is rapid, has no entrance barrier, and yields the triacetylene molecule via indirect scattering dynamics through complex formation in a single collision event. Photochemical models of Titan's atmosphere imply that triacetylene may serve as a building block to synthesize even more complex polyynes such as tetraacetylene (HCCCCCCCCH). PMID:19805262

Chemical dynamics of triacetylene formation and implications to the synthesis of polyynes in Titan's atmosphere.

PubMed

Gu, X; Kim, Y S; Kaiser, R I; Mebel, A M; Liang, M C; Yung, Y L

2009-09-22

For the last four decades, the role of polyynes such as diacetylene (HCCCCH) and triacetylene (HCCCCCCH) in the chemical evolution of the atmosphere of Saturn's moon Titan has been a subject of vigorous research. These polyacetylenes are thought to serve as an UV radiation shield in planetary environments; thus, acting as prebiotic ozone, and are considered as important constituents of the visible haze layers on Titan. However, the underlying chemical processes that initiate the formation and control the growth of polyynes have been the least understood to date. Here, we present a combined experimental, theoretical, and modeling study on the synthesis of the polyyne triacetylene (HCCCCCCH) via the bimolecular gas phase reaction of the ethynyl radical (CCH) with diacetylene (HCCCCH). This elementary reaction is rapid, has no entrance barrier, and yields the triacetylene molecule via indirect scattering dynamics through complex formation in a single collision event. Photochemical models of Titan's atmosphere imply that triacetylene may serve as a building block to synthesize even more complex polyynes such as tetraacetylene (HCCCCCCCCH).

Biosynthetic versatility and coordinated action of 5'-deoxyadenosyl radicals in deazaflavin biosynthesis.

PubMed

Philmus, Benjamin; Decamps, Laure; Berteau, Olivier; Begley, Tadhg P

2015-04-29

Coenzyme F420 is a redox cofactor found in methanogens and in various actinobacteria. Despite the major biological importance of this cofactor, the biosynthesis of its deazaflavin core (8-hydroxy-5-deazaflavin, F(o)) is still poorly understood. F(o) synthase, the enzyme involved, is an unusual multidomain radical SAM enzyme that uses two separate 5'-deoxyadenosyl radicals to catalyze F(o) formation. In this paper, we report a detailed mechanistic study on this complex enzyme that led us to identify (1) the hydrogen atoms abstracted from the substrate by the two radical SAM domains, (2) the second tyrosine-derived product, (3) the reaction product of the CofH-catalyzed reaction, (4) the demonstration that this product is a substrate for CofG, and (5) a stereochemical study that is consistent with the formation of a p-hydroxybenzyl radical at the CofH active site. These results enable us to propose a mechanism for F(o) synthase and uncover a new catalytic motif in radical SAM enzymology involving the use of two 5'-deoxyadenosyl radicals to mediate the formation of a complex heterocycle.

Density functional theory study of HfCl4, ZrCl4, and Al(CH3)3 decomposition on hydroxylated SiO2: Initial stage of high-k atomic layer deposition

NASA Astrophysics Data System (ADS)

Jeloaica, L.; Estève, A.; Djafari Rouhani, M.; Estève, D.

2003-07-01

The initial stage of atomic layer deposition of HfO2, ZrO2, and Al2O3 high-k films, i.e., the decomposition of HfCl4, ZrCl4, and Al(CH3)3 precursor molecules on an OH-terminated SiO2 surface, is investigated within density functional theory. The energy barriers are determined using artificial activation of vibrational normal modes. For all precursors, reaction proceeds through the formation of intermediate complexes that have equivalent formation energies (˜-0.45 eV), and results in HCl and CH4 formation with activation energies of 0.88, 0.91, and 1.04 eV for Hf, Zr, and Al based precursors, respectively. The reaction product of Al(CH3)3 decomposition is found to be more stable (by -1.45 eV) than the chemisorbed intermediate complex compared to the endothermic decomposition of HfCl4 and ZrCl4 chemisorbed precursors (0.26 and 0.29 eV, respectively).

Pulse radiolysis studies of the reactions of bromine atoms and dimethyl sulfoxide bromine atom complexes with alcohols

NASA Astrophysics Data System (ADS)

Sumiyoshi, Takashi; Fujiyoshi, Ryoko; Katagiri, Miho; Sawamura, Sadashi

2007-05-01

Dimethylsulfoxide (DMSO)-Br complexes were generated by pulse radiolysis of DMSO/bromomethane mixtures and the formation mechanism and spectral characteristics of the formed complexes were investigated in detail. The rate constant for the reaction of bromine atoms with DMSO and the extinction coefficient of the complex were obtained to be 4.6×10 9 M -1 s -1 and 6300 M -1 cm -1 at the absorption maximum of 430 nm. Rate constants for the reaction of bromine atoms with a series of alcohols were determined in CBrCl 3 solutions applying a competitive kinetic method using the DMSO-Br complex as the reference system. The obtained rate constants were ˜10 8 M -1 s -1, one or two orders larger than those reported for highly polar solvents. Rate constants of DMSO-Br complexes with alcohols were determined to be ˜ 10 7 M -1 s -1. A comparison of the reactivities of Br atoms and DMSO-Br complexes with those of chlorine atoms and chlorine atom complexes which are ascribed to hydrogen abstracting reactants strongly indicates that hydrogen abstraction from alcohols is not the rate determining step in the case of Br atoms and DMSO-Br complexes.

Bimetallic redox synergy in oxidative palladium catalysis.

PubMed

Powers, David C; Ritter, Tobias

2012-06-19

Polynuclear transition metal complexes, which are embedded in the active sites of many metalloenzymes, are responsible for effecting a diverse array of oxidation reactions in nature. The range of chemical transformations remains unparalleled in the laboratory. With few noteworthy exceptions, chemists have primarily focused on mononuclear transition metal complexes in developing homogeneous catalysis. Our group is interested in the development of carbon-heteroatom bond-forming reactions, with a particular focus on identifying reactions that can be applied to the synthesis of complex molecules. In this context, we have hypothesized that bimetallic redox chemistry, in which two metals participate synergistically, may lower the activation barriers to redox transformations relevant to catalysis. In this Account, we discuss redox chemistry of binuclear Pd complexes and examine the role of binuclear intermediates in Pd-catalyzed oxidation reactions. Stoichiometric organometallic studies of the oxidation of binuclear Pd(II) complexes to binuclear Pd(III) complexes and subsequent C-X reductive elimination from the resulting binuclear Pd(III) complexes have confirmed the viability of C-X bond-forming reactions mediated by binuclear Pd(III) complexes. Metal-metal bond formation, which proceeds concurrently with oxidation of binuclear Pd(II) complexes, can lower the activation barrier for oxidation. We also discuss experimental and theoretical work that suggests that C-X reductive elimination is also facilitated by redox cooperation of both metals during reductive elimination. The effect of ligand modification on the structure and reactivity of binuclear Pd(III) complexes will be presented in light of the impact that ligand structure can exert on the structure and reactivity of binuclear Pd(III) complexes. Historically, oxidation reactions similar to those discussed here have been proposed to proceed via mononuclear Pd(IV) intermediates, and the hypothesis of mononuclear Pd(II/IV) catalysis has guided the successful development of many reactions. Herein we discuss differences between monometallic Pd(IV) and bimetallic Pd(III) redox catalysis. We address whether appreciation of the relevance of bimetallic Pd(III) redox catalysis is of academic interest exclusively, serving to provide a more nuanced description of catalysis, or if the new insight regarding bimetallic Pd(III) chemistry can be a platform to enable future reaction development. To this end, we describe an example in which the hypothesis of bimetallic redox chemistry guided reaction development, leading to the discovery of reactivity distinct from monometallic catalysts.

Transformation of 2,4,6-Trinitrotoluene by Purified Xenobiotic Reductase B from Pseudomonas fluorescens I-C

PubMed Central

Pak, Jeong W.; Knoke, Kyle L.; Noguera, Daniel R.; Fox, Brian G.; Chambliss, Glenn H.

2000-01-01

The enzymatic transformation of 2,4,6-trinitrotoluene (TNT) by purified XenB, an NADPH-dependent flavoprotein oxidoreductase from Pseudomonas fluorescens I-C, was evaluated by using natural abundance and [U-14C]TNT preparations. XenB catalyzed the reduction of TNT either by hydride addition to the aromatic ring or by nitro group reduction, with the accumulation of various tautomers of the protonated dihydride-Meisenheimer complex of TNT, 2-hydroxylamino-4,6-dinitrotoluene, and 4-hydroxylamino-2,6-dinitrotoluene. Subsequent reactions of these metabolites were nonenzymatic and resulted in predominant formation of at least three dimers with an anionic m/z of 376 as determined by negative-mode electrospray ionization mass spectrometry and the release of ∼0.5 mol of nitrite per mol of TNT consumed. The extents of the initial enzymatic reactions were similar in the presence and in the absence of O2, but the dimerization reaction and the release of nitrite were favored under aerobic conditions or under anaerobic conditions in the presence of NADP+. Reactions of chemically and enzymatically synthesized and high-pressure liquid chromatography-purified TNT metabolites showed that both a hydroxylamino-dinitrotoluene isomer and a tautomer of the protonated dihydride-Meisenheimer complex of TNT were required precursors for the dimerization and nitrite release reactions. The m/z 376 dimers also reacted with either dansyl chloride or N-1-naphthylethylenediamine HCl, providing evidence for an aryl amine functional group. In combination, the experimental results are consistent with assigning the chemical structures of the m/z 376 species to various isomers of amino-dimethyl-tetranitrobiphenyl. A mechanism for the formation of these proposed TNT metabolites is presented, and the potential enzymatic and environmental significance of their formation is discussed. PMID:11055918

Functionalized Anodic Aluminum Oxide Membrane–Electrode System for Enzyme Immobilization

PubMed Central

2015-01-01

A nanoporous membrane system with directed flow carrying reagents to sequentially attached enzymes to mimic nature’s enzyme complex system was demonstrated. Genetically modified glycosylation enzyme, OleD Loki variant, was immobilized onto nanometer-scale electrodes at the pore entrances/exits of anodic aluminum oxide membranes through His6-tag affinity binding. The enzyme activity was assessed in two reactions—a one-step “reverse” sugar nucleotide formation reaction (UDP-Glc) and a two-step sequential sugar nucleotide formation and sugar nucleotide-based glycosylation reaction. For the one-step reaction, enzyme specific activity of 6–20 min–1 on membrane supports was seen to be comparable to solution enzyme specific activity of 10 min–1. UDP-Glc production efficiencies as high as 98% were observed at a flow rate of 0.5 mL/min, at which the substrate residence time over the electrode length down pore entrances was matched to the enzyme activity rate. This flow geometry also prevented an unwanted secondary product hydrolysis reaction, as observed in the test homogeneous solution. Enzyme utilization increased by a factor of 280 compared to test homogeneous conditions due to the continuous flow of fresh substrate over the enzyme. To mimic enzyme complex systems, a two-step sequential reaction using OleD Loki enzyme was performed at membrane pore entrances then exits. After UDP-Glc formation at the entrance electrode, aglycon 4-methylumbelliferone was supplied at the exit face of the reactor, affording overall 80% glycosylation efficiency. The membrane platform showed the ability to be regenerated with purified enzyme as well as directly from expression crude, thus demonstrating a single-step immobilization and purification process. PMID:25025628

The kinetics and mechanism of the organo-iridium-catalysed enantioselective reduction of imines.

PubMed

Stirling, Matthew J; Sweeney, Gemma; MacRory, Kerry; Blacker, A John; Page, Michael I

2016-04-14

The iridium complex of pentamethylcyclopentadiene and (S,S)-1,2-diphenyl-N'-tosylethane-1,2-diamine is an effective catalyst for the asymmetric transfer hydrogenation of imine substrates under acidic conditions. Using the Ir catalyst and a 5 : 2 ratio of formic acid : triethylamine as the hydride source for the asymmetric transfer hydrogenation of 1-methyl-3,4-dihydroisoquinoline and its 6,7-dimethoxy substituted derivative, in either acetonitrile or dichloromethane, shows unusual enantiomeric excess (ee) profiles for the product amines. The reactions initially give predominantly the (R) enantiomer of the chiral amine products with >90% ee but which then decreases significantly during the reaction. The decrease in ee is not due to racemisation of the product amine, but because the rate of formation of the (R)-enantiomer follows first-order kinetics whereas that for the (S)-enantiomer is zero-order. This difference in reaction order explains the change in selectivity as the reaction proceeds - the rate formation of the (R)-enantiomer decreases exponentially with time while that for the (S)-enantiomer remains constant. A reaction scheme is proposed which requires rate-limiting hydride transfer from the iridium hydride to the iminium ion for the first-order rate of formation of the (R)-enantiomer amine and rate-limiting dissociation of the product for the zero-order rate of formation of the (S)-enantiomer.

Photocatalytic CO2 reduction with high turnover frequency and selectivity of formic acid formation using Ru(II) multinuclear complexes

PubMed Central

Tamaki, Yusuke; Morimoto, Tatsuki; Koike, Kazuhide; Ishitani, Osamu

2012-01-01

Previously undescribed supramolecules constructed with various ratios of two kinds of Ru(II) complexes—a photosensitizer and a catalyst—were synthesized. These complexes can photocatalyze the reduction of CO2 to formic acid with high selectivity and durability using a wide range of wavelengths of visible light and NADH model compounds as electron donors in a mixed solution of dimethylformamide–triethanolamine. Using a higher ratio of the photosensitizer unit to the catalyst unit led to a higher yield of formic acid. In particular, of the reported photocatalysts, a trinuclear complex with two photosensitizer units and one catalyst unit photocatalyzed CO2 reduction (ΦHCOOH = 0.061, TONHCOOH = 671) with the fastest reaction rate (TOFHCOOH = 11.6 min-1). On the other hand, photocatalyses of a mixed system containing two kinds of model mononuclear Ru(II) complexes, and supramolecules with a higher ratio of the catalyst unit were much less efficient, and black oligomers and polymers were produced from the Ru complexes during photocatalytic reactions, which reduced the yield of formic acid. The photocatalytic formation of formic acid using the supramolecules described herein proceeds via two sequential processes: the photochemical reduction of the photosensitizer unit by NADH model compounds and intramolecular electron transfer to the catalyst unit. PMID:22908243

A DEVELOPMENTAL STUDY OF THE RELATIONSHIP BETWEEN REACTION-TIME AND PROBLEM-SOLVING EFFICIENCY. FINAL REPORT.

ERIC Educational Resources Information Center

FRIEDMAN, STANLEY R.

MANY STUDIES HAVE INDICATED THE PRESENCE OF A SLUMP OR INVERSION IN THE PROBLEM-SOLVING EFFICIENCY OF CHILDREN AT THE FOURTH GRADE LEVEL. IT HAS BEEN SUGGESTED THAT THIS MAY BE DUE TO THE INTERFERING EFFECT OF THE FORMATION OF COMPLEX HYPOTHESES BY THE CHILDREN. SINCE A TENDENCY TO RESPOND RAPIDLY WOULD PRESUMABLY INHIBIT THE FORMATION OF COMPLEX…

Ionization of doped helium nanodroplets: Complexes of C60 with water clusters

NASA Astrophysics Data System (ADS)

Denifl, S.; Zappa, F.; Mähr, I.; Mauracher, A.; Probst, M.; Urban, J.; Mach, P.; Bacher, A.; Bohme, D. K.; Echt, O.; Märk, T. D.; Scheier, P.

2010-06-01

Water clusters are known to undergo an autoprotonation reaction upon ionization by photons or electron impact, resulting in the formation of (H2O)nH3O+. Ejection of OH cannot be quenched by near-threshold ionization; it is only partly quenched when clusters are complexed with inert gas atoms. Mass spectra recorded by electron ionization of water-doped helium droplets show that the helium matrix also fails to quench OH loss. The situation changes drastically when helium droplets are codoped with C60. Charged C60-water complexes are predominantly unprotonated; C60(H2O)4+ and (C60)2(H2O)4+ appear with enhanced abundance. Another intense ion series is due to C60(H2O)nOH+; dehydrogenation is proposed to be initiated by charge transfer between the primary He+ ion and C60. The resulting electronically excited C60+∗ leads to the formation of a doubly charged C60-water complex either via emission of an Auger electron from C60+∗, or internal Penning ionization of the attached water complex, followed by charge separation within {C60(H2O)n}2+. This mechanism would also explain previous observations of dehydrogenation reactions in doped helium droplets. Mass-analyzed ion kinetic energy scans reveal spontaneous (unimolecular) dissociation of C60(H2O)n+. In addition to the loss of single water molecules, a prominent reaction channel yields bare C60+ for sizes n=3, 4, or 6. Ab initio Hartree-Fock calculations for C60-water complexes reveal negligible charge transfer within neutral complexes. Cationic complexes are well described as water clusters weakly bound to C60+. For n=3, 4, or 6, fissionlike desorption of the entire water complex from C60(H2O)n+ energetically competes with the evaporation of a single water molecule.

Post-Self-Assembly Cross-Linking to Integrate Molecular Nanofibers with Copolymers in Oscillatory Hydrogels

DTIC Science & Technology

2013-05-09

The BZ reaction provides a model system to mimic a variety of complex processes, such as biological morphogenesis, in monodisperse microemulsions .15...surfaces, ion-exchange resins, membranes, and microemulsions . For example, in addition to minimizing the hydrodynamic effects and formation of bubbles...Reaction-Diffusion Microemulsions Reveals Three-Dimensional Tu- ring Patterns. Science (Washington, DC, U.S.) 2011, 331, 1309−1312. (16) Agladze, K. I

Enhancing the efficiency of sortase-mediated ligations through nickel-peptide complex formation.

PubMed

David Row, R; Roark, Travis J; Philip, Marina C; Perkins, Lorena L; Antos, John M

2015-08-14

A modified sortase A recognition motif containing a masked Ni(2+)-binding peptide was employed to boost the efficiency of sortase-catalyzed ligation reactions. Deactivation of the Ni(2+)-binding peptide using a Ni(2+) additive improved reaction performance at low to equimolar ratios of the glycine amine nucleophile and sortase substrate. The success of this approach was demonstrated with both peptide and protein substrates.

Well-Defined Heterobimetallic Reactivity at Unsupported Ruthenium-Indium Bonds.

PubMed

Riddlestone, Ian M; Rajabi, Nasir A; Macgregor, Stuart A; Mahon, Mary F; Whittlesey, Michael K

2018-02-01

The hydride complex [Ru(IPr) 2 (CO)H][BAr F 4 ], 1, reacts with InMe 3 with loss of CH 4 to form [Ru(IPr) 2 (CO)(InMe)(Me)][BAr F 4 ], 4, featuring an unsupported Ru-In bond with unsaturated Ru and In centres. 4 reacts with H 2 to give [Ru(IPr) 2 (CO)(η 2 -H 2 )(InMe)(H)][BAr F 4 ], 5, while CO induces formation of the indyl complex [Ru(IPr) 2 (CO) 3 (InMe 2 )][BAr F 4 ], 7. These observations highlight the ability of Me to shuttle between Ru and In centres and are supported by DFT calculations on the mechanism of formation of 4 and its reactions with H 2 and CO. An analysis of Ru-In bonding in these species is also presented. Reaction of 1 with GaMe 3 also involves CH 4 loss but, in contrast to its In congener, sees IPr transfer from Ru to Ga to give a gallyl complex featuring an η 6 interaction of one aryl substituent with Ru. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Oxidation of ZrB2 SiC TaSi2 Materials at Ultra High Temperatures

NASA Technical Reports Server (NTRS)

Opila, E.; Smith, J.; Levine, S.; Lorincz, J.; Reigel, M.

2008-01-01

ZrB2 - 20v% SiC - 20v% TaSi2 was oxidized in stagnant air for ten minute cycles for times up to 100 minutes at 1627 C and 1927 C. The sample oxidized at 1627 C showed oxidation resistance better than that of the standard ZrB2 - 20v% SiC. The sample oxidized at 1927 C, however, showed evidence of liquid phase formation and complex oxidation products. The sample exposed at 1927 C was analyzed in detail by scanning electron microprobe and wavelength dispersive spectroscopy to understand the complex oxidation and melting reactions occurring during exposure. The as hot-pressed material shows the formation of a Zr(Ta)B2 phase in addition to the three phases in the nominal composition already noted. After oxidation, the TaSi2 in the matrix was completely reacted to form Ta(Zr)C. The layered oxidation products included SiO2, ZrO2, Ta2O5, and a complex oxide containing both Zr and Ta. Likely reactions are proposed based on thermodynamic phase stability and phase morphology.

[Studies by means of 1H NMR spectroscopy of complex formation of aromatic biologically active compounds with antibiotic topotecan].

PubMed

Mosunov, A A; Kostiukov, V V; Evstigneev, M P

2012-01-01

The analysis of heteroassociation of antibiotic topotecan (TPT) with aromatic biologically active compounds (BAC): caffeine, mutagens ethidium bromide and proflavine, antibiotic daunomycin, vitamins flavin-mononucleotide and nicotinamide, has been carried out in the work using 1H NMR spectroscopy data. The equilibrium constants of heteroassociation and induced chemical shifts of the protons have been obtained in the complexes with BAC. It is found that the complex formation TPT-BAC has the nature of stacking of the chromophores, additionally stabilized in the case of proflavine by intermolecular hydrogen bond. Calculation of the basic components of the Gibbs free energy of the complexation reactions is carried out, and the factors which stabilize and destabilize the heterocomplexes of molecules are revealed.

Zirconocene-iridium hydrido complexes: arene carbon-hydrogen bond activation and formation of a planar square Zr2Ir2 complex.

PubMed

Oishi, Masataka; Suzuki, Hiroharu

2009-03-16

New early-late heterobimetallic hydrides (L(2)ZrCl)(Cp*Ir)(mu-H)(3) (1; L = Cp derivative, Cp* = eta(5)-C(5)Me(5)) were synthesized from zirconocene derivatives (L(2)ZrCl(2)) and LiCp*IrH(3) via a salt elimination reaction and structurally characterized by NMR and X-ray analyses. Upon treatment of 1 with an alkyllithium reagent, hydride abstraction complex 4 underwent thermolytic ligand elimination at the Zr-Ir system to yield a novel planar square complex (L(2)Zr)(2)(Cp*Ir)(2)(mu(3)-H)(4) (2). When a labeling study of the reaction was conducted, it was found that the conversion of 1 to 2 involves rapid aromatic and benzylic C-H activation by a coordinatively unsaturated dinuclear complex (L(2)Zr)(Cp*Ir)(H)(2) (3).

Supramolecular reactivity in the gas phase: investigating the intrinsic properties of non-covalent complexes.

PubMed

Cera, Luca; Schalley, Christoph A

2014-03-21

The high vacuum inside a mass spectrometer offers unique conditions to broaden our view on the reactivity of supramolecules. Because dynamic exchange processes between complexes are efficiently suppressed, the intrinsic and intramolecular reactivity of the complexes of interest is observed. Besides this, the significantly higher strength of non-covalent interactions in the absence of competing solvent allows processes to occur that are unable to compete in solution. The present review highlights a series of examples illustrating different aspects of supramolecular gas-phase reactivity ranging from the dissociation and formation of covalent bonds in non-covalent complexes through the reactivity in the restricted inner phase of container molecules and step-by-step mechanistic studies of organocatalytic reaction cycles to cage contraction reactions, processes induced by electron capture, and finally dynamic molecular motion within non-covalent complexes as unravelled by hydrogen-deuterium exchange processes performed in the gas phase.

Elementary Reactions and Their Role in Gas-Phase Prebiotic Chemistry

PubMed Central

Balucani, Nadia

2009-01-01

The formation of complex organic molecules in a reactor filled with gaseous mixtures possibly reproducing the primitive terrestrial atmosphere and ocean demonstrated more than 50 years ago that inorganic synthesis of prebiotic molecules is possible, provided that some form of energy is provided to the system. After that groundbreaking experiment, gas-phase prebiotic molecules have been observed in a wide variety of extraterrestrial objects (including interstellar clouds, comets and planetary atmospheres) where the physical conditions vary widely. A thorough characterization of the chemical evolution of those objects relies on a multi-disciplinary approach: 1) observations allow us to identify the molecules and their number densities as they are nowadays; 2) the chemistry which lies behind their formation starting from atoms and simple molecules is accounted for by complex reaction networks; 3) for a realistic modeling of such networks, a number of experimental parameters are needed and, therefore, the relevant molecular processes should be fully characterized in laboratory experiments. A survey of the available literature reveals, however, that much information is still lacking if it is true that only a small percentage of the elementary reactions considered in the models have been characterized in laboratory experiments. New experimental approaches to characterize the relevant elementary reactions in laboratory are presented and the implications of the results are discussed. PMID:19564951

Exploring the reaction channels between arsine and the hydroxyl radical

NASA Astrophysics Data System (ADS)

Viana, Rommel B.

2017-10-01

The aim of this study was to present the reaction mechanism channels between arsine (AsH3) and hydroxyl (OH) which was evaluated at CCSD(T)/CBS//CCSD/cc-pVTZ level. One potential channel is the hydrogen abstraction pathway (R1), leading to AsH2 and H2O products, which occurs due to the formation of an entrance complex (AsH3OH) followed by a 1,2-hydrogen shift pathway (involving the proton transfer from the arsine group to hydroxyls, with one leading to the products). Additional channels are accessed via H-elimination pathways of the entrance complexes, forming arsinous acid (AsH2OH; R2) and arsine oxide (AsH3O; R3). In this respect, R2 is the only exoergic route of the three exit channels, representing the major branching ratio at 200-1000 K and, after 2000 K, R1 increases gradually becoming the major route of this reaction. In contrast, even at 4000 K, R3 is a highly unfeasible pathway. Therefore, the information predicted here provides new insights into the neutral-neutral chemical reaction dynamics regarding the Group V hydrides. On the other side, the R2 pathway may have some potential to solve the arsine oxidation puzzle as a possible primary pathway to the arsenic-oxygen species formation.

Solid State Pathways towards Molecular Complexity in Space

NASA Astrophysics Data System (ADS)

Linnartz, Harold; Bossa, Jean-Baptiste; Bouwman, Jordy; Cuppen, Herma M.; Cuylle, Steven H.; van Dishoeck, Ewine F.; Fayolle, Edith C.; Fedoseev, Gleb; Fuchs, Guido W.; Ioppolo, Sergio; Isokoski, Karoliina; Lamberts, Thanja; Öberg, Karin I.; Romanzin, Claire; Tenenbaum, Emily; Zhen, Junfeng

2011-12-01

It has been a long standing problem in astrochemistry to explain how molecules can form in a highly dilute environment such as the interstellar medium. In the last decennium more and more evidence has been found that the observed mix of small and complex, stable and highly transient species in space is the cumulative result of gas phase and solid state reactions as well as gas-grain interactions. Solid state reactions on icy dust grains are specifically found to play an important role in the formation of the more complex ``organic'' compounds. In order to investigate the underlying physical and chemical processes detailed laboratory based experiments are needed that simulate surface reactions triggered by processes as different as thermal heating, photon (UV) irradiation and particle (atom, cosmic ray, electron) bombardment of interstellar ice analogues. Here, some of the latest research performed in the Sackler Laboratory for Astrophysics in Leiden, the Netherlands is reviewed. The focus is on hydrogenation, i.e., H-atom addition reactions and vacuum ultraviolet irradiation of interstellar ice analogues at astronomically relevant temperatures. It is shown that solid state processes are crucial in the chemical evolution of the interstellar medium, providing pathways towards molecular complexity in space.

New group 6 metal carbonyl complexes with 4,5-dimethyl-N,N-bis(pyridine-2-yl-methylene)benzene-1,2-diimine Schiff base: synthesis, spectral, cyclic voltammetry and biological activity studies.

PubMed

Mohamed, Rania G; Elantabli, Fatma M; Helal, Nadia H; El-Medani, Samir M

2015-04-15

Thermal reaction of M(CO)6 (M=Cr, Mo or W) with a Schiff base (DMPA) derived from the condensation of 4,5-dimethyl-1,2-phenylenediamine and pyridine-2-carboxaldehyde in THF in absence and presence of a secondary ligand; 2-aminobenzimidazole (Abz), thiourea (Tu) or 2-(2'-pyridyl)benzimidazole (pybz) were studied. The reaction of Cr(CO)6 gave the four complexes Cr2(CO)2(DMPA)2; 1, Cr(DMPA)2(Abz)2; 2, Cr2(CO)4(DMPA)2(Tu)2; 3 and Cr(DMPA)2(Pybz); 4, while the thermal reaction of Mo(CO)6 resulted in the formation of the two complexes Mo2(O)6(DMPA)2; 5, and Mo2(O)2(CO)2(DMPA)2(Tu)2; 6. Thermal reaction of W(CO)6 and the Schiff base DMPA gave the complex W(O)2(DMPA)2; 7. The ligand DMPA and its metal complexes have been reported and characterized based on elemental analyses, IR, (1)H NMR, magnetic measurements, and thermal analysis. Cyclic voltammetry and biological activity were also investigated. Copyright © 2015 Elsevier B.V. All rights reserved.

Model-based analysis of coupled equilibrium-kinetic processes: indirect kinetic studies of thermodynamic parameters using the dynamic data.

PubMed

Emami, Fereshteh; Maeder, Marcel; Abdollahi, Hamid

2015-05-07

Thermodynamic studies of equilibrium chemical reactions linked with kinetic procedures are mostly impossible by traditional approaches. In this work, the new concept of generalized kinetic study of thermodynamic parameters is introduced for dynamic data. The examples of equilibria intertwined with kinetic chemical mechanisms include molecular charge transfer complex formation reactions, pH-dependent degradation of chemical compounds and tautomerization kinetics in micellar solutions. Model-based global analysis with the possibility of calculating and embedding the equilibrium and kinetic parameters into the fitting algorithm has allowed the complete analysis of the complex reaction mechanisms. After the fitting process, the optimal equilibrium and kinetic parameters together with an estimate of their standard deviations have been obtained. This work opens up a promising new avenue for obtaining equilibrium constants through the kinetic data analysis for the kinetic reactions that involve equilibrium processes.

Catalytic reduction of dinitrogen to ammonia at a single molybdenum center

PubMed Central

Weare, Walter W.; Dai, Xuliang; Byrnes, Matthew J.; Chin, Jia Min; Schrock, Richard R.; Müller, Peter

2006-01-01

Since our discovery of the catalytic reduction of dinitrogen to ammonia at a single molybdenum center, we have embarked on a variety of studies designed to further understand this complex reaction cycle. These include studies of both individual reaction steps and of ligand variations. An important step in the reaction sequence is exchange of ammonia for dinitrogen in neutral molybdenum(III) compounds. We have found that this exchange reaction is first order in dinitrogen and relatively fast (complete in <1 h) at 1 atm of dinitrogen. Variations of the terphenyl substituents in the triamidoamine ligand demonstrate that the original ligand is not unique in its ability to yield successful catalysts. However, complexes that contain sterically less demanding ligands fail to catalyze formation of ammonia from dinitrogen; it is proposed as a consequence of a base-catalyzed decomposition of a diazenido (MoNNH) intermediate. PMID:17085586

Complex formation between the protein components of methane monooxygenase from Methylosinus trichosporium OB3b. Identification of sites of component interaction.

PubMed

Fox, B G; Liu, Y; Dege, J E; Lipscomb, J D

1991-01-05

Kinetic, spectroscopic, and chemical evidence for the formation of specific catalytically essential complexes between the three protein components of the soluble form of methane monooxygenase from Methylosinus trichosporium OB3b is reported. The effects of the concentrations of the reductase and component B on the hydroxylation activity of the reconstituted enzyme system has been numerically simulated based on a kinetic model which assumes formation of multiple high affinity complexes with the hydroxylase component during catalysis. The formation of several of these complexes has been directly demonstrated. By using EPR spectroscopy, the binding of approximately 2 mol of component B/mol of hydroxylase (subunit structure (alpha beta gamma)2) is shown to significantly change the electronic environment of the mu-(H/R)-oxo-bridged binuclear iron cluster of the hydroxylase in both the mixed valent (Fe(II).Fe(III)) and fully reduced (Fe(II).Fe(II)) states. Protein-protein complexes between the reductase and component B as well as between the reductase and hydroxylase have been shown to form by monitoring quenching of the tryptophan fluorescence spectrum of either the component B (KD approximately 0.4 microM) or hydroxylase (two binding sites, KDa approximately 10 nM, KDb approximately 8 microM). The observed KD values are in agreement with the best fit values from the kinetic simulation. Through the use of the covalent zero length cross-linking reagent 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC), the binding sites of the component B and reductase were shown to be on the hydroxylase alpha and beta subunits, respectively. The alpha and beta subunits of the hydroxylase are cross-linked by EDC suggesting that they are juxtaposed. EDC also caused the rapid loss of the ability of the monomeric component B to stimulate the hydroxylation reaction suggesting that cross-linking of reactive groups on the protein surface had occurred. This effect was inhibited by the presence of hydroxylase and was accompanied by a loss of the ability of the component B to bind to the hydroxylase. Thus, formation of a component B-hydroxylase complex is apparently required for effective catalysis linked to NADH oxidation. When present in concentrations greater than required to saturate the initial hydroxylase complex, component B inhibited both the rate of the enzymic reaction and the cross-linking of the reductase to the hydroxylase. This suggests that a second complex involving component B can form that negatively regulates catalysis by preventing formation of the reductase-hydroxylase complex.

Efficient hydrogenation of organic carbonates, carbamates and formates indicates alternative routes to methanol based on CO2 and CO

NASA Astrophysics Data System (ADS)

Balaraman, Ekambaram; Gunanathan, Chidambaram; Zhang, Jing; Shimon, Linda J. W.; Milstein, David

2011-08-01

Catalytic hydrogenation of organic carbonates, carbamates and formates is of significant interest both conceptually and practically, because these compounds can be produced from CO2 and CO, and their mild hydrogenation can provide alternative, mild approaches to the indirect hydrogenation of CO2 and CO to methanol, an important fuel and synthetic building block. Here, we report for the first time catalytic hydrogenation of organic carbonates to alcohols, and carbamates to alcohols and amines. Unprecedented homogeneously catalysed hydrogenation of organic formates to methanol has also been accomplished. The reactions are efficiently catalysed by dearomatized PNN Ru(II) pincer complexes derived from pyridine- and bipyridine-based tridentate ligands. These atom-economical reactions proceed under neutral, homogeneous conditions, at mild temperatures and under mild hydrogen pressures, and can operate in the absence of solvent with no generation of waste, representing the ultimate ‘green’ reactions. A possible mechanism involves metal-ligand cooperation by aromatization-dearomatization of the heteroaromatic pincer core.

Efficient hydrogenation of organic carbonates, carbamates and formates indicates alternative routes to methanol based on CO2 and CO.

PubMed

Balaraman, Ekambaram; Gunanathan, Chidambaram; Zhang, Jing; Shimon, Linda J W; Milstein, David

2011-07-22

Catalytic hydrogenation of organic carbonates, carbamates and formates is of significant interest both conceptually and practically, because these compounds can be produced from CO2 and CO, and their mild hydrogenation can provide alternative, mild approaches to the indirect hydrogenation of CO2 and CO to methanol, an important fuel and synthetic building block. Here, we report for the first time catalytic hydrogenation of organic carbonates to alcohols, and carbamates to alcohols and amines. Unprecedented homogeneously catalysed hydrogenation of organic formates to methanol has also been accomplished. The reactions are efficiently catalysed by dearomatized PNN Ru(II) pincer complexes derived from pyridine- and bipyridine-based tridentate ligands. These atom-economical reactions proceed under neutral, homogeneous conditions, at mild temperatures and under mild hydrogen pressures, and can operate in the absence of solvent with no generation of waste, representing the ultimate 'green' reactions. A possible mechanism involves metal-ligand cooperation by aromatization-dearomatization of the heteroaromatic pincer core.

Pattern formation in mass conserving reaction-diffusion systems

NASA Astrophysics Data System (ADS)

Brauns, Fridtjof; Halatek, Jacob; Frey, Erwin

We present a rigorous theoretical framework able to generalize and unify pattern formation for quantitative mass conserving reaction-diffusion models. Mass redistribution controls chemical equilibria locally. Separation of diffusive mass redistribution on the level of conserved species provides a general mathematical procedure to decompose complex reaction-diffusion systems into effectively independent functional units, and to reveal the general underlying bifurcation scenarios. We apply this framework to Min protein pattern formation and identify the mechanistic roles of both involved protein species. MinD generates polarity through phase separation, whereas MinE takes the role of a control variable regulating the existence of MinD phases. Hence, polarization and not oscillations is the generic core dynamics of Min proteins in vivo. This establishes an intrinsic mechanistic link between the Min system and a broad class of intracellular pattern forming systems based on bistability and phase separation (wave-pinning). Oscillations are facilitated by MinE redistribution and can be understood mechanistically as relaxation oscillations of the polarization direction.

Ellagic acid inhibits iron-mediated free radical formation

NASA Astrophysics Data System (ADS)

Dalvi, Luana T.; Moreira, Daniel C.; Andrade, Roberto; Ginani, Janini; Alonso, Antonio; Hermes-Lima, Marcelo

2017-02-01

Polyphenols are reported to have some health benefits, which are link to their antioxidant properties. In the case of ellagic acid (EA), there is evidence that it has free radical scavenger properties and that it is able to form complexes with metal ions. However, information on a possible link between the formation of iron-EA complexes and their interference in Haber-Weiss/Fenton reactions was not yet determined. Thus, the present study investigated the in vitro antioxidant mechanism of EA in a system containing ascorbate, Fe(III) and different iron ligands (EDTA, citrate and NTA). Iron-mediated oxidative degradation of 2-deoxyribose was poorly inhibited (by 12%) in the presence of EA (50 μM) and EDTA. When citrate or NTA - which form weak iron complexes - were used, the 2-deoxyribose protection increased to 89-97% and 45%, respectively. EA also presented equivalent inhibitory effects on iron-mediated oxygen uptake and ascorbyl radical formation. Spectral analyses of iron-EA complexes show that EA removes Fe(III) from EDTA within hours, and from citrate within 1 min. This difference in the rate of iron-EA complex formation may explain the antioxidant effects of EA. Furthermore, the EA antioxidant effectiveness was inversely proportional to the Fe(III) concentration, suggesting a competition with EDTA. In conclusion, the results indicate that EA may prevent in vitro free radical formation when it forms a complex with iron ions.

trans-[Pt(BCat')Me(PCy3)2]: an experimental case study of reductive elimination processes in Pt-Boryls through associative mechanisms.

PubMed

Braunschweig, Holger; Bertermann, Rüdiger; Brenner, Peter; Burzler, Michael; Dewhurst, Rian D; Radacki, Krzysztof; Seeler, Fabian

2011-10-10

A stable trans-(alkyl)(boryl) platinum complex trans-[Pt(BCat')Me(PCy(3))(2)] (Cat'=Cat-4-tBu; Cy=cyclohexyl=C(6)H(11)) was synthesised by salt metathesis reaction of trans-[Pt(BCat')Br(PCy(3))(2)] with LiMe and was fully characterised. Investigation of the reactivity of the title compound showed complete reductive elimination of Cat'BMe at 80 °C within four weeks. This process may be accelerated by the addition of a variety of alkynes, thereby leading to the formation of the corresponding η(2) -alkyne platinum complexes, of which [Pt(η(2)-MeCCMe)(PCy(3))(2)] was characterised by X-ray crystallography. Conversion of the trans-configured title compound to a cis derivative remained unsuccessful due to an instantaneous reductive elimination process during the reaction with chelating phosphines. Treatment of trans-[Pt(BCat')Me(PCy(3))(2)] with Cat(2)B(2) led to the formation of CatBMe and Cat'BMe. In the course of further investigations into this reaction, indications for two indistinguishable reaction mechanisms were found: 1) associative formation of a six-coordinate platinum centre prior to reductive elimination and 2) σ-bond metathesis of B-B and C-Pt bonds. Mechanism 1 provides a straightforward explanation for the formation of both methylboranes. Scrambling of diboranes(4) Cat(2)B(2) and Cat'(2)B(2) in the presence of [Pt(PCy(3))(2)], fully reductive elimination of CatBMe or Cat'BMe from trans-[Pt(BCat')Me(PCy(3))(2)] in the presence of sub-stoichiometric amounts of Cat(2)B(2), and evidence for the reversibility of the oxidative addition of Cat(2)B(2) to [Pt(PCy(3))(2)] all support mechanism 2, which consists of sequential equilibria reactions. Furthermore, the solid-state molecular structure of cis-[Pt(BCat)(2)(PCy(3))(2)] and cis-[Pt(BCat')(2)(PCy(3))(2)] were investigated. The remarkably short B-B separations in both bis(boryl) complexes suggest that the two boryl ligands in each case are more loosely bound to the Pt(II) centre than in related bis(boryl) species. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Surface reaction of SnII on goethite (α-FeOOH): surface complexation, redox reaction, reductive dissolution, and phase transformation.

PubMed

Dulnee, Siriwan; Scheinost, Andreas C

2014-08-19

To elucidate the potential risk of (126)Sn migration from nuclear waste repositories, we investigated the surface reactions of Sn(II) on goethite as a function of pH and Sn(II) loading under anoxic condition with O2 level < 2 ppmv. Tin redox state and surface structure were investigated by Sn K edge X-ray absorption spectroscopy (XAS), goethite phase transformations were investigated by high-resolution transmission electron microscopy and selected area electron diffraction. The results demonstrate the rapid and complete oxidation of Sn(II) by goethite and formation of Sn(IV) (1)E and (2)C surface complexes. The contribution of (2)C complexes increases with Sn loading. The Sn(II) oxidation leads to a quantitative release of Fe(II) from goethite at low pH, and to the precipitation of magnetite at higher pH. To predict Sn sorption, we applied surface complexation modeling using the charge distribution multisite complexation approach and the XAS-derived surface complexes. Log K values of 15.5 ± 1.4 for the (1)E complex and 19.2 ± 0.6 for the (2)C complex consistently predict Sn sorption across pH 2-12 and for two different Sn loadings and confirm the strong retention of Sn(II) even under anoxic conditions.

Monitoring dediazoniation product formation by high-performance liquid chromatography after derivatization.

PubMed

Bravo-Díaz, Carlos; González-Romero, Elisa

2003-03-14

A derivatization protocol that exploits the rapid reaction between arenediazonium ions and a suitable coupling agent followed by high-performance liquid chromatography analyses of the reaction mixture was employed to determine the product distribution, the rate constants for product formation and the association constant of 4-nitrobenzenediazonium, PNBD, ion with beta-cyclodextrin, beta-CD. The derivatization of PNBD with the coupling agent leads to the formation of a stable azo dye that prevents by-side reactions of PNBD with the solvents of the mobile phase, including water, or the metallic parts of the chromatographic system that would eventually lead to erroneous identification and quantification of dediazoniation products. The results show that in the presence of beta-CD, nitrobenzene is formed at the expense of 4-nitrophenol, which is the major product in its absence. The observed rate constants for the interaction between PNBD and beta-CD increase upon increasing [beta-CD] showing a saturation profile indicative of the formation of an inclusion complex between PNBD and beta-CD. By fitting the experimental data to a simplified Lineaweaver-Burk equation, the corresponding association constant and the maximum acceleration rate of beta-CD towards PNBD were estimated. The protocol is applicable under a variety of experimental conditions provided that the rate of the coupling reaction is much faster than that of dediazoniation.

9-Triptycenecarboxylate-Bridged Diiron(II) Complexes

PubMed Central

Friedle, Simone; Kodanko, Jeremy J.; Fornace, Kyrstin L.; Lippard, Stephen J.

2008-01-01

The synthesis and characterization of diiron(II) complexes supported by 9-triptycenecarboxylate ligands (-O2CTrp) is described. The interlocking nature of the triptycenecarboxylates facilitates formation of quadruply bridged diiron(II) complexes of the type [Fe2(μ-O2CTrp)4(L)2] (L = THF, pyridine or imidazole derivative) with a paddlewheel geometry. A systematic lengthening of the Fe-Fe distance occurs with the increase in steric bulk of the neutral donor L, resulting in values of up to 3 Å without disassembly of the paddlewheel structure. Reactions with an excess of water do not lead to decomposition of the diiron(II) core, indicating that these quadruply bridged complexes are of exceptional stability. The red-colored complexes [Fe2(μ-O2CTrp)4(4-AcPy)2] (10) and [Fe2(μ-O2CTrp)4(4-CNPy)2] (11) exhibit solvent-dependent thermochromism in coordinating solvents that was studied by variable temperature UV-vis spectroscopy. Reaction of [Fe2(μ-O2CTrp)4(THF)2] with N,N,N’,N’-tetramethylethylenediamine (TMEDA), tetra-n-butyl ammonium thiocyanate, or excess 2-methylimidazole resulted in the formation of mononuclear complexes [Fe(O2CTrp)2(TMEDA)] (13), (n-Bu4N)2[Fe(O2CTrp)2(SCN)2] (14), and [Fe(O2CTrp)2(2-MeIm)2] (15) having an O4/N2 coordination sphere composition. PMID:19915653

Coordination Chemistry of Disilylated Germylenes with Group 4 Metallocenes

PubMed Central

2013-01-01

Reaction of the PEt3 adduct of a disilylated five-membered cyclic germylene with group 4 metallocene dichlorides in the presence of magnesium led to the formation of the respective germylene metallocene phosphine complexes of titanium, zirconium, and hafnium. Attempts to react the related NHC adduct of a disilylated four-membered cyclic germylene under the same conditions with Cp2TiCl2 did not give the expected germylene NHC titanocene complex. This complex was, however, obtained in the reaction of Cp2Ti(btmsa) with the NHC germylene adduct. A computational analysis of the structure of the group 4 metallocene germylene complexes revealed the multiple-bond character of the M–Ge(II) linkage, which can be rationalized with the classical σ-donor/π-acceptor interaction. The strength of the M–Ge(II) bond increases descending group 4. PMID:23874053

Adaptive Correction from Virtually Complex Dynamic Libraries: The Role of Noncovalent Interactions in Structural Selection and Folding.

PubMed

Lafuente, Maria; Atcher, Joan; Solà, Jordi; Alfonso, Ignacio

2015-11-16

The hierarchical self-assembling of complex molecular systems is dictated by the chemical and structural information stored in their components. This information can be expressed through an adaptive process that determines the structurally fittest assembly under given environmental conditions. We have set up complex disulfide-based dynamic covalent libraries of chemically and topologically diverse pseudopeptidic compounds. We show how the reaction evolves from very complex mixtures at short reaction times to the almost exclusive formation of a major compound, through the establishment of intramolecular noncovalent interactions. Our experiments demonstrate that the systems evolve through error-check and error-correction processes. The nature of these interactions, the importance of the folding and the effects of the environment are also discussed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Detailed reaction mechanism of macrophomate synthase. Extraordinary enzyme catalyzing five-step transformation from 2-pyrones to benzoates.

PubMed

Watanabe, K; Mie, T; Ichihara, A; Oikawa, H; Honma, M

2000-12-08

Macrophomate synthase from the fungus Macrophoma commelinae IFO 9570 is a Mg(II)-dependent dimeric enzyme that catalyzes an extraordinary, complex five-step chemical transformation from 2-pyrone and oxalacetate to benzoate involving decarboxylation, C-C bond formation, and dehydration. The catalytic mechanism of the whole pathway was investigated in three separate chemical steps. In the first decarboxylation step, the enzyme loses oxalacetate decarboxylation activity upon incubation with EDTA. Activity is fully restored by addition of Mg(II) and is not restored with other divalent metal cations. The dissociation constant of 0.93 x 10(-)(7) for Mg(II) and atomic absorption analysis established a 1:1 stoichiometric complex. Inhibition of pyruvate formation with 2-pyrone revealed that the actual product in the first step is a pyruvate enolate, which undergoes C-C bond formation in the presence of 2-pyrone. Incubation of substrate analogs provided aberrant adducts that were produced via C-C bond formation and rearrangement. This strongly indicates that the second step is two C-C bond formations, affording a bicyclic intermediate. Based on the stereospecificity, involvement of a Diels-Alder reaction at the second step is proposed. Incubation of the stereospecifically deuterium-labeled malate with 2-pyrones in the presence of malate dehydrogenase provided information for the stereochemical course of the reaction catalyzed by macrophomate synthase, indicating that the first decarboxylation provides pyruvate (Z)-[3-(2)H]enolate and that dehydration at the final step occurs with anti-elimination accompanied by concomitant decarboxylation. Examination of kinetic parameters in the individual steps suggests that the third step is the rate-determining step of the overall transformation.

NADPH-cytochrome P450 reductase-mediated denitration reaction of 2,4,6-trinitrotoluene to yield nitrite in mammals.

PubMed

Shinkai, Yasuhiro; Nishihara, Yuya; Amamiya, Masahiro; Wakayama, Toshihiko; Li, Song; Kikuchi, Tomohiro; Nakai, Yumi; Shimojo, Nobuhiro; Kumagai, Yoshito

2016-02-01

While the biodegradation of 2,4,6-trinitrotoluene (TNT) via the release of nitrite is well established, mechanistic details of the reaction in mammals are unknown. To address this issue, we attempted to identify the enzyme from rat liver responsible for the production of nitrite from TNT. A NADPH-cytochrome P450 reductase (P450R) was isolated and identified from rat liver microsomes as the enzyme responsible for not only the release of nitrite from TNT but also formation of superoxide and 4-hydroxyamino-2,6-dinitrotoluene (4-HADNT) under aerobic conditions. In this context, reactive oxygen species generated during P450R-catalyzed TNT reduction were found to be, at least in part, a mediator for the production of 4-HADNT from TNT via formation of 4-nitroso-2,6-dinitrotoluene. P450R did not catalyze the formation of the hydride-Meisenheimer complex (H(-)-TNT) that is thought to be an intermediate for nitrite release from TNT. Furthermore, in a time-course experiment, 4-HADNT formation reached a plateau level and then declined during the reaction between TNT and P450R with NADPH, while the release of nitrite was subjected to a lag period. Notably, the produced 4-HADNT can react with the parent compound TNT to produce nitrite and dimerized products via formation of a Janovsky complex. Our results demonstrate for the first time that P450R-mediated release of nitrite from TNT results from the process of chemical interaction of TNT and its 4-electron reduction metabolite 4-HADNT. Copyright © 2015 Elsevier Inc. All rights reserved.

Astrochemistry and the Role of Laboratory and Theoretical Support

NASA Technical Reports Server (NTRS)

Herbst, E.

2006-01-01

We emphasize some current needs of astrochemists for laboratory data. The data are urgently required both to detect molecules in assorted regions and to produce robust models of these regions. Three areas of laboratory-based research are particularly crucial and yet are not being studied in the United States: (i) reactions more complex than the formation of molecular hydrogen occurring on interstellar grain analogs, (ii) molecular spectroscopy in the THz (far-infrared) region of the electromagnetic spectrum, and (iii) gas-phase kinetics of reactions leading to complex molecules. Without solid knowledge of many unstudied but key reactions, both in the gas and on grains, astrochemists will not be in position to keep up with the large amount of new information expected to come from the next generation of telescopes.

Complex Organic Parents during Star-Forming Infall

NASA Astrophysics Data System (ADS)

Drozdovskaya, Maria; Walsh, Catherine; Visser, Ruud; Harsono, Daniel; van Dishoeck, Ewine

2013-07-01

Stars are born upon the gravitation infall of clumps in molecular clouds. Complex organic compounds have been observed to accompany star formation and are also believed to be the simplest ingredients to life. Therefore understanding complex organics under star forming conditions is fundamentally interesting. This work models the formation and distribution of several potential parent species for complex organic compounds, such as formaldehyde (H2CO) and methanol (CH3OH), along trajectories of matter parcels, as they undergo infall from the cold outer envelope towards the hot core region and eventually onto the disk. The code from Visser et al. (2009, 2011) serves as the basis for this research. The gas-phase chemistry network has now been expanded with grain-surface reactions to form CH3OH and, ultimately, larger organics such as methyl formate (HCOOCH3) and dimethyl ether (CH3OCH3). The intention behind this work is to obtain information on complex organic parents in the star formation scenario by means of a physically and chemically robust model. The availability of complex organic compounds will vary depending on where the parent species are abundant, such as in the pre-stellar stage, hot-core, or only in the disk; and where they are available for a sufficient amount of time for the complexity enhancement. Such model-based conclusions can then be used in order to explain the observational data on complex organic compounds.

Energetic Processing of Interstellar Ices: A Route to Complexity

NASA Technical Reports Server (NTRS)

Moore, Marla H.; Hudson, Reggie L.

2009-01-01

More than 140 gas-phase molecules have been detected in the interstellar (IS) medium or in circumstellar environments including inorganics, organics, ions, and radicals. The significant abundance of large, complex organic molecules, and families of isomers in these regions makes the origin and formation history of these species the subject of debate. Observationally determined condensed-phase species are H2O, CO, CO2, NH3 and CH30H, with CH4, HCOOH, OCS, OCN-, H2CO and NH4(+) present at trace levels. These ices can undergo energetic processing with cosmic rays or far-UV photons to form larger complex organics with abundance levels that make them undetectable in icy mantles. Once warmed, however, it is likely that these complex species would enter the gas-phase where they might be detected by Herschel or Alma. Understanding the role of radiation chemistry and thermal processing of ices and identifying new products are the goals of our laboratory research. In the Cosmic lee Laboratory at NASA Goddard Space Plight Center, we can study both the photo-and radiation chemistries of ices from 8 -- 300 K. Using dear- and mid-IR spectroscopy we can follow the destruction of primary molecules and the formation of radicals and secondary products as a function of energetic processing. During warming we can monitor the trapping of species and the results of any thermal chemistry. An overview of recent and past work will focus on complex secondary radiation products from small condensed-phase IS species. Likely reactions include dimerization, isomerization, H-addition and H-elimination. Another focus of our work is the development of reaction schemes for the formation of complex molecules and the use of such schemes to predict new molecules awaiting detection by Herschel and Alma.

Computed Potential Energy Surfaces and Minimum Energy Pathway for Chemical Reactions

NASA Technical Reports Server (NTRS)

Walch, Stephen P.; Langhoff, S. R. (Technical Monitor)

1994-01-01

Computed potential energy surfaces are often required for computation of such observables as rate constants as a function of temperature, product branching ratios, and other detailed properties. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method with the Dunning correlation consistent basis sets to obtain accurate energetics, gives useful results for a number of chemically important systems. Applications to complex reactions leading to NO and soot formation in hydrocarbon combustion are discussed.

The Differential Gibbs Free Energy of Activation and its Implications in the Transition-State of Enzymatic Reactions

NASA Astrophysics Data System (ADS)

Maggi, F.; Riley, W. J.

2016-12-01

We propose a mathematical framework to introduce the concept of differential free energy of activation in enzymatically catalyzed reactions, and apply it to N uptake by microalgae and bacteria. This framework extends the thermodynamic capabilities of the classical transition-state theory in and harmonizes the consolidated definitions of kinetic parameters with their thermodynamic and physical meaning. Here, the activation energy is assumed to be a necessary energetic level for equilibrium complexation between reactants and activated complex; however, an additional energy contribution is required for the equilibrium activated complex to release reaction products. We call this "differential free energy of activation"; it can be described by a Boltzmann distribution, and corresponds to a free energy level different from that of complexation. Whether this level is above or below the free energy of activation depends on the reaction, and defines energy domains that correspond to "superactivated", "activated", and "subactivated" complexes. The activated complex reaching one of those states will eventually release the products from an energy level different than that of activation. The concept of differential free energy of activation was tested on 57 independent experiments of NH­4+ and NO3- uptake by various microalgae and bacteria at temperatures ranging between 1 and 45oC. Results showed that the complexation equilibrium always favored the activated complex, but the differential energy of activation led to an apparent energy barrier consistent with observations. Temperature affected all energy levels within this framework but did not alter substantially these thermodynamic features. Overall the approach: (1) provides a thermodynamic and mathematical link between Michaelis-Menten and rate constants; (2) shows that both kinetic parameters can be described or approximated by Arrhenius' like equations; (3) describes the likelihood of formation of sub-, super-, and activated complexes; and (4) shows direction and thermodynamic likelihood of each reaction branch within the transition state. The approach suites particularly well for calibration of kinetic parameters against experimentally acquired reaction dynamics measurements of nutrient biogeochemical cycles.

Hydride-Meisenheimer Complex Formation and Protonation as Key Reactions of 2,4,6-Trinitrophenol Biodegradation by Rhodococcus erythropolis

PubMed Central

Rieger, Paul-Gerhard; Sinnwell, Volker; Preuß, Andrea; Francke, Wittko; Knackmuss, Hans-Joachim

1999-01-01

Biodegradation of 2,4,6-trinitrophenol (picric acid) by Rhodococcus erythropolis HLPM-1 proceeds via initial hydrogenation of the aromatic ring system. Here we present evidence for the formation of a hydride-Meisenheimer complex (anionic ς-complex) of picric acid and its protonated form under physiological conditions. These complexes are key intermediates of denitration and productive microbial degradation of picric acid. For comparative spectroscopic identification of the hydride complex, it was necessary to synthesize this complex for the first time. Spectroscopic data revealed the initial addition of a hydride ion at position 3 of picric acid. This hydride complex readily picks up a proton at position 2, thus forming a reactive species for the elimination of nitrite. Cell extracts of R. erythropolis HLPM-1 transform the chemically synthesized hydride complex into 2,4-dinitrophenol. Picric acid is used as the sole carbon, nitrogen, and energy source by R. erythropolis HLPM-1. PMID:9973345

Redox Equilibria Involving Chromium Minerals in Aqueous Fluids in the Deep Earth - Implications for Diamond Formation

NASA Astrophysics Data System (ADS)

Huang, J.; Huang, F.; Hao, J.; Sverjensky, D. A.

2017-12-01

Diamonds are often associated with inclusions of garnet that are characteristically Cr-rich and Ca-poor, suggesting metasomatic reactions involving fluids [1]. To investigate these reactions, we developed a thermodynamic characterization of Cr-bearing minerals and integrated it with our database for the thermodynamic properties of aqueous Cr-species [2]. We retrieved thermodynamic properties of picrochromite (MgCr2O4), and knorringite (Mg3Cr2Si3O12) consistent with minerals in the Berman (1988) using calorimetric data and experimental phase equilibria involving the reactions: MgCr2O4 + SiO2 = Cr2O3 + MgSiO3 [2] and MgCr2O4 + 4MgSiO3 = Mg3Cr2Si3O12 + Mg2SiO4 [3], respectively.At high temperatures and pressures, neutral pH and FMQ, the predicted solubilities of eskolaite and knorringite equilibrium with Cr2+ in a pure water system are very low. However, we found that complexes of Cr2+ and Cl- could increase the solubilities of chromium minerals significantly. At 500°C and 0.2 - 1.0 GPa, we retrieved the CrCl(OH)0 neutral complex from experiments on the solubility of Cr2O3 in HCl solutions [4]. At 1,000°C and 4.0 GPa, we retrieved the properties of a CrCl3- complex from experiments on the solubility of Cr2O3 in KCl solutions [5]. The predicted solubility of a garnet containing 23 mole% of knorringite in equilibrium with CrCl3- in a peridotitic diamond-forming fluid is 22 millimolal (1,144 ppm). This result suggests that a redox reaction relating to diamond formation might involveMg3Al2Si3O12 + 0.5CO2(aq) + 2 CrCl3- + 2H+ = Mg3Cr2Si3O12 + 0.5C-Diamond + 2Al3+ + 6Cl-. In this way, high temperature and pressure fluids containing Cr(II)-complexes might promote the mobility of chromium and be involved in metasomatic reactions and diamond formation.[1]Boyd et al. (1993)[2] Hao et al. (submitted to Geochem. Persp. Letters)[3] Berman (1988)[4] Klemme et al. (2000)[5] Klemme et al. (2004)[6] Watenphul et al. (2014)[7] Klein-BenDavid et al. (2011)

The equilibrium constant of complex formation in solution: A study utilizing a dielectric constant method

NASA Astrophysics Data System (ADS)

Loh, C. W.

1980-03-01

A method was developed for determining equilibrium constants, heat of reaction, and change in free energy and entropy during a 1:1 complex formation in solutions. The measurements were carried out on ternary systems containing two interacting solutes in an inert solvent. The procedures was applied to the investigation of hydrogen bond complex formations in two mixtures systems, phenol and pyridine in carbon tetrachloride, and 4, 5, 6, 7-tetrachloro-2-trifluoromethylbenzimidazole (TTFB) and alkyl acetate in styrene. The first mixture system was studied in order to compare the results with those obtained by other methods. Results for the second mixture system indicated strong association between molecules of TTFB and alkyl acetate and suggested that the blocking of valinomycin-mediated bilayer membrane conductance by substituted benzimidazoles was due to competition for a limited number of adsorption sites on the membrane surface.

Trapping in water - an important prerequisite for complex reactivity in astrophysical ices: the case of acetone (CH3)2C = O and ammonia NH3

NASA Astrophysics Data System (ADS)

Fresneau, Aurélien; Danger, Grégoire; Rimola, Albert; Theule, Patrice; Duvernay, Fabrice; Chiavassa, Thierry

2014-10-01

Water is the most abundant compound in interstellar and cometary ices. Laboratory experiments on ice analogues have shown that water has a great influence on the chemical activity of these ices. In this study, we investigated the reactivity of acetone-ammonia ices, showing that water is an essential component in chemical reactions with high activation energies. In a water-free binary ice, acetone and ammonia do not react due to high activation energy, as the reactants desorb before reacting (at 120 and 140 K, respectively). By contrast, our study shows that under experimental conditions of ˜150 K, this reaction does occur in the presence of water. Here, water traps reactants in the solid phase above their desorption temperatures, allowing them to gather thermal energy as the reaction proceeds. Using infrared spectroscopy and mass spectrometry associated with isotopic labelling, as well as quantum chemical calculations, 2-aminopropan-2-ol (2HN-C(CH3)2-OH) was identified as the acetone-ammonia reaction product. The formation of this product may represent the first step towards formation of 2-aminoisobutyric acid (AIB) in the Strecker synthesis. The activation energy for the formation of 2-aminopropan-2-ol was measured to be 42 ± 3 kJ mol-1, while its desorption energy equalled 61.3 ± 0.1 kJ mol-1. Our work demonstrates that astrophysical water, rather than being a non-thermally reactive species, is crucial for the evolution of complex chemistry occurring in the Universe.

Rethinking pattern formation in reaction-diffusion systems

NASA Astrophysics Data System (ADS)

Halatek, J.; Frey, E.

2018-05-01

The present theoretical framework for the analysis of pattern formation in complex systems is mostly limited to the vicinity of fixed (global) equilibria. Here we present a new theoretical approach to characterize dynamical states arbitrarily far from (global) equilibrium. We show that reaction-diffusion systems that are driven by locally mass-conserving interactions can be understood in terms of local equilibria of diffusively coupled compartments. Diffusive coupling generically induces lateral redistribution of the globally conserved quantities, and the variable local amounts of these quantities determine the local equilibria in each compartment. We find that, even far from global equilibrium, the system is well characterized by its moving local equilibria. We apply this framework to in vitro Min protein pattern formation, a paradigmatic model for biological pattern formation. Within our framework we can predict and explain transitions between chemical turbulence and order arbitrarily far from global equilibrium. Our results reveal conceptually new principles of self-organized pattern formation that may well govern diverse dynamical systems.

Astrochemistry

NASA Astrophysics Data System (ADS)

Millar, T. J.

2015-08-01

In the last 40 years a wide range of molecules, including neutrals, cations and anions, containing up to 13 atoms—in addition to detections of {{\\text{C}}60} and {{\\text{C}}70} —have been found in the harsh environment of the interstellar medium. The exquisite sensitivity and very high spectral and, more recently, spatial resolution, of modern telescopes has enabled the physics of star formation to be probed through rotational line emission. In this article, I review the basic properties of interstellar clouds and the processes that initiate the chemistry and generate chemical complexity, particularly in regions of star and planet formation. Our understanding of astrochemistry has evolved over the years. Before 1990, the general consensus was that molecules were formed in binary, gas-phase, or volume, reactions, most importantly ion-neutral reactions despite the very low ionization in clouds. Since then, observations have indicated unambiguously that there is also a contribution from surface processes, particularly on the icy mantles that form around refractory grain cores in cold, dense gas. The balance between these two processes depends on particular physical conditions and can vary during the life cycle of a particular volume of interstellar cloud. The complex chemistry that occurs in space is driven mostly through interaction of the gas with cosmic ray protons, a source of ionization that enables a rich ion-neutral chemistry. In addition, I show that the interaction between the gas and the dust in cold, dense regions also leads to additional chemical complexity through reactions that take place in ices at only a few tens of degrees above absolute zero. Although densities are low compared to those in terrestrial environments, the extremely long life times of interstellar clouds and their enormous sizes, enable complex molecules to be synthesised and detected. I show that in some instances, particularly in reactions involving deuterium, the rotational populations of reactants, together with spin-selection rules, can determine the detailed abundances. Although the review is mainly focused on regions associated with star formation, I also consider chemistry in other interesting astronomical regions—in the early Universe and in the envelopes formed by mass loss during the final stages of stellar evolution.

Mechanisms of proton transfer in Nafion: elementary reactions at the sulfonic acid groups.

PubMed

Sagarik, Kritsana; Phonyiem, Mayuree; Lao-ngam, Charoensak; Chaiwongwattana, Sermsiri

2008-04-21

Proton transfer reactions at the sulfonic acid groups in Nafion were theoretically studied, using complexes formed from triflic acid (CF3SO3H), H3O+ and H2O, as model systems. The investigations began with searching for potential precursors and transition states at low hydration levels, using the test-particle model (T-model), density functional theory (DFT) and ab initio calculations. They were employed as starting configurations in Born-Oppenheimer molecular dynamics (BOMD) simulations at 298 K, from which elementary reactions were analyzed and categorized. For the H3O+-H2O complexes, BOMD simulations suggested that a quasi-dynamic equilibrium could be established between the Eigen and Zundel complexes, and that was considered to be one of the most important elementary reactions in the proton transfer process. The average lifetime of H3O+ obtained from BOMD simulations is close to the lowest limit, estimated from low-frequency vibrational spectroscopy. It was demonstrated that proton transfer reactions at -SO3H are not concerted, due to the thermal energy fluctuation and the existence of various quasi-dynamic equilibria, and -SO3H could directly and indirectly mediate proton transfer reactions through the formation of proton defects, as well as the -SO3- and -SO3H2+ transition states.

Autocatalytic formation of an iron(IV)-oxo complex via scandium ion-promoted radical chain autoxidation of an iron(II) complex with dioxygen and tetraphenylborate.

PubMed

Nishida, Yusuke; Lee, Yong-Min; Nam, Wonwoo; Fukuzumi, Shunichi

2014-06-04

A non-heme iron(IV)-oxo complex, [(TMC)Fe(IV)(O)](2+) (TMC = 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane), was formed by oxidation of an iron(II) complex ([(TMC)Fe(II)](2+)) with dioxygen (O2) and tetraphenylborate (BPh4(-)) in the presence of scandium triflate (Sc(OTf)3) in acetonitrile at 298 K via autocatalytic radical chain reactions rather than by a direct O2 activation pathway. The autocatalytic radical chain reaction is initiated by scandium ion-promoted electron transfer from BPh4(-) to [(TMC)Fe(IV)(O)](2+) to produce phenyl radical (Ph(•)). The chain propagation step is composed of the addition of O2 to Ph(•) and the reduction of the resulting phenylperoxyl radical (PhOO(•)) by scandium ion-promoted electron transfer from BPh4(-) to PhOO(•) to produce phenyl hydroperoxide (PhOOH), accompanied by regeneration of phenyl radical. PhOOH reacts with [(TMC)Fe(II)](2+) to yield phenol (PhOH) and [(TMC)Fe(IV)(O)](2+). Biphenyl (Ph-Ph) was formed via the radical chain autoxidation of BPh3 by O2. The induction period of the autocatalytic radical chain reactions was shortened by addition of a catalytic amount of [(TMC)Fe(IV)(O)](2+), whereas addition of a catalytic amount of ferrocene that can reduce [(TMC)Fe(IV)(O)](2+) resulted in elongation of the induction period. Radical chain autoxidation of BPh4(-) by O2 also occurred in the presence of Sc(OTf)3 without [(TMC)Fe(IV)(O)](2+), initiating the autocatalytic oxidation of [(TMC)Fe(II)](2+) with O2 and BPh4(-) to yield [(TMC)Fe(IV)(O)](2+). Thus, the general view for formation of non-heme iron(IV)-oxo complexes via O2-binding iron species (e.g., Fe(III)(O2(•-))) without contribution of autocatalytic radical chain reactions should be viewed with caution.

Synthesis of branched iminosugars through a hypervalent iodine(III)-mediated radical-polar crossover reaction.

PubMed

Santana, Andrés G; Paz, Nieves R; Francisco, Cosme G; Suárez, Ernesto; González, Concepción C

2013-08-02

The synthesis of a novel type of branched iminosugars is described. This synthetic strategy is based on two key reactions: first, an aldol reaction with formaldehyde in order to introduce selectively the hydroxymethyl branch, and second, a tandem β-fragmentation-intramolecular cyclization reaction. The combination of both reactions afforded a battery of compounds exhibiting a great structural complexity, with the concomitant formation of a quaternary center, starting from readily available aldoses. With this approach we have demonstrated the usefulness of the fragmentation of anomeric alkoxyl radicals (ARF) promoted by the PhIO/I2 system for the preparation of new compounds with potential interest for both medicinal and synthetic chemists.

Formation of an Oxidant-Sensible Pd(II) Coordination Compound and Its [superscript 1]H NMR Specific Characterization: A Preparative and Analytical Challenge in Current Coordination Chemistry

ERIC Educational Resources Information Center

Abraham, Maria L.; Oppel, Iris M.

2014-01-01

A three-part experiment that leads to the synthesis of palladium(II) complex starting from a C[subscript 3]-symmetric triaminoguanidinium-based ligand is presented. In the first part, the preparation of tris-benzylidenetriaminoguanidinium chloride ([H[subscript 6]Br[subscript 3]L]Cl) by an acidic catalyzed 3-fold imine formation reaction of…

Enzymology below 200 K: The kinetics and thermodynamics of the photochemistry catalyzed by protochlorophyllide oxidoreductase

PubMed Central

Heyes, Derren J.; Ruban, Alexander V.; Wilks, Helen M.; Hunter, C. Neil

2002-01-01

The chlorophyll biosynthesis enzyme protochlorophyllide reductase (POR) catalyzes the light-dependent reduction of protochlorophyllide (Pchlide) into chlorophyllide in the presence of NADPH. As POR is light-dependent, catalysis can be initiated by illumination of the enzyme-substrate complex at low temperatures, making it an attractive model for studying aspects of biological proton and hydride transfers. The early stages in the photoreduction, involving Pchlide binding and an initial photochemical reaction, have been studied in vitro by using low-temperature fluorescence and absorbance measurements. Formation of the ternary POR-NADPH-Pchlide complex produces red shifts in the fluorescence and absorbance maxima of Pchlide, allowing the dissociation constant for Pchlide binding to be measured. We demonstrate that the product of an initial photochemical reaction, which can occur below 200 K, is a nonfluorescent intermediate with a broad absorbance band at 696 nm (A696) that is suggested to represent an ion radical complex. The temperature dependence of the rate of A696 formation has allowed the activation energy for the photochemical step to be calculated and has shown that POR catalysis can proceed at much lower temperatures than previously thought. Calculations of differences in free energy between various reaction intermediates have been calculated; these, together with the quantum efficiency for Pchlide conversion, suggest a quantitative model for the thermodynamics of the light-driven step of Pchlide reduction. PMID:12177453

Are Nonadiabatic Reaction Dynamics the Key to Novel Organosilicon Molecules? The Silicon (Si(3P))-Dimethylacetylene (C4H6(X1A1g)) System as a Case Study.

PubMed

Thomas, Aaron M; Dangi, Beni B; Yang, Tao; Kaiser, Ralf I; Lin, Lin; Chou, Tzu-Jung; Chang, Agnes H H

2018-06-06

The bimolecular gas phase reaction of ground-state silicon (Si; 3 P) with dimethylacetylene (C 4 H 6 ; X 1 A 1g ) was investigated under single collision conditions in a crossed molecular beams machine. Merged with electronic structure calculations, the data propose nonadiabatic reaction dynamics leading to the formation of singlet SiC 4 H 4 isomer(s) and molecular hydrogen (H 2 ) via indirect scattering dynamics along with intersystem crossing (ISC) from the triplet to the singlet surface. The reaction may lead to distinct energetically accessible singlet SiC 4 H 4 isomers ( 1 p8- 1 p24) in overall exoergic reaction(s) (-107 -20 +12 kJ mol -1 ). All feasible reaction products are either cyclic, carry carbene analogous silylene moieties, or carry C-Si-H or C-Si-C bonds that would require extensive isomerization from the initial collision complex(es) to the fragmenting singlet intermediate(s). The present study demonstrates the first successful crossed beams study of an exoergic reaction channel arising from bimolecular collisions of silicon, Si( 3 P), with a hydrocarbon molecule.

IRON AND FREE RADICAL OXIDATIONS IN CELL MEMBRANES

PubMed Central

Schafer, Freya Q.; Yue Qian, Steven; Buettner, Garry R.

2013-01-01

Brain tissue being rich in polyunsaturated fatty acids, is very susceptible to lipid peroxidation. Iron is well known to be an important initiator of free radical oxidations. We propose that the principal route to iron-mediated lipid peroxidations is via iron-oxygen complexes rather than the reaction of iron with hydrogen peroxide, the Fenton reaction. To test this hypothesis, we enriched leukemia cells (K-562 and L1210 cells) with docosahexaenoic acid (DHA) as a model for brain tissue, increasing the amount of DHA from approximately 3 mole % to 32 mole %. These cells were then subjected to ferrous iron and dioxygen to initiate lipid peroxidation in the presence or absence of hydrogen peroxide. Lipid-derived radicals were detected using EPR spin trapping with α-(4-pyridyl-1-oxide)-N-t-butylnitrone (POBN). As expected, lipid-derived radical formation increases with increasing cellular lipid unsaturation. Experiments with Desferal demonstrate that iron is required for the formation of lipid radicals from these cells. Addition of iron to DHA-enriched L1210 cells resulted in significant amounts of radical formation; radical formation increased with increasing amount of iron. However, the exposure of cells to hydrogen peroxide before the addition of ferrous iron did not increase cellular radical formation, but actually decreased spin adduct formation. These data suggest that iron-oxygen complexes are the primary route to the initiation of biological free radical oxidations. This model proposes a mechanism to explain how catalytic iron in brain tissue can be so destructive. PMID:10872752

Characteristics of pattern formation and evolution in approximations of Physarum transport networks.

PubMed

Jones, Jeff

2010-01-01

Most studies of pattern formation place particular emphasis on its role in the development of complex multicellular body plans. In simpler organisms, however, pattern formation is intrinsic to growth and behavior. Inspired by one such organism, the true slime mold Physarum polycephalum, we present examples of complex emergent pattern formation and evolution formed by a population of simple particle-like agents. Using simple local behaviors based on chemotaxis, the mobile agent population spontaneously forms complex and dynamic transport networks. By adjusting simple model parameters, maps of characteristic patterning are obtained. Certain areas of the parameter mapping yield particularly complex long term behaviors, including the circular contraction of network lacunae and bifurcation of network paths to maintain network connectivity. We demonstrate the formation of irregular spots and labyrinthine and reticulated patterns by chemoattraction. Other Turing-like patterning schemes were obtained by using chemorepulsion behaviors, including the self-organization of regular periodic arrays of spots, and striped patterns. We show that complex pattern types can be produced without resorting to the hierarchical coupling of reaction-diffusion mechanisms. We also present network behaviors arising from simple pre-patterning cues, giving simple examples of how the emergent pattern formation processes evolve into networks with functional and quasi-physical properties including tensionlike effects, network minimization behavior, and repair to network damage. The results are interpreted in relation to classical theories of biological pattern formation in natural systems, and we suggest mechanisms by which emergent pattern formation processes may be used as a method for spatially represented unconventional computation.

Isomerization of Cyclooctadiene to Cyclooctyne with a Zinc/Zirconium Heterobimetallic Complex.

PubMed

Butler, Michael J; White, Andrew J P; Crimmin, Mark R

2016-06-06

Reaction of a zinc/zirconium heterobimetallic complex with 1,5-cyclooctadiene (1,5-COD) results in slow isomerization to 1,3-cyclooctadiene (1,3-COD), along with the formation of a new complex that includes a cyclooctyne ligand bridging two metal centers. While analogous magnesium/zirconium and aluminum/zirconium heterobimetallic complexes are competent for the catalytic isomerization of 1,5-COD to 1,3-COD, only in the case of the zinc species is the cyclooctyne adduct observed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Isomerization of Cyclooctadiene to Cyclooctyne with a Zinc/Zirconium Heterobimetallic Complex

PubMed Central

Butler, Michael J.; White, Andrew J. P.

2016-01-01

Abstract Reaction of a zinc/zirconium heterobimetallic complex with 1,5‐cyclooctadiene (1,5‐COD) results in slow isomerization to 1,3‐cyclooctadiene (1,3‐COD), along with the formation of a new complex that includes a cyclooctyne ligand bridging two metal centers. While analogous magnesium/zirconium and aluminum/zirconium heterobimetallic complexes are competent for the catalytic isomerization of 1,5‐COD to 1,3‐COD, only in the case of the zinc species is the cyclooctyne adduct observed. PMID:27071992

Oxidation of benzoin catalyzed by oxovanadium(IV) schiff base complexes

PubMed Central

2013-01-01

Background The oxidative transformation of benzoin to benzil has been accomplished by the use of a wide variety of reagents or catalysts and different reaction procedures. The conventional oxidizing agents yielded mainly benzaldehyde or/and benzoic acid and only a trace amount of benzil. The limits of practical utilization of these reagents involves the use of stoichiometric amounts of corrosive acids or toxic metallic reagents, which in turn produce undesirable waste materials and required high reaction temperatures. In recent years, vanadium complexes have attracted much attention for their potential utility as catalysts for various types of reactions. Results Active and selective catalytic systems of new unsymmetrical oxovanadium(IV) Schiff base complexes for the oxidation of benzoin is reported. The Schiff base ligands are derived between 2-aminoethanol and 2-hydroxy-1-naphthaldehyde (H2L1) or 3-ethoxy salicylaldehyde (H2L3); and 2-aminophenol and 3-ethoxysalicylaldehyde (H2L2) or 2-hydroxy-1-naphthaldehyde (H2L4). The unsymmetrical Schiff bases behave as tridentate dibasic ONO donor ligands. Reaction of these Schiff base ligands with oxovanadyl sulphate afforded the mononuclear oxovanadium(IV) complexes (VIVOLx.H2O), which are characterized by various physico-chemical techniques. The catalytic oxidation activities of these complexes for benzoin were evaluated using H2O2 as an oxidant. The best reaction conditions are obtained by considering the effect of solvent, reaction time and temperature. Under the optimized reaction conditions, VOL4 catalyst showed high conversion (>99%) with excellent selectivity to benzil (~100%) in a shorter reaction time compared to the other catalysts considered. Conclusion Four tridentate ONO type Schiff base ligands were synthesized. Complexation of these ligands with vanadyl(IV) sulphate leads to the formation of new oxovanadium(IV) complexes of type VIVOL.H2O. Elemental analyses and spectral data of the free ligands and their oxovanadium(IV) complexes were found to be in good agreement with their structures, indicating high purity of all the compounds. Oxovanadium complexes were screened for the oxidation of benzoin to benzil using H2O2 as oxidant. The effect of time, solvent and temperature were optimized to obtain maximum yield. The catalytic activity results demonstrate that these catalytic systems are both highly active and selective for the oxidation of benzoin under mild reaction conditions. PMID:23294561

Oxidation of benzoin catalyzed by oxovanadium(IV) schiff base complexes.

PubMed

Alsalim, Tahseen A; Hadi, Jabbar S; Ali, Omar N; Abbo, Hanna S; Titinchi, Salam Jj

2013-01-07

The oxidative transformation of benzoin to benzil has been accomplished by the use of a wide variety of reagents or catalysts and different reaction procedures. The conventional oxidizing agents yielded mainly benzaldehyde or/and benzoic acid and only a trace amount of benzil. The limits of practical utilization of these reagents involves the use of stoichiometric amounts of corrosive acids or toxic metallic reagents, which in turn produce undesirable waste materials and required high reaction temperatures.In recent years, vanadium complexes have attracted much attention for their potential utility as catalysts for various types of reactions. Active and selective catalytic systems of new unsymmetrical oxovanadium(IV) Schiff base complexes for the oxidation of benzoin is reported. The Schiff base ligands are derived between 2-aminoethanol and 2-hydroxy-1-naphthaldehyde (H2L1) or 3-ethoxy salicylaldehyde (H2L3); and 2-aminophenol and 3-ethoxysalicylaldehyde (H2L2) or 2-hydroxy-1-naphthaldehyde (H2L4). The unsymmetrical Schiff bases behave as tridentate dibasic ONO donor ligands. Reaction of these Schiff base ligands with oxovanadyl sulphate afforded the mononuclear oxovanadium(IV) complexes (VIVOLx.H2O), which are characterized by various physico-chemical techniques.The catalytic oxidation activities of these complexes for benzoin were evaluated using H2O2 as an oxidant. The best reaction conditions are obtained by considering the effect of solvent, reaction time and temperature. Under the optimized reaction conditions, VOL4 catalyst showed high conversion (>99%) with excellent selectivity to benzil (~100%) in a shorter reaction time compared to the other catalysts considered. Four tridentate ONO type Schiff base ligands were synthesized. Complexation of these ligands with vanadyl(IV) sulphate leads to the formation of new oxovanadium(IV) complexes of type VIVOL.H2O.Elemental analyses and spectral data of the free ligands and their oxovanadium(IV) complexes were found to be in good agreement with their structures, indicating high purity of all the compounds.Oxovanadium complexes were screened for the oxidation of benzoin to benzil using H2O2 as oxidant. The effect of time, solvent and temperature were optimized to obtain maximum yield. The catalytic activity results demonstrate that these catalytic systems are both highly active and selective for the oxidation of benzoin under mild reaction conditions.

Group 4 Metalloporphyrin diolato Complexes and Catalytic Application of Metalloporphyrins and Related Transition Metal Complexes

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

Du, Guodong

In this work, the first examples of group 4 metalloporphyrin 1,2-diolato complexes were synthesized through a number of strategies. In general, treatment of imido metalloporphyrin complexes, (TTP)M=NR, (M = Ti, Zr, Hf), with vicinal diols led to the formation of a series of diolato complexes. Alternatively, the chelating pinacolate complexes could be prepared by metathesis of (TTP)MCl 2 (M = Ti, Hf) with disodium pinacolate. These complexes were found to undergo C-C cleavage reactions to produce organic carbonyl compounds. For titanium porphyrins, treatment of a titanium(II) alkyne adduct, (TTP)Ti(η 2-PhC≡CPh), with aromatic aldehydes or aryl ketones resulted in reductive couplingmore » of the carbonyl groups to produce the corresponding diolato complexes. Aliphatic aldehydes or ketones were not reactive towards (TTP)Ti(η 2-PhC≡CPh). However, these carbonyl compounds could be incorporated into a diolato complex on reaction with a reactive precursor, (TTP)Ti[O(Ph) 2C(Ph) 2O] to provide unsymmetrical diolato complexes via cross coupling reactions. In addition, an enediolato complex (TTP)Ti(OCPhCPhO) was obtained from the reaction of (TTP)Ti(η 2-PhC≡CPh) with benzoin. Titanium porphyrin diolato complexes were found to be intermediates in the (TTP)Ti=O-catalyzed cleavage reactions of vicinal diols, in which atmospheric oxygen was the oxidant. Furthermore, (TTP)Ti=O was capable of catalyzing the oxidation of benzyl alcohol and α-hydroxy ketones to benzaldehyde and α-diketones, respectively. Other high valent metalloporphyrin complexes also can catalyze the oxidative diol cleavage and the benzyl alcohol oxidation reactions with dioxygen. A comparison of Ti(IV) and Sn(IV) porphyrin chemistry was undertaken. While chelated diolato complexes were invariably obtained for titanium porphyrins on treatment with 1,2-diols, the reaction of vicinal diols with tin porphyrins gave a number of products, including mono-, bis-alkoxo, and chelating diolato complexes, depending on the identity of diols and the stoichiometry employed. It was also found that tin porphyrin complexes promoted the oxidative cleavage of vicinal diols and the oxidation of α-ketols to α-diketones with dioxygen. In extending the chemistry of metalloporphyrins and analogous complexes, a series of chiral tetraaza macrocyclic ligands and metal complexes were designed and synthesized. Examination of iron(II) complexes showed that they were efficient catalysts for the cyclopropanation of styrene by diazo reagents. Good yields and high diastereoselectivity were obtained with modest enantioselectivity. A rationalization of the stereoselectivity was presented on the basis of structural factors in a carbene intermediate.« less

A Simplified Representation of the Chemical Nature and Reactions of Soil Humus.

ERIC Educational Resources Information Center

Stevenson, F. J.; Olsen, R. A.

1989-01-01

Presented is a comprehensible structural representation of humic substances. A number of important roles of soil organic matter, including contribution to the cation-exchange capacity, binding of pesticides, and formation of complexes with micronutrient cations, are illustrated. (Author/CW)

Reactions of vitamin A with acceptors of electrons. Interactions with iodine and the formation of iodide

PubMed Central

Lucy, J. A.; Lichti, F. Ulrike

1969-01-01

1. The reactions of retinol and retinoic acid with iodine were investigated since knowledge of the chemical reactions of vitamin A with acceptors of electrons may shed light on its biochemical mode of action. 2. Colloidal retinol, but not retinoic acid, reacts with iodine to yield a blue–green complex that rapidly decomposes, giving iodide and an unknown species with λmax. at 870mμ. 3. In addition, both retinol and retinoic acid reduce iodine to iodide by a reaction that does not involve an intermediate coloured complex; this reaction appears to yield unstable carbonium ion derivatives of the vitamin. 4. The presence of water greatly facilitates the production of iodide from vitamin A and iodine. 5. Possible chemical pathways involved in these reactions are discussed. 6. It is suggested that the chemical properties of retinol and retinoic acid that underlie their biochemical behaviour might be apparent only when the molecules are at a lipid–water interface, and that vitamin A might be expected to react with a number of different electron acceptors in vivo. PMID:5801297

Perturbation theory in the catalytic rate constant of the Henri-Michaelis-Menten enzymatic reaction.

PubMed

Bakalis, Evangelos; Kosmas, Marios; Papamichael, Emmanouel M

2012-11-01

The Henry-Michaelis-Menten (HMM) mechanism of enzymatic reaction is studied by means of perturbation theory in the reaction rate constant k (2) of product formation. We present analytical solutions that provide the concentrations of the enzyme (E), the substrate (S), as well as those of the enzyme-substrate complex (C), and the product (P) as functions of time. For k (2) small compared to k (-1), we properly describe the entire enzymatic activity from the beginning of the reaction up to longer times without imposing extra conditions on the initial concentrations E ( o ) and S ( o ), which can be comparable or much different.

Syntheses, structures and luminescent properties of zero-/two-dimensional Cd(II) and Eu(III) complexes

NASA Astrophysics Data System (ADS)

Fan, Rui-Qing; Wang, Li-Yuan; Wang, Ping; Chen, Hong; Sun, Cun-fa; Yang, Yu-Lin; Su, Qing

2012-12-01

Three metal-organic complexes Cd(HBIDC)(phen)2·4H2O (1), [Cd(BIC)(phen)]n (2) and {[Eu(HBIDC)(H2BIDC)(H2O)]·H2O}n (3) (H3BIDC=benzimidazole-5,6-dicarboxylic acid, H2BIC=benzimidazole-6-carboxylic acid, phen=1,10-phenanthroline) have been synthesized under hydro(solvo)thermal conditions and structurally characterized by elemental analysis, IR spectrum, and single-crystal X-ray diffraction. With similar reaction conditions, reactions of the same ligand with different metal cations selected from different blocks (d-block and f-block) result in different coordination modes of carboxylate groups and final frameworks of complexes 1 and 3. The decarboxylation was observed in complex 2 and resulted in the formation of BIC2- ligand. Complexes 1-3 have intense fluorescent emissions at room temperature in dimethylsulfoxide (DMSO) solution and in the solid-state, which indicate they are potential fluorescence materials. The quantum yields and fluorescence lifetimes of these three complexes were systematically studied.

Chromium(IV)–Peroxo Complex Formation and Its Nitric Oxide Dioxygenase Reactivity

PubMed Central

Yokoyama, Atsutoshi; Han, Jung Eun; Cho, Jaeheung; Kubo, Minoru; Ogura, Takashi; Siegler, Maxime A.; Karlin, Kenneth D.; Nam, Wonwoo

2012-01-01

The O2 and NO reactivity of a Cr(II) complex bearing a 12-membered tetraazamacrocyclic TMC ligand, [CrII(12-TMC)(Cl)]+ (1), and the NO reactivity of its peroxo derivative, [CrIV(12-TMC)(O2)(Cl)]+ (2), are described. By contrast to the previously reported Cr(III)-superoxo complex, [CrIII(14-TMC)(O2)(Cl)]+, a Cr(IV)-peroxo complex (2) is formed in the reaction of 1 and O2. Full spectroscopic and X-ray analysis reveals that 2 possesses a side-on η2-peroxo ligation. A quantitative reaction of 2 with NO affords a reduction in Cr oxidation state and production of a Cr(III)-nitrato complex, [CrIII(12-TMC)(NO3)(Cl)]+ (3). The latter is suggested to form via a Cr(III)-peroxynitrite intermediate. A Cr(II)-nitrosyl complex, [CrII(12-TMC)(NO)(Cl)]+ (4), derived from 1 andNO could also be synthesized; however, it does not react with O2. PMID:22950528

The Role of Coordination Environment and pH in Tuning the Oxidation Rate of Europium(II).

PubMed

Ekanger, Levi A; Basal, Lina A; Allen, Matthew J

2017-01-23

The Eu II/III redox couple offers metal-based oxidation-sensing with magnetic resonance imaging making the study of Eu II oxidation chemistry important in the design of new probes. Accordingly, we explored oxidation reactions with a set of Eu II -containing complexes. Superoxide formation from the reaction between Eu II and dioxygen was observed using electron paramagnetic resonance spectroscopy. Additionally, oxidation kinetics of three Eu II -containing complexes with bromate and glutathione disulfide at pH values, including 5 and 7, is reported. In the reaction with bromate, the oxidation rate of two of the complexes increased by 7.3 and 6.7 times upon decreasing pH from 7 to 5, but the rate increased by 17 times for a complex containing amide functional groups over the same pH range. The oxidation rate of a fluorobenzo-functionalized cryptate was relatively slow, indicating that the ligand used to impart thermodynamic oxidative stability might also be useful for controlling oxidation kinetics. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Investigation of interaction between the Pt(II) ions and aminosilane-modified silica surface in heterogeneous system

NASA Astrophysics Data System (ADS)

Nowicki, Waldemar; Gąsowska, Anna; Kirszensztejn, Piotr

2016-05-01

UV-vis spectroscopy measurements confirmed the reaction in heterogeneous system between Pt(II) ions and ethylenediamine type ligand, n-(2-aminoethyl)-3-aminopropyl-trimethoxysilane, immobilized at the silica surface. The formation of complexes is a consequence of interaction between the amine groups from the ligand grafted onto SiO2 and ions of platinum. A potentiometric titration technique was to determine the stability constants of complexes of Pt(II) with immobilized insoluble ligand (SG-L), on the silica gel. The results show the formation of three surface complexes of the same type (PtHSG-L, Pt(HSG-L)2, PtSG-L) with SG-L ligand, in a wide range of pH for different Debye length. The concentration distribution of the complexes in a heterogeneous system is evaluated.

Role of Mediator and Effects of Temperature on ortho-C-N Bond Fusion Reactions of Aniline Using Ruthenium Templates: Isolation and Characterization of New Ruthenium Complexes of the in-Situ-Generated Ligands.

PubMed

Roy, Suman K; Sengupta, Debabrata; Rath, Santi Prasad; Saha, Tanushri; Samanta, Subhas; Goswami, Sreebrata

2017-05-01

In this work, ortho-C-N bond fusion reactions of aniline are followed by the use of two different ruthenium mediators. Reaction of aniline with [Ru III (terpy)Cl 3 ] (terpy = 2,2':6',2″-terpyridine) resulted in a trans bis-aniline ruthenium(II) complex [1] + which upon oxidation with H 2 O 2 produced compound [2] + of a bidentate ligand, N-phenyl-1,2-benzoquinonediimine, due to an oxidative ortho-C-N bond fusion reaction. Complex [1] + and aniline (neat) at 185 °C produced a bis-chelated ruthenium complex (3). A previously reported complex [Ru II (N-phenyl-1,2-benzoquinonediimine)(aniline) 2 (Cl) 2 ] (5) undergoes similar oxidation by air at 185 °C to produce complex [3]. A separate chemical reaction between aniline and strongly oxidizing tetra-n-propylammonium perruthenate [(n-pr) 4 N] + [RuO 4 ] - in air produced a ruthenium complex [4] of a N 4 -tetraamidophenylmacrocycle ligand via multiple ortho-C-N bond fusion reaction. Notably, the yield of this product is low (5%) at 100 °C but increases to 25% in refluxing aniline. All these complexes are characterized fully by their physicochemical characterizations and X-ray structure determination. From their structural parameters and other spectroscopic studies, complex [2] + is assigned as [Ru II (terpy)(N-phenyl-1,2-benzoquinonediimine)(Cl)] + whereas complex [4] is described as a ruthenium(VI) complex comprised of a reduced deprotonated N-phenyl-1,2-diamidobenzene and N 4 -tetraamidophenylmacrocyclic ligand. Complex [2] + exhibits one reversible oxidation at 1.32 V and one reversible reduction at -0.75 V vs Ag/AgCl reference electrode. EPR of the electrogenerated complexes has revealed that the oxidized complex is a ruthenium(III) complex with an axial EPR spectrum at g av = 2.06. The reduced complex [2], on the other hand, shows a single-line EPR signal at g av = 1.998. In contrast, complex [4] shows two successive one-electron oxidation waves at 0.5 and 0.8 V and an irreversible reduction wave at -0.9 V. EPR studies of the oxidized complexes [4] + and [4] 2+ reveal that oxidations are ligand centered. DFT calculations were employed to elucidate the electronic structures as well as the redox processes associated with the above complexes. Aerial ortho-C-N bond fusion reactions of aniline using two different mediators, viz. [Ru III (terpy)Cl 3 ] and [(n-pr) 4 N] + [RuO 4 ] - , have been followed. It is found that in the case of oxidizable Ru(III) mediator complex, C-N bond fusion is limited only to dimerization reaction whereas the high-valent Ru(VII) salt mediates multiple C-N bond fusion reactions leading to the formation of a novel tetradentate N 4 -tetraamidophenylmacrocyclic ligand. Valence ambiguity in the complexes of the resultant redox-active ligands is scrutinized.

The short-term reduction of uranium by nanoscale zero-valent iron (nZVI): role of oxide shell, reduction mechanism and the formation of U( v )-carbonate phases

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

Tsarev, Sergey; Collins, Richard N.; Ilton, Eugene S.

Nanoscale zero-valent iron (nZVI) is a potential remediation agent for uranium-contaminated groundwaters, however, a complete mechanistic understanding of the processes that lead to uranium immobilization has yet to be achieved. In this study, the short-term anoxic reaction of U(VI) with fresh, (anoxic) aged and corroded nZVI particles was investigated under aqueous conditions conducive to the formation of thermodynamically stable U(VI)-Ca-CO3 ternary aqueous complexes. The first stage of the reaction between U(VI) and nZVI was assigned to sorption processes with the formation of surface U(VI)-carbonate complexes. Aged nZVI removed U(VI) faster than either fresh or corroded nZVI and it is hypothesizedmore » that U reduction initially occurs through the transfer of one electron from Fe(II) in the nZVI surface oxide layer. Evidence for reduction to U(V) was obtained through X-ray photoelectron spectroscopy and by determination of U-O bond distances of ~2.05 Å and 2.27 Å by U LIII-edge X-ray absorption spectroscopy detection of U-O bond distances at ~2.05 Å and 2.27 Å with these distances , similar to thoseat observed for the U(V) site in the mixed U(V)/U(VI) carbonate mineral wyartite. Scanning transmission electron microscopy also demonstrated that U was present as a nanoparticulate phase after one day of reaction, rather than a surface complex. Further reduction to U(IV), as observed in previous studies, would appear to be rate-limiting and coincident with the transformation of this meta-stable U-carbonate phase to uraninite (UO2).« less

Copper-phospholipid interaction at cell membrane model hydrophobic surfaces.

PubMed

Mlakar, Marina; Cuculić, Vlado; Frka, Sanja; Gašparović, Blaženka

2018-04-01

Detailed investigation of Cu (II) binding with natural lipid phosphatidylglycerol (PG) in aqueous solution was carried out by voltammetric measurements at the mercury drop electrode, complemented by monolayer studies in a Langmuir trough and electrophoretic measurements, all used as models for hydrophobic cell membranes. Penetration of copper ions into the PG layer was facilitated by the formation of hydrophilic Cu-Phenanthroline (Phen) complex in the subphase, followed by the mixed ligand Cu-Phen-PG complex formation at the hydrophobic interface. Electrophoretic measurements indicated a comparatively low abundance of the formed mixed ligand complex within the PG vesicles, resulting it the zeta potential change of +0.83mV, while monolayer studies confirmed their co-existence at the interface. The Cu-Phen-PG complex was identified in the pH range from 6 to 9. The stoichiometry of the complex ([PhenCuOHPG]), as well as its stability and kinetics of formation, were determined at the mercury drop electrode. Cu-Phen-PG reduces quasireversibly at about -0.7V vs. Ag/AgCl including reactant adsorption, followed by irreversible mixed complex dissociation, indicating a two-electron transfer - chemical reaction (EC mechanism). Consequently, the surface concentration (γ) of the adsorbed [PhenCuOHPG] complex at the hydrophobic electrode surface was calculated to be (3.35±0.67)×10 -11 molcm -2 . Information on the mechanism of Cu (II) - lipid complex formation is a significant contribution to the understanding of complex processes at natural cell membranes. Copyright © 2017 Elsevier B.V. All rights reserved.

Catalytic and inhibiting effect of amino acids on the porphyrin metallation reactions

NASA Astrophysics Data System (ADS)

Mamardashvili, Galina M.; Zhdanova, Daria Yu.; Mamardashvili, Nugzar Zh.; Koifman, Oskar I.; Dehaen, Wim

In the present work, using the interaction of tetra-(4-sulfophenyl)porphyrin with copper(II) chloride as an example, it has been shown how different amino acid additives (glycine, valine, leucine and tryptophan) catalyze or inhibit the formation of Cu-porphyrin as a function of the chemical environment (borate buffer (pH7.4), DMSO) and the concentration of the additive. It has been demonstrated that the type of amino acid affects the complexation reaction rate. Possible mechanisms of metalloporphyrin formation and the ways of their acceleration are discussed. Ways in which different amino acid additives catalyze or inhibit the interaction of tetra-(4-sulfophenyl)porphyrin with copper(II) chloride are examined.

Carbon-hydrogen activation of cycloalkanes by cyclopentadienylcarbonylrhodium--a lifetime enigma.

PubMed

Pitts, Amanda L; Wriglesworth, Alisdair; Sun, Xue-Zhong; Calladine, James A; Zarić, Snežana D; George, Michael W; Hall, Michael B

2014-06-18

Carbon-hydrogen bond activation reactions of four cycloalkanes (C5H10, C6H12, C7H14, and C8H16) by the Cp'Rh(CO) fragments (Cp' = η(5)-C5H5 (Cp) or η(5)-C5Me5 (Cp*)) were modeled theoretically by combining density functional and coupled cluster theories, and their reaction rates were measured by fast time-resolved infrared spectroscopy. The reaction has two steps, starting with the formation of a σ-complex intermediate, followed by oxidative addition of the C-H bond by the rhodium. A range of σ-complex stabilities among the electronically unique C-H bonds in a cycloalkane were calculated and are related to the individual strengths of the C-H bond's interactions with the Rh fragment and the steric repulsion that is incurred upon forming the specific σ-complex. The unexpectedly large increase in the lifetimes of the σ-complexes from cyclohexane to cycloheptane was predicted to be due to the large range of stabilities of the different σ-complexes found for cycloheptane. The reaction lifetimes were simulated with two mechanisms, with and without migrations among the different σ-complexes, to determine if ring migrations prior to C-H activation were influencing the rate. Both mechanisms predicted similar lifetimes for cyclopentane, cyclohexane, and, to a lesser extent, cycloheptane, suggesting ring migrations do not have a large impact on the rate of C-H activation for these cycloalkanes. For cyclooctane, the inclusion of ring migrations in the reaction mechanism led to a more accurate prediction of the lifetime, indicating that ring migrations did have an effect on the rate of C-H activation for this alkane, and that migration among the σ-complexes is faster than the C-H activation for this larger cycloalkane.

Formation of methemoglobin and metmyoglobin using 8-aminoquinoline derivatives or sodium nitrite and subsequent reaction with cyanide.

PubMed

Steinhaus, R K; Baskin, S I; Clark, J H; Kirby, S D

1990-10-01

The kinetics of the oxidation of hemoglobin (Hb) and myoglobin (Mb) by sodium nitrite, 8-[(4-amino-1-methylbutyl)amino]-6-methoxy-quinoline diphosphate (primaquine), 6-methoxy-8-(6-diethylaminohexylamino)-4-methyl-quinoline dihydrochloride (WR6026) and 8-[(4-amino-1-methylbutyl)amino]-2,6-dimethoxy-4-methyl- 5-[(3-trifluoromethyl)phenoxy]quinoline succinate (WR238,605) were studied at pH values ranging from 7.4 to 7.6 and at 37 +/- 1 degrees C. The reaction between Hb and primaquine, WR6026 and WR238,605 resulted in precipitation, as did the reaction between Mb and WR238,605. The reaction between nitrite ion (NO2-) and Hb showed a lag period followed by an autocatalytic phase. The data in this study are consistent with and substantiate the proposed mechanism for the Hb-NO2- oxidation reaction. The reaction between Mb and NO2- at higher NO2- concentrations also showed a lag period followed by an autocatalytic period, while at lower NO2- concentrations no lag period was seen. The data suggest a shift in rate constant at these lower NO2- concentrations. The reaction between Mb and both WR6026 and primaquine followed a two-term rate law with oxidant-dependent and -independent terms. Concentration-effect curve data, along with these results, suggest the presence of a catalytic pathway. The rates of formation of cyanomethemoglobin and cyanometmyoglobin complexes from cyanide ion and methemoglobin (MHb) and metmyoglobin (MMb), respectively, were followed in the presence of the heme oxidants. The rate constants were all within a narrow range and suggest that complexation of cyanide by MHb and MMb is not affected by the presence of oxidants.

Reactions of Ground State Nitrogen Atoms N(4S) with Astrochemically-Relevant Molecules on Interstellar Dusts

NASA Astrophysics Data System (ADS)

Krim, Lahouari; Nourry, Sendres

2015-06-01

In the last few years, ambitious programs were launched to probe the interstellar medium always more accurately. One of the major challenges of these missions remains the detection of prebiotic compounds and the understanding of reaction pathways leading to their formation. These complex heterogeneous reactions mainly occur on icy dust grains, and their studies require the coupling of laboratory experiments mimicking the extreme conditions of extreme cold and dilute media. For that purpose, we have developed an original experimental approach that combine the study of heterogeneous reactions (by exposing neutral molecules adsorbed on ice to non-energetic radicals H, OH, N...) and a neon matrix isolation study at very low temperatures, which is of paramount importance to isolate and characterize highly reactive reaction intermediates. Such experimental approach has already provided answers to many questions raised about some astrochemically-relevant reactions occurring in the ground state on the surface of dust grain ices in dense molecular clouds. The aim of this new present work is to show the implication of ground state atomic nitrogen on hydrogen atom abstraction reactions from some astrochemically-relevant species, at very low temperatures (3K-20K), without providing any external energy. Under cryogenic temperatures and with high barrier heights, such reactions involving N(4S) nitrogen atoms should not occur spontaneously and require an initiating energy. However, the detection of some radicals species as byproducts, in our solid samples left in the dark for hours at 10K, proves that hydrogen abstraction reactions involving ground state N(4S) nitrogen atoms may occur in solid phase at cryogenic temperatures. Our results show the efficiency of radical species formation stemming from non-energetic N-atoms and astrochemically-relevant molecules. We will then discuss how such reactions, involving nitrogen atoms in their ground states, might be the first key step towards complex organic molecules production in the interstellar medium.

Cationic dirhodium(II,II) complexes for the electrocatalytic reduction of CO 2 to HCOOH

DOE PAGES

Witt, Suzanne E.; White, Travis A.; Li, Zhanyong; ...

2016-09-22

Two formamidinate bridged dirhodium(II,II) complexes with chelating diimine ligands L, [Rh 2(μ-DTolF) 2(L) 2] 2+, were shown to electrocatalytically reduce CO 2 in the presence of H 2O. Analysis of the reaction mixture and headspace following bulk electrolysis revealed H 2 and HCOOH as the major products. Finally, the variation in relative product formation is discussed.

Development of an ELISA assay for screening inhibitors against divalent metal ion dependent alphavirus capping enzyme.

PubMed

Kaur, Ramanjit; Mudgal, Rajat; Narwal, Manju; Tomar, Shailly

2018-06-26

Alphavirus non-structural protein, nsP1 has a distinct molecular mechanism of capping the viral RNAs than the conventional capping mechanism of host. Thus, alphavirus capping enzyme nsP1 is a potential drug target. nsP1 catalyzes the methylation of guanosine triphosphate (GTP) by transferring the methyl group from S-adenosylmethionine (SAM) to a GTP molecule at its N7 position with the help of nsP1 methyltransferase (MTase) followed by guanylylation (GT) reaction which involves the formation of m 7 GMP-nsP1 covalent complex by nsP1 guanylyltransferase (GTase). In subsequent reactions, m 7 GMP moiety is added to the 5' end of the viral ppRNA by nsP1 GTase resulting in the formation of cap0 structure. In the present study, chikungunya virus (CHIKV) nsP1 MTase and GT reactions were confirmed by an indirect non-radioactive colorimetric assay and western blot assay using an antibody specific for the m 7 G cap, respectively. The purified recombinant CHIKV nsP1 has been used for the development of a rapid and sensitive non-radioactive enzyme linked immunosorbent assay (ELISA) to identify the inhibitors of CHIKV nsP1. The MTase reaction is followed by GT reaction and resulted in m 7 GMP-nsP1 covalent complex formation. The developed ELISA nsP1 assay measures this m 7 GMP-nsP1 complex by utilizing anti-m 7 G cap monoclonal antibody. The mutation of a conserved residue Asp63 to Ala revealed its role in nsP1 enzyme reaction. Inductively coupled plasma mass spectroscopy (ICP-MS) was used to determine the presence of magnesium ions (Mg 2+ ) in the purified nsP1 protein. The divalent metal ion selectivity and investigation show preference for Mg 2+ ion by CHIKV nsP1. Additionally, using the developed ELISA nsP1 assay, the inhibitory effects of sinefungin, aurintricarboxylic acid (ATA) and ribavirin were determined and the IC 50 values were estimated to be 2.69 µM, 5.72 µM and 1.18 mM, respectively. Copyright © 2018. Published by Elsevier B.V.

Formation of cyanoallene (buta-2, 3-dienenitrile) in the interstellar medium: a quantum chemical and spectroscopic study

NASA Astrophysics Data System (ADS)

Singh, Amresh; Shivani; Misra, Alka; Tandon, Poonam

2014-03-01

The interstellar medium, filling the vast space between stars, is a rich reservoir of molecular material ranging from simple diatomic molecules to more complex, astrobiologically important molecules such as vinylcyanide, methylcyanodiaccetylene, cyanoallene, etc. Interstellar molecular cyanoallene is one of the most stable isomers of methylcynoacetylene. An attempt has been made to explore the possibility of forming cyanoallene in interstellar space by radical-radical and radical-molecule interaction schemes in the gaseous phase. The formation of cyanoallene starting from some simple, neutral interstellar molecules and radicals has been studied using density functional theory. The reaction energies and structures of the reactants and products show that the formation of cyanoallene is possible in the gaseous phase. Both of the considered reaction paths are totally exothermic and barrierless, thus giving rise to a high probability of occurrence. Rate constants for each step in the formation process of cyanoallene in both the reaction paths are estimated. A full vibrational analysis has been attempted for cyanoallene in the harmonic and anharmonic approximations. Anharmonic spectroscopic parameters such as rotational constants, rotation-vibration coupling constants and centrifugal distortion constants have been calculated.

A combinatorial approach of inclusion complexation and dendrimer synthesization for effective targeting EGFR-TK.

PubMed

Shende, Pravin; Patil, Sampada; Gaud, R S

2017-07-01

The aim of the present study was to use a combinatorial approach of inclusion complexation and dendrimer synthesization of gefitinib using solvent-free technique for targeting EGFR-TK to treat Non-Small-Cell Lung Cancer (NSCLC). The inclusion complex of gefitinib with β-cyclodextrin was prepared by trituration method. This complex encapsulated G4 PAMAM dendrimers were synthesized by Michael addition and amidation reactions using green chemistry and then PEGylated by conjugation reaction. FTIR and DSC confirmed the formation of inclusion complex of gefitinib and β-cyclodextrin and PEGylation of G4 PAMAM dendrimers. Gefitinib showed higher solubility, encapsulation efficiency and controlled release profile from PEGylated dendrimers compared to inclusion complex. The PEGylated dendrimers of inclusion complex of gefitinib were found to reduce hemolytic toxicity and lesser GI 50 value on Human lung cancer cell line A-549 by effective targeting EGFR-TK. A combinatorial approach of inclusion complexation and dendrimer synthesization is one of the alternative advanced approaches to treat NSCLC. Copyright © 2017 Elsevier B.V. All rights reserved.

Intermolecular hydrogen bond complexes by in situ charge transfer complexation of o-tolidine with picric and chloranilic acids

NASA Astrophysics Data System (ADS)

Refat, Moamen S.; Saad, Hosam A.; Adam, Abdel Majid A.

2011-08-01

A two new charge transfer complexes formed from the interactions between o-tolidine (o-TOL) and picric (PA) or chloranilic (CA) acids, with the compositions, [(o-TOL)(PA) 2] and [(o-TOL)(CA) 2] have been prepared. The 13C NMR, 1H NMR, 1H-Cosy, and IR show that the charge-transfer chelation occurs via the formation of chain structures O-H⋯N intermolecular hydrogen bond between 2NH 2 groups of o-TOL molecule and OH group in each PA or CA units. Photometric titration measurements concerning the two reactions in methanol were performed and the measurements show that the donor-acceptor molar ratio was found to be 1:2 using the modified Benesi-Hildebrand equation. The spectroscopic data were discussed in terms of formation constant, molar extinction coefficient, oscillator strength, dipole moment, standard free energy, and ionization potential. Thermal behavior of both charge transfer complexes showed that the complexes were more stable than their parents. The thermodynamic parameters were estimated from the differential thermogravimetric curves. The results indicated that the formation of molecular charge transfer complexes is spontaneous and endothermic.

Intermolecular hydrogen bond complexes by in situ charge transfer complexation of o-tolidine with picric and chloranilic acids.

PubMed

Refat, Moamen S; Saad, Hosam A; Adam, Abdel Majid A

2011-08-01

A two new charge transfer complexes formed from the interactions between o-tolidine (o-TOL) and picric (PA) or chloranilic (CA) acids, with the compositions, [(o-TOL)(PA)(2)] and [(o-TOL)(CA)(2)] have been prepared. The (13)C NMR, (1)H NMR, (1)H-Cosy, and IR show that the charge-transfer chelation occurs via the formation of chain structures O-H⋯N intermolecular hydrogen bond between 2NH(2) groups of o-TOL molecule and OH group in each PA or CA units. Photometric titration measurements concerning the two reactions in methanol were performed and the measurements show that the donor-acceptor molar ratio was found to be 1:2 using the modified Benesi-Hildebrand equation. The spectroscopic data were discussed in terms of formation constant, molar extinction coefficient, oscillator strength, dipole moment, standard free energy, and ionization potential. Thermal behavior of both charge transfer complexes showed that the complexes were more stable than their parents. The thermodynamic parameters were estimated from the differential thermogravimetric curves. The results indicated that the formation of molecular charge transfer complexes is spontaneous and endothermic. Copyright © 2011 Elsevier B.V. All rights reserved.

Differences and Comparisons of the Properties and Reactivities of Iron(III)–hydroperoxo Complexes with Saturated Coordination Sphere

PubMed Central

Faponle, Abayomi S; Quesne, Matthew G; Sastri, Chivukula V; Banse, Frédéric; de Visser, Sam P

2015-01-01

Heme and nonheme monoxygenases and dioxygenases catalyze important oxygen atom transfer reactions to substrates in the body. It is now well established that the cytochrome P450 enzymes react through the formation of a high-valent iron(IV)–oxo heme cation radical. Its precursor in the catalytic cycle, the iron(III)–hydroperoxo complex, was tested for catalytic activity and found to be a sluggish oxidant of hydroxylation, epoxidation and sulfoxidation reactions. In a recent twist of events, evidence has emerged of several nonheme iron(III)–hydroperoxo complexes that appear to react with substrates via oxygen atom transfer processes. Although it was not clear from these studies whether the iron(III)–hydroperoxo reacted directly with substrates or that an initial O–O bond cleavage preceded the reaction. Clearly, the catalytic activity of heme and nonheme iron(III)–hydroperoxo complexes is substantially different, but the origins of this are still poorly understood and warrant a detailed analysis. In this work, an extensive computational analysis of aromatic hydroxylation by biomimetic nonheme and heme iron systems is presented, starting from an iron(III)–hydroperoxo complex with pentadentate ligand system (L52). Direct C–O bond formation by an iron(III)–hydroperoxo complex is investigated, as well as the initial heterolytic and homolytic bond cleavage of the hydroperoxo group. The calculations show that [(L52)FeIII(OOH)]2+ should be able to initiate an aromatic hydroxylation process, although a low-energy homolytic cleavage pathway is only slightly higher in energy. A detailed valence bond and thermochemical analysis rationalizes the differences in chemical reactivity of heme and nonheme iron(III)–hydroperoxo and show that the main reason for this particular nonheme complex to be reactive comes from the fact that they homolytically split the O–O bond, whereas a heterolytic O–O bond breaking in heme iron(III)–hydroperoxo is found. PMID:25399782

Rule-based modeling and simulations of the inner kinetochore structure.

PubMed

Tschernyschkow, Sergej; Herda, Sabine; Gruenert, Gerd; Döring, Volker; Görlich, Dennis; Hofmeister, Antje; Hoischen, Christian; Dittrich, Peter; Diekmann, Stephan; Ibrahim, Bashar

2013-09-01

Combinatorial complexity is a central problem when modeling biochemical reaction networks, since the association of a few components can give rise to a large variation of protein complexes. Available classical modeling approaches are often insufficient for the analysis of very large and complex networks in detail. Recently, we developed a new rule-based modeling approach that facilitates the analysis of spatial and combinatorially complex problems. Here, we explore for the first time how this approach can be applied to a specific biological system, the human kinetochore, which is a multi-protein complex involving over 100 proteins. Applying our freely available SRSim software to a large data set on kinetochore proteins in human cells, we construct a spatial rule-based simulation model of the human inner kinetochore. The model generates an estimation of the probability distribution of the inner kinetochore 3D architecture and we show how to analyze this distribution using information theory. In our model, the formation of a bridge between CenpA and an H3 containing nucleosome only occurs efficiently for higher protein concentration realized during S-phase but may be not in G1. Above a certain nucleosome distance the protein bridge barely formed pointing towards the importance of chromatin structure for kinetochore complex formation. We define a metric for the distance between structures that allow us to identify structural clusters. Using this modeling technique, we explore different hypothetical chromatin layouts. Applying a rule-based network analysis to the spatial kinetochore complex geometry allowed us to integrate experimental data on kinetochore proteins, suggesting a 3D model of the human inner kinetochore architecture that is governed by a combinatorial algebraic reaction network. This reaction network can serve as bridge between multiple scales of modeling. Our approach can be applied to other systems beyond kinetochores. Copyright © 2013 Elsevier Ltd. All rights reserved.

Photochemical activity of a key donor-acceptor complex can drive stereoselective catalytic α-alkylation of aldehydes.

PubMed

Arceo, Elena; Jurberg, Igor D; Alvarez-Fernández, Ana; Melchiorre, Paolo

2013-09-01

Asymmetric catalytic variants of sunlight-driven photochemical processes hold extraordinary potential for the sustainable preparation of chiral molecules. However, the involvement of short-lived electronically excited states inherent to any photochemical reaction makes it challenging for a chiral catalyst to dictate the stereochemistry of the products. Here, we report that readily available chiral organic catalysts, with well-known utility in thermal asymmetric processes, can also confer a high level of stereocontrol in synthetically relevant intermolecular carbon-carbon bond-forming reactions driven by visible light. A unique mechanism of catalysis is proposed, wherein the catalyst is involved actively in both the photochemical activation of the substrates (by inducing the transient formation of chiral electron donor-acceptor complexes) and the stereoselectivity-defining event. We use this approach to enable transformations that are extremely difficult under thermal conditions, such as the asymmetric α-alkylation of aldehydes with alkyl halides, the formation of all-carbon quaternary stereocentres and the control of remote stereochemistry.

Non-covalent and coordination interactions in Cu(II) systems with uridine, uridine 5'-monophosphate and triamine or tetramine as biogenic amine analogues in aqueous solutions.

PubMed

Łomozik, Lechosław; Jastrzab, Renata

2003-10-01

Reactions of metallation and non-covalent interactions have been studied in ternary systems of Cu(II) ions with uridine, uridine 5'-monophosphate and diamines or triamines. It has been found that in metal-free systems the reaction centres of the nucleoside with the polyamine are the donor nitrogen atoms N(3) and protonated -NH(x) groups of the amines. In comparison to systems with adenosine or cytidine, the pH range of complex formation is shifted towards higher values. It is a consequence of significantly higher basicity of uridine and in agreement with the ion-ion, ion-dipole interaction model assumed. Formation of molecular complexes of uridine 5'-monophosphate with polyamines at a low pH is the result of activity of the phosphate group which plays the role of a negatively charged reaction site. Non-covalent interactions interfere in processes of bioligand metallation. Centres of weak interactions are simultaneously binding sites of metal ions. In protonated Cu(Urd)(PA)H(x) complexes, coordination has been found to involve the N(3) atom from the nucleoside and two donor nitrogen atoms from the polyamine (PA). In the heteroligand species Cu(Urd)(PA), despite deprotonation of all amine groups, one of these groups is located outside the inner coordination sphere. In complexes with uridine-5'-monophosphate, the phosphate group is active in metallation. Moreover, in certain coordination compounds this group is engaged in non-covalent interactions with PA molecules, despite binding Cu ions, as has been shown on the basis of equilibrium and spectral studies.

In Situ FTIR and NMR Spectroscopic Investigations on Ruthenium-Based Catalysts for Alkene Hydroformylation.

PubMed

Kubis, Christoph; Profir, Irina; Fleischer, Ivana; Baumann, Wolfgang; Selent, Detlef; Fischer, Christine; Spannenberg, Anke; Ludwig, Ralf; Hess, Dieter; Franke, Robert; Börner, Armin

2016-02-18

Homogeneous ruthenium complexes modified by imidazole-substituted monophosphines as catalysts for various highly efficient hydroformylation reactions were characterized by in situ IR spectroscopy under reaction conditions and NMR spectroscopy. A proper protocol for the preformation reaction from [Ru3 (CO)12] is decisive to prevent the formation of inactive ligand-modified polynuclear complexes. During catalysis, ligand-modified mononuclear ruthenium(0) carbonyls were detected as resting states. Changes in the ligand structure have a crucial impact on the coordination behavior of the ligand and consequently on the catalytic performance. The substitution of CO by a nitrogen atom of the imidazolyl moiety in the ligand is not a general feature, but it takes place when structural prerequisites of the ligand are fulfilled. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chemical modelling of glycolaldehyde and ethylene glycol in star-forming regions

NASA Astrophysics Data System (ADS)

Coutens, A.; Viti, S.; Rawlings, J. M. C.; Beltrán, M. T.; Holdship, J.; Jiménez-Serra, I.; Quénard, D.; Rivilla, V. M.

2018-04-01

Glycolaldehyde (HOCH2CHO) and ethylene glycol ((CH2OH)2) are two complex organic molecules detected in the hot cores and hot corinos of several star-forming regions. The ethylene glycol/glycolaldehyde abundance ratio seems to show an increase with the source luminosity. In the literature, several surface-chemistry formation mechanisms have been proposed for these two species. With the UCLCHEM chemical code, we explored the different scenarios and compared the predictions for a range of sources of different luminosities with the observations. None of the scenarios reproduce perfectly the trend. A better agreement is, however, found for a formation through recombination of two HCO radicals followed by successive hydrogenations. The reaction between HCO and CH2OH could also contribute to the formation of glycolaldehyde in addition to the hydrogenation pathway. The predictions are improved when a trend of decreasing H2 density within the core region with T≥100 K as a function of luminosity is included in the model. Destruction reactions of complex organic molecules in the gas phase would also need to be investigated, since they can affect the abundance ratios once the species have desorbed in the warm inner regions of the star-forming regions.

Charge–transfer reaction of 2,3-dichloro-1,4-naphthoquinone with crizotinib: Spectrophotometric study, computational molecular modeling and use in development of microwell assay for crizotinib

PubMed Central

Alzoman, Nourah Z.; Alshehri, Jamilah M.; Darwish, Ibrahim A.; Khalil, Nasr Y.; Abdel-Rahman, Hamdy M.

2014-01-01

The reaction of 2,3-dichloro-1,4-naphthoquinone (DCNQ) with crizotinib (CZT; a novel drug used for treatment of non-small cell lung cancer) was investigated in different solvents of varying dielectric constants and polarity indexes. The reaction produced a red-colored product. Spectrophotometric investigations confirmed that the reaction proceeded through charge–transfer (CT) complex formation. The molar absorptivity of the complex was found to be linearly correlated with the dielectric constant and polarity index of the solvent; the correlation coefficients were 0.9567 and 0.9069, respectively. The stoichiometric ratio of DCNQ:CZT was found to be 2:1 and the association constant of the complex was found to be 1.07 × 102 l/mol. The kinetics of the reaction was studied; the order of the reaction, rate and rate constant were determined. Computational molecular modeling for the complex between DCNQ and CZT was conducted, the sites of interaction on CZT molecule were determined, and the mechanism of the reaction was postulated. The reaction was employed as a basis in the development of a novel 96-microwell assay for CZT in a linear range of 4–500 μg/ml. The assay limits of detection and quantitation were 2.06 and 6.23 μg/ml, respectively. The assay was validated as per the guidelines of the International Conference on Harmonization (ICH) and successfully applied to the analysis of CZT in its bulk and capsules with good accuracy and precision. The assay has high throughput and consumes a minimum volume of organic solvents thus it reduces the exposures of the analysts to the toxic effects of organic solvents, and significantly reduces the analysis cost. PMID:25685046

Study of intermediates from transition metal excited-state electron-transfer reactions

NASA Astrophysics Data System (ADS)

Hoffman, M. Z.

1984-03-01

Attention during the past year focused on MV(+)., the reduced methyl viologen radical cation, which is a precursor to the formation of H2 in the photosensitized reduction of water. Through the use of photochemical and radiation chemical techniques, the efficiency of interaction of MV(+). with colloidal Pt, the stability of MV(+). as a function of pH, the quantum yield of formation of MV(+). in the Ru(bpy)3(2+)/MV(2+)/EDTA system, and the formation of photoactive charge-transfer complexes between MV(2+) and sacrificial electron donors were studied.

Catalyst activation, deactivation, and degradation in palladium-mediated Negishi cross-coupling reactions.

PubMed

Böck, Katharina; Feil, Julia E; Karaghiosoff, Konstantin; Koszinowski, Konrad

2015-03-27

Pd-mediated Negishi cross-coupling reactions were studied by a combination of kinetic measurements, electrospray-ionization (ESI) mass spectrometry, (31)P NMR and UV/Vis spectroscopy. The kinetic measurements point to a rate-determining oxidative addition. Surprisingly, this step seems to involve not only the Pd catalyst and the aryl halide substrate, but also the organozinc reagent. In this context, the ESI-mass spectrometric observation of heterobimetallic Pd-Zn complexes [L2 PdZnR](+) (L=S-PHOS, R=Bu, Ph, Bn) is particularly revealing. The inferred presence of these and related neutral complexes with a direct Pd-Zn interaction in solution explains how the organozinc reagent can modulate the reactivity of the Pd catalyst. Previous theoretical calculations by González-Pérez et al. (Organometallics- 2012, 31, 2053) suggest that the complexation by the organozinc reagent lowers the activity of the Pd catalyst. Presumably, a similar effect also causes the rate decrease observed upon addition of ZnBr2 . In contrast, added LiBr apparently counteracts the formation of Pd-Zn complexes and restores the high activity of the Pd catalyst. At longer reaction times, deactivation processes due to degradation of the S-PHOS ligand and aggregation of the Pd catalyst come into play, thus further contributing to the appreciable complexity of the title reaction. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effect of ultrasonic waves on the water turbidity during the oxidation of phenol. Formation of (hydro)peroxo complexes.

PubMed

Villota, Natalia; Lomas, Jose M; Camarero, Luis M

2017-11-01

Analysis of the kinetics of aqueous phenol oxidation by a sono-Fenton process reveals that the via involving ortho-substituted intermediates prevails: catechol (25.0%), hydroquinone (7.7%) and resorcinol (0.6%). During the oxidation, water rapidly acquires color that reaches its maximum intensity at the maximum concentration of p-benzoquinone. Turbidity formation occurs at a slower rate. Oxidant dosage determines the nature of the intermediates, being trihydroxylated benzenes (pyrogallol, hydroxyhydroquinone) and muconic acid the main precursors causing turbidity. It is found that the concentration of iron species and ultrasonic waves affects the intensity of the turbidity. The pathway of (hydro)peroxo-iron(II) complexes formation is proposed. Operating with 20.0-27.8mgFe 2+ /kW rates leads to formation of (hydro)peroxo-iron(II) complexes, which induce high turbidity levels. These species would dissociate into ZZ-muconic acid and ferrous ions. Applying relationships around 13.9mgFe 2+ /kW, the formation of (hydro)peroxo-iron(III) complexes would occur, which could react with carboxylic acids (2,5-dioxo-3-hexenedioic acid). That reaction induces turbidity slower. This is due to the organic substrate reacting with two molecules of the (hydro)peroxo complex. Therefore, it is necessary to accelerate the iron regeneration, intensifying the ultrasonic irradiation. Afterwards, this complex would dissociate into maleic acid and ferric ions. Copyright © 2017 Elsevier B.V. All rights reserved.

Copper(II) complexes with uridine, uridine 5'-monophosphate, spermidine, or spermine in aqueous solution.

PubMed

Lomozik, Lechoslaw; Jastrzab, Renata

2003-01-15

Molecular complexes of the types (Urd)H(x)(PA) and (UMP)H(x)(PA) are formed in the uridine (Urd) or uridine 5'-monophosphate (UMP) plus spermidine or spermine systems, as shown by the results of equilibrium and spectral studies. Overall stability constants of the adducts and equilibrium constants of their formation have been determined. An increase in the efficiency of the reaction between the bioligands is observed with increasing length of the polyamine. The pH range of adduct formation is found to coincide with that in which the polyamine is protonated while uridine or its monophosphate is deprotonated. The -NH(x)(+) groups from PA and the N(3) atom of the purine base as well as phosphate groups from the nucleotides have been identified as the significant centres of non-covalent interactions. Compared to cytidine, the pH range of Urd adduct formation is shifted significantly higher due to differences in the protonation constants of the endocyclic N(3) donor atoms of particular nucleosides. Overall stability constants of the Cu(II) complexes with uridine and uridine 5'-monophosphate in ternary systems with spermidine or spermine have been determined. It has been found from spectral data that in the Cu(II) ternary complexes with nucleosides and polyamines the reaction of metallation involves mainly N(3) atoms from the pyrimidine bases, as well as the amine groups of PA. This unexpected type of interaction has been evidenced in the coordination mode of the complexes forming in the Cu-UMP systems including spermidine or spermine. Results of spectral and equilibrium studies indicate that the phosphate groups taking part in metallation are at the same time involved in non-covalent interaction with the protonated polyamine.

Zinc(II)-methimazole complexes: synthesis and reactivity.

PubMed

Isaia, Francesco; Aragoni, Maria Carla; Arca, Massimiliano; Bettoschi, Alexandre; Caltagirone, Claudia; Castellano, Carlo; Demartin, Francesco; Lippolis, Vito; Pivetta, Tiziana; Valletta, Elisa

2015-06-07

The tetrahedral S-coordinated complex [Zn(MeImHS)4](ClO4)2, synthesised from the reaction of [Zn(ClO4)2] with methimazole (1-methyl-3H-imidazole-2-thione, MeImHS), reacts with triethylamine to yield the homoleptic complex [Zn(MeImS)2] (MeImS = anion methimazole). ESI-MS and MAS (13)C-NMR experiments supported MeImS acting as a (N,S)-chelating ligand. The DFT-optimised structure of [Zn(MeImS)2] is also reported and the main bond lengths compared to those of related Zn-methimazole complexes. The complex [Zn(MeImS)2] reacts under mild conditions with methyl iodide and separates the novel complex [Zn(MeImSMe)2I2] (MeImSMe = S-methylmethimazole). X-ray diffraction analysis of the complex shows a ZnI2N2 core, with the methyl thioethers uncoordinated to zinc. Conversely, the reaction of [Zn(MeImS)2] with hydroiodic acid led to the formation of the complex [Zn(MeImHS)2I2] having a ZnI2S2 core with the neutral methimazole units S-coordinating the metal centre. The Zn-coordinated methimazole can markedly modify the coordination environment when changing from its thione to thionate form and vice versa. The study of the interaction of the drug methimazole with the complex [Zn(MeIm)4](2+) (MeIm = 1-methylimidazole) - as a model for Zn-enzymes containing a N4 donor set from histidine residues - shows that methimazole displaces only one of the coordinated MeIm molecules; the formation constant of the mixed complex [Zn(MeIm)3(MeImHS)](2+) was determined.

Pd(II) and Pt(II) complexes of α-keto stabilized sulfur ylide: Synthesis, structural, theoretical and catalytic activity studies

NASA Astrophysics Data System (ADS)

Sabounchei, Seyyed Javad; Hashemi, Ali; Sedghi, Asieh; Bayat, Mehdi; Akhlaghi Bagherjeri, Fateme; Gable, Robert W.

2017-05-01

Reaction of dimethyl sulfide with 2, 3‧-dibromoacetophenone led to formation of sulfonium salt [Me2SCH2C(O)C6H4-m-Br]Br (1). The resulted sulfonium salt was treated with NaOH and gave the α-keto stabilized sulfur ylide Me2SC(H)C(O)C6H4-m-Br (2). This ligand was reacted with [MCl2(cod)] (M = Pd, Pt; cod = 1,5-cyclooctadiene) to form the new cis- and trans-[MCl2(ylide)2] (M = Pd (cis- and trans-3), Pt (cis- and trans-4)) complexes. Characterization of the obtained compounds was performed by elemental analysis, IR, 1H and 13C NMR. Recrystallization of dichlorobis(ylide) palladium(II) and platinum(II) complexes from DMSO solution yielded the crystalline products, which X-ray diffraction data revealed that the both compounds were crystallized as cis-[MCl2(ylide)(DMSO)] (M = Pd (5), Pt (6)) complexes. Also, a theoretical study on structure and nature of the Msbnd C bonding between the Y ligand (ylide) and [MCl2·DMSO] fragments in [YMCl2·DMSO] (M = Pd, Pt) complexes has been reported via NBO and energy-decomposition analysis (EDA). Furthermore, the palladium catalyzed Suzuki-Miyaura reaction of various aryl chlorides with arylboronic acids was performed. The results showed that the Pd(II) complexes cis- and trans-3 catalyzed efficiently coupling reactions at low catalyst loading and short reaction time.

A quantum dynamical study of the He++2He-->He2++He reaction

NASA Astrophysics Data System (ADS)

Xie, Junkai; Poirier, Bill; Gellene, Gregory I.

2003-11-01

The temperature dependent rate of the He++2He→He2++He three-body association reaction is studied using two complementary quantum dynamical models. Model I presumes a two-step, reverse Lindemann mechanism, where the intermediate energized complex, He2+*, is interpreted as the rotational resonance states of He2+. The energy and width of these resonances are determined via "exact" quantum calculation using highly accurate potential-energy curves. Model II uses an alternate quantum rate expression as the thermal average of the cumulative recombination probability, N(E). This microcanonical quantity is computed approximately, over the He2+ space only, with the third-body interaction modeled using a special type of absorbing potential. Because Model II implicitly incorporates both the two-step reverse Lindemann mechanism, and a one-step, reverse collision induced dissociation mechanism, the relative importance of the two formation mechanisms can be estimated by a comparison of the Model I and Model II results. For T<300 K, the reaction is found to be dominated by the two-step mechanism, and a formation rate in good agreement with the available experimental results is obtained with essentially no adjustable parameters in the theory. Interestingly, a nonmonotonic He2+ formation rate is observed, with a maximum identified near 25 K. This maximum is associated with just two reaction intermediate resonance states, the lowest energy states that can contribute significantly to the formation kinetics.

Reactivity of molecular dioxygen towards a series of isostructural dichloroiron(III) complexes with tripodal tetraamine ligands: general access to mu-oxodiiron(III) complexes and effect of alpha-fluorination on the reaction kinetics.

PubMed

Thallaj, Nasser K; Rotthaus, Olaf; Benhamou, Leila; Humbert, Nicolas; Elhabiri, Mourad; Lachkar, Mohammed; Welter, Richard; Albrecht-Gary, Anne-Marie; Mandon, Dominique

2008-01-01

We have synthesized the mono, di-, and tri-alpha-fluoro ligands in the tris(2-pyridylmethyl)amine (TPA) series, namely, FTPA, F(2)TPA and F(3)TPA, respectively. Fluorination at the alpha-position of these nitrogen-containing tripods shifts the oxidation potential of the ligand by 45-70 mV per added fluorine atom. The crystal structures of the dichloroiron(II) complexes with FTPA and F(2)TPA reveal that the iron center lies in a distorted octahedral geometry comparable to that already found in TPAFeCl(2). All spectroscopic data indicate that the geometry is retained in solution. These three isostructural complexes all react with molecular dioxygen to yield stable mu-oxodiiron(III) complexes. Crystal structure analyses are reported for each of these three mu-oxo compounds. With TPA, a symmetrical structure is obtained for a dicationic compound with the tripod coordinated in the kappa(4)N coordination mode. With FTPA, the compound is a neutral mu-oxodiiron(III) complex with a kappa(3)N coordination mode of the ligand. Oxygenation of the F(2)TPA complex gave a neutral unsymmetrical compound, the structure of which is reminiscent of that already found with the trifluorinated ligand. On reduction, all mu-oxodiiron(III) complexes revert to the starting iron(II) species. The oxygenation reaction parallels the well-known formation of mu-oxo derivatives from dioxygen in the chemistry of porphyrins reported almost three decades ago. The striking feature of the series of iron(II) precursors is the effect of the ligand on the kinetics of oxygenation of the complexes. Whereas the parent complex undergoes 90 % conversion over 40 h, the monofluorinated ligand provides a complex that has fully reacted after 30 h, whereas the reaction time for the complex with the difluorinated ligand is only 10 h. Analysis of the spectroscopic data reveals that formation of the mu-oxo complexes proceeds in two distinct reversible kinetic steps with k(1) approximately 10 k(2). For TPAFeCl(2) and FTPAFeCl(2) only small variations in the k(1) and k(2) values are observed. By contrast, F(2)TPAFeCl(2) exhibits k(1) and k(2) values that are ten times higher. These differences in kinetics are interpreted in the light of structural and electronic effects, especially the Lewis acidity at the metal center. Our results suggest coordination of dioxygen as an initial step in the process leading to formation of mu-oxodiiron(III) compounds, by contrast with an unlikely outer-sphere reduction of dioxygen, which generally occurs at negative potentials.

Catalytic Activity of μ-Carbido-Dimeric Iron(IV) Octapropylporphyrazinate in the 3,5,7,2',4'-Pentahydroxyflavone Oxidation Reaction with tert-Butyl Hydroperoxide

NASA Astrophysics Data System (ADS)

Tyurin, D. V.; Zaitseva, S. V.; Kudrik, E. V.

2018-05-01

It is found for the first time that μ-carbido-dimeric iron(IV) octapropylporphyrazinate displays catalytic activity in the oxidation reaction of natural flavonol morin with tert-butyl hydroperoxide, with the catalyst being stable under conditions of the reaction. The kinetics of this reaction are studied. It is shown the reaction proceeds via tentative formation of a complex between the catalyst and the oxidant, followed by O‒O bond homolytic cleavage. The kinetics of the reaction is described in the coordinates of the Michaelis-Menten equation. A linear dependence of the apparent reaction rate constant on the concentration of the catalyst is observed, testifying to its participation in the limiting reaction step. The equilibrium constants and rates of interaction are found. A mechanism is proposed for the reaction on the basis of the experimental data.

Theoretical survey of the reaction between osmium and acetaldehyde

NASA Astrophysics Data System (ADS)

Dai, Guo-Liang; Wang, Chuan-Feng

2012-05-01

The mechanism of the reaction of osmium atom with acetaldehyde has been investigated with a DFT approach. All the stationary points are determined at the UB3LYP/ sdd/6-311++G** level of the theory. Both ground and excited state potential energy surfaces are investigated in detail. The present results show that the title reaction start with the formation of a CH3CHO-metal complex followed by C-C, aldehyde C-H, C-O, and methyl C-H activation. These reactions can lead to four different products (HOsCH3 + CO, OsCO + CH4, OsCOCH3 + H, and OsO + C2H4). The minimum energy reaction path is found to involve the spin inversion in the initial reaction step. This potential energy curve-crossing dramatically affects reaction exothermic. The present results may be helpful in understanding the mechanism of the title reaction and further experimental investigation of the reaction.

Effect of amino acids on the interaction between cobalamin(II) and dehydroascorbic acid

NASA Astrophysics Data System (ADS)

Dereven'kov, I. A.; Thi, Thu Thuy Bui; Salnikov, D. S.; Makarov, S. V.

2016-03-01

The kinetics of the reaction between one-electron-reduced cobalamin (cobalamin(II), Cb(II)) and the two-electron-oxidized form of vitamin C (dehydroascorbic acid, DHA) with amino acids in an acidic medium is studied by conventional UV-Vis spectroscopy. It is shown that the oxidation of Cbl(II) by dehydroascorbic acid proceeds only in the presence of sulfur-containing amino acids (cysteine, acetylcysteine). A proposed reaction mechanism includes the step of amino acid coordination on the Co(II)-center through the sulfur atom, along with that of the interaction between this complex and DHA molecules, which results in the formation of ascorbyl radical and the corresponding Co(III) thiolate complex.

NADP-Specific Electron-Bifurcating [FeFe]-Hydrogenase in a Functional Complex with Formate Dehydrogenase in Clostridium autoethanogenum Grown on CO

PubMed Central

Wang, Shuning; Huang, Haiyan; Kahnt, Jörg; Mueller, Alexander P.; Köpke, Michael

2013-01-01

Flavin-based electron bifurcation is a recently discovered mechanism of coupling endergonic to exergonic redox reactions in the cytoplasm of anaerobic bacteria and archaea. Among the five electron-bifurcating enzyme complexes characterized to date, one is a heteromeric ferredoxin- and NAD-dependent [FeFe]-hydrogenase. We report here a novel electron-bifurcating [FeFe]-hydrogenase that is NADP rather than NAD specific and forms a complex with a formate dehydrogenase. The complex was found in high concentrations (6% of the cytoplasmic proteins) in the acetogenic Clostridium autoethanogenum autotrophically grown on CO, which was fermented to acetate, ethanol, and 2,3-butanediol. The purified complex was composed of seven different subunits. As predicted from the sequence of the encoding clustered genes (fdhA/hytA-E) and from chemical analyses, the 78.8-kDa subunit (FdhA) is a selenocysteine- and tungsten-containing formate dehydrogenase, the 65.5-kDa subunit (HytB) is an iron-sulfur flavin mononucleotide protein harboring the NADP binding site, the 51.4-kDa subunit (HytA) is the [FeFe]-hydrogenase proper, and the 18.1-kDa (HytC), 28.6-kDa (HytD), 19.9-kDa (HytE1), and 20.1-kDa (HytE2) subunits are iron-sulfur proteins. The complex catalyzed both the reversible coupled reduction of ferredoxin and NADP+ with H2 or formate and the reversible formation of H2 and CO2 from formate. We propose the complex to have two functions in vivo, namely, to normally catalyze CO2 reduction to formate with NADPH and reduced ferredoxin in the Wood-Ljungdahl pathway and to catalyze H2 formation from NADPH and reduced ferredoxin when these redox mediators get too reduced during unbalanced growth of C. autoethanogenum on CO (E0′ = −520 mV). PMID:23893107

NADP-specific electron-bifurcating [FeFe]-hydrogenase in a functional complex with formate dehydrogenase in Clostridium autoethanogenum grown on CO.

PubMed

Wang, Shuning; Huang, Haiyan; Kahnt, Jörg; Mueller, Alexander P; Köpke, Michael; Thauer, Rudolf K

2013-10-01

Flavin-based electron bifurcation is a recently discovered mechanism of coupling endergonic to exergonic redox reactions in the cytoplasm of anaerobic bacteria and archaea. Among the five electron-bifurcating enzyme complexes characterized to date, one is a heteromeric ferredoxin- and NAD-dependent [FeFe]-hydrogenase. We report here a novel electron-bifurcating [FeFe]-hydrogenase that is NADP rather than NAD specific and forms a complex with a formate dehydrogenase. The complex was found in high concentrations (6% of the cytoplasmic proteins) in the acetogenic Clostridium autoethanogenum autotrophically grown on CO, which was fermented to acetate, ethanol, and 2,3-butanediol. The purified complex was composed of seven different subunits. As predicted from the sequence of the encoding clustered genes (fdhA/hytA-E) and from chemical analyses, the 78.8-kDa subunit (FdhA) is a selenocysteine- and tungsten-containing formate dehydrogenase, the 65.5-kDa subunit (HytB) is an iron-sulfur flavin mononucleotide protein harboring the NADP binding site, the 51.4-kDa subunit (HytA) is the [FeFe]-hydrogenase proper, and the 18.1-kDa (HytC), 28.6-kDa (HytD), 19.9-kDa (HytE1), and 20.1-kDa (HytE2) subunits are iron-sulfur proteins. The complex catalyzed both the reversible coupled reduction of ferredoxin and NADP(+) with H2 or formate and the reversible formation of H2 and CO2 from formate. We propose the complex to have two functions in vivo, namely, to normally catalyze CO2 reduction to formate with NADPH and reduced ferredoxin in the Wood-Ljungdahl pathway and to catalyze H2 formation from NADPH and reduced ferredoxin when these redox mediators get too reduced during unbalanced growth of C. autoethanogenum on CO (E0' = -520 mV).

Chemical reaction CO+OH • → CO 2+H • autocatalyzed by carbon dioxide: Quantum chemical study of the potential energy surfaces

DOE PAGES

Masunov, Artem E.; Wait, Elizabeth; Vasu, Subith S.

2016-06-28

The supercritical carbon dioxide medium, used to increase efficiency in oxy combustion fossil energy technology, may drastically alter both rates and mechanisms of chemical reactions. Here we investigate potential energy surface of the second most important combustion reaction with quantum chemistry methods. Two types of effects are reported: formation of the covalent intermediates and formation of van der Waals complexes by spectator CO 2 molecule. While spectator molecule alter the activation barrier only slightly, the covalent bonding opens a new reaction pathway. The mechanism includes sequential covalent binding of CO 2 to OH radical and CO molecule, hydrogen transfer frommore » oxygen to carbon atoms, and CH bond dissociation. This reduces the activation barrier by 11 kcal/mol at the rate-determining step and is expected to accelerate the reaction rate. The finding of predicted catalytic effect is expected to play an important role not only in combustion but also in a broad array of chemical processes taking place in supercritical CO 2 medium. Furthermore, tt may open a new venue for controlling reaction rates for chemical manufacturing.« less

Cell proteins bind to multiple sites within the 5' untranslated region of poliovirus RNA.

PubMed Central

del Angel, R M; Papavassiliou, A G; Fernández-Tomás, C; Silverstein, S J; Racaniello, V R

1989-01-01

The 5' noncoding region of poliovirus RNA contains sequences necessary for translation and replication. These functions are probably carried out by recognition of poliovirus RNA by cellular and/or viral proteins. Using a mobility-shift electrophoresis assay and 1,10-phenanthroline/Cu+ footprinting, we demonstrate specific binding of cytoplasmic factors with a sequence from nucleotides 510-629 within the 5' untranslated region (UTR). Complex formation was also observed with a second sequence (nucleotides 97-182) within the 5' UTR. These two regions of the 5' UTR appear to be recognized by distinct cell factors as determined by competition analysis and the effects of ionic strength on complex formation. However, both complexes contain eukaryotic initiation factor 2 alpha, as revealed by their reaction with specific antibody. Images PMID:2554308

Silanones and silanethiones from the reactions of transient silylenes with oxiranes and thiiranes in solution. The direct detection of diphenylsilanethione.

PubMed

Kostina, Svetlana S; Leigh, William J

2011-03-30

The transient silylenes SiMe(2) and SiPh(2) react with cyclohexene oxide (CHO), propylene oxide (PrO), and propylene sulfide (PrS) in hydrocarbon solvents to form products consistent with the formation of the corresponding transient silanones and silanethiones, respectively. Laser flash photolysis studies show that these reactions proceed via multistep sequences involving the intermediacy of the corresponding silylene-oxirane or -thiirane complexes, which are formed with rate constants close to the diffusion limit in all cases and exhibit UV absorption spectra similar to those of the corresponding complexes with the nonreactive O- and S-donors, tetrahydrofuran and tetrahydrothiophene. The SiMe(2)-PrO and SiPh(2)-PrO complexes both exhibit lifetimes of ca. 300 ns, and are longer-lived than the corresponding complexes with CHO, which are both in the range of 230-240 ns. On the other hand, the silylene-PrS complexes are considerably shorter-lived and vary with silyl substituent; the SiMe(2)-PrS complex decays with the excitation laser pulse (i.e., τ ≤ 25 ns), while the SiPh(2)-PrS complex exhibits τ = 48 ± 3 ns. The decay of the SiPh(2)-PrS complex affords a long-lived transient product exhibiting λ(max) ≈ 275 nm, which has been assigned to diphenylsilanethione (Ph(2)Si═S) on the basis of its second order decay kinetics and absolute rate constants for reaction with methanol, tert-butanol, acetic acid, and n-butyl amine, for which values in the range of 1.4 × 10(8) to 3.2 × 10(9) M(-1) s(-1) are reported. The experimental rate constants for decay of the SiMe(2)-epoxide and -PrS complexes indicate free energy barriers (ΔG(‡)) of ca. 8.5 and ≤7.1 kcal mol(-1) for the rate-determining steps leading to dimethylsilanone and -silanethione, respectively, which are compared to the results of DFT (B3LYP/6-311+G(d,p)) calculations of the reactions of SiH(2) and SiMe(2) with oxirane and thiirane. The calculations predict a stepwise C-O cleavage mechanism involving singlet biradical intermediates for the silylene-oxirane complexes, and a concerted mechanism for silanethione formation from the silylene-thiirane complexes, in agreement with earlier ab initio studies of the SiH(2)-oxirane and -thiirane systems.

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.

Enantioselective Diels-Alder reactions of unsaturated beta-ketoesters catalyzed by chiral ruthenium PNNP complexes.

PubMed

Schotes, Christoph; Mezzetti, Antonio

2011-01-01

We report here dicationic ruthenium PNNP complexes that promote the enantioselective Diels-Alder reaction of alpha-methylene beta-ketoesters with various dienes. Complex [Ru(OEt2)2(PNNP)](PF6)2, formed in situ from [RuCl2,(PNNP)] and (Et3O)PF6 (2 equiv.), catalyzes the Diels-Alder reaction of such unsaturated beta-ketoesters to give novel alkoxycarbonyltetrahydro-1-indanone derivatives (nine examples) with up to 93% ee. The crystal structure of the substrate-catalyst adduct shows that the lower face of the substrate is shielded by a phenyl ring of the PNNP ligand, which accounts for the high enantioselectivity. The attack of the diene from the open re enantioface of the unsaturated beta-ketoester is consistent with the absolute configuration of the product. A useful application of this method is the reaction with Dane's diene to give estrone derivatives with up to 99% ee and an ester-exo:endo ratio of up to 145:1 (after recrystallization). Besides the enantioselective formation of all-carbon quaternary centers, this methodology is notable because unsaturated beta-ketoesters have been rarely used in Diels-Alder reactions. Furthermore, enantiomerically pure estrone derivatives are interesting in view of their potential applications, including the treatment of breast cancer.

An experimental design method leading to chemical Turing patterns.

PubMed

Horváth, Judit; Szalai, István; De Kepper, Patrick

2009-05-08

Chemical reaction-diffusion patterns often serve as prototypes for pattern formation in living systems, but only two isothermal single-phase reaction systems have produced sustained stationary reaction-diffusion patterns so far. We designed an experimental method to search for additional systems on the basis of three steps: (i) generate spatial bistability by operating autoactivated reactions in open spatial reactors; (ii) use an independent negative-feedback species to produce spatiotemporal oscillations; and (iii) induce a space-scale separation of the activatory and inhibitory processes with a low-mobility complexing agent. We successfully applied this method to a hydrogen-ion autoactivated reaction, the thiourea-iodate-sulfite (TuIS) reaction, and noticeably produced stationary hexagonal arrays of spots and parallel stripes of pH patterns attributed to a Turing bifurcation. This method could be extended to biochemical reactions.

Formation of {eta}-mesic nuclei by the ({pi},N) reaction and properties of N*(1535) in medium

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

Nagahiro, Hideko; Jido, Daisuke; Hirenzaki, Satoru

2009-08-15

We calculate formation spectra of the {eta}-nucleus systems in the ({pi},N) reactions with nuclear targets, which can be performed at existing and/or forthcoming facilities, including the Japan Proton Accelerator Research Complex, to investigate the {eta}-nucleus interaction. Based on the N*(1535) dominance in the {eta}N system, the {eta}-mesic nuclei are suitable systems for the study of in-medium properties of the N*(1535) baryon resonance, such as reduction of the mass difference of N and N* in the nuclear medium, which affects the level structure of the {eta} and N*-hole modes. We find that clear information on the in-medium N*- and {eta}-nucleus interactionsmore » can be obtained through the formation spectra of the {eta}-mesic nuclei. We also discuss the experimental feasibilities by showing several spectra of the ({pi},N) reactions calculated with possible experimental settings. Coincident measurements of the N{pi} pairs from the N* decays in nuclei help us to reduce backgrounds.« less

Microfluidic Technology: Uncovering the Mechanisms of Nanocrystal Nucleation and Growth.

PubMed

Lignos, Ioannis; Maceiczyk, Richard; deMello, Andrew J

2017-05-16

The controlled and reproducible formation of colloidal semiconductor nanocrystals (or quantum dots) is of central importance in nanoscale science and technology. The tunable size- and shape-dependent properties of such materials make them ideal candidates for the development of efficient and low-cost displays, solar cells, light-emitting devices, and catalysts. The formidable difficulties associated with the macroscale preparation of semiconductor nanocrystals (possessing bespoke optical and chemical properties) result from the fact that underlying reaction mechanisms are complex and that the reactive environment is difficult to control. Automated microfluidic reactors coupled with monitoring systems and optimization algorithms aim to elucidate complex reaction mechanisms that govern both nucleation and growth of nanocrystals. Such platforms are ideally suited for the efficient optimization of reaction parameters, assuring the reproducible synthesis of nanocrystals with user-defined properties. This Account aims to inform the nanomaterials community about how microfluidic technologies can supplement flask experimentation for the ensemble investigation of formation mechanisms and design of semiconductor nanocrystals. We present selected studies outlining the preparation of quantum dots using microfluidic systems with integrated analytics. Such microfluidic reaction systems leverage the ability to extract real-time information regarding optical, structural, and compositional characteristics of quantum dots during nucleation and growth stages. The Account further highlights our recent research activities focused on the development and application of droplet-based microfluidics with integrated optical detection systems for the efficient and rapid screening of reaction conditions and a better understanding of the mechanisms of quantum dot synthesis. We describe the features and operation of fully automated microfluidic reactors and their subsequent application to high-throughput parametric screening of metal chalcogenides (CdSe, PbS, PbSe, CdSeTe), ternary and core/shell heavy metal-free quantum dots (CuInS 2 , CuInS 2 /ZnS), and all-inorganic perovskite nanocrystals (CsPbX 3 , X = Cl, Br, I) syntheses. Critically, concurrent absorption and photoluminescence measurements on millisecond to second time scales allow the extraction of basic parameters governing nanocrystal formation. Moreover, experimental data obtained from such microfluidic platforms can be directly supported by theoretical models of nucleation and growth. To this end, we also describe the use of metamodeling algorithms able to accurately predict optimized conditions of CdSe synthesis using a minimal number of sample parameters. Importantly, we discuss future challenges that must be addressed before microfluidic technologies are in a position to be widely adopted for the on-demand formation of nanocrystals. From a technology perspective, these challenges include the development of novel engineering platforms for the formation of complex architectures, the integration of monitoring systems able to harvest photophysical and structural information, the incorporation of continuous purification systems, and the application of optimization algorithms to multicomponent quantum dot systems.

Three-dimensional simulations of void collapse in energetic materials

NASA Astrophysics Data System (ADS)

Rai, Nirmal Kumar; Udaykumar, H. S.

2018-03-01

The collapse of voids in porous energetic materials leads to hot-spot formation and reaction initiation. This work advances the current knowledge of the dynamics of void collapse and hot-spot formation using 3D reactive void collapse simulations in HMX. Four different void shapes, i.e., sphere, cylinder, plate, and ellipsoid, are studied. For all four shapes, collapse generates complex three-dimensional (3D) baroclinic vortical structures. The hot spots are collocated with regions of intense vorticity. The differences in the vortical structures for the different void shapes are shown to significantly impact the relative sensitivity of the voids. Voids of high surface area generate hot spots of greater intensity; intricate, highly contorted vortical structures lead to hot spots of corresponding tortuosity and therefore enhanced growth rates of reaction fronts. In addition, all 3D voids are shown to be more sensitive than their two-dimensional (2D) counterparts. The results provide physical insights into hot-spot formation and growth and point to the limitations of 2D analyses of hot-spot formation.

Enhanced hydroxyl radical production by dihydroxybenzene-driven Fenton reactions: implications for wood biodegradation.

PubMed

Contreras, David; Rodríguez, Jaime; Freer, Juanita; Schwederski, Brigitte; Kaim, Wolfgang

2007-09-01

Brown rot fungi degrade wood, in initial stages, mainly through hydroxyl radicals (.OH) produced by Fenton reactions. These Fenton reactions can be promoted by dihydroxybenzenes (DHBs), which can chelate and reduce Fe(III), increasing the reactivity for different substrates. This mechanism allows the extensive degradation of carbohydrates and the oxidation of lignin during wood biodegradation by brown rot fungi. To understand the enhanced reactivity in these systems, kinetics experiments were carried out, measuring .OH formation by the spin-trapping technique of electron paramagnetic resonance spectroscopy. As models of the fungal DHBs, 1,2-dihydroxybenzene (catechol), 2,3-dihydroxybenzoic acid and 3,4-dihydroxybenzoic acid were utilized as well as 1,2-dihydroxy-3,5-benzenedisulfonate as a non-Fe(III)-reducing substance for comparison. Higher amounts and maintained concentrations of .OH were observed in the driven Fenton reactions versus the unmodified Fenton process. A linear correlation between the logarithms of complex stability constants and the .OH production was observed, suggesting participation of such complexes in the radical production.

Factors affecting catalysis of copper corrosion products in NDMA formation from DMA in simulated premise plumbing.

PubMed

Zhang, Hong; Andrews, Susan A

2013-11-01

This study investigated the effects of corrosion products of copper, a metal commonly employed in household plumbing systems, on N-nitrosodimethylamine (NDMA) formation from a known NDMA precursor, dimethylamine (DMA). Copper-catalyzed NDMA formation increased with increasing copper concentrations, DMA concentrations, alkalinity and hardness, but decreased with increasing natural organic matter (NOM) concentration. pH influenced the speciation of chloramine and the interactions of copper with DMA. The transformation of monochloramine (NH2Cl) to dichloramine and complexation of copper with DMA were involved in elevating the formation of NDMA by copper at pH 7.0. The inhibiting effect of NOM on copper catalysis was attributed to the rapid consumption of NH2Cl by NOM and/or the competitive complexation of NOM with copper to limit the formation of DMA-copper complexes. Hardness ions, as represented by Ca(2+), also competed with copper for binding sites on NOM, thereby weakening the inhibitory effect of NOM on NDMA formation. Common copper corrosion products also participated in these reactions but in different ways. Aqueous copper released from malachite [Cu2CO3(OH)2] was shown to promote NDMA formation while NDMA formation decreased in the presence of CuO, most likely due to the adsorption of DMA. Copyright © 2013 Elsevier Ltd. All rights reserved.

CAPS drives trans-SNARE complex formation and membrane fusion through syntaxin interactions.

PubMed

James, Declan J; Kowalchyk, Judith; Daily, Neil; Petrie, Matt; Martin, Thomas F J

2009-10-13

Ca(2+)-dependent activator protein for secretion (CAPS) is an essential factor for regulated vesicle exocytosis that functions in priming reactions before Ca(2+)-triggered fusion of vesicles with the plasma membrane. However, the precise events that CAPS regulates to promote vesicle fusion are unclear. In the current work, we reconstituted CAPS function in a SNARE-dependent liposome fusion assay using VAMP2-containing donor and syntaxin-1/SNAP-25-containing acceptor liposomes. The CAPS stimulation of fusion required PI(4,5)P(2) in acceptor liposomes and was independent of Ca(2+), but Ca(2+) dependence was restored by inclusion of synaptotagmin. CAPS stimulated trans-SNARE complex formation concomitant with the stimulation of full membrane fusion at physiological SNARE densities. CAPS bound syntaxin-1, and CAPS truncations that competitively inhibited syntaxin-1 binding also inhibited CAPS-dependent fusion. The results revealed an unexpected activity of a priming protein to accelerate fusion by efficiently promoting trans-SNARE complex formation. CAPS may function in priming by organizing SNARE complexes on the plasma membrane.

Improving Secondary Organic Aerosol (SOA) Models using Global Sensitivity Analysis and by Comparison to Chamber Data.

NASA Astrophysics Data System (ADS)

Miller, D. O.; Brune, W. H.

2017-12-01

Accurate estimates of secondary organic aerosol (SOA) from atmospheric models is a major research challenge due to the complexity of the chemical and physical processes involved in the SOA formation and continuous aging. The primary uncertainties of SOA models include those associated with the formation of gas-phase products, the conversion between gas phase and particle phase, the aging mechanisms of SOA, and other processes related to the heterogeneous and particle-phase reactions. To address this challenge, we us a modular modeling framework that combines both simple and near-explicit gas-phase reactions and a two-dimensional volatility basis set (2D-VBS) to simulate the formation and evolution of SOA. Global sensitivity analysis is used to assess the relative importance of the model input parameters. In addition, the model is compared to the measurements from the Focused Isoprene eXperiment at the California Institute of Technology (FIXCIT).

The first chiral diene-based metal-organic frameworks for highly enantioselective carbon-carbon bond formation reactions

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

Sawano, Takahiro; Ji, Pengfei; McIsaac, Alexandra R.

2016-02-01

We have designed the first chiral diene-based metal–organic framework (MOF), E₂-MOF, and postsynthetically metalated E₂-MOF with Rh(I) complexes to afford highly active and enantioselective single-site solid catalysts for C–C bond formation reactions. Treatment of E₂-MOF with [RhCl(C₂H₄)₂]₂ led to a highly enantioselective catalyst for 1,4-additions of arylboronic acids to α,β-unsaturated ketones, whereas treatment of E₂-MOF with Rh(acac)(C₂H₄)₂ afforded a highly efficient catalyst for the asymmetric 1,2-additions of arylboronic acids to aldimines. Interestingly, E₂-MOF·Rh(acac) showed higher activity and enantioselectivity than the homogeneous control catalyst, likely due to the formation of a true single-site catalyst in the MOF. E₂-MOF·Rh(acac) was also successfullymore » recycled and reused at least seven times without loss of yield and enantioselectivity.« less

Pentachlorophenol radical cations generated on Fe(III)-montmorillonite initiate octachlorodibenzo-p-dioxin formation in clays: DFT and FTIR studies

PubMed Central

Gu, Cheng; Liu, Cun; Johnston, Cliff T.; Teppen, Brian J.; Li, Hui; Boyd, Stephen A.

2011-01-01

Octachlorodibenzodioxin (OCDD) forms spontaneously from pentachlorophenol (PCP) on the surfaces of Fe(III)-saturated smectite clay (1). Here, we used in situ FTIR methods and quantum mechanical calculations to determine the mechanism by which this reaction is initiated. As the clay was dehydrated, vibrational spectra showed new peaks that grew and then reversibly disappeared as the clay rehydrated. First principle DFT calculations of hydrated Fe-PCP clusters reproduced these transient FTIR peaks when inner-sphere complexation and concomitant electron transfer produced Fe(II) and PCP radical cations. Thus, our experimental (FTIR) and theoretical (quantum mechanical) results mutually support the hypothesis that OCDD formation on Fe-smectite surfaces is initiated by the reversible formation of metastable PCP radical cations via single electron transfer from PCP to Fe(III). The negatively charged clay surface apparently selects for this reaction mechanism by stabilizing PCP radical cations. PMID:21254769

Simulation studies of the Cl- + CH3I SN2 nucleophilic substitution reaction: Comparison with ion imaging experiments

NASA Astrophysics Data System (ADS)

Zhang, Jiaxu; Lourderaj, Upakarasamy; Sun, Rui; Mikosch, Jochen; Wester, Roland; Hase, William L.

2013-03-01

In the previous work of Mikosch et al. [Science 319, 183 (2008)], 10.1126/science.1150238, ion imaging experiments were used to study the Cl- + CH3I → ClCH3 + I- reaction at collision energies Erel of 0.39, 0.76, 1.07, and 1.9 eV. For the work reported here MP2(fc)/ECP/d direct dynamics simulations were performed to obtain an atomistic understanding of the experiments. There is good agreement with the experimental product energy and scattering angle distributions for the highest three Erel, and at these energies 80% or more of the reaction is direct, primarily occurring by a rebound mechanism with backward scattering. At 0.76 eV there is a small indirect component, with isotropic scattering, involving formation of the pre- and post-reaction complexes. All of the reaction is direct at 1.07 eV. Increasing Erel to 1.9 eV opens up a new indirect pathway, the roundabout mechanism. The product energy is primarily partitioned into relative translation for the direct reactions, but to CH3Cl internal energy for the indirect reactions. The roundabout mechanism transfers substantial energy to CH3Cl rotation. At Erel = 0.39 eV both the experimental product energy partitioning and scattering are statistical, suggesting the reaction is primarily indirect with formation of the pre- and post-reaction complexes. However, neither MP2 nor BhandH/ECP/d simulations agree with experiment and, instead, give reaction dominated by direct processes as found for the higher collision energies. Decreasing the simulation Erel to 0.20 eV results in product energy partitioning and scattering which agree with the 0.39 eV experiment. The sharp transition from a dominant direct to indirect reaction as Erel is lowered from 0.39 to 0.20 eV is striking. The lack of agreement between the simulations and experiment for Erel = 0.39 eV may result from a distribution of collision energies in the experiment and/or a shortcoming in both the MP2 and BhandH simulations. Increasing the reactant rotational temperature from 75 to 300 K for the 1.9 eV collisions, results in more rotational energy in the CH3Cl product and a larger fraction of roundabout trajectories. Even though a ClCH3-I- post-reaction complex is not formed and the mechanistic dynamics are not statistical, the roundabout mechanism gives product energy partitioning in approximate agreement with phase space theory.

A mechanistic and kinetic study on the formation of PBDD/Fs from PBDEs.

PubMed

Altarawneh, Mohammednoor; Dlugogorski, Bogdan Z

2013-05-21

This study presents a detailed mechanistic and kinetic investigation that explains the experimentally observed high yields of formation of polybrominated dibenzo-p-dioxins and dibenzofurans (PBDD/Fs) from the polybrominated diphenyl ethers (PBDEs), commonly deployed in brominated flame retardants (BFRs). Theoretical calculations involved the accurate meta hybrid functional of M05-2X. The previously suggested pathways of debromination and generation of bromophenols/bromophenoxys/bromobenzenes were found to be unimportant corridors for the formation of PBDD/Fs. A loss of an ortho Br or H atom from PBDEs, followed by a ring-closure reaction, is the most accessible pathway for the production of PBDFs via modest reaction barriers. The initially formed peroxy-type adduct (RO₂) is found to evolve in a complex, nevertheless very exoergic, mechanism to produce PBDDs. Results indicate that, degree and pattern of bromination, in the vicinity of the ether oxygen bridge, has a minor influence on governing mechanisms and that even fully brominated isomers of BFRs are capable of forming PBDD/Fs. We thoroughly discuss bimolecular reactions of PBDEs with Br and H, as well as the Br-displacement reaction by triplet oxygen. The rate of the Br-displacement reaction significantly exceeds that of the unimolecular inititiation reactions due to loss of ortho Br or H. Results presented herein address conclusively the intriguing question of how PBDEs form PBDD/Fs, a matter that has been in the center of much debate among environmental chemists.

Kinetic Evidence of an Apparent Negative Activation Enthalpy in an Organocatalytic Process

PubMed Central

Han, Xiao; Lee, Richmond; Chen, Tao; Luo, Jie; Lu, Yixin; Huang, Kuo-Wei

2013-01-01

A combined kinetic and computational study on our tryptophan-based bifunctional thiourea catalyzed asymmetric Mannich reactions reveals an apparent negative activation enthalpy. The formation of the pre-transition state complex has been unambiguously confirmed and these observations provide an experimental support for the formation of multiple hydrogen bonding network between the substrates and the catalyst. Such interactions allow the creation of a binding cavity, a key factor to install high enantioselectivity. PMID:23990028

Forming metal-intermetallic or metal-ceramic composites by self-propagating high-temperature reactions

DOEpatents

Rawers, James C.; Alman, David E.; Petty, Jr., Arthur V.

1996-01-01

Industrial applications of composites often require that the final product have a complex shape. In this invention intermetallic or ceramic phases are formed from sheets of unreacted elemental metals. The process described in this invention allows the final product shape be formed prior to the formation of the composite. This saves energy and allows formation of shaped articles of metal-intermetallic composites composed of brittle materials that cannot be deformed without breaking.

The role of shock waves in the formation of organic compounds in the primeval atmosphere.

NASA Technical Reports Server (NTRS)

Hochstim, A. R.

1971-01-01

It is shown that shock waves from micrometeorites, meteors, meteorites, and thunder are of interest from the viewpoint of contributing significantly to the total accumulation of organic compounds in primeval times. The multitude of recombination reactions occurring in connection with shock waves could be an important factor in the formation of more complex compounds. Lower bound kinetic energies available to micrometeorites, cometary meteorites, stony and iron meteorites are calculated.

Cationic cluster formation versus disproportionation of low-valent indium and gallium complexes of 2,2'-bipyridine

PubMed Central

Lichtenthaler, Martin R.; Stahl, Florian; Kratzert, Daniel; Heidinger, Lorenz; Schleicher, Erik; Hamann, Julian; Himmel, Daniel; Weber, Stefan; Krossing, Ingo

2015-01-01

Group 13 MI compounds often disproportionate into M0 and MIII. Here, however, we show that the reaction of the MI salt of the weakly coordinating alkoxyaluminate [GaI(C6H5F)2]+[Al(ORF)4]− (RF=C(CF3)3) with 2,2'-bipyridine (bipy) yields the paramagnetic and distorted octahedral [Ga(bipy)3]2+•{[Al(ORF)4]−}2 complex salt. While the latter appears to be a GaII compound, both, EPR and DFT investigations assign a ligand-centred [GaIII{(bipy)3}•]2+ radical dication. Surprisingly, the application of the heavier homologue [InI(C6H5F)2]+[Al(ORF)4]− leads to aggregation and formation of the homonuclear cationic triangular and rhombic [In3(bipy)6]3+, [In3(bipy)5]3+ and [In4(bipy)6]4+ metal atom clusters. Typically, such clusters are formed under strongly reductive conditions. Analysing the unexpected redox-neutral cationic cluster formation, DFT studies suggest a stepwise formation of the clusters, possibly via their triplet state and further investigations attribute the overall driving force of the reactions to the strong In−In bonds and the high lattice enthalpies of the resultant ligand stabilized [M3]3+{[Al(ORF)4]−}3 and [M4]4+{[Al(ORF)4]−}4 salts. PMID:26478464

Reaction of iminopropadienones with amines: mechanistic explanations of zwitterionic intermediate, ketene and ketenimine formation.

PubMed

Koch, Rainer; Finnerty, Justin J; Bruhn, Torsten; Borget, Fabien; Wentrup, Curt

2008-09-25

The complex reaction of thermally generated iminopropadienones with amines in the gas phase and upon matrix deposition and its varying product composition is investigated using density functional theory. In the high energy gas phase addition a single amine molecule reacts readily with iminopropadienone with the decisive step being a 1,3-hydrogen shift and activation barriers of at least 100 kJ/mol. In accordance with the experiment, the formation of ketenes is favored. In the condensed phase of an amine matrix, the utilization of amine dimers both as reagents and as explicit solvents lowers the activation energy required to a feasible 20-30 kJ/mol and predicts ketenimines as the main products, as observed experimentally.

Highly Selective Coupling of Alkenes and Aldehydes Catalyzed by NHC–Ni–P(OPh)3: Synergy Between a Strong σ-Donor and a Strong π-Acceptor**

PubMed Central

Ho, Chun-Yu; Jamison, Timothy F.

2011-01-01

Both a strong electron donor (IPr) and a strong electron acceptor (P(OPh)3) are necessary for a highly selective, nickel-catalyzed coupling reaction between alkenes, aldehydes, and silyltriflates. Without the phosphite, catalysis is not observed and several side reactions are observed. The phosphite appears to suppress the formation of these byproducts and rescue the catalytic cycle by accelerating reductive elimination from an (IPr–Ni–H)(OTf) complex. PMID:17154217

Mechanism of Ras Activation by TGFBeta

DTIC Science & Technology

2002-07-01

32P-labeled oligonucleotides to each reaction. The reactions were incubated at room temperature for 20 min. For supershift assays, 1 p\\ of antibodies ...formation of this TGFß3-inducible complex. In addition, as shown in Fig. 4A, left side, addition of either a pan-Fos or pan-Jun antibody completely blocked...addition to c-Jun 30770 A Ras/MAPK/Smads and TGFß1 Production RasNI7E3 -RasN17 +RiisN17 Antibodies TGFß I " - Jun Fits Ig(J

Preparation of cell-free splicing extracts from Saccharomyces cerevisiae.

PubMed

Ares, Manuel

2013-10-01

Much of our understanding of the mechanism of splicing comes from the analysis of cell extracts able to carry out splicing complex formation and splicing reactions in vitro using exogenously added synthetic model pre-mRNA transcripts. This protocol describes the preparation of whole-cell extracts from the budding yeast Saccharomyces cerevisiae. These extracts can be used to dissect the biochemical steps of the splicing reaction and to determine the macromolecules, cofactors, and substrate features necessary for successful splicing.

Millimeter and Submillimeter Studies of O(^1D) Insertion Reactions to Form Molecules of Astrophysical Interest

NASA Astrophysics Data System (ADS)

Hays, Brian; Wehres, Nadine; Deprince, Bridget Alligood; Roy, Althea A. M.; Laas, Jacob; Widicus Weaver, Susanna L.

2015-06-01

While both the number of detected interstellar molecules and their chemical complexity continue to increase, understanding of the processes leading to their formation is lacking. Our research group combines laboratory spectroscopy, observational astronomy, and astrochemical modeling for an interdisciplinary examination of the chemistry of star and planet formation. This talk will focus on our laboratory studies of O(^1D) insertion reactions with organic molecules to produce molecules of astrophysical interest. By employing these reactions in a supersonic expansion, we are able to produce interstellar organic reaction intermediates that are unstable under terrestrial conditions; we then probe the products using millimeter and submillimeter spectroscopy. We benchmarked this setup using the well-studied O(^1D) + methane reaction to form methanol. After optimizing methanol production, we moved on to study the O(^1D) + ethylene reaction to form vinyl alcohol (CH_2CHOH), and the O(^1D) + methyl amine reaction to form aminomethanol (NH_2CH_2OH). Vinyl alcohol measurements have now been extended up to 450 GHz, and the associated spectral analysis is complete. A possible detection of aminomethanol has also been made, and continued spectral studies and analysis are underway. We will present the results from these experiments and discuss future applications of these molecular and spectroscopic techniques.

Associative charge transfer reactions. Temperature effects and mechanism of the gas-phase polymerization of propene initiated by a benzene radical cation.

PubMed

Ibrahim, Yehia; Meot-Ner Mautner, Michael; El-Shall, M Samy

2006-07-13

In associative charge transfer (ACT) reactions, a core ion activates ligand molecules by partial charge transfer. The activated ligand polymerizes, and the product oligomer takes up the full charge from the core ion. In the present system, benzene(+*) (Bz(+*)) reacts with two propene (Pr) molecules to form a covalently bonded ion, C(6)H(6)(+*) + 2 C(3)H(6) --> C(6)H(12)(+*) + C(6)H(6). The ACT reaction is activated by a partial charge transfer from Bz(+*) to Pr in the complex, and driven to completion by the formation of a covalent bond in the polymerized product. An alternative channel forms a stable association product (Bz.Pr)(+*), with an ACT/association product ratio of 60:40% that is independent of pressure and temperature. In contrast to the Bz(+*)/propene system, ACT polymerization is not observed in the Bz(+*)/ethylene (Et) system since charge transfer in the Bz(+*)(Et) complex is inefficient to activate the reaction. The roles of charge transfer in these complexes are verified by ab initio calculations. The overall reaction of Bz(+*) with Pr follows second-order kinetics with a rate constant of k (304 K) = 2.1 x 10(-12) cm(3) s(-1) and a negative temperature coefficient of k = aT(-5.9) (or an activation energy of -3 kcal/mol). The kinetic behavior is similar to sterically hindered reactions and suggests a [Bz(+*) (Pr)]* activated complex that proceeds to products through a low-entropy transition state. The temperature dependence shows that ACT reactions can reach a unit collision efficiency below 100 K, suggesting that ACT can initiate polymerization in cold astrochemical environments.

Bonds Between Metal Atoms: A New Mode of Transition Metal Chemistry.

ERIC Educational Resources Information Center

Cotton, F. Albert; Chisholm, Malcolm H.

1982-01-01

Discusses polynuclear metal clusters (containing two or more metal atoms bonded to one another as well as to nonmetallic elements), including their formation and applications. Studies of bonds between metal atoms reveal superconductors, organic-reaction catalysts, and photosensitive complexes that may play a role in solar energy. (JN)

Origin of Complexity in Multicellular Organisms

NASA Astrophysics Data System (ADS)

Furusawa, Chikara; Kaneko, Kunihiko

2000-06-01

Through extensive studies of dynamical system modeling cellular growth and reproduction, we find evidence that complexity arises in multicellular organisms naturally through evolution. Without any elaborate control mechanism, these systems can exhibit complex pattern formation with spontaneous cell differentiation. Such systems employ a ``cooperative'' use of resources and maintain a larger growth speed than simple cell systems, which exist in a homogeneous state and behave ``selfishly.'' The relevance of the diversity of chemicals and reaction dynamics to the growth of a multicellular organism is demonstrated. Chaotic biochemical dynamics are found to provide the multipotency of stem cells.

Preparation of microcapsules by complex coacervation of gum Arabic and chitosan.

PubMed

Butstraen, Chloé; Salaün, Fabien

2014-01-01

Gum Arabic-chitosan microcapsules containing a commercially available blend of triglycerides (Miglyol 812 N) as core phase were synthesized by complex coacervation. This study was conducted to clarify the influence of different parameters on the encapsulation process, i.e. during the emulsion formation steps and during the shell formation, using conductometry, zeta potential, surface and interface tension measurement and Fourier-transform infrared spectroscopy. By carefully analyzing the influencing factors including phase volume ratio, stirring rate and time, pH, reaction time, biopolymer ratio and crosslinking effect, the optimum synthetic conditions were found out. For the emulsion step, the optimum phase volume ratio chosen was 0.10 and an emulsion time of 15 min at 11,000 rpm was selected. The results also indicated that the optimum formation of these complexes appears at a pH value of 3.6 and a weight ratio of chitosan to gum Arabic mixtures of 0.25. Copyright © 2013 Elsevier Ltd. All rights reserved.

Vacancy clustering and its dissociation process in electroless deposited copper films studied by monoenergetic positron beams

NASA Astrophysics Data System (ADS)

Uedono, A.; Yamashita, Y.; Tsutsui, T.; Dordi, Y.; Li, S.; Oshima, N.; Suzuki, R.

2012-05-01

Positron annihilation was used to probe vacancy-type defects in electroless deposited copper films. For as-deposited films, two different types of vacancy-type defects were found to coexist; these were identified as vacancy aggregates (V3-V4) and larger vacancy clusters (˜V10). After annealing at about 200 °C, the defects started to diffuse toward the surface and aggregate. The same tendency has been observed for sulfur only, suggesting the formation of complexes between sulfur and vacancies. The defect concentration near the Cu/barrier-metal interface was high even after annealing above 600 °C, and this was attributed to an accumulation of vacancy-impurity complexes. The observed defect reactions were attributed to suppression of the vacancy diffusion to sinks through the formation of impurity-vacancy complexes. It was shown that electroless plating has a high potential to suppress the formation of voids/hillocks caused by defect migration.

Protonation of a peroxodiiron(III) complex and conversion to a diiron(III/IV) intermediate: implications for proton-assisted O-O bond cleavage in nonheme diiron enzymes.

PubMed

Cranswick, Matthew A; Meier, Katlyn K; Shan, Xiaopeng; Stubna, Audria; Kaizer, Jószef; Mehn, Mark P; Münck, Eckard; Que, Lawrence

2012-10-01

Oxygenation of a diiron(II) complex, [Fe(II)(2)(μ-OH)(2)(BnBQA)(2)(NCMe)(2)](2+) [2, where BnBQA is N-benzyl-N,N-bis(2-quinolinylmethyl)amine], results in the formation of a metastable peroxodiferric intermediate, 3. The treatment of 3 with strong acid affords its conjugate acid, 4, in which the (μ-oxo)(μ-1,2-peroxo)diiron(III) core of 3 is protonated at the oxo bridge. The core structures of 3 and 4 are characterized in detail by UV-vis, Mössbauer, resonance Raman, and X-ray absorption spectroscopies. Complex 4 is shorter-lived than 3 and decays to generate in ~20% yield of a diiron(III/IV) species 5, which can be identified by electron paramagnetic resonance and Mössbauer spectroscopies. This reaction sequence demonstrates for the first time that protonation of the oxo bridge of a (μ-oxo)(μ-1,2-peroxo)diiron(III) complex leads to cleavage of the peroxo O-O bond and formation of a high-valent diiron complex, thereby mimicking the steps involved in the formation of intermediate X in the activation cycle of ribonucleotide reductase.

MurD ligase from E. coli: Tetrahedral intermediate formation study by hybrid quantum mechanical/molecular mechanical replica path method.

PubMed

Perdih, Andrej; Hodoscek, Milan; Solmajer, Tom

2009-02-15

MurD (UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase), a three-domain bacterial protein, catalyses a highly specific incorporation of D-glutamate to the cytoplasmic intermediate UDP-N-acetyl-muramoyl-L-alanine (UMA) utilizing ATP hydrolysis to ADP and P(i). This reaction is part of a biosynthetic path yielding bacterial peptidoglycan. On the basis of structural studies of MurD complexes, a stepwise catalytic mechanism was proposed that commences with a formation of the acyl-phosphate intermediate, followed by a nucleophilic attack of D-glutamate that, through the formation of a tetrahedral reaction intermediate and subsequent phosphate dissociation, affords the final product, UDP-N-acetyl-muramoyl-L-alanine-D-glutamate (UMAG). A hybrid quantum mechanical/molecular mechanical (QM/MM) molecular modeling approach was utilized, combining the B3LYP QM level of theory with empirical force field simulations to evaluate three possible reaction pathways leading to tetrahedral intermediate formation. Geometries of the starting structures based on crystallographic experimental data and tetrahedral intermediates were carefully examined together with a role of crucial amino acids and water molecules. The replica path method was used to generate the reaction pathways between the starting structures and the corresponding tetrahedral reaction intermediates, offering direct comparisons with a sequential kinetic mechanism and the available structural data for this enzyme. The acquired knowledge represents new and valuable information to assist in the ongoing efforts leading toward novel inhibitors of MurD as potential antibacterial drugs. (c) 2008 Wiley-Liss, Inc.

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

Kanzler, Charlotte R.; Lian, Peng; Trainer, Emma Leverich

Alkylated mercury species (monomethylmercury, MeHg, and dimethylmercury, DMeHg) exhibit significant bioaccumulation, and pose significant risks to ecosystems and human health. Although decades of research have been devoted to understanding MeHg formation and degradation, little is known about the DMeHg formation in aquatic systems. Here, we combine complementary experimental and computational approaches to examine MeHg speciation and DMeHg formation in sulfidic aqueous solutions, with an emphasis on the formation and decomposition of the binuclear bis(methylmercuric(II)) sulfide complex (CH3Hg)2S. Experimental data indicate that the reaction 2CH3Hg+ + HS- = (CH3Hg)2S has a log K = 26.0. Thus, the binuclear (CH3Hg)2S complex ismore » likely to be the dominant MeHg species under high MeHg concentrations typically used in experimental investigations of MeHg degradation by sulfate-reducing bacteria (SRB). Our finding of a significant abiotic removal mechanism for MeHg in sulfidic solutions through the formation of relatively insoluble (CH3Hg)2S suggests careful reexamination of reported “oxidative demethylation” of MeHg by SRB and perhaps other obligate anaerobes. We provide evidence for slow decomposition of (CH3Hg)2S to DMeHg and HgS, with a first-order rate constant k = 1.5 0.4 x 10-6 h-1. Quantum chemical calculations suggest that the reaction proceeds by a novel mechanism involving rearrangement of the (CH3Hg)2S complex facilitated by strong Hg-Hg interactions that activate a methyl group for intramolecular transfer. Predictions of DMeHg formation rates under a variety of field and laboratory conditions indicate that this pathway for DMeHg formation will be significant in laboratory experiments utilizing high MeHg concentrations, favoring (CH3Hg)2S formation. In natural systems with relatively high MeHg/[H2S]T ratios (the oxic/anoxic interface, for example), DMeHg production may be observed, and warrants further investigation.Experimental and computational evidence show that dimethylmercury is produced from decomposition of bis(methylmercury(ii)) sulfide.« less

Synthesis, characterization, spectroscopic and antioxidation studies of Cu(II)-morin complex

NASA Astrophysics Data System (ADS)

Panhwar, Qadeer Khan; Memon, Shahabuddin; Bhanger, M. I.

2010-04-01

Complex formation between copper (II) sulfate and morin (3,5,7,2',4'-pentahydroxyflavone) have been studied in methanol. Structure of the complex was determined through various analytical techniques including UV-vis, IR, 1H NMR, thermal, gravimetric and elemental analyses. The stoichiometric ratio for the reaction between the flavonoid and the metal ion in methanol has been determined by Job's method and elemental analysis for metal content of complex by titration with EDTA, which confirm that morin forms a 1:1 metal:ligand complex. 1H NMR study reveals that, 3OH and 4CO groups of morin take part in complexation with a copper ion. Individual stress was given to the site of central ion and composition of the complex. Antioxidant activity of the complex was evaluated by using 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging method, which showed that the antioxidant activity of complexed morin has higher value as compared to the free morin. Moreover, it was observed that the metal complex is sufficiently stable as well as the data indicates the spontaneous formation of complex (-Δ G) that is exothermic in nature (-Δ H) and entropically unfavourable (-Δ S).

Mechanistic investigations of CO-photoextrusion and oxidative addition reactions of early transition-metal carbonyls: (η(5)-C5H5)M(CO)4 (M = V, Nb, Ta).

PubMed

Su, Shih-Hao; Su, Ming-Der

2016-06-28

The mechanisms for the photochemical Si-H bond activation reaction are studied theoretically using a model system of the group 5 organometallic compounds, η(5)-CpM(CO)4 (M = V, Nb, and Ta), with the M06-2X method and the Def2-SVPD basis set. Three types of reaction pathways that lead to final insertion products are identified. The structures of the intersystem crossings, which play a central role in these photo-activation reactions, are determined. The intermediates and transitional structures in either the singlet or triplet states are also calculated to provide a mechanistic explanation of the reaction pathways. All of the potential energy surfaces for the group 5 η(5)-CpM(CO)4 complexes are quite similar. In particular, the theoretical evidence suggests that after irradiation using light, η(5)-CpM(CO)4 quickly loses one CO ligand to yield two tricarbonyls, in either the singlet or the triplet states. The triplet tricarbonyl 16-electron intermediates, ([η(5)-CpM(CO)3](3)), play a key role in the formation of the final oxidative addition product, η(5)-CpM(CO)3(H)(SiMe3). However, the singlet counterparts, ([η(5)-CpM(CO)3](1)), play no role in the formation of the final product molecule, but their singlet metal centers interact weakly with solvent molecules ((Me3)SiH) to produce alkyl-solvated organometallic complexes, which are observable experimentally. This theoretical evidence is in accordance with the available experimental observations.

Adventures on the C 3H 5O potential energy surface: OH+propyne, OH+allene and related reactions

DOE PAGES

Zádor, Judit; Miller, James A.

2014-06-25

We mapped out the stationary points and the corresponding conformational space on the C 3H 5O potential energy surface relevant for the OH + allene and OH + propyne reactions systematically and automatically using the KinBot software at the UCCSD(T)-F12b/cc-pVQZ-F12//M06-2X/6-311++G(d,p) level of theory. We used RRKM-based 1-D master equations to calculate pressure- and temperature-dependent, channel-specific phenomenological rate coefficients for the bimolecular reactions propyne + OH and allene + OH, and for the unimolecular decomposition of the CH 3CCHOH, CH 3C(OH)CH, CH 2CCH 2OH, CH 2C(OH)CH 2 primary adducts, and also for the related acetonyl, propionyl, 2-methylvinoxy, and 3-oxo-1-propyl radicals. Themore » major channel of the bimolecular reactions at high temperatures is the formation propargyl + H 2O, which makes the title reactions important players in soot formation at high temperatures. However, below ~1000 K the chemistry is more complex, involving the competition of stabilization, isomerization and dissociation processes. We found that the OH addition to the central carbon of allene has a particularly interesting and complex pressure dependence, caused by the low-lying exit channel to form ketene + CH 3 bimolecular products. In this study, we compared our results to a wide range of experimental data and assessed possible uncertainties arising from certain aspects of the theoretical framework.« less

Spectroscopic investigation confirms retaining the pristine nature of single-walled carbon nanotubes on dissolution in aniline

NASA Astrophysics Data System (ADS)

Singha, Somdutta; Ghosh, Swapankumar

2017-09-01

Carbon nanotubes in all forms are very much insoluble in both organic and inorganic solvents due to its high agglomeration and entangled morphology. General methods for dissolution of single-walled carbon nanotubes (SWNTs) are mostly associated with complexation or polymerization or addition of macromolecules which change the physical or chemical properties of SWNTs and the pristine nature of SWNTs is lost. Dissolution of SWNTs in a solvent like aniline is practiced here which is a very simple reaction method. Here aniline is capable to form a SWNT-aniline charge transfer complex without attachment of macromolecules or polymer which is also soluble in other organic solvents. Solvation of SWNTs by this method is also capable of maintaining the similarity between the structure of SWNTs before and after the dissolution, which means that the pristine nature of SWNTs is preserved. Formation of charge transfer complex in this reaction has been proven by UV-Vis/NIR absorption and photoluminescence spectroscopy. Raman spectroscopy and electron microscopy (FESEM and TEM) are the evidences for protection of the pristine nature of SWNTs even after high-temperature complexation reaction with aniline and also after solubilization in organic solvents.

Formation of doubly and triply bonded unsaturated compounds HCN, HNC, and CH2NH via N + CH4 low-temperature solid state reaction: from molecular clouds to solar system objects

NASA Astrophysics Data System (ADS)

Mencos, Alejandro; Krim, Lahouari

2018-06-01

We show in the current study carried out in solid phase at cryogenic temperatures that methane (CH4) ice exposed to nitrogen atoms is a source of two acids HCN, HNC, and their corresponding hydrogenated unsaturated species CH2NH, in addition to CH3, C2H6, CN-, and three nitrogen hydrides NH, NH2, and NH3. The solid state N + CH4 reaction taken in the ground state seems to be strongly temperature dependent. While at temperatures lower than 10 K only CH3, NH, NH2, and NH3 species formation is promoted due to CH bond dissociation and NH bond formation, stable compounds with CN bonds are formed at temperatures ranged between 10 and 40 K. Many of these reaction products, resulting from CH4 + N reaction, have already been observed in N2-rich regions such as the atmospheres of Titan, Kuiper belt objects, and molecular clouds of the interstellar medium. Our results show the power of the solid state N-atom chemistry in the transformation of simple astrochemical relevant species, such as CH4 molecules and N atoms into complex organic molecules which are also potentially prebiotic species.

Kinetic mechanism of the dimeric ATP sulfurylase from plants

PubMed Central

Ravilious, Geoffrey E.; Herrmann, Jonathan; Goo Lee, Soon; Westfall, Corey S.; Jez, Joseph M.

2013-01-01

In plants, sulfur must be obtained from the environment and assimilated into usable forms for metabolism. ATP sulfurylase catalyses the thermodynamically unfavourable formation of a mixed phosphosulfate anhydride in APS (adenosine 5′-phosphosulfate) from ATP and sulfate as the first committed step of sulfur assimilation in plants. In contrast to the multi-functional, allosterically regulated ATP sulfurylases from bacteria, fungi and mammals, the plant enzyme functions as a mono-functional, non-allosteric homodimer. Owing to these differences, here we examine the kinetic mechanism of soybean ATP sulfurylase [GmATPS1 (Glycine max (soybean) ATP sulfurylase isoform 1)]. For the forward reaction (APS synthesis), initial velocity methods indicate a single-displacement mechanism. Dead-end inhibition studies with chlorate showed competitive inhibition versus sulfate and non-competitive inhibition versus APS. Initial velocity studies of the reverse reaction (ATP synthesis) demonstrate a sequential mechanism with global fitting analysis suggesting an ordered binding of substrates. ITC (isothermal titration calorimetry) showed tight binding of APS to GmATPS1. In contrast, binding of PPi (pyrophosphate) to GmATPS1 was not detected, although titration of the E•APS complex with PPi in the absence of magnesium displayed ternary complex formation. These results suggest a kinetic mechanism in which ATP and APS are the first substrates bound in the forward and reverse reactions, respectively. PMID:23789618

Pulse radiolytic study of the oxidation reactions of uric acid in presence of bovine serum albumin. Evidence of possible complex formation in the transient state

NASA Astrophysics Data System (ADS)

Adhikari, S.; Joshi, R.; Gopinathan, C.

1997-01-01

The pulse radiolytic and spectrophotometric study of uric acid in presence of bovine serum albumin (BSA) has been carried out. In the spectrophotometric study there is no evidence for ground state interaction between BSA and uric acid. The oxidation reactions of uric acid in presence and absence of BSA employing CCl 3OO and Br radicals have been carried out. In a composition of equal concentration of uric acid and BSA, the CCl 3OO and Br radicals produce a transient absorption spectrum which show two peaks at 330 and 360 nm. The peak at 360 nm is ascribed due to weak complex formation between semioxidised BSA and uric acid radicals. The rate constant of CCl 3OO . radical with uric acid increases with the increase in BSA concentration which is explained as protection of BSA by uric acid from radical attack. The Br radical attacks uric acid and BSA in a manner similar to CCl 3OO radical. The bimolecular rate constants for the reaction of Br radical with BSA and uric acid have been found as 2.9 × 10 10 dm 3 mol -1 s -1 and 6.33 × 10 9 dm 3 mol -1 s -, respectively.

From a Dy(III) single molecule magnet (SMM) to a ferromagnetic [Mn(II)Dy(III)Mn(II)] trinuclear complex.

PubMed

Bhunia, Asamanjoy; Gamer, Michael T; Ungur, Liviu; Chibotaru, Liviu F; Powell, Annie K; Lan, Yanhua; Roesky, Peter W; Menges, Fabian; Riehn, Christoph; Niedner-Schatteburg, Gereon

2012-09-17

The Schiff base compound 2,2'-{[(2-aminoethyl)imino]bis[2,1-ethanediyl-nitriloethylidyne]}bis-2-hydroxy-benzoic acid (H(4)L) as a proligand was prepared in situ. This proligand has three potential coordination pockets which make it possible to accommodate from one to three metal ions allowing for the possible formation of mono-, di-, and trinuclear complexes. Reaction of in situ prepared H(4)L with Dy(NO(3))(3)·5H(2)O resulted in the formation of a mononuclear complex [Dy(H(3)L)(2)](NO(3))·(EtOH)·8(H(2)O) (1), which shows SMM behavior. In contrast, reaction of in situ prepared H(4)L with Mn(ClO(4))(2)·6H(2)O and Dy(NO(3))(3)·5H(2)O in the presence of a base resulted in a trinuclear mixed 3d-4f complex (NHEt(3))(2)[Dy{Mn(L)}(2)](ClO(4))·2(H(2)O) (2). At low temperatures, compound 2 is a weak ferromagnet. Thus, the SMM behavior of compound 1 can be switched off by incorporating two Mn(II) ions in close proximity either side of the Dy(III). This quenching behavior is ascribed to the presence of the weak ferromagnetic interactions between the Mn(II) and Dy(III) ions, which at T > 2 K act as a fluctuating field causing the reversal of magnetization on the dysprosium ion. Mass spectrometric ion signals related to compounds 1 and 2 were both detected in positive and negative ion modes via electrospray ionization mass spectrometry. Hydrogen/deuterium exchange (HDX) reactions with ND(3) were performed in a FT-ICR Penning-trap mass spectrometer.

Study of complex formation of 5,5'-(2 E, 2' E)-2,2'-(ethane-1,2-diylidene)bis(hydrazine-1-yl-2-ylidene)bis(4-amino-4H-1,2,4-triazole-3-thiol) (HYT) macrocyclic ligand with Cd2+ cation in non-aqueous solution by spectroscopic and conductometric methods

NASA Astrophysics Data System (ADS)

Mallaekeh, Hassan; Shams, Alireza; Shaker, Mohammad; Bahramzadeh, Ehsan; Arefi, Donya

2014-12-01

In this paper the complexation reaction of the 5,5'-(2 E,2' E)-2,2'-(ethane-1,2-diylidene)bis(hydrazine-1-yl-2-ylidene)bis(4-amino-4H-1,2,4-triazole-3-thiol) ligand (HYT) with Cd2+ education was studied in some binary mixtures of methanol (MeOH), n-propanol (PrOH) and dimethyl-formamide (DMF) at different temperatures using the conductometry and spectrophotometry. The stability constants of the complex was determined using a GENPLOT computer program. The conductance data and absorbance-mole ratio plots show that in all solvent systems, the stoichiometry of the complex formed between (HYT) and Cd2+ cation is 1: 1. The obtained results show that the stability of (HYT)-Cd complex is sensitive to the mixed solvents composition. The values of thermodynamic parameters (Δ G ∘, Δ H ∘, and Δ S ∘) for formation of (HYT)-Cd complex were obtained from temperature dependence of the stability constant using the van't Hoff plots. The results show that in most cases, the complex are enthalpy destabilized but entropy stabilized and the complex formation is affected by pH, time, temperature and the nature of the solvent.

Interactions of Enolizable Barbiturate Dyes.

PubMed

Schade, Alexander; Schreiter, Katja; Rüffer, Tobias; Lang, Heinrich; Spange, Stefan

2016-04-11

The specific barbituric acid dyes 1-n-butyl-5-(2,4-dinitro-phenyl) barbituric acid and 1-n-butyl-5-{4-[(1,3-dioxo-1H-inden-(3 H)-ylidene)methyl]phenyl}barbituric acid were used to study complex formation with nucleobase derivatives and related model compounds. The enol form of both compounds shows a strong bathochromic shift of the UV/Vis absorption band compared to the rarely coloured keto form. The keto-enol equilibria of the five studied dyes are strongly dependent on the properties of the environment as shown by solvatochromic studies in ionic liquids and a set of organic solvents. Enol form development of the barbituric acid dyes is also associated with alteration of the hydrogen bonding pattern from the ADA to the DDA type (A=hydrogen bond acceptor site, D=donor site). Receptor-induced altering of ADA towards DDA hydrogen bonding patterns of the chromophores are utilised to study supramolecular complex formation. As complementary receptors 9-ethyladenine, 1-n-butylcytosine, 1-n-butylthymine, 9-ethylguanidine and 2,6-diacetamidopiridine were used. The UV/Vis spectroscopic response of acid-base reaction compared to supramolecular complex formation is evaluated by (1)H NMR titration experiments and X-ray crystal structure analyses. An increased acidity of the barbituric acid derivative promotes genuine salt formation. In contrast, supramolecular complex formation is preferred for the weaker acidic barbituric acid. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

η(6) -Arene-Zirconium-PNP-Pincer Complexes: Mechanism of Their Hydrogenolytic Formation and Their Reactivity as Zirconium(II) Synthons.

PubMed

Plundrich, Gudrun T; Wadepohl, Hubert; Clot, Eric; Gade, Lutz H

2016-06-27

The cyclometalated monobenzyl complexes [(Cbzdiphos(R) -CH)ZrBnX] 1 (iPr) Cl and 1 (Ph) I reacted with dihydrogen (10 bar) to yield the η(6) -toluene complexes [(Cbzdiphos(R) )Zr(η(6) -tol)X] 2 (iPr) Cl and 2 (Ph) I (cbzdiphos=1,8-bis(phosphino)-3,6-di-tert-butyl-9H-carbazole). The arene complexes were also found to be directly accessible from the triiodide [(Cbzdiphos(Ph) )ZrI3 ] through an in situ reaction with a dibenzylmagnesium reagent and subsequent hydrogenolysis, as exemplified for the η(6) -mesitylene complex [(Cbzdiphos(Ph) )Zr(η(6) -mes)I] (3 (Ph) I). The tolyl-ring in 2 (iPr) Cl adopts a puckered arrangement (fold angle 23.3°) indicating significant arene-1,4-diido character. Deuterium labeling experiments were consistent with an intramolecular reaction sequence after the initial hydrogenolysis of a Zr-C bond by a σ-bond metathesis. A DFT study of the reaction sequence indicates that hydrogenolysis by σ-bond metathesis first occurs at the cyclometalated ancillary ligand giving a hydrido-benzyl intermediate, which subsequently reductively eliminates toluene that then coordinates to the Zr atom as the reduced arene ligand. Complex 2 (Ph) I was reacted with 2,6-diisopropylphenyl isocyanide giving the deep blue, diamagnetic Zr(II) -diisocyanide complex [(Cbzdiphos(Ph) )Zr(CNDipp)2 I] (4 (Ph) I). DFT modeling of 4 (Ph) I demonstrated that the HOMO of the complex is primarily located as a "lone pair on zirconium", with some degree of back-bonding into the C≡N π* bond, and the complex is thus most appropriately described as a zirconium(II) species. Reaction of 2 (Ph) I with trimethylsilylazide (N3 TMS) and 2 (iPr) Cl with 1-azidoadamantane (N3 Ad) resulted in the formation of the imido complexes [(Cbzdiphos(R) )Zr=NR'(X)] 5 (iPr) Cl-NAd and 5 (Ph) I-NTMS, respectively. Reaction of 2 (iPr) Cl with azobenzene led to N-N bond scission giving 6 (iPr) Cl, in which one of the NPh-fragments is coupled with the carbazole nitrogen to form a central η(2) -bonded hydrazide(-1), whereas the other NPh-fragment binds to zirconium acting as an imido-ligand. Finally, addition of pyridine to 2 (iPr) Cl yielded the dark purple complex [(Cbzdiphos(iPr) )Zr(bpy)Cl] (7 (iPr) Cl) through a combination of CH-activation and C-C-coupling. The structural data and UV/Vis spectroscopic properties of 7 (iPr) Cl indicate that the bpy (bipyridine) may be regarded as a (dianionic) diamido-type ligand. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Formation of ternary CaUO2(CO3)3(2-) and Ca2UO2(CO3)3(aq) complexes under neutral to weakly alkaline conditions.

PubMed

Lee, Jun-Yeop; Yun, Jong-Il

2013-07-21

The chemical behavior of ternary Ca-UO2-CO3 complexes was investigated by using time-resolved laser fluorescence spectroscopy (TRLFS) in combination with EDTA complexation at pH 7-9. A novel TRLFS revealed two distinct fluorescence lifetimes of 12.7 ± 0.2 ns and 29.2 ± 0.4 ns for uranyl complexes which were formed increasingly dependent upon the calcium ion concentration, even though nearly indistinguishable fluorescence peak shapes and positions were measured for both Ca-UO2-CO3 complexes. For identifying the stoichiometric number of complexed calcium ions, slope analysis in terms of relative fluorescence intensity versus calcium concentration was employed in a combination with the complexation reaction of CaEDTA(2-) by adding EDTA. The formation of CaUO2(CO3)3(2-) and Ca2UO2(CO3)3(aq) was identified under given conditions and their formation constants were determined at I = 0.1 M Na/HClO4 medium, and extrapolated to infinitely dilute solution using specific ion interaction theory (SIT). As a result, the formation constants for CaUO2(CO3)3(2-) and Ca2UO2(CO3)3(aq) were found to be log β113(0) = 27.27 ± 0.14 and log β213(0) = 29.81 ± 0.19, respectively, providing that the ternary Ca-UO2-CO3 complexes were predominant uranium(vi) species at neutral to weakly alkaline pH in the presence of Ca(2+) and CO3(2-) ions.

Formation of a Criegee intermediate in the low-temperature oxidation of dimethyl sulfoxide.

PubMed

Asatryan, Rubik; Bozzelli, Joseph W

2008-04-07

Dimethyl sulfoxide (DMSO) is the major sulfur-containing constituent of the Marine Boundary Layer. It is a significant source of H2SO4 aerosol/particles and methane sulfonic acid via atmospheric oxidation processes, where the mechanism is not established. In this study, several new, low-temperature pathways are revealed in the oxidation of DMSO using CBS-QB3 and G3MP2 multilevel and B3LYP hybrid density functional quantum chemical methods. Unlike analogous hydrocarbon peroxy radicals the chemically activated DMSO peroxy radical, [CH3S(=O)CH2OO*]*, predominantly undergoes simple dissociation to a methylsulfinyl radical CH3S*(=O) and a Criegee intermediate, CH2OO, with the barrier to dissociation 11.3 kcal mol(-1) below the energy of the CH3S(=O)CH2* + O2 reactants. The well depth for addition of O2 to the CH3S(=O)CH2 precursor radical is 29.6 kcal mol(-1) at the CBS-QB3 level of theory. We believe that this reaction may serve an important role in atmospheric photochemical and irradiated biological (oxygen-rich) media where formation of initial radicals is facilitated even at lower temperatures. The Criegee intermediate (carbonyl oxide, peroxymethylene) and sulfinyl radical can further decompose, resulting in additional chain branching. A second reaction channel important for oxidation processes includes formation (via intramolecular H atom transfer) and further decomposition of hydroperoxide methylsulfoxide radical, *CH2S(=O)CH2OOH over a low barrier of activation. The initial H-transfer reaction is similar and common in analogous hydrocarbon radical + O2 reactions; but the subsequent very low (3-6 kcal mol(-1)) barrier (14 kcal mol(-1) below the initial reagents) to beta-scission products is not common in HC systems. The low energy reaction of the hydroperoxide radical is a beta-scission elimination of *CH2S(=O)CH2OOH into the CH2=S=O + CH2O + *OH product set. This beta-scission barrier is low, because of the delocalization of the *CH2 radical center through the -S(=O) group, to the -CH2OOH fragment in the transition state structure. The hydroperoxide methylsulfoxide radical can also decompose via a second reaction channel of intramolecular OH migration, yielding formaldehyde and a sulfur-centered hydroxymethylsulfinyl radical HOCH2S*(=O). The barrier of activation relative to initial reagents is 4.2 kcal mol(-1). Heats of formation for DMSO, DMSO carbon-centered radical and Criegee intermediate are evaluated at 298 K as -35.97 +/- 0.05, 13.0 +/- 0.2 and 25.3 +/- 0.7 kcal mol(-1) respectively using isodesmic reaction analysis. The [CH3S*(=O) + CH2OO] product set is shown to form a van der Waals complex that results in O-atom transfer reaction and the formation of new products CH3SO2* radical and CH2O. Proper orientation of the Criegee intermediate and methylsulfinyl radical, as a pre-stabilized pre-reaction complex, assist the process. The DMSO radical reaction is also compared to that of acetonyl radical.

Formation of W(3)A(1) electron-transferring flavoprotein (ETF) hydroquinone in the trimethylamine dehydrogenase x ETF protein complex.

PubMed

Jang, M H; Scrutton, N S; Hille, R

2000-04-28

The electron-transferring flavoprotein (ETF) from Methylophilus methylotrophus (sp. W(3)A(1)) exhibits unusual oxidation-reduction properties and can only be reduced to the level of the semiquinone under most circumstances (including turnover with its physiological reductant, trimethylamine dehydrogenase (TMADH), or reaction with strong reducing reagents such as sodium dithionite). In the present study, we demonstrate that ETF can be reduced fully to its hydroquinone form both enzymatically and chemically when it is in complex with TMADH. Quantitative titration of the TMADH x ETF protein complex with sodium dithionite shows that a total of five electrons are taken up by the system, indicating that full reduction of ETF occurs within the complex. The results indicate that the oxidation-reduction properties of ETF are perturbed upon binding to TMADH, a conclusion further supported by the observation of a spectral change upon formation of the TMADH x ETF complex that is due to a change in the environment of the FAD of ETF. The results are discussed in the context of ETF undergoing a conformational change during formation of the TMADH x ETF electron transfer complex, which modulates the spectral and oxidation-reduction properties of ETF such that full reduction of the protein can take place.

Solution Synthesis, Structure, and CO2 Reduction Reactivity of a Scandium(II) Complex, {Sc[N(SiMe3 )2 ]3 }.

PubMed

Woen, David H; Chen, Guo P; Ziller, Joseph W; Boyle, Timothy J; Furche, Filipp; Evans, William J

2017-02-13

The first crystallographically characterizable complex of Sc 2+ , [Sc(NR 2 ) 3 ] - (R=SiMe 3 ), has been obtained by LnA 3 /M reactions (Ln=rare earth metal; A=anionic ligand; M=alkali metal) involving reduction of Sc(NR 2 ) 3 with K in the presence of 2.2.2-cryptand (crypt) and 18-crown-6 (18-c-6) and with Cs in the presence of crypt. Dark maroon [K(crypt)] + , [K(18-c-6)] + , and [Cs(crypt)] + salts of the [Sc(NR 2 ) 3 ] - anion are formed, respectively. The formation of this oxidation state of Sc is also indicated by the eight-line EPR spectra arising from the I=7/2 45 Sc nucleus. The Sc(NR 2 ) 3 reduction differs from Ln(NR 2 ) 3 reactions (Ln=Y and lanthanides) in that it occurs under N 2 without formation of isolable reduced dinitrogen species. [K(18-c-6)][Sc(NR 2 ) 3 ] reacts with CO 2 to produce an oxalate complex, {K 2 (18-c-6) 3 }{[(R 2 N) 3 Sc] 2 (μ-C 2 O 4 -κ 1 O:κ 1 O'')}, and a CO 2 - radical anion complex, [(R 2 N) 3 Sc(μ-OCO-κ 1 O:κ 1 O')K(18-c-6)] n . © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Gas phase reaction of nitric acid with hydroxyl radical without and with water. A theoretical investigation.

PubMed

Gonzalez, Javier; Anglada, Josep M

2010-09-02

The gas phase reaction between nitric acid and hydroxyl radical, without and with a single water molecule, has been investigated theoretically using the DFT-B3LYP, MP2, QCISD, and CCSD(T) theoretical approaches with the 6-311+G(2df,2p) and aug-cc-pVTZ basis sets. The reaction without water begins with the formation of a prereactive hydrogen-bonded complex and has several elementary reactions processes. They include proton coupled electron transfer, hydrogen atom transfer, and proton transfer mechanisms, and our kinetic study shows a quite good agreement of the behavior of the rate constant with respect to the temperature and to the pressure with the experimental results from the literature. The addition of a single water molecule results in a much more complex potential energy surface although the different elementary reactions found have the same electronic features that the naked reaction. Two transition states are stabilized by the effect of a hydrogen bond interaction originated by the water molecule, and in the prereactive hydrogen bond region there is a geometrical rearrangement necessary to prepare the HO and HNO(3) moieties to react to each other. This step contributes the reaction to be slower than the reaction without water and explains the experimental finding, pointing out that there is no dependence for the HNO(3) + HO reaction on water vapor.

Tunable catalytic properties of bi-functional mixed oxides in ethanol conversion to high value compounds

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

Ramasamy, Karthikeyan K.; Gray, Michel J.; Job, Heather M.

2016-04-10

tA highly versatile ethanol conversion process to selectively generate high value compounds is pre-sented here. By changing the reaction temperature, ethanol can be selectively converted to >C2alcohols/oxygenates or phenolic compounds over hydrotalcite derived bi-functional MgO–Al2O3cata-lyst via complex cascade mechanism. Reaction temperature plays a role in whether aldol condensationor the acetone formation is the path taken in changing the product composition. This article containsthe catalytic activity comparison between the mono-functional and physical mixture counterpart to thehydrotalcite derived mixed oxides and the detailed discussion on the reaction mechanisms.

Wave reflection in a reaction-diffusion system: breathing patterns and attenuation of the echo.

PubMed

Tsyganov, M A; Ivanitsky, G R; Zemskov, E P

2014-05-01

Formation and interaction of the one-dimensional excitation waves in a reaction-diffusion system with the piecewise linear reaction functions of the Tonnelier-Gerstner type are studied. We show that there exists a parameter region where the established regime of wave propagation depends on initial conditions. Wave phenomena with a complex behavior are found: (i) the reflection of waves at a growing distance (the remote reflection) upon their collision with each other or with no-flux boundaries and (ii) the periodic transformation of waves with the jumping from one regime of wave propagation to another (the periodic trigger wave).

Wave reflection in a reaction-diffusion system: Breathing patterns and attenuation of the echo

NASA Astrophysics Data System (ADS)

Tsyganov, M. A.; Ivanitsky, G. R.; Zemskov, E. P.

2014-05-01

Formation and interaction of the one-dimensional excitation waves in a reaction-diffusion system with the piecewise linear reaction functions of the Tonnelier-Gerstner type are studied. We show that there exists a parameter region where the established regime of wave propagation depends on initial conditions. Wave phenomena with a complex behavior are found: (i) the reflection of waves at a growing distance (the remote reflection) upon their collision with each other or with no-flux boundaries and (ii) the periodic transformation of waves with the jumping from one regime of wave propagation to another (the periodic trigger wave).

Tunable catalytic properties of bi-functional mixed oxides in ethanol conversion to high value compounds

DOE PAGES

Ramasamy, Karthikeyan K.; Gray, Michel; Job, Heather; ...

2016-02-03

Here, a highly versatile ethanol conversion process to selectively generate high value compounds is presented here. By changing the reaction temperature, ethanol can be selectively converted to >C 2 alcohols/oxygenates or phenolic compounds over hydrotalcite derived bi-functional MgO–Al 2O 3 catalyst via complex cascade mechanism. Reaction temperature plays a role in whether aldol condensation or the acetone formation is the path taken in changing the product composition. This article contains the catalytic activity comparison between the mono-functional and physical mixture counterpart to the hydrotalcite derived mixed oxides and the detailed discussion on the reaction mechanisms.

Insight into ethylene interactions with molybdenum suboxide cluster anions from photoelectron spectra of chemifragments

NASA Astrophysics Data System (ADS)

Schaugaard, Richard N.; Topolski, Josey E.; Ray, Manisha; Raghavachari, Krishnan; Jarrold, Caroline Chick

2018-02-01

Recent studies on reactions between MoxOy- cluster anions and H2O/C2H4 mixtures revealed a complex web of addition, hydrogen evolution, and chemifragmentation reactions, with chemifragments unambiguously connected to cluster reactions with C2H4. To gain insight into the molecular-scale interactions along the chemifragmentation pathways, the anion photoelectron (PE) spectra of MoC2H2-, MoC4H4-, MoOC2H2-, and MoO2C2H2- formed directly in MoxOy- + C2H4 (x > 1; y ≥ x) reactions, along with supporting CCSD(T) and density functional theory calculations, are presented and analyzed. The complexes have spectra that are all consistent with η2-acetylene complexes, though for all but MoC4H4-, the possibility that vinylidene complexes are also present cannot be definitively ruled out. Structures that are consistent with the PE spectrum of MoC2H2- differ from the lowest energy structure, suggesting that the fragment formation is under kinetic control. The PE spectrum of MoO2C2H2- additionally exhibits evidence that photodissociation to MoO2- + C2H2 may be occurring. The results suggest that oxidative dehydrogenation of ethylene is initiated by Lewis acid/base interactions between the Mo centers in larger clusters and the π orbitals in ethylene.

Kirromycin, an Inhibitor of Protein Biosynthesis that Acts on Elongation Factor Tu

PubMed Central

Wolf, Heinz; Chinali, Gianni; Parmeggiani, Andrea

1974-01-01

Kirromycin, a new inhibitor of protein synthesis, is shown to interfere with the peptide transfer reaction by acting on elongation factor Tu (EF-Tu). All the reactions associated with this elongation factor are affected. Formation of the EF-Tu·GTP complex is strongly stimulated. Peptide bond formation is prevented only when Phe-tRNAPhe is bound enzymatically to ribosomes, presumably because GTP hydrolysis associated with enzymatic binding of Phe-tRNAPhe is not followed by release of EF-Tu·GDP from the ribosome. This antibiotic also enables EF-Tu to catalyze the binding of Phe-tRNAPhe to the poly(U)·ribosome complex even in the absence of GTP. EF-Tu activity in the GTPase reaction is dramatically affected by kirromycin: GTP hydrolysis, which normally requires ribosomes and aminoacyl-tRNA, takes place with the elongation factor alone. This GTPase shows the same Km for GTP as the one dependent on Phe-tRNAPhe and ribosomes in the absence of the antibiotic. Ribosomes and Phe-tRNAPhe, but not tRNAPhe or Ac-Phe-tRNAPhe, stimulate the kirromycin-induced EF-Tu GTPase. These results indicate that the catalytic center of EF-Tu GTPase that is dependent upon aminoacyl-tRNA and ribosomes is primarily located on the elongation factor. In conclusion, kirromycin can substitute for GTP, aminoacyl-tRNA, or ribosomes in various reactions involving EF-Tu, apparently by affecting the allosteric controls between the sites on the EF-Tu molecule interacting with these components. PMID:4373734

A GAS-PHASE FORMATION ROUTE TO INTERSTELLAR TRANS-METHYL FORMATE

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

Cole, Callie A.; Wehres, Nadine; Yang Zhibo

2012-07-20

The abundance of methyl formate in the interstellar medium has previously been underpredicted by chemical models. Additionally, grain surface chemistry cannot account for the relative abundance of the cis- and trans-conformers of methyl formate, and the trans-conformer is not even formed at detectable abundance on these surfaces. This highlights the importance of studying formation pathways to methyl formate in the gas phase. The rate constant and branching fractions are reported for the gas-phase reaction between protonated methanol and formic acid to form protonated trans-methyl formate and water as well as adduct ion: Rate constants were experimentally determined using a flowingmore » afterglow-selected ion flow tube apparatus at 300 K and a pressure of 530 mTorr helium. The results indicate a moderate overall rate constant of (3.19 {+-} 0.39) Multiplication-Sign 10{sup -10} cm{sup 3} s{sup -1} ({+-} 1{sigma}) and an average branching fraction of 0.05 {+-} 0.04 for protonated trans-methyl formate and 0.95 {+-} 0.04 for the adduct ion. These experimental results are reinforced by ab initio calculations at the MP2(full)/aug-cc-pVTZ level of theory to examine the reaction coordinate and complement previous density functional theory calculations. This study underscores the need for continued observational studies of trans-methyl formate and for the exploration of other gas-phase formation routes to complex organic molecules.« less

Linear pi-Acceptor-Templated Dynamic Clipping to Macrobicycles and[2]Rotaxanes

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

Klivansky, Liana M.; Koshkakaryan, Gayane; Cao, Dennis

2009-04-30

Functional rotaxanes are one of the representative nanoscale molecular machines that have found applications in many areas, including molecular electronics, nanoelectromechanical systems (NEMS), photo controllable smart surfaces, and nanovalves. With the advent of molecular recognition and self-assembly, such molecular compounds can now be obtained efficiently through template-directed synthesis. One of the common strategies of making [2]rotaxanes involves the clipping of a macrocycle around a preformed dumbbell-shaped template in a [1+1] or [2+2] manner. While early examples were based on irreversible kinetic pathway through covalent bond formation, recent advances on reversible dynamic covalent chemistry (DCC) has attracted great attention to thismore » field. By virtue of thermodynamically controlled equilibria, DCC has provided highly efficient and versatile synthetic routes in the selection of specific products from a complex system. Among the several reversible reactions in the category of DCC reactions, the imine formation has proven to be very versatile in macrocyclization to give complex interlocked molecular compounds. Cryptands are three dimensional bicyclic hosts with preorganized cavities capable of inclusion of ions and small molecules. Replacing the nitrogen bridgeheads in common cryptands with aromatic ring systems gives cyclophane-based macrobicycles. The introduction of aromatic ring systems into a preorganized cage-like geometry facilitates ion-{pi} interactions and {pi}-{pi} interactions, resulting in novel metal sandwiches, fluoride receptors, and host-guest complexes. In particular, the seminal work by Gibson, Huang and coworkers on cryptand complexation with paraquat and diquat guests have resulted in the efficient synthesis of mechanically interlocked rotaxanes. The synthesis of cyclophane-based macrobicycles, however, was mostly realized through multiple reaction steps and in high-dilution conditions, which often suffered from low yield and tedious workup. Thus, a one-step, five-component [2+3] clipping reaction that can give the desired macrobicycle is highly desirable. We are motivated by a {pi}-guest templating protocol, because not only {pi}-{pi} interactions can contribute to the formation of macrobicycles, but also the resulting host-guest system holds great promise as a forerunner in the construction of interlocked molecules. (Scheme 1c) Very simple precursors, namely 1,3,5-benzenetrialdehyde (1) and 2,2{prime}-(ethylenedioxy)diethylamine (2) were chosen as the components for desired macrobicycle. (Scheme 2) The formation of six imine bonds would connect the five components to give a macrobicycle while extending the conjugation in the C{sub 3}-symmetric aromatic 'ceiling' and 'floor', which is suitable for enhancing the {pi}-{pi} interactions with a complementary aromatic template. Meanwhile, the ethylene glycol 'pillars' can provide sufficient flexibility, proper spacing, and polar binding sites to assist guest encapsulation. Initial screening of ?-templates engaged several C{sub 3} symmetric aromatic compounds in order to match the symmetry of the desired macrobicycle, which only resulted in nonspecific mixtures. It was found instead that linear bipyridinium (BPY) containing guests effectively templated the [2+3] clipping reaction. Based on this protocol, a [2]rotaxane was successfully assembled as the single product from the six-component reaction.« less

Evidence for the complex relationship between free amino acid and sugar concentrations and acrylamide-forming potential in potato

PubMed Central

Muttucumaru, N; Powers, SJ; Elmore, JS; Briddon, A; Mottram, DS; Halford, NG

2014-01-01

Free amino acids and reducing sugars participate in the Maillard reaction during high-temperature cooking and processing. This results not only in the formation of colour, aroma and flavour compounds, but also undesirable contaminants, including acrylamide, which forms when the amino acid that participates in the reaction is asparagine. In this study, tubers of 13 varieties of potato (Solanum tuberosum), which had been produced in a field trial in 2010 and sampled immediately after harvest or after storage for 6 months, were analysed to show the relationship between the concentrations of free asparagine, other free amino acids, sugars and acrylamide-forming potential. The varieties comprised five that are normally used for crisping, seven that are used for French fry production and one that is used for boiling. Acrylamide formation was measured in heated flour, and correlated with glucose and fructose concentration. In French fry varieties, which contain higher concentrations of sugars, acrylamide formation also correlated with free asparagine concentration, demonstrating the complex relationship between precursor concentration and acrylamide-forming potential in potato. Storage of the potatoes for 6 months at 9°C had a significant, variety-dependent impact on sugar and amino acid concentrations and acrylamide-forming potential. PMID:25540460

Single-Molecule Analysis for RISC Assembly and Target Cleavage.

PubMed

Sasaki, Hiroshi M; Tadakuma, Hisashi; Tomari, Yukihide

2018-01-01

RNA-induced silencing complex (RISC) is a small RNA-protein complex that mediates silencing of complementary target RNAs. Biochemistry has been successfully used to characterize the molecular mechanism of RISC assembly and function for nearly two decades. However, further dissection of intermediate states during the reactions has been warranted to fill in the gaps in our understanding of RNA silencing mechanisms. Single-molecule analysis with total internal reflection fluorescence (TIRF) microscopy is a powerful imaging-based approach to interrogate complex formation and dynamics at the individual molecule level with high sensitivity. Combining this technique with our recently established in vitro reconstitution system of fly Ago2-RISC, we have developed a single-molecule observation system for RISC assembly. In this chapter, we summarize the detailed protocol for single-molecule analysis of chaperone-assisted assembly of fly Ago2-RISC as well as its target cleavage reaction.

Bimetallic iron–iron and iron–zinc complexes of the redox-active ONO pincer ligand† †Electronic supplementary information (ESI) available: Complete experimental procedures and magnetic measurements and models. CCDC 1417565–1417567. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c5sc03006d Click here for additional data file. Click here for additional data file.

PubMed Central

Wong, Janice L.; Higgins, Robert F.; Bhowmick, Indrani; Cao, David Xi; Szigethy, Géza; Ziller, Joseph W.

2016-01-01

A new bimetallic platform comprising a six-coordinate Fe(ONO)2 unit bound to an (ONO)M (M = Fe, Zn) has been discovered ((ONOcat)H3 = bis(3,5-di-tert-butyl-2-phenol)amine). Reaction of Fe(ONO)2 with either (ONOcat)Fe(py)3 or with (ONOq)FeCl2 under reducing conditions led to the formation of the bimetallic complex Fe2(ONO)3, which includes unique five- and six-coordinate iron centers. Similarly, the reaction of Fe(ONO)2 with the new synthon (ONOsq˙)Zn(py)2 led to the formation of the heterobimetallic complex FeZn(ONO)3, with a six-coordinate iron center and a five-coordinate zinc center. Both bimetallic complexes were characterized by single-crystal X-ray diffraction studies, solid-state magnetic measurements, and multiple spectroscopic techniques. The magnetic data for FeZn(ONO)3 are consistent with a ground state S = 3/2 spin system, generated from a high-spin iron(ii) center that is antiferromagnetically coupled to a single (ONOsq˙)2– radical ligand. In the case of Fe2(ONO)3, the magnetic data revealed a ground state S = 7/2 spin system arising from the interactions of one high-spin iron(ii) center, one high-spin iron(iii) center, and two (ONOsq˙)2– radical ligands. PMID:28808535

The impact of dihydrogen phosphate anions on the excited-state proton transfer of harmane. Effect of β-cyclodextrin on these photoreactions.

PubMed

Reyman, Dolores; Viñas, Montserrat H; Tardajos, Gloria; Mazario, Eva

2012-01-12

Photoinduced proton transfer reactions of harmane (1-methyl-9H-pyrido[3,4-b]indole) (HAR) in the presence of a proton donor/acceptor such as dihydrogen phosphate anions in aqueous solution have been studied by stationary and time-resolved fluorescence spectroscopy. The presence of high amounts of dihydrogen phosphate ions modifies the acid/base properties of this alkaloid. Thus, by keeping the pH constant at pH 8.8 and by increasing the amount of NaH(2)PO(4) in the solution, it is possible to reproduce the same spectral profiles as those obtained in high alkaline solutions (pH >12) in the absence of NaH(2)PO(4). Under these conditions, a new fluorescence profile appears at around 520 nm. This result could be related to the results of a recent investigation which suggests that a high intake of phosphates may promote skin tumorigenesis. The presence of β-cyclodextrin (β-CD) avoids the proton transfer reactions in this alkaloid by means the formation of an inclusion complex between β-CD and HAR. The formation of this complex originates a remarkable enhancement of the emission intensity from the neutral form in contrast to the cationic and zwitterionic forms. A new lifetime was obtained at 360 nm (2.5 ns), which was associated with the emission of this inclusion complex. At this wavelength, the fluorescence intensity decay of HAR can be described by a linear combination of two exponentials. From the ratio between the pre-exponential factors, we have obtained a value of K = 501 M for the equilibrium of formation of this complex.

IMMUNOREACTIONS INVOLVING PLATELETS

PubMed Central

Shulman, N. Raphael

1958-01-01

A steric and kinetic model for the sequence and mechanism of reactions leading to formation of a complex from an antibody, a haptene (quinidine), and a cell membrane (platelets), and to fixation of complement by the complex was deduced from the effects of varying the initial concentration of each component of the complex on the amount of complement fixed, from kinetic aspects of the sequential reactions, and from other chemical and physical properties of the various components involved. Theoretical results calculated using equations based on the model, which were derived by Dr. Terrell L. Hill, were similar in all respects to experimental results. Results of this study were consistent with the possibilities that the protein moiety of a haptenic antigen involved in development of an antibody which attaches to a cell is not necessarily a component of the cell, and that the cell reacts with the antibody by virtue of having a surface favorable for non-specific adsorption of certain haptene-antibody complexes. PMID:13525578

Gold(I) Complexes of the Geminal Phosphinoborane tBu2PCH2BPh2.

PubMed

Boom, Devin H A; Ehlers, Andreas W; Nieger, Martin; Devillard, Marc; Bouhadir, Ghenwa; Bourissou, Didier; Slootweg, J Chris

2018-04-30

In this work, we explored the coordination properties of the geminal phosphinoborane t Bu 2 PCH 2 BPh 2 ( 2 ) toward different gold(I) precursors. The reaction of 2 with an equimolar amount of the sulfur-based complex (Me 2 S)AuCl resulted in displacement of the SMe 2 ligand and formation of linear phosphine gold(I) chloride 3 . Using an excess of ligand 2 , bisligated complex 4 was formed and showed dynamic behavior at room temperature. Changing the gold(I) metal precursor to the phosphorus-based complex, (Ph 3 P)AuCl impacted the coordination behavior of ligand 2 . Namely, the reaction of ligand 2 with (Ph 3 P)AuCl led to the heterolytic cleavage of the gold-chloride bond, which is favored over PPh 3 ligand displacement. To the best of our knowledge, 2 is the first example of a P/B-ambiphilic ligand capable of cleaving the gold-chloride bond. The coordination chemistry of 2 was further analyzed by density functional theory calculations.

Zwitterion formation in titan ice analogs: reaction between HC3N and NH3.

PubMed

Couturier-Tamburelli, Isabelle; Sessouma, Bintou; Chiavassa, Thierry; Piétri, Nathalie

2012-11-08

A zwitterion is formed in the laboratory at low temperatures in the solid phase from the thermal reaction of HC(3)N and NH(3). We report for the first time its infrared spectrum. We study its reaction using Fourier transform infrared spectroscopy. Its reaction rate is estimated to be k(T) = 2.9 × 10(5) exp(-2.3 ± 0.1 (kJ mol(-1))/RT). Calculations using density functional theory (B3LYP/6-31g**) are used to characterize all the species (complexes, zwitterions, and transition states) and are in good agreement with the infrared spectra. The structure of the zwitterion is determined planar and it is characterized by a N-C bond around 1.5 Å.

A Stopped-Flow Apparatus with Light-Scattering Detection and Its Application to Biochemical Reactions

PubMed Central

Riesner, Detlev; Buenemann, Hans

1973-01-01

A stopped-flow apparatus utilizing light-scattering for following the progress of a reaction is described. The method is applicable to all reactions that result in a significant change of the average molecular weight. It was possible due to several modifications of a conventional stopped-flow system to obtain a sensitivity comparable to that of commercial instruments for static light-scattering measurements. Experiments on three reactions are reported: association and dissociation of mercury ligands with DNA, dissociation of the dimers of DNA-dependent RNA polymerase, and complex formation of tRNASer (yeast) with the cognate aminoacyl-tRNA synthetase. The changes in the intensities of the scattered light are calculated and compared with the measured amplitudes. PMID:4577138

The reaction mechanism of methyl-coenzyme M reductase: How an enzyme enforces strict binding order

DOE PAGES

Wongnate, Thanyaporn; Ragsdale, Stephen W.

2015-02-17

Methyl-coenzyme M reductase (MCR) is a nickel tetrahydrocorphinoid (coenzyme F430) containing enzyme involved in the biological synthesis and anaerobic oxidation of methane. MCR catalyzes the conversion of methyl-2-mercaptoethanesulfonate (methyl-SCoM) and N-7-mercaptoheptanoylthreonine phosphate (CoB 7SH) to CH 4 and the mixed disulfide CoBS-SCoM. In this study, the reaction of MCR from Methanothermobacter marburgensis, with its native substrates was investigated using static binding, chemical quench, and stopped-flow techniques. Rate constants were measured for each step in this strictly ordered ternary complex catalytic mechanism. Surprisingly, in the absence of the other substrate, MCR can bind either substrate; however, only one binary complex (MCR·methyl-SCoM)more » is productive whereas the other (MCR·CoB 7SH) is inhibitory. Moreover, the kinetic data demonstrate that binding of methyl-SCoM to the inhibitory MCR·CoB 7SH complex is highly disfavored ( Kd = 56 mM). However, binding of CoB 7SH to the productive MCR·methyl-SCoM complex to form the active ternary complex (CoB 7SH·MCR(Ni I)·CH 3SCoM) is highly favored ( Kd = 79 μM). Only then can the chemical reaction occur ( kobs = 20 s -1 at 25 °C), leading to rapid formation and dissociation of CH 4 leaving the binary product complex (MCR(Ni II)·CoB 7S -·SCoM), which undergoes electron transfer to regenerate Ni(I) and the final product CoBS-SCoM. In conclusion, this first rapid kinetics study of MCR with its natural substrates describes how an enzyme can enforce a strictly ordered ternary complex mechanism and serves as a template for identification of the reaction intermediates.« less

Structural, luminescence, thermodynamic and theoretical studies on mononuclear complexes of Eu(III) with pyridine monocarboxylate-N-oxides in aqueous solution

NASA Astrophysics Data System (ADS)

Dumpala, Rama Mohana Rao; Rawat, Neetika; Boda, Anil; Ali, Sk. Musharaf; Tomar, B. S.

2018-02-01

The mononuclear complexes formed by Eu(III) with three isomeric pyridine monocarboxylate-N-oxides namely picolinic acid-N-oxide (PANO), nicotinic acid-N-oxide (NANO) and isonicotinic acid-N-oxide (IANO) in aqueous solutions were studied by potentiometry, luminescence spectroscopy and isothermal titration calorimetry (ITC) to determine the speciation, coordination, luminescence properties and thermodynamic parameters of the complexes formed during the course of the reaction. More stable six membered chelate complexes with stoichiometry (MLi, i = 1-4) are formed by Eu(III) with PANO while non chelating ML and ML2 complexes are formed by NANO and IANO. The stability of Eu(III) complexes follow the order PANO > IANO > NANO. The ITC studies inferred an endothermic and innersphere complex formation of Eu(III)-PANO and Eu(III)-IANO whereas an exothermic and outer-sphere complex formation for Eu(III)-NANO. The luminescence life time data further supported the ITC results. Density functional theoretical calculations were carried out to optimize geometries of the complexes and to estimate the energies, structural parameters (bond distances, bond angles) and charges on individual atoms of the same. Theoretical approximations are found to be in good agreement with the experimental observations.

Formation of a Ruthenium-Arene Complex, Cyclometallation with a Substituted Benzylamine, and Insertion of an Alkyne

ERIC Educational Resources Information Center

Chetcuti, Michael J.; Ritleng, Vincent

2007-01-01

The three step synthesis is presented to allow the functionalization of an aromatic amine by forming new C-C and C-N bonds via an intramolecular C-H activation under mild conditions. The reactions are stoichiometric and allow the students to isolate the different organometallic intermediates.

Transient Kinetic Analysis of Hydrogen Sulfide Oxidation Catalyzed by Human Sulfide Quinone Oxidoreductase*

PubMed Central

Mishanina, Tatiana V.; Yadav, Pramod K.; Ballou, David P.; Banerjee, Ruma

2015-01-01

The first step in the mitochondrial sulfide oxidation pathway is catalyzed by sulfide quinone oxidoreductase (SQR), which belongs to the family of flavoprotein disulfide oxidoreductases. During the catalytic cycle, the flavin cofactor is intermittently reduced by sulfide and oxidized by ubiquinone, linking H2S oxidation to the electron transfer chain and to energy metabolism. Human SQR can use multiple thiophilic acceptors, including sulfide, sulfite, and glutathione, to form as products, hydrodisulfide, thiosulfate, and glutathione persulfide, respectively. In this study, we have used transient kinetics to examine the mechanism of the flavin reductive half-reaction and have determined the redox potential of the bound flavin to be −123 ± 7 mV. We observe formation of an unusually intense charge-transfer (CT) complex when the enzyme is exposed to sulfide and unexpectedly, when it is exposed to sulfite. In the canonical reaction, sulfide serves as the sulfur donor and sulfite serves as the acceptor, forming thiosulfate. We show that thiosulfate is also formed when sulfide is added to the sulfite-induced CT intermediate, representing a new mechanism for thiosulfate formation. The CT complex is formed at a kinetically competent rate by reaction with sulfide but not with sulfite. Our study indicates that sulfide addition to the active site disulfide is preferred under normal turnover conditions. However, under pathological conditions when sulfite concentrations are high, sulfite could compete with sulfide for addition to the active site disulfide, leading to attenuation of SQR activity and to an alternate route for thiosulfate formation. PMID:26318450

Transient Kinetic Analysis of Hydrogen Sulfide Oxidation Catalyzed by Human Sulfide Quinone Oxidoreductase.

PubMed

Mishanina, Tatiana V; Yadav, Pramod K; Ballou, David P; Banerjee, Ruma

2015-10-09

The first step in the mitochondrial sulfide oxidation pathway is catalyzed by sulfide quinone oxidoreductase (SQR), which belongs to the family of flavoprotein disulfide oxidoreductases. During the catalytic cycle, the flavin cofactor is intermittently reduced by sulfide and oxidized by ubiquinone, linking H2S oxidation to the electron transfer chain and to energy metabolism. Human SQR can use multiple thiophilic acceptors, including sulfide, sulfite, and glutathione, to form as products, hydrodisulfide, thiosulfate, and glutathione persulfide, respectively. In this study, we have used transient kinetics to examine the mechanism of the flavin reductive half-reaction and have determined the redox potential of the bound flavin to be -123 ± 7 mV. We observe formation of an unusually intense charge-transfer (CT) complex when the enzyme is exposed to sulfide and unexpectedly, when it is exposed to sulfite. In the canonical reaction, sulfide serves as the sulfur donor and sulfite serves as the acceptor, forming thiosulfate. We show that thiosulfate is also formed when sulfide is added to the sulfite-induced CT intermediate, representing a new mechanism for thiosulfate formation. The CT complex is formed at a kinetically competent rate by reaction with sulfide but not with sulfite. Our study indicates that sulfide addition to the active site disulfide is preferred under normal turnover conditions. However, under pathological conditions when sulfite concentrations are high, sulfite could compete with sulfide for addition to the active site disulfide, leading to attenuation of SQR activity and to an alternate route for thiosulfate formation. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

State-of-the-art thermochemical and kinetic computations for astrochemical complex organic molecules: formamide formation in cold interstellar clouds as a case study

PubMed Central

Vazart, Fanny; Calderini, Danilo; Puzzarini, Cristina; Skouteris, Dimitrios

2017-01-01

We propose an integrated computational strategy aimed at providing reliable thermochemical and kinetic information on the formation processes of astrochemical complex organic molecules. The approach involves state-of-the-art quantum-mechanical computations, second-order vibrational perturbation theory, and kinetic models based on capture and transition state theory together with the master equation approach. Notably, tunneling, quantum reflection, and leading anharmonic contributions are accounted for in our model. Formamide has been selected as a case study in view of its interest as a precursor in the abiotic amino acid synthesis. After validation of the level of theory chosen for describing the potential energy surface, we have investigated several pathways of the OH+CH2NH and NH2+HCHO reaction channels. Our results indicate that both reaction channels are essentially barrier-less (in the sense that all relevant transition states lie below or only marginally above the reactants) and can, therefore, occur under the low temperature conditions of interstellar objects provided that tunneling is taken into the proper account. PMID:27689448

Exact model reduction of combinatorial reaction networks

PubMed Central

Conzelmann, Holger; Fey, Dirk; Gilles, Ernst D

2008-01-01

Background Receptors and scaffold proteins usually possess a high number of distinct binding domains inducing the formation of large multiprotein signaling complexes. Due to combinatorial reasons the number of distinguishable species grows exponentially with the number of binding domains and can easily reach several millions. Even by including only a limited number of components and binding domains the resulting models are very large and hardly manageable. A novel model reduction technique allows the significant reduction and modularization of these models. Results We introduce methods that extend and complete the already introduced approach. For instance, we provide techniques to handle the formation of multi-scaffold complexes as well as receptor dimerization. Furthermore, we discuss a new modeling approach that allows the direct generation of exactly reduced model structures. The developed methods are used to reduce a model of EGF and insulin receptor crosstalk comprising 5,182 ordinary differential equations (ODEs) to a model with 87 ODEs. Conclusion The methods, presented in this contribution, significantly enhance the available methods to exactly reduce models of combinatorial reaction networks. PMID:18755034

Exploring reaction pathways in the hydrothermal growth of phase-pure bismuth ferrites

NASA Astrophysics Data System (ADS)

Goldman, Abby R.; Fredricks, Jeremy L.; Estroff, Lara A.

2017-06-01

Phase-pure bismuth ferrites (BiFeO3 and Bi2Fe4O9) are grown using hydrothermal synthesis. In addition to varying the KOH, bismuth, and iron salt concentrations to tune which crystalline phases are formed, we identified that a 48 h, pre-furnace, room temperature reaction is critical for the formation of phase-pure BiFeO3. To understand the reaction pathways leading to the different bismuth ferrite phases, we investigate the changes in composition of the intermediate products as a function of reagent concentrations and room temperature reaction times. During the syntheses that included a room temperature reaction, Bi25FeO40 is formed in the intermediate products, and BiFeO3 is the majority phase of the final products. The BiFeO3 crystals grown using this method are clusters of faceted subunits. These results indicate that forming Bi25FeO40 is a productive route to the formation of BiFeO3. Bi2Fe4O9 is formed via an alternate reaction pathway that proceeded via an amorphous precursor. This improved understanding of how hydrothermal synthesis can be used to control the phase-purity and morphology of bismuth ferrites opens doors to explore the multiferroic properties of BiFeO3 with complex morphologies.

Towards understanding the role of amines in the SO2 hydration and the contribution of the hydrated product to new particle formation in the Earth's atmosphere.

PubMed

Lv, Guochun; Nadykto, Alexey B; Sun, Xiaomin; Zhang, Chenxi; Xu, Yisheng

2018-08-01

By theoretical calculations, the gas-phase SO 2 hydration reaction assisted by methylamine (MA) and dimethylamine (DMA) was investigated, and the potential contribution of the hydrated product to new particle formation (NPF) also was evaluated. The results show that the energy barrier for aliphatic amines (MA and DMA) assisted SO 2 hydration reaction is lower than the corresponding that of water and ammonia assisted SO 2 hydration. In these hydration reactions, nearly barrierless reaction (only a barrier of 0.1 kcal mol -1 ) can be found in the case of SO 2  + 2H 2 O + DMA. These lead us to conclude that the SO 2 hydration reaction assisted by MA and DMA is energetically facile. The temporal evolution for hydrated products (CH 3 NH 3 + -HSO 3 - -H 2 O or (CH 3 ) 2 NH 2 + -HSO 3 - -H 2 O) in molecular dynamics simulations indicates that these complexes can self-aggregate into bigger clusters and can absorb water and amine molecules, which means that these hydrated products formed by the hydration reaction may serve as a condensation nucleus to initiate the NPF. Copyright © 2018 Elsevier Ltd. All rights reserved.

The measles virus N(TAIL)-XD complex: an illustrative example of fuzziness.

PubMed

Longhi, Sonia

2012-01-01

In this chapter, I focus on the biochemical and structural characterization of the complex between the intrinsically disordered C-terminal domain of the measles virus nucleoprotein (N(TAIL)) and the C-terminal X domain (XD) of the viral phosphoprotein (P). I summarize the main experimental data available so far pointing out the prevalently disordered nature of N(TAIL) even after complex formation and the role of the flexible C-terminal appendage in the binding reaction. I finally discuss the possible functional role of these residual disordered regions within the complex in terms of their ability to capture other regulatory, binding partners.

Discovery of a Significant Acetone•Hydroperoxy Adduct Chaperone Effect and Its Impact on the Determination of Room Temperature Rate Constants for Acetonylperoxy/Hydroperoxy Self-Reactions and Cross Reaction Via Infrared Kinetic Spectroscopy.

NASA Astrophysics Data System (ADS)

Grieman, F. J.; Hui, A. O.; Okumura, M.; Sander, S. P.

2017-12-01

In order to model the upper troposphere/lower stratosphere in regions containing acetone properly, the kinetics of the acetonylperoxy/hydroperoxy self-reactions and cross reaction have been studied over a wide temperature range using Infrared Kinetic Spectroscopy. We report here the determination of different rate constants for the acetonylperoxy chemistry that we obtained at 298 K compared to currently accepted values. A considerable increase in the observed HO2 self-reaction rate constant due to rate enhancement via the chaperone effect from the reaction between HO2 and the (CH3)2CO•HO2 hydrogen-bonded adduct, even at room temperature, was discovered that was previously ignored. Correct determination of the acetonylperoxy and hydroperoxy kinetics must include this dependence of the HO2 self-reaction rate on acetone concentration. Via excimer laser flash photolysis to create the radical reactants, HO2 absorption was monitored in the infrared by diode laser wavelength modulation detection simultaneously with CH3C(O)CH2O2absorption monitored in the ultraviolet at 300 nm as a function of time. Resulting decay curves were fit concurrently first over a short time scale to obtain the rate constants minimizing subsequent product reactions. Modeling/fitting with a complete reaction scheme was then performed to refine the rate constants and test their veracity. Experiments were carried out over a variety of concentrations of acetone and methanol. Although no effect due to methanol concentration was found at room temperature, the rate constant for the hydroperoxy self-reaction was found to increase linearly with acetone concentration which is interpreted as the adduct being formed and resulting in a chaperone mechanism that enhances the self-reaction rate: (CH3)2CO·HO2 + HO2 → H2O2 + O2 + (CH3)2CO Including this effect, the resulting room temperature rate constants for the cross reaction and the acetonylperoxy self-reaction were found to be 2-3 times smaller than previously reported. This complex formation/chaperone mechanism is similar to that found for methanol, but different in that it occurs at room temperature. No precursor concentration dependence was found for the acetonylperoxy radical reactions. The equilibrium constant for the complex formation will also be presented.

An ab initio molecular orbital study of the mechanism for the gas-phase water-mediated decomposition and the formation of hydrates of peroxyacetyl nitrate (PAN).

PubMed

Li, Yumin; Francisco, Joseph S

2005-08-31

There is uncertainty in the mechanism for the hydrolysis of peroxyacetyl nitrate (PAN), and experimental attempts to detect products of the direct reaction have been unsuccessful. Ab initio calculations are used to examine the energetics of water-mediated decomposition of gas-phase PAN into acetic acid and peroxynitric acid. On the basis of ab initio calculations, an alternative reaction mechanism for the decomposition of PAN is proposed. The calculations indicate that the barrier for one water addition to PAN is large. However, including additional water molecules reveals a substantially lower energy route. The calculations suggest that the formation of PAN hydrate complexes are energetically favorable and stable. Additional waters are increasingly efficient at stabilizing hydrated PAN.

Master stability functions reveal diffusion-driven pattern formation in networks

NASA Astrophysics Data System (ADS)

Brechtel, Andreas; Gramlich, Philipp; Ritterskamp, Daniel; Drossel, Barbara; Gross, Thilo

2018-03-01

We study diffusion-driven pattern formation in networks of networks, a class of multilayer systems, where different layers have the same topology, but different internal dynamics. Agents are assumed to disperse within a layer by undergoing random walks, while they can be created or destroyed by reactions between or within a layer. We show that the stability of homogeneous steady states can be analyzed with a master stability function approach that reveals a deep analogy between pattern formation in networks and pattern formation in continuous space. For illustration, we consider a generalized model of ecological meta-food webs. This fairly complex model describes the dispersal of many different species across a region consisting of a network of individual habitats while subject to realistic, nonlinear predator-prey interactions. In this example, the method reveals the intricate dependence of the dynamics on the spatial structure. The ability of the proposed approach to deal with this fairly complex system highlights it as a promising tool for ecology and other applications.

Mechanisms and Kinetics of Alkaline Hydrolysis of the Energetic Nitroaromatic Compounds 2,4,6-Trinitrotoluene (TNT) and 2,4-Dinitroanisole (DNAN)

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

Salter-Blanc, Alexandra J.; Bylaska, Eric J.; Ritchie, Julia J.

2013-07-02

The environmental impacts of energetic compounds can be minimized through the design and selection of new energetic materials with favorable fate properties. Building predictive models to inform this process, however, is difficult because of uncertainties and complexities in some major fate-determining transformation reactions such as the alkaline hydrolysis of energetic nitroaromatic compounds (NACs). Prior work on the mechanisms of the reaction between NACs and OH– has yielded inconsistent results. In this study, the alkaline hydrolysis of 2,4,6-trinitrotoluene (TNT) and 2,4-dinitroanisole (DNAN) was investigated with coordinated experimental kinetic measurements and molecular modeling calculations. For TNT, the results suggest reversible formation ofmore » an initial product, which is likely either a Meisenheimer complex or a TNT anion formed by abstraction of a methyl proton by OH–. For DNAN, the results suggest that a Meisenheimer complex is an intermediate in the formation of 2,4-dinitrophenolate. Despite these advances, the remaining uncertainties in the mechanisms of these reactions—and potential variability between the hydrolysis mechanisms for different NACs—mean that it is not yet possible to generalize the results into predictive models (e.g., quantitative structure–activity relationships, QSARs) for hydrolysis of other NACs.« less

Reactivity of the parent amido complexes of iridium with olefins: C-NH2 bond formation versus C-H activation.

PubMed

Mena, Inmaculada; García-Orduña, Pilar; Polo, Víctor; Lahoz, Fernando J; Casado, Miguel A; Oro, Luis A

2017-08-29

Herein we report on the different chemical reactivity displayed by two mononuclear terminal amido compounds depending on the nature of the coordinated diene. Hence, treatment of amido-bridged iridium complexes [{Ir(μ-NH 2 )(tfbb)} 3 ] (1; tfbb = tetrafluorobenzobarrelene) with dppp (dppp = bis(diphenylphosphane)propane) leads to the rupture of the amido bridges forming the mononuclear terminal amido compound [Ir(NH 2 )(dppp)(tfbb)] (3) in the first stage. On changing the reaction conditions, the formation of a C-NH 2 bond between the amido moiety and the coordinated diene is observed and a new dinuclear complex [{Ir(1,2-η 2 -4-κ-C 12 H 8 F 4 N)(dppp)} 2 (μ-dppp)] (4) has been isolated. On the contrary, the diiridium amido-bridged complex [{Ir(μ-NH 2 )(cod)} 2 ] (2; cod = 1,5-cyclooctadiene) in the presence of dppb (dppb = bis(diphenylphosphane)butane) allows the isolation of a mononuclear complex [Ir(1,2,3-η 3 -6-κ-C 8 H 10 )H(dppb)] (5), as a consequence of the extrusion of ammonia. The monitoring of the reaction of 2 with dppb (and dppp) allowed us to detect terminal amido complexes [Ir(NH 2 )(P-P)(cod)] (P-P = dppb (6), dppp (7)) in solution, as confirmed by an X-ray analysis of 7. Complex 7 was observed to evolve into hydrido species 5 at room temperature. DFT studies showed that C-H bond activation occurs through the deprotonation of one methylene fragment of the cod ligand by the highly basic terminal amido moiety instead of C-H oxidative addition to the Ir(i) center.

Solvent influence on complex formation between Cd2+ and 2-hydroxy-1,4-naphthoquinone in binary mixed nonaqueous solvents at 15-45°C

NASA Astrophysics Data System (ADS)

Farazandeh, R.; Rounaghi, G. H.; Ebrahimi, M.; Basafa, S.

2017-04-01

The complexation reaction of Cd2+ cation with 2-hydroxy-1,4-naphthoquinone (HNQ) was studied in acetonitrile (AN), 2-PrOH, ethyl acetate (EtOAc), EtOH, dimethylformamide (DMF) and in binary solutions AN-2-PrOH, AN-DMF, AN-EtOH, and AN-EtOAc using conductometric method at 15-45°C. The conductance data show that the stoichiometry of the Cd2+ complex with HNQ in all solvent systems is 1 : 1. In the pure solvents the stability of the complex changes in the order AN > 2-PrOH > EtOH > DMF. The stability of the complex at 25°C in the studied mixtures changes in the following order : AN-EtOAc > AN-2-PrOH > AN-EtOH > AN-DMF. These orders are affected by the nature and composition of the solvent systems and by the temperature. From the temperature dependence data, the thermodynamic functions values (Δ H° and Δ S°) for the complex formation were calculated.

B. subtilis as a Model for Studying the Assembly of Fe-S Clusters in Gram-Positive Bacteria.

PubMed

Dos Santos, Patricia C

2017-01-01

Complexes of iron and sulfur (Fe-S clusters) are widely distributed in nature and participate in essential biochemical reactions. The biological formation of Fe-S clusters involves dedicated pathways responsible for the mobilization of sulfur, the assembly of Fe-S clusters, and the transfer of these clusters to target proteins. Genomic analysis of Bacillus subtilis and other Gram-positive bacteria indicated the presence of only one Fe-S cluster biosynthesis pathway, which is distinct in number of components and organization from previously studied systems. B. subtilis has been used as a model system for the characterization of cysteine desulfurases responsible for sulfur mobilization reactions in the biogenesis of Fe-S clusters and other sulfur-containing cofactors. Cysteine desulfurases catalyze the cleavage of the C-S bond from the amino acid cysteine and subsequent transfer of sulfur to acceptor molecules. These reactions can be monitored by the rate of alanine formation, the first product in the reaction, and sulfide formation, a byproduct of reactions performed under reducing conditions. The assembly of Fe-S clusters on protein scaffolds and the transfer of these clusters to target acceptors are determined through a combination of spectroscopic methods probing the rate of cluster assembly and transfer. This chapter provides a description of reactions promoting the assembly of Fe-S clusters in bacteria as well as methods used to study functions of each biosynthetic component and identify mechanistic differences employed by these enzymes across different pathways. © 2017 Elsevier Inc. All rights reserved.

A quantum-rovibrational-state-selected study of the reaction in the collision energy range of 0.05-10.00 eV: translational, rotational, and vibrational energy effects.

PubMed

Xu, Yuntao; Xiong, Bo; Chang, Yih-Chung; Pan, Yi; Lo, Po Kam; Lau, Kai Chung; Ng, C Y

2017-04-12

We report detailed absolute integral cross sections (σ's) for the quantum-rovibrational-state-selected ion-molecule reaction in the center-of-mass collision energy (E cm ) range of 0.05-10.00 eV, where (vvv) = (000), (100), and (020), and . Three product channels, HCO + + OH, HOCO + + H, and CO + + H 2 O, are identified. The measured σ(HCO + ) curve [σ(HCO + ) versus E cm plot] supports the hypothesis that the formation of the HCO + + OH channel follows an exothermic pathway with no potential energy barriers. Although the HOCO + + H channel is the most exothermic, the σ(HOCO + ) is found to be significantly lower than the σ(HCO + ). The σ(HOCO + ) curve is bimodal, indicating two distinct mechanisms for the formation of HOCO + . The σ(HOCO + ) is strongly inhibited at E cm < 0.4 eV, but is enhanced at E cm > 0.4 eV by (100) vibrational excitation. The E cm onsets of σ(CO + ) determined for the (000) and (100) vibrational states are in excellent agreement with the known thermochemical thresholds. This observation, along with the comparison of the σ(CO + ) curves for the (100) and (000) states, shows that kinetic and vibrational energies are equally effective in promoting the CO + channel. We have also performed high-level ab initio quantum calculations on the potential energy surface, intermediates, and transition state structures for the titled reaction. The calculations reveal potential barriers of ≈0.5-0.6 eV for the formation of HOCO + , and thus account for the low σ(HOCO + ) and its bimodal profile observed. The E cm enhancement for σ(HOCO + ) at E cm ≈ 0.5-5.0 eV can be attributed to the direct collision mechanism, whereas the formation of HOCO + at low E cm < 0.4 eV may involve a complex mechanism, which is mediated by the formation of a loosely sticking complex between HCO + and OH. The direct collision and complex mechanisms proposed also allow the rationalization of the vibrational inhibition at low E cm and the vibrational enhancement at high E cm observed for the σ(HOCO + ).

Negative kinetic temperature effect on the hydride transfer from NADH analogue BNAH to the radical cation of N-benzylphenothiazine in acetonitrile.

PubMed

Zhu, Xiao-Qing; Zhang, Jian-Yu; Cheng, Jin-Pei

2006-09-01

The reaction rates of 1-(p-substituted benzyl)-1,4-dihydronicotinamide (G-BNAH) with N-benzylphenothiazine radical cation (PTZ(*+)) in acetonitrile were determined. The results show that the reaction rates (k(obs)) decreased from 2.80 x 10(7) to 2.16 x 10(7) M(-1) s(-1) for G = H as the reaction temperature increased from 298 to 318 K. The activation enthalpies of the reactions were estimated according to Eyring equation to give negative values (-3.4 to -2.9 kcal/mol). Investigation of the reaction intermediate shows that the charge-transfer complex (CT-complex) between G-BNAH and PTZ(*+) was formed in front of the hydride transfer from G-BNAH to PTZ(*+). The formation enthalpy of the CT-complex was estimated by using the Benesi-Hildebrand equation to give the values from -6.4 to -6.0 kcal/mol when the substituent G in G-BNAH changes from CH(3)O to Br. Detailed thermodynamic analyses on each elementary step in the possible reaction pathways suggest that the hydride transfer from G-BNAH to PTZ(*+) occurs by a concerted hydride transfer via a CT-complex. The effective charge distribution on the pyridine ring in G-BNAH at the various stages-the reactant G-BNAH, the charge-transfer complex, the transition-state, and the product G-BNA(+)-was estimated by using the method of Hammett-type linear free energy analysis, and the results show that the pyridine ring carries relative effective positive charges of 0.35 in the CT-complex and 0.45 in the transition state, respectively, which indicates that the concerted hydride transfer from G-BNAH to PTZ(*+) was practically performed by the initial charge (-0.35) transfer from G-BNAH to PTZ(*+) and then followed by the transfer of hydrogen atom with partial negative charge (-0.65). It is evident that the present work would be helpful in understanding the nature of the negative temperature effect, especially on the reaction of NADH coenzyme with the drug phenothiazine in vivo.

Reactivity pathways for nitric oxide and nitrosonium with iron complexes in biologically relevant sulfur coordination spheres.

PubMed

Harrop, Todd C; Song, Datong; Lippard, Stephen J

2007-11-01

The interaction of nitric oxide (NO) with iron-sulfur cluster proteins results in the formation of dinitrosyl iron complexes (DNICs) coordinated by cysteine residues from the peptide backbone or with low molecular weight sulfur-containing molecules like glutathione. Such DNICs are among the modes available in biology to store, transport, and deliver NO to its relevant targets. In order to elucidate the fundamental chemistry underlying the formation of DNICs and to characterize possible intermediates in the process, we have investigated the interaction of NO (g) and NO(+) with iron-sulfur complexes having the formula [Fe(SR)(4)](2-), where R=(t)Bu, Ph, or benzyl, chosen to mimic sulfur-rich iron sites in biology. The reaction of NO (g) with [Fe(S(t)Bu)(4)](2-) or [Fe(SBz)(4)](2-) cleanly affords the mononitrosyl complexes (MNICs), [Fe(S(t)Bu)(3)(NO)](-) (1) and [Fe(SBz)(3)(NO)](-) (3), respectively, by ligand displacement. Mononitrosyl species of this kind were previously unknown. These complexes further react with NO (g) to generate the corresponding DNICs, [Fe(SPh)(2)(NO)(2)](-) (4) and [Fe(SBz)(2)(NO)(2)](-) (5), with concomitant reductive elimination of the coordinated thiolate donors. Reaction of [Fe(SR)(4)](2-) complexes with NO(+) proceeds by a different pathway to yield the corresponding dinitrosyl S-bridged Roussin red ester complexes, [Fe(2)(mu-S(t)Bu)(2)(NO)(4)] (2), [Fe(2)(mu-SPh)(2)(NO)(4)] (7) and [Fe(2)(mu-SBz)(2)(NO)(4)] (8). The NO/NO(+) reactivity of an Fe(II) complex with a mixed nitrogen/sulfur coordination sphere was also investigated. The DNIC and red ester species, [Fe(S-o-NH(2)C(6)H(4))(2)(NO)(2)](-) (6) and [Fe(2)(mu-S-o-NH(2)C(6)H(4))(2)(NO)(4)] (9), were generated. The structures of 8 and 9 were verified by X-ray crystallography. The MNIC complex 1 can efficiently deliver NO to iron-porphyrin complexes like [Fe(TPP)Cl], a reaction that is aided by light. Removal of the coordinated NO ligand of 1 by photolysis and addition of elemental sulfur generates higher nuclearity Fe/S clusters.

The Role of Oxygen in the Formation of TNT Product Ions in Ion Mobility Spectrometry

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

Daum, Keith Alvin; Atkinson, David Alan; Ewing, Robert Gordon

2002-03-01

The atmospheric pressure ionization of 2,4,6-trinitrotoluene (TNT) in air yields the (TNT-H)- product ion. It is generally accepted that this product ion is formed by the direct proton abstraction of neutral TNT by O2- reactant ions. Data presented here demonstrate the reaction involves the formation of an intermediate (TNT·O2)-, from the association of either TNT+O2- or TNT-+O2. This intermediate has two subsequent reaction branches. One of these branches involves simple dissociation of the intermediate to TNT-; the other branch is a terminal reaction that forms the typically observed (TNT-H)- ion via proton abstraction. The dissociation reaction involving electron transfer tomore » TNT- appeared to be kinetically favored and prevailed at low concentrations of oxygen (less than 2%). The presence of significant amounts of oxygen, however, resulted in the predominant formation of the (TNT-H)- ion by the terminal reaction branch. With TNT- in the system, either from direct electron attachment or by simple dissociation of the intermediate, increasing levels of oxygen in the system will continue to reform the intermediate, allowing the cycle to continue until proton abstraction occurs. Key to understanding this complex reaction pathway is that O2- was observed to transfer an electron directly to neutral TNT to form the TNT-. At oxygen levels of less than 2%, the TNT- ion intensity increased with increasing levels of oxygen (and O2-) and was larger than the (TNT-H)- ion intensity. As the oxygen level increased from 2 to 10%, the (TNT-H)- product ion became predominant. The potential reaction mechanisms were investigated with an ion mobility spectrometer, which was configured to independently evaluate the ionization pathways.« less

Studies on the reaction mechanism of lactate oxidase. Formation of two covalent flavin-substrate adducts on reaction with glycollate.

PubMed

Massey, V; Ghisla, S; Kieschke, K

1980-04-10

L-Lactate oxidase from Mycobacterium smegmatis catalyzes the oxidative decarboxylation of glycollate, with formate, CO2, and H2O as the major products. In addition, some "uncoupling" of the normal reaction occurs, with glyoxylate and H2O adition, some "uncoupling" of the normal reaction occurs, with glyoxylate and H2O2 as products. Glyoxylate is also a substrate (presumably as its hydrate); in this case, the reaction products are oxalate and H2O2. Evidence is presented that the enzyme recognizes glycollate as a prochiral substrate, differentiating between the Re- and Si-faces of the alpha carbon atom. Two highly fluorescent species are formed concomitantly from the reaction with glycollate; they are proposed to be covalent alpha-glycollyl adducts to the reduced flavin position N(5). One of these adducts is labile and in rapid equilibrium with oxidized enzyme and glycollate, and with the complex of reduced enzyme and glyoxylate; this adduct is a catalytically competent intermediate. The other adduct is comparatively stable (t 1/2 for decay = 20 min at 25 degrees C) and does not react with O2. It is formed at a rate approximately 1% that of the catalytic adduct, but because of its lack of reaction with O2 and its stability, it gradually accumulates during catalytic turnover, resulting in catalytically incompetent enzyme. An isotope effect of approximately 4 is found in the reduction of oxidized enzyme flavin and in the formation of the labile fluorescent adduct, when alpha-2H2-glycollate or (R)-glycollate-2-d is used, but not with the (S)-glycollate-2-d enantiomer. It is concluded that the catalytic adduct is formed by hydrogen abstraction from the Re-face of glycollate.

Evidence for Carbonate Surface Complexation during Forsterite Carbonation in Wet Supercritical Carbon Dioxide

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

Loring, John S.; Chen, Jeffrey; Benezeth, Pascale

Continental flood basalts are attractive formations for geologic sequestration of carbon dioxide because of their reactive divalent-cation containing silicates, such as forsterite (Mg2SiO4), suitable for long-term trapping of CO2 mineralized as metal carbonates. The goal of this study was to investigate at a molecular level the carbonation products formed during the reaction of forsterite with supercritical CO2 (scCO2) as a function of the concentration of H2O adsorbed to the forsterite surface. Experiments were performed at 50 °C and 90 bar using an in situ IR titration capability, and post-reaction samples were examined by ex situ techniques, including SEM, XPS, FIB-TEM,more » TGA-MS, and MAS-NMR. Carbonation products and reaction extents varied greatly with adsorbed H2O. We show for the first time evidence of Mg-carbonate surface complexation under wet scCO2 conditions. Carbonate is found to be coordinated to Mg at the forsterite surface in a predominately bidentate fashion at adsorbed H2O concentrations below 27 µmol/m2. Above this concentration and up to 76 µmol/m2, monodentate coordinated complexes become dominant. Beyond a threshold adsorbed H2O concentration of 76 µmol/m2, crystalline carbonates continuously precipitate as magnesite, and the particles that form are hundreds of times larger than the estimated thicknesses of the adsorbed water films of about 7 to 15 Å. At an applied level, the implication of these results is that mineral trapping in scCO2 dominated fluids will be insignificant and limited to surface complexation unless adsorbed H2O concentrations are high enough to promote crystalline carbonate formation. At a fundamental level, the surface complexes and their dependence on adsorbed H2O concentration give insights regarding forsterite dissolution processes and magnesite nucleation and growth.« less

Evidence for Carbonate Surface Complexation during Forsterite Carbonation in Wet Supercritical Carbon Dioxide

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

Loring, John S.; Chen, Jeffrey; Benezeth Ep Gisquet, Pascale

Continental flood basalts are attractive formations for geologic sequestration of carbon dioxide because of their reactive divalent-cation containing silicates, such as forsterite (Mg2SiO4), suitable for long-term trapping of CO2 mineralized as metal carbonates. The goal of this study was to investigate at a molecular level the carbonation products formed during the reaction of forsterite with supercritical CO2 (scCO2) as a function of the concentration of H2O adsorbed to the forsterite surface. Experiments were performed at 50 °C and 90 bar using an in situ IR titration capability, and post-reaction samples were examined by ex situ techniques, including SEM, XPS, FIB-TEM,more » TGA-MS, and MAS-NMR. Carbonation products and reaction extents varied greatly with adsorbed H2O. We show for the first time evidence of Mg-carbonate surface complexation under wet scCO2 conditions. Carbonate is found to be coordinated to Mg at the forsterite surface in a predominately bidentate fashion at adsorbed H2O concentrations below 27 µmol/m2. Above this concentration and up to 76 µmol/m2, monodentate coordinated complexes become dominant. Beyond a threshold adsorbed H2O concentration of 76 µmol/m2, crystalline carbonates continuously precipitate as magnesite, and the particles that form are hundreds of times larger than the estimated thicknesses of the adsorbed water films of about 7 to 15 Å. At an applied level, these results suggest that mineral carbonation in scCO2 dominated fluids near the wellbore and adjacent to caprocks will be insignificant and limited to surface complexation, unless adsorbed H2O concentrations are high enough to promote crystalline carbonate formation. At a fundamental level, the surface complexes and their dependence on adsorbed H2O concentration give insights regarding forsterite dissolution processes and magnesite nucleation and growth.« less

Reduced Uranium Phases Produced from Anaerobic Reaction with Nanoscale Zerovalent Iron.

PubMed

Tsarev, Sergey; Collins, Richard N; Fahy, Adam; Waite, T David

2016-03-01

Nanoscale zerovalent iron (nZVI) has shown potential to be an effective remediation agent for uranium-contaminated subsurface environments, however, the nature of the reaction products and their formation kinetics have not been fully elucidated over a range of environmentally relevant conditions. In this study, the oxygen-free reaction of U(VI) with varying quantities of nZVI was examined at pH 7 in the presence of both calcium and carbonate using a combination of X-ray absorption spectroscopy, X-ray diffraction and transmission electron microscopy. It was observed that the structure of the reduced U solid phases was time dependent and largely influenced by the ratio of nZVI to U in the system. At the highest U:Fe molar ratio examined (1:4), nanoscale uraninite (UO2) was predominantly formed within 1 day of reaction. At lower U:Fe molar ratios (1:21), evidence was obtained for the formation of sorbed U(IV) and U(V) surface complexes which slowly transformed to UO2 nanoparticles that were stable for up to 1 year of anaerobic incubation. After 8 days of reaction at the lowest U:Fe molar ratio examined (1:110), sorbed U(IV) was still the major form of U associated with the solid phase. Regardless of the U:Fe molar ratio, the anaerobic corrosion of nZVI resulted in the slow formation of micron-sized fibrous chukanovite (Fe2(OH)2CO3) particles.

Secondary organic aerosol formation from isoprene photooxidation

NASA Astrophysics Data System (ADS)

Kroll, J. H.; Ng, N. L.; Murphy, S. M.; Flagan, R. C.; Seinfeld, J. H.

2005-12-01

We report chamber studies of the formation of secondary organic aerosol (SOA) from the oxidation of isoprene (2-methyl-1,3-butadiene). Isoprene is the most abundant non-methane hydrocarbon emitted into the troposphere (source strength of ~500 Tg/year), so even small SOA yields may have a large impact on global SOA production. Reactions are carried out in Caltech's dual 28 m3 Teflon chambers, and aerosol growth is monitored by a differential mobility analyzer (DMA) and an Aerodyne time-of-flight aerosol mass spectrometer (AMS). Isoprene oxidation is initiated by the UV irradiation of isoprene in the presence of hydrogen peroxide, with NO added for high-NOx experiments. These conditions ensure that isoprene oxidation is initiated by reaction with the OH radical, with negligible interference from other oxidants (ozone, nitrate radicals, and O atoms). Aerosol growth is observed under both high-NOx and low-NOx conditions, at isoprene concentrations lower than measured in previous studies (down to 8 ppb). SOA yields are found to be in the range of 1-2%. Yields exhibit a complex dependence on NOx concentration, likely a result of changes in the chemistry of organic peroxy radicals. It is shown that condensable compounds are formed from further reactions of first-generation isoprene oxidation products; the rates and products of such gas-phase reactions are at present poorly understood. Additionally, measurements of SOA composition indicate that these products undergo reactions in the aerosol phase, leading to the formation of low-volatility oligomeric products.

Analysis of the complex formation of heparin with protamine by light scattering and analytical ultracentrifugation: implications for blood coagulation management.

PubMed

Maurer, Jürgen; Haselbach, Stephanie; Klein, Oliver; Baykut, Doan; Vogel, Vitali; Mäntele, Werner

2011-02-02

Heparin, a linear glycosaminoglycan, is used in different forms in anticoagulation treatment. Protamine, a highly positive charged peptide containing about 32 amino acids, acts as an antagonist for heparin to restore normal blood coagulation. The complex formation of protamine with heparin was analyzed by a combination of analytical ultracentrifugation and light scattering. Titration of heparin with protamine in blood plasma preparations results in a drastic increase of turbidity, indicating the formation of nanoscale particles. A similar increase of turbidity was observed in physiological saline solution with or without human serum albumin (HSA). Particle size analysis by analytical ultracentrifugation revealed a particle radius of approximately 30 nm for unfractionated heparin and of approximately 60 nm for low molecular weight heparin upon complexation with excess protamine, in agreement with atomic force microscopy data. In the absence of HSA, larger and more heterogeneous particles were observed. The particles obtained were found to be stable for hours. The particle formation kinetics was analyzed by light scattering at different scattering angles and was found to be complete within several minutes. The time course of particle formation suggests a condensation reaction, with sigmoidal traces for low heparin concentrations and quasi-first-order reaction for high heparin concentrations. Under all conditions, the final scattering intensity reached after several minutes was found to be proportional to the amount of heparin in the blood plasma or buffer solution, provided that excess protamine was available and no multiple scattering occurred. On the basis of a direct relation between particle concentration and the heparin concentration present before protaminization, a light scattering assay was developed which permits the quantitative analysis of the heparin concentration in blood plasma and which could complement or even replace the activated clotting time test, which is currently the most commonly used method for blood coagulation management.

Microstructures and formation history of melilite-rich calcium-aluminum-rich inclusions from the ALHA77307 CO3.0 chondrite

NASA Astrophysics Data System (ADS)

Han, Jangmi; Brearley, Adrian J.

2017-03-01

We have studied four melilite-rich calcium-aluminum-rich inclusions (CAIs) from the Allan Hills A77307 CO3.0 chondrite using transmission electron microscopy with the focused ion beam sample preparation technique. This type of CAI represents one of the dominant types of refractory inclusions in CO3 chondrites. Individual melilite-rich CAIs 04-07 record complex formational histories involving high-temperature gas-solid condensation that occurred under both equilibrium and disequilibrium conditions. CAI 04 contains two texturally- and compositionally-distinct occurrences of perovskite: fine-grained perovskite within a melilite-rich core and aggregates of perovskite grains that surround the core. The perovskite in the core was probably involved in a disequilibrium reaction with early equilibrium condensates (e.g., melilite and spinel) and a nebular gas to form Al-Ti-rich diopside, followed by a later condensation of the perovskite aggregates under equilibrium conditions. CAI 05 has a compact melilite-rich core surrounded by a porous mantle, and likely formed by at least two different condensation events under equilibrium and disequilibrium conditions. In CAI 06, complex intergrowth layers of spinel and diopside surrounding a melilite-rich core indicate disequilibrium reaction of spinel and melilite with a nebular gas to form Al-Ti-rich diopside following core formation by equilibrium condensation. CAI 07 is dominated by melilite with a narrow compositional range and equilibrated textures, suggesting its formation by equilibrium condensation over a limited temperature range. Collectively, we infer that the melilite-rich inclusions formed by a generalized sequence of high-temperature gas-solid condensation that involved: (1) formation of CAI cores by aggregation of primary equilibrium condensates (i.e., perovskite, spinel, and melilite), (2) back-reactions of the primary core minerals with a nebular gas under disequilibrium conditions, forming diopside that evolves in composition from Al-Ti-rich at the interface with the inclusion core to Al-Ti-poor on the exterior of the inclusions. The change in formation conditions may have been achieved by transport and injection of the core materials into a region of a partially-condensed gas that still contained refractory elements in the gas phase.

Predictions of diagenetic reactions in the presence of organic acids

NASA Astrophysics Data System (ADS)

Harrison, Wendy J.; Thyne, Geoffrey D.

1992-02-01

Stability constants have been estimated for cation complexes with anions of monofunctional and difunctional acids (combinations of Ca, Mg, Fe, Al, Sr, Mn, U, Th, Pb, Cu, Zn with formate, acetate, propionate, oxalate, malonate, succinate, and salicylate) between 0 and 200°C. Difunctional acid anions form much more stable complexes than monofunctional acid anions with aluminum; the importance of the aluminum-acetate complex is relatively minor in comparison to aluminum oxalate and malonate complexes. Divalent metal cations such as Mg, Ca, and Fe form more stable complexes with acetate than with difunctional acid anions. Aluminum-oxalate can dominate the species distribution of aluminum under acidic pH conditions, whereas the divalent cation-acetate and oxalate complexes rarely account for more than 60% of the total dissolved cation, and then only in more alkaline waters. Mineral thermodynamic affinities were calculated using the reaction path model EQ3/6 for waters having variable organic acid anion (OAA) contents under conditions representative of those found during normal burial diagenesis. The following scenarios are possible: 1) K-feldspar and albite are stable, anorthite dissolves 2) All feldpars are stable 3) Carbonates can be very unstable to slightly unstable, but never increase in stability. Organic acid anions are ineffective at neutral to alkaline pH in modifying stabilities of aluminosilicate minerals whereas the anions are variably effective under a wide range of pH in modifying carbonate mineral stabilities. Reaction path calculations demonstrate that the sequence of mineral reactions occurring in an arkosic sandstone-fluid system is only slightly modified by the presence of OAA. A spectrum of possible sandstone alteration mineralogies can be obtained depending on the selected boundary conditions: EQ3/6 predictions include quartz overgrowth, calcite replacement of plagioclase, albitization of plagioclase, and the formation of porosity-occluding calcite cement, smectite, and illite, all of which are commonly documented in rocks. Under some circumstances, OAA-bearing waters are less effective at producing porosity in an arkosic sandstone than are OAA-free waters. In the scenarios modeled in this study the role of OAA in fluid-rock interactions is to contribute to the total alteration assemblage but not necessarily to dominate it, except under exceptional circumstances that might include, for example, hydrocarbon contaminant plumes in aquifers, wetland environments, and within hydrocarbon source-rocks.

Determination of the formation of dark state via depleted spontaneous emission in a complex solvated molecule.

PubMed

Guo, Xunmin; Wang, Sufan; Xia, Andong; Su, Hongmei

2007-07-05

We present a general two-color two-pulse femtosecond pump-dump approach to study the specific population transfer along the reaction coordinate through the higher vibrational energy levels of excited states of a complex solvated molecule via the depleted spontaneous emission. The time-dependent fluorescence depletion provides the correlated dynamical information between the monitored fluorescence state and the SEP "dumped" dark states, and therefore allow us to obtain the dynamics of the formation of the dark states corresponding to the ultrafast photoisomerization processes. The excited-state dynamics of LDS 751 have been investigated as a function of solvent viscosity and solvent polarity, where a cooperative two-step isomerization process is clearly identified within LDS 751 upon excitation.

Interface Reactions and Synthetic Reaction of Composite Systems

PubMed Central

Park, Joon Sik; Kim, Jeong Min

2010-01-01

Interface reactions in composite systems often determine their overall properties, since product phases usually formed at interfaces during composite fabrication processing make up a large portion of the composites. Since most composite materials represent a ternary or higher order materials system, many studies have focused on analyses of diffusion phenomena and kinetics in multicomponent systems. However, the understanding of the kinetic behavior increases the complexity, since the kinetics of each component during interdiffusion reactions need to be defined for interpreting composite behaviors. From this standpoint, it is important to clarify the interface reactions for producing compatible interfaces with desired product phases. A thermodynamic evaluation such as a chemical potential of involving components can provide an understanding of the diffusion reactions, which govern diffusion pathways and product phase formation. A strategic approach for designing compatible interfaces is discussed in terms of chemical potential diagrams and interface morphology, with some material examples.

Single-Molecule Probing the Energy Landscape of Enzymatic Reaction and Non-Covalent Interactions

NASA Astrophysics Data System (ADS)

Lu, H. Peter; Hu, Dehong; Chen, Yu; Vorpagel, Erich R.

2002-03-01

We have applied single-molecule spectroscopy under physiological conditions to study the mechanisms and dynamics of T4 lysozyme enzymatic reactions, characterizing mode-specific protein conformational dynamics. Enzymatic reaction turnovers and the associated structure changes of individual protein molecules were observed simultaneously in real-time. The overall reaction rates were found to vary widely from molecule-to-molecule, and the initial non-specific binding of the enzyme to the substrate was seen to dominate this inhomogeneity. The reaction steps subsequent to the initial binding were found to have homogeneous rates. Molecular dynamics simulation has been applied to elucidate the mechanism and intermediate states of the single-molecule enzymatic reaction. Combining the analysis of single-molecule experimental trajectories, MD simulation trajectories, and statistical modeling, we have revealed the nature of multiple intermediate states involved in the active enzyme-substrate complex formation and the associated conformational change mechanism and dynamics.

Achieving One-Electron Oxidation of a Mononuclear Nonheme Iron(V)-Imido Complex

DOE PAGES

Hong, Seungwoo; Lu, Xiaoyan; Lee, Yong -Min; ...

2017-09-29

Here, a mononuclear nonheme iron(V)-imido complex bearing a tetraamido macrocyclic ligand (TAML), [Fe V(NTs)(TAML)] – (1), was oxidized by one-electron oxidants, affording formation of an iron(V)-imido TAML cation radical species, [Fe V(NTs)(TAML +•)] (2); 2 is a diamagnetic (S = 0) complex, resulting from the antiferromagnetic coupling of the low-spin iron(V) ion (S = 1/2) with the one-electron oxidized ligand (TAML +•). 2 is a competent oxidant in C–H bond functionalization and nitrene transfer reaction, showing that the reactivity of 2 is greater than that of 1.

Pyrene synthesis in circumstellar envelopes and its role in the formation of 2D nanostructures

NASA Astrophysics Data System (ADS)

Zhao, Long; Kaiser, Ralf I.; Xu, Bo; Ablikim, Utuq; Ahmed, Musahid; Joshi, Dharati; Veber, Gregory; Fischer, Felix R.; Mebel, Alexander M.

2018-05-01

For the past decades, the hydrogen-abstraction/acetylene-addition (HACA) mechanism has been instrumental in attempting to untangle the origin of polycyclic aromatic hydrocarbons (PAHs) as identified in carbonaceous meteorites such as Allende and Murchison. However, the fundamental reaction mechanisms leading to the synthesis of PAHs beyond phenanthrene (C14H10) are still unknown. By exploring the reaction of the 4-phenanthrenyl radical (C14H9•) with acetylene (C2H2) under conditions prevalent in carbon-rich circumstellar environments, we show evidence of a facile, isomer-selective formation of pyrene (C16H10). Along with the hydrogen-abstraction/vinylacetylene-addition (HAVA) mechanism, molecular mass growth processes from pyrene may lead through systematic ring expansions not only to more complex PAHs, but ultimately to 2D graphene-type structures. These fundamental reaction mechanisms are crucial to facilitate an understanding of the origin and evolution of the molecular universe and, in particular, of carbon in our Galaxy.

Theoretical studies on atmospheric chemistry of HFE-245mc and perfluoro-ethyl formate: Reaction with OH radicals, atmospheric fate of alkoxy radical and global warming potential

NASA Astrophysics Data System (ADS)

Lily, Makroni; Baidya, Bidisha; Chandra, Asit K.

2017-02-01

Theoretical studies have been performed on the kinetics, mechanism and thermochemistry of the hydrogen abstraction reactions of CF3CF2OCH3 (HFE-245mc) and CF3CF2OCHO with OH radical using DFT based M06-2X method. IRC calculation shows that both hydrogen abstraction reactions proceed via weakly bound hydrogen-bonded complex preceding to the formation of transition state. The rate coefficients calculated by canonical transition state theory along with Eckart's tunnelling correction at 298 K: k1(CF3CF2OCH3 + OH) = 1.09 × 10-14 and k2(CF3CF2OCHO + OH) = 1.03 × 10-14 cm3 molecule-1 s-1 are in very good agreement with the experimental values. The atmospheric implications of CF3CF2OCH3 and CF3CF2OCHO are also discussed.

Gas-Phase Amidation of Carboxylic Acids with Woodward’s Reagent K Ions

PubMed Central

Peng, Zhou; Pilo, Alice L.; Luongo, Carl A.; McLuckey, Scott A.

2015-01-01

Gas-phase amidation of carboxylic acids in multiply-charged peptides is demonstrated via ion/ion reactions with Woodward’s reagent K (wrk) in both positive and negative mode. Woodward’s reagent K, N-ethyl-3-phenylisoxazolium-3′-sulfonate, is a commonly used reagent that activates carboxylates to form amide bonds with amines in solution. Here, we demonstrate that the analogous gas-phase chemistry occurs upon reaction of the wrk ions and doubly protonated (or doubly deprotonated) peptide ions containing the carboxylic acid functionality. The reaction involves the formation of the enol ester intermediate in the electrostatic complex. Upon collisional activation, the ethyl amine on the reagent is transferred to the activated carbonyl carbon on the peptide, resulting in the formation of an ethyl amide (addition of 27 Da to the peptide) with loss of a neutral ketene derivative. Further collision-induced dissociation (CID) of the products and comparison with solution-phase amidation product confirms the structure of the ethyl amide. PMID:26122523

Arenium ions are not obligatory intermediates in electrophilic aromatic substitution

PubMed Central

Galabov, Boris; Koleva, Gergana; Simova, Svetlana; Hadjieva, Boriana; Schaefer, Henry F.; Schleyer, Paul von Ragué

2014-01-01

Our computational and experimental investigation of the reaction of anisole with Cl2 in nonpolar CCl4 solution challenges two fundamental tenets of the traditional SEAr (arenium ion) mechanism of aromatic electrophilic substitution. Instead of this direct substitution process, the alternative addition–elimination (AE) pathway is favored energetically. This AE mechanism rationalizes the preferred ortho and para substitution orientation of anisole easily. Moreover, neither the SEAr nor the AE mechanisms involve the formation of a σ-complex (Wheland-type) intermediate in the rate-controlling stage. Contrary to the conventional interpretations, the substitution (SEAr) mechanism proceeds concertedly via a single transition state. Experimental NMR investigations of the anisole chlorination reaction course at various temperatures reveal the formation of tetrachloro addition by-products and thus support the computed addition–elimination mechanism of anisole chlorination in nonpolar media. The important autocatalytic effect of the HCl reaction product was confirmed by spectroscopic (UV-visible) investigations and by HCl-augmented computational modeling. PMID:24972792

Iterative reactions of transient boronic acids enable sequential C-C bond formation

NASA Astrophysics Data System (ADS)

Battilocchio, Claudio; Feist, Florian; Hafner, Andreas; Simon, Meike; Tran, Duc N.; Allwood, Daniel M.; Blakemore, David C.; Ley, Steven V.

2016-04-01

The ability to form multiple carbon-carbon bonds in a controlled sequence and thus rapidly build molecular complexity in an iterative fashion is an important goal in modern chemical synthesis. In recent times, transition-metal-catalysed coupling reactions have dominated in the development of C-C bond forming processes. A desire to reduce the reliance on precious metals and a need to obtain products with very low levels of metal impurities has brought a renewed focus on metal-free coupling processes. Here, we report the in situ preparation of reactive allylic and benzylic boronic acids, obtained by reacting flow-generated diazo compounds with boronic acids, and their application in controlled iterative C-C bond forming reactions is described. Thus far we have shown the formation of up to three C-C bonds in a sequence including the final trapping of a reactive boronic acid species with an aldehyde to generate a range of new chemical structures.

Modeling Interfacial Glass-Water Reactions: Recent Advances and Current Limitations

DOE PAGES

Pierce, Eric M.; Frugier, Pierre; Criscenti, Louise J.; ...

2014-07-12

Describing the reactions that occur at the glass-water interface and control the development of the altered layer constitutes one of the main scientific challenges impeding existing models from providing accurate radionuclide release estimates. Radionuclide release estimates are a critical component of the safety basis for geologic repositories. The altered layer (i.e., amorphous hydrated surface layer and crystalline reaction products) represents a complex region, both physically and chemically, sandwiched between two distinct boundaries pristine glass surface at the inner most interface and aqueous solution at the outer most interface. Computational models, spanning different length and time-scales, are currently being developed tomore » improve our understanding of this complex and dynamic process with the goal of accurately describing the pore-scale changes that occur as the system evolves. These modeling approaches include geochemical simulations [i.e., classical reaction path simulations and glass reactivity in allowance for alteration layer (GRAAL) simulations], Monte Carlo simulations, and Molecular Dynamics methods. Finally, in this manuscript, we discuss the advances and limitations of each modeling approach placed in the context of the glass-water reaction and how collectively these approaches provide insights into the mechanisms that control the formation and evolution of altered layers.« less

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

The Ionic Building Blocks of Life: Exploring Astrochemistry through Mass Spectrometry

NASA Astrophysics Data System (ADS)

Cole, Callie A.

The first polyatomic molecule was discovered in interstellar space in 1968, catalyzing the growth of a new scientific field called astrochemistry. Since its inception, collaborations among laboratory chemists, astrophysical modelers, and observational astronomers in this field have led to the detection of nearly 200 molecules in the interstellar medium (ISM). Similarly, detections of complex biomolecules in cometary dust and meteorites have sparked theories of the origin of terrestrial life, a central focus of the recently-established field of astrobiology. Chemical processing occurs in a variety of environments within our galaxy. The purpose of this work is to explore the chemistry of ions and molecules that are pertinent to a multitude of these regions including nebulae, prestellar cores, and the atmosphere of Saturn's moon, Titan. This thesis presents mass spectrometric investigations of gas-phase ion chemistry that contribute to the fields of both astrochemistry and astrobiology. Many gas-phase chemical reactions are initiated by ions due to the attractive forces induced by their charge on a reacting partner. This attraction often lowers the barriers of ion-neutral reactions, and can lead to high reaction rates even at low temperatures. The ions examined herein increase in complexity starting with simple species (CN-) and concluding with larger biomolecules, the deprotonated nucleobases. This work begins with a series of Flowing Afterglow-Selected Ion Flow Tube (FA-SIFT) experiments exploring nitrogen-containing carbanion (C xNy-) chemistry and the formation of interstellar propene and methyl formate (Chapters 3 and 4). Reactions between CxN y- and H atoms reveal pathways for destruction of several CxN- and CxN2 - anions, but no reactions are observed for CxN3 - species. Two previously-proposed reactions between organic cations and H2 are shown to be immeasurably slow and unlikely to produce propene. Lastly, a reaction pathway producing protonated trans-methyl formate is experimentally and computationally verified. The later chapters describe studies of heterocyclic biomolecules performed using a modified ion trap apparatus. These ions include deprotonated azoles, pyrimidines, and purines (Chapters 5-7). In addition to their reactivity, the dissociation processes and fragments of these anions provide clues to potential precursors and abiotic syntheses. Notably, nearly all fragments observed are detected interstellar species.

Epitope reactions can be gauged by relative antibody discriminating specificity (RADS) values supported by deletion, substitution and cysteine bridge formation analyses: potential uses in pathogenesis studies

PubMed Central

2012-01-01

Background Epitope-mapping of infectious agents is essential for pathogenesis studies. Since polyclonal antibodies (PAbs) and monoclonal antibodies (MAbs) are always polyspecific and can react with multiple epitopes, it is important to distinguish between specific and non-specific reactions. Relative antibody discriminating specificity (RADS) values, obtained from their relative ELISA reactions with L-amino acid peptides prepared in the natural versus reverse orientations (x-fold absorbance natural/absorbance reverse = RADS value) may be valuable for this purpose. PAbs generated against the dengue type-2 virus (DENV-2) nonstructural-1 (NS1) glycoprotein candidate vaccine also reacted with both DENV envelope (E) glycoproteins and blood-clotting proteins. New xKGSx/xSGKx amino acid motifs were identified on DENV-2 glycoproteins, HIV-1 gp41 and factor IXa. Their potential roles in DENV and HIV-1 antibody-enhanced replication (AER) and auto-immunity were assessed. In this study, a) RADS values were determined for MAbs and PAbs, generated in congeneic (H2: class II) mice against DENV NS1 glycoprotein epitopes, to account for their cross-reaction patterns, and b) MAb 1G5.3 reactions with xKGSx/xSGKx motifs present in the DENV-4 NS1, E and HIV-1 glycoproteins and factor IXa were assessed after the introduction of amino acid substitutions, deletions, or intra-/inter-cysteine (C-C) bridges. Results MAbs 1H7.4, 5H4.3, 3D1.4 and 1G5.3 had high (4.23- to 16.83-fold) RADS values against single epitopes on the DENV-2 NS1 glycoprotein, and MAb 3D1.4 defined the DENV complex-conserved LX1 epitope. In contrast, MAbs 1G5.4-A1-C3 and 1C6.3 had low (0.47- to 1.67-fold) RADS values against multiple epitopes. PAb DENV complex-reactions occurred through moderately-high (2.77- and 3.11-fold) RADS values against the LX1 epitope. MAb 1G5.3 reacted with xSGKx motifs present in DENV-4 NS1 and E glycoproteins, HIV-1 gp41 and factor IXa, while natural C-C bridge formations or certain amino acid substitutions increased its binding activity. Conclusions These results: i) were readily obtained using a standard 96-well ELISA format, ii) showed the LX1 epitope to be the immuno-dominant DENV complex determinant in the NS1 glycoprotein, iii) supported an antigenic co-evolution of the DENV NS1 and E glycoproteins, and iv) identified methods that made it possible to determine the role of anti-DENV PAb reactions in viral pathogenesis. PMID:22546090

Microhydration Effects on the Intermediates of the SN2 Reacation of Iodide Anion with Methyl Iodine

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

Doi, Keisuke; Togano, Eijiro; Xantheas, Sotiris S.

2013-04-15

Reactions of halide anions with methyl halides (X- + CH3Y → XCH3 + Y-) are bimolecular nucleophilic substitution (SN2) reactions that have been well investigated in the last few decades.[1] Figure 1 shows typical potential energy surfaces (PESs) proposed for symmetric (X- + CH3X → XCH3 + X-) SN2 reactions along the reaction coordinate. In the gas phase, the PES has two minima corresponding to the stable X-(CH3X) complexes.[2] The PES is substantially distorted by the solvation. Since the negative charge is delocalized over the [X•••CH3•••X]- moiety at the transition state the stabilization energy gained by the solvation is smallermore » for the transition state than that for the (X- + CH3X) reactants or the X- (CH3X) complexes. In solution, a large potential barrier exists between the reactants and products. The rate constants of these reactions in protic solvents were reported to be a few orders of magnitude smaller than those in aprotic solvents; this trend was explained by the formation of solvation shells of protic molecules around the halide anions.[1,3] Morokuma has previously reported a theoretical study on the PES of the (Cl- + CH3Cl → ClCH3 + Cl-) SN2 reaction with a few H2O molecules. The attachment of H2O molecules to the Cl-(CH3Cl) reactive system produces metastable isomers, which affect the reaction mechanism.[4] Johnson and coworkers extensively investigated the structure and reactions of halide anion complexes in the gas phase using photodissociation spectroscopy.« less

LOW TEMPERATURE FORMATION OF NITROGEN-SUBSTITUTED POLYCYCLIC AROMATIC HYDROCARBONS (PANHs)—BARRIERLESS ROUTES TO DIHYDRO(iso)QUINOLINES

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

Parker, Dorian S. N.; Yang, Tao; Dangi, Beni B.

Meteorites contain bio-relevant molecules such as vitamins and nucleobases, which consist of aromatic structures with embedded nitrogen atoms. Questions remain over the chemical mechanisms responsible for the formation of nitrogen-substituted polycyclic aromatic hydrocarbons (PANHs) in extraterrestrial environments. By exploiting single collision conditions, we show that a radical mediated bimolecular collision between pyridyl radicals and 1,3-butadiene in the gas phase forms nitrogen-substituted polycyclic aromatic hydrocarbons (PANHs) 1,4-dihydroquinoline and to a minor amount 1,4-dihydroisoquinoline. The reaction proceeds through the formation of a van der Waals complex, which circumnavigates the entrance barrier implying it can operate at very low kinetic energy and thereforemore » at low temperatures of 10 K as present in cold molecular clouds such as TMC-1. The discovery of facile de facto barrierless exoergic reaction mechanisms leading to PANH formation could play an important role in providing a population of aromatic structures upon which further photo-processing of ice condensates could occur to form nucleobases.« less

Calcium manganese oxides as oxygen evolution catalysts: O2 formation pathways indicated by 18O-labelling studies.

PubMed

Shevela, Dmitriy; Koroidov, Sergey; Najafpour, M Mahdi; Messinger, Johannes; Kurz, Philipp

2011-05-02

Oxygen evolution catalysed by calcium manganese and manganese-only oxides was studied in (18)O-enriched water. Using membrane-inlet mass spectrometry, we monitored the formation of the different O(2) isotopologues (16)O(2), (16)O(18)O and (18)O(2) in such reactions simultaneously with good time resolution. From the analysis of the data, we conclude that entirely different pathways of dioxygen formation catalysis exist for reactions involving hydrogen peroxide (H(2)O(2)), hydrogen persulfate (HSO(5)(-)) or single-electron oxidants such as Ce(IV) and [Ru(III) (bipy)(3)](3+) . Like the studied oxide catalysts, the active sites of manganese catalase and the oxygen-evolving complex (OEC) of photosystem II (PSII) consist of μ-oxido manganese or μ-oxido calcium manganese sites. The studied processes show very similar (18)O-labelling behaviour to the natural enzymes and are therefore interesting model systems for in vivo oxygen formation by manganese metalloenzymes such as PSII. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Monitoring of protease catalyzed reactions by quantitative MALDI MS using metal labeling.

PubMed

Gregorius, Barbara; Jakoby, Thomas; Schaumlöffel, Dirk; Tholey, Andreas

2013-05-21

Quantitative mass spectrometry is a powerful tool for the determination of enzyme activities as it does not require labeled substrates and simultaneously allows for the identification of reaction products. However, major restrictions are the limited number of samples which can be measured in parallel due to the need for isotope labeled internal standards. Here we describe the use of metal labeling of peptides for the setup of multiplexed enzyme activity assays. After proteolytic reaction, using the protease trypsin, remaining substrates and peptide products formed in the reaction were labeled with metal chelators complexing rare earth metal ions. Labeled peptides were quantified with high accuracy and over a wide dynamic range (at least 2 orders of magnitude) using MALDI MS in case of simple peptide mixtures or by LC-MALDI MS for complex substrate mixtures and used for the monitoring of time-dependent product formation and substrate consumption. Due to multiplexing capabilities and accuracy, the presented approach will be useful for the determination of enzyme activities with a wide range of biochemical and biotechnological applications.

In situ formation of the amino sugars 1-amino-1-deoxy-fructose and 2-amino-2-deoxy-glucose under Maillard reaction conditions in the absence of ammonia.

PubMed

Nashalian, Ossanna; Yaylayan, Varoujan A

2016-04-15

Replacing amino acids with their binary metal complexes during the Maillard reaction can initiate various processes, including the oxidative degradation of their glucose conjugates, generating 1-amino-1-deoxy-fructose and its derivatives. These reactive amino sugars are not easily accessible under Maillard reaction conditions and are only formed in the presence of ammonia. To explore the generality of this observation and to study in particular the ability of fructose to generate glucosamine, the amino acid-metal complexes were heated in aqueous solutions with three aldohexoses and two ketohexoses at 110°C for 2 h and the dry residues were analysed by ESI/qTOF/MS/MS. All the sugars generated relatively intense ions at [M+H](+) 180 (C6H14NO5); those ions originating from ketohexoses exhibited MS/MS fragmentations identical to glucosamine and those originating form aldohexoses showed ions identical to fructosamine. Furthermore, the amino sugars were found to form fructosazine, react with other sugars and undergo dehydration reactions. Copyright © 2015 Elsevier Ltd. All rights reserved.

Dynamics and Novel Mechanisms of SN2 Reactions on ab Initio Analytical Potential Energy Surfaces.

PubMed

Szabó, István; Czakó, Gábor

2017-11-30

We describe a novel theoretical approach to the bimolecular nucleophilic substitution (S N 2) reactions that is based on analytical potential energy surfaces (PESs) obtained by fitting a few tens of thousands high-level ab initio energy points. These PESs allow computing millions of quasi-classical trajectories thereby providing unprecedented statistical accuracy for S N 2 reactions, as well as performing high-dimensional quantum dynamics computations. We developed full-dimensional ab initio PESs for the F - + CH 3 Y [Y = F, Cl, I] systems, which describe the direct and indirect, complex-forming Walden-inversion, the frontside attack, and the new double-inversion pathways as well as the proton-transfer channels. Reaction dynamics simulations on the new PESs revealed (a) a novel double-inversion S N 2 mechanism, (b) frontside complex formation, (c) the dynamics of proton transfer, (d) vibrational and rotational mode specificity, (e) mode-specific product vibrational distributions, (f) agreement between classical and quantum dynamics, (g) good agreement with measured scattering angle and product internal energy distributions, and (h) significant leaving group effect in accord with experiments.

Reprint of "How do components of real cloud water affect aqueous pyruvate oxidation?"

NASA Astrophysics Data System (ADS)

Boris, Alexandra J.; Desyaterik, Yury; Collett, Jeffrey L.

2015-01-01

Chemical oxidation of dissolved volatile or semi-volatile organic compounds within fog and cloud droplets in the atmosphere could be a major pathway for secondary organic aerosol (SOA) formation. This proposed pathway consists of: (1) dissolution of organic chemicals from the gas phase into a droplet; (2) reaction with an aqueous phase oxidant to yield low volatility products; and (3) formation of particle phase organic matter as the droplet evaporates. The common approach to simulating aqueous SOA (aqSOA) reactions is photo-oxidation of laboratory standards in pure water. Reactions leading to aqSOA formation should be studied within real cloud and fog water to determine whether additional competing processes might alter apparent rates of reaction as indicated by rates of reactant loss or product formation. To evaluate and identify the origin of any cloud water matrix effects on one example of observed aqSOA production, pyruvate oxidation experiments simulating aqSOA formation were monitored within pure water, real cloud water samples, and an aqueous solution of inorganic salts. Two analysis methods were used: online electrospray ionization high-resolution time-of-flight mass spectrometry (ESI-HR-ToF-MS), and offline anion exchange chromatography (IC) with quantitative conductivity and qualitative ESI-HR-ToF-MS detection. The apparent rate of oxidation of pyruvate was slowed in cloud water matrices: overall measured degradation rates of pyruvate were lower than in pure water. This can be at least partially accounted for by the observed formation of pyruvate from reactions of other cloud water components. Organic constituents of cloud water also compete for oxidants and/or UV light, contributing to the observed slowed degradation rates of pyruvate. The oxidation of pyruvate was not significantly affected by the presence of inorganic anions (nitrate and sulfate) at cloud-relevant concentrations. Future bulk studies of aqSOA formation reactions using simplified simulated cloud solutions and model estimates of generated aqSOA mass should take into account possible generation of, or competition for, oxidant molecules by organic components found in the complex matrices typically associated with real atmospheric water droplets. Additionally, it is likely that some components of real atmospheric waters have not yet been identified as aqSOA precursors, but could be distinguished through further simplified bulk oxidations of known atmospheric water components.

Making the invisible visible: improved electrospray ion formation of metalloporphyrins/-phthalocyanines by attachment of the formate anion (HCOO(-)).

PubMed

Hitzenberger, Jakob Felix; Dammann, Claudia; Lang, Nina; Lungerich, Dominik; García-Iglesias, Miguel; Bottari, Giovanni; Torres, Tomás; Jux, Norbert; Drewello, Thomas

2016-02-21

A protocol is developed for the coordination of the formate anion (HCOO(-)) to neutral metalloporphyrins (Pors) and -phthalocyanines (Pcs) containing divalent metals as a means to improve their ion formation in electrospray ionization (ESI). This method is particularly useful when the oxidation of the neutral metallomacrocycle fails. While focusing on Zn(II)Pors and Zn(II)Pcs, we show that formate is also readily attached to Mn(II), Mg(II) and Co(II)Pcs. However, for the Co(II)Pc secondary reactions can be observed. Upon collision-induced dissociation (CID), Zn(II)Por/Pc·formate supramolecular complexes can undergo the loss of CO2 in combination with transfer of a hydride anion (H(-)) to the zinc metal center. Further dissociation leads to electron transfer and hydrogen atom loss, generating a route to the radical anion of the Zn(II)Por/Pc without the need for electrochemical reduction, although the Zn(II)Por/Pc may have a too low electron affinity to allow electron transfer directly from the formate anion. In addition to single Por molecules, multi Por arrays were successfully analyzed by this method. In this case, multiple addition of formate occurs, giving rise to multiply charged species. In these multi Por arrays, complexation of the formate anion occurs by two surrounding Por units (sandwich). Therefore, the maximum attainment of formate anions in these arrays corresponds to the number of such sandwich complexes rather than the number of porphyrin moieties. The same bonding motif leads to dimers of the composition [(Zn(II)Por/Pc)2·HCOO](-). In these, the formate anion can act as a structural probe, allowing the distinction of isomeric ions with the formate bridging two macrocycles or being attached to a dimer of directly connected macrocycles.

Single Turnover Kinetics of Tryptophan Hydroxylase: Evidence for a New Intermediate in the Reaction of the Aromatic Amino Acid Hydroxylases

PubMed Central

Pavon, Jorge Alex; Eser, Bekir; Huynh, Michaela T.; Fitzpatrick, Paul F.

2010-01-01

Tryptophan hydroxylase (TrpH) uses a non-heme mononuclear iron center to catalyze the tetrahydropterin-dependent hydroxylation of tryptophan to 5-hydroxytryptophan. The reactions of the TrpH·Fe(II), TrpH·Fe(II)·tryptophan, TrpH·Fe(II)·6MePH4·tryptophan, and TrpH·Fe(II)·6MePH4·phenylalanine complexes with O2 were monitored by stopped-flow absorbance spectroscopy and rapid quench methods. The second-order rate constant for the oxidation of TrpH·Fe(II) has a value of 104 M−1s−1 irrespective of the presence of tryptophan. Stopped-flow absorbance analyses of the reaction of the TrpH·Fe(II)·6MePH4·tryptophan complex with oxygen are consistent with the initial step being reversible binding of oxygen, followed by the formation with a rate constant of 65 s−1 of an intermediate I that has maximal absorbance at 420 nm. The rate constant for decay of I, 4.4 s−1, matches that for formation of the 4a-hydroxypterin product monitored at 248 nm. Chemical-quench analyses show that 5-hydroxytryptophan forms with a rate constant of 1.3 s−1, and that overall turnover is limited by a subsequent slow step, presumably product release, with a rate constant of 0.2 s−1. All of the data with tryptophan as substrate can be described by a five-step mechanism. In contrast, with phenylalanine as substrate, the reaction can be described by three steps: a second-order reaction with oxygen to form I, decay of I as tyrosine forms, and slow product release. PMID:20687613

Spectroscopic study of the reaction mechanism of buspirone interaction with iodine and tetracyanoethylene reagents and its applications.

PubMed

Zayed, M A; El-Habeeb, Abeer A

2009-06-01

The reactions between the drug buspirone (busp) in its base form and iodine amphoteric reagent (n-donor and/or sigma-acceptor) and with tetracyanoethylene as a pi-acceptor reagent (TCNE) have been studied spectrophotometrically at different reactant concentrations, time intervals, temperatures, and with different solvents and wavelengths, with the aim of selecting the conditions that give the most suitable molar extinction coefficients. This study aims chiefly to throw light on the nature of these reactions and to select the most proper conditions for spectrophotometric application of these reagents to determine this biologically active drug used in treating different diseases. The reaction mechanism involves the formation of busp-I(2) outer and inner sphere complexes. The separated busp-I(2) solid product obtained was investigated using elemental analyses, FT-IR, thermal analyses (TA) and electron ionization mass spectrometry (EI-MS) and was found to be biologically active. The reaction mechanism of busp-TCNE involves the formation of a charge transfer (CT) complex. The analytical parameters of the proposed spectrophotometric procedures were calculated. These procedures were applied in the analysis of busp in its formulations as a drug used to treat psychiatric illnesses. The values of the Sandell sensitivity, standard deviation (SD), relative standard deviation (RSD) and recovery percentage show the high sensitivity of these procedures. This study also presents a promising new busp-I(2) drug derivative that can be used more efficiently for the same purposes as its parent. It gives a clear idea about the possible metabolites and metabolic pathways of busp and its derivative that may occur in vivo. Copyright 2009 John Wiley & Sons, Ltd.

Evolution of an RNP assembly system: A minimal SMN complex facilitates formation of UsnRNPs in Drosophila melanogaster

PubMed Central

Kroiss, Matthias; Schultz, Jörg; Wiesner, Julia; Chari, Ashwin; Sickmann, Albert; Fischer, Utz

2008-01-01

In vertebrates, assembly of spliceosomal uridine-rich small nuclear ribonucleoproteins (UsnRNPs) is mediated by the SMN complex, a macromolecular entity composed of the proteins SMN and Gemins 2–8. Here we have studied the evolution of this machinery using complete genome assemblies of multiple model organisms. The SMN complex has gained complexity in evolution by a blockwise addition of Gemins onto an ancestral core complex composed of SMN and Gemin2. In contrast to this overall evolutionary trend to more complexity in metazoans, orthologs of most Gemins are missing in dipterans. In accordance with these bioinformatic data a previously undescribed biochemical purification strategy elucidated that the dipteran Drosophila melanogaster contains an SMN complex of remarkable simplicity. Surprisingly, this minimal complex not only mediates the assembly reaction in a manner very similar to its vertebrate counterpart, but also prevents misassembly onto nontarget RNAs. Our data suggest that only a minority of Gemins are required for the assembly reaction per se, whereas others may serve additional functions in the context of UsnRNP biogenesis. The evolution of the SMN complex is an interesting example of how the simplification of a biochemical process contributes to genome compaction. PMID:18621711

Metal-promoted binuclear C-H activation of ethylene and formation of a novel heterobimetallic Ir-Pt complex. X-ray crystal structure of ((Ph sub 3 P) sub 2 (CO)Ir(. mu. -H)(. mu. -. eta. sup 2 :. eta. sup 1 -CH double bond CH sub 2 )Pt(PPh sub 3 ) sub 2 ) sup + CF sub 3 SO sub 3 sup minus

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

Huang, Yohsin; Stang, P.J.; Arif, A.M.

1990-07-04

Heterobimetallic complexes containing asymmetric metal-metal bonds as well as homogeneous C-H bond activation by organometallic compounds are of considerable current interest largely because of their relevance to catalysis. Although coordination of an alkene to transition metal systems is generally considered a necessary activation step in many catalytic and stoichiometric organometallic reactions, little is known about alkene C-H bond activation of precomplexed olefin substrates. In this paper the authors report the first intermolecular example of olefin C-H activation by a second, different metal system of a precomplexed {pi}-ethylene transition-metal complex and the concomitant formation of a novel alkene-bridged heterobimetallic Ir-Pt complex.

Spectroscopic studies on [(DD18C6H 2)(HPA) 2](PA) 2 and [(DD18C6H 2)(DDQ) 2](DDQH) 2 formed in the reaction of N, N'-dibenzyl-1,4,10,13-tetraoxa-7,16-diazacyclooctadecane with HPA and DDQ

NASA Astrophysics Data System (ADS)

Teleb, Said M.; Gaballa, Akmal S.; Elmosallamy, M. A. F.; Nour, El-Metwally

2005-09-01

The interaction of the mixed oxygen-nitrogen cyclic base, N, N'-dibenzyl-1,4,10,13-tetraoxa-7,16-diazacyclooctadecane (DD18C6) with π-acceptors such as picric acid (HPA) and 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) has been studied spectrophotometrically in chloroform at 25 °C. The results obtained indicate the formation of 1:4 charge-transfer complexes with the general formula (DD18C6)(acceptor) 4. The electronic and infrared spectra of charge-transfer complexes along with the 1H NMR spectra were recorded and discussed. Based on the data obtained, the complexes were formulated as [(DD18C6H 2)(HPA) 2](PA) 2 and [(DD18C6H 2)(DDQ) 2](DDQH) 2. A general mechanism explaining the formation of the DDQ complex has been suggested.

Spectroscopic and thermal investigations of charge-transfer complexes formed between sulfadoxine drug and different types of acceptors

NASA Astrophysics Data System (ADS)

Refat, Moamen S.

2011-01-01

Charge-transfer reactions between sulfadoxine (SDOX) as a donor with iodine (I 2), 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ), p-chloranil (CHL) and picric acid (PA) have been studied in solid and solution forms. The stoichiometry of all complexes was found to be 1:1 by molar ratio method between donor and acceptor at a CT-band absorption bands. The data are discussed in terms of formation constant ( KCT), molar extinction coefficient ( ɛCT), standard free energy (Δ Go), oscillator strength (ƒ), transition dipole moment ( μ), resonance energy ( RN) and ionization potential ( ID). The results indicate that the formation constant ( KCT) for the complexes were shown to be dependent upon the nature of electron acceptor, donor and polarity of solvents which were used. IR, 1H NMR and UV-Vis spectroscopic techniques, Elemental analyses (CHN) and TG-DTG investigation were used to characterize the four sulfadoxine charge-transfer complexes.

Enhanced chlorine dioxide decay in the presence of metal oxides: relevance to drinking water distribution systems.

PubMed

Liu, Chao; von Gunten, Urs; Croué, Jean-Philippe

2013-08-06

Chlorine dioxide (ClO2) decay in the presence of typical metal oxides occurring in distribution systems was investigated. Metal oxides generally enhanced ClO2 decay in a second-order process via three pathways: (1) catalytic disproportionation with equimolar formation of chlorite and chlorate, (2) reaction to chlorite and oxygen, and (3) oxidation of a metal in a reduced form (e.g., cuprous oxide) to a higher oxidation state. Cupric oxide (CuO) and nickel oxide (NiO) showed significantly stronger abilities than goethite (α-FeOOH) to catalyze the ClO2 disproportionation (pathway 1), which predominated at higher initial ClO2 concentrations (56-81 μM). At lower initial ClO2 concentrations (13-31 μM), pathway 2 also contributed. The CuO-enhanced ClO2 decay is a base-assisted reaction with a third-order rate constant of 1.5 × 10(6) M(-2) s(-1) in the presence of 0.1 g L(-1) CuO at 21 ± 1 °C, which is 4-5 orders of magnitude higher than in the absence of CuO. The presence of natural organic matter (NOM) significantly enhanced the formation of chlorite and decreased the ClO2 disproportionation in the CuO-ClO2 system, probably because of a higher reactivity of CuO-activated ClO2 with NOM. Furthermore, a kinetic model was developed to simulate CuO-enhanced ClO2 decay at various pH values. Model simulations that agree well with the experimental data include a pre-equilibrium step with the rapid formation of a complex, namely, CuO-activated Cl2O4. The reaction of this complex with OH(-) is the rate-limiting and pH-dependent step for the overall reaction, producing chlorite and an intermediate that further forms chlorate and oxygen in parallel. These novel findings suggest that the possible ClO2 loss and the formation of chlorite/chlorate should be carefully considered in drinking water distribution systems containing copper pipes.

Fe(II) sorption on pyrophyllite: Effect of structural Fe(III) (impurity) in pyrophyllite on nature of layered double hydroxide (LDH) secondary mineral formation

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

Starcher, Autumn N.; Li, Wei; Kukkadapu, Ravi K.

Fe(II)-Al(III)-LDH (layered double hydroxide) phases have been shown to form from reactions of aqueous Fe(II) with Fe-free Al-bearing minerals (phyllosilicate/clays and Al-oxides). To our knowledge, the effect of small amounts of structural Fe(III) impurities in “neutral” clays on such reactions, however, were not studied. In this study to understand the role of structural Fe(III) impurity in clays, laboratory batch studies with pyrophyllite (10 g/L), an Al-bearing phyllosilicate, containing small amounts of structural Fe(III) impurities and 0.8 mM and 3 mM Fe(II) (both natural and enriched in 57Fe) were carried out at pH 7.5 under anaerobic conditions (4% H2 – 96%more » N2 atmosphere). Samples were taken up to 4 weeks for analysis by Fe-X-ray absorption spectroscopy and 57Fe Mössbauer spectroscopy. In addition to the precipitation of Fe(II)-Al(III)-LDH phases as observed in earlier studies with pure minerals (no Fe(III) impurities in the minerals), the analyses indicated formation of small amounts of Fe(III) containing solid(s), most probably hybrid a Fe(II)-Al(III)/Fe(III)-LDH phase. The mechanism of Fe(II) oxidation was not apparent but most likely was due to interfacial electron transfer from the sorbed Fe(II) to the structural Fe(III) and/or surface-sorption-induced electron-transfer from the sorbed Fe(II) to the clay lattice. Increase in the Fe(II)/Al ratio of the LDH with reaction time further indicated the complex nature of the samples. This research provides evidence for the formation of both Fe(II)-Al(III)-LDH and Fe(II)-Fe(III)/Al(III)-LDH-like phases during reactions of Fe(II) in systems that mimic the natural environments. Better understanding Fe phase formation in complex laboratory studies will improve models of natural redox systems.« less

Copper complexes of anionic nitrogen ligands in the amidation and imidation of aryl halides.

PubMed

Tye, Jesse W; Weng, Zhiqiang; Johns, Adam M; Incarvito, Christopher D; Hartwig, John F

2008-07-30

Copper(I) imidate and amidate complexes of chelating N,N-donor ligands, which are proposed intermediates in copper-catalyzed amidations of aryl halides, have been synthesized and characterized by X-ray diffraction and detailed solution-phase methods. In some cases, the complexes adopt neutral, three-coordinate trigonal planar structures in the solid state, but in other cases they adopt an ionic form consisting of an L 2Cu (+) cation and a CuX 2 (-) anion. A tetraalkylammonium salt of the CuX 2 (-) anion in which X = phthalimidate was also isolated. Conductivity measurements and (1)H NMR spectra of mixtures of two complexes all indicate that the complexes exist predominantly in the ionic form in DMSO and DMF solutions. One complex was sufficiently soluble for conductance measurements in less polar solvents and was shown to adopt some degree of the ionic form in THF and predominantly the neutral form in benzene. The complexes containing dative nitrogen ligands reacted with iodoarenes and bromoarenes to form products from C-N coupling, but the ammonium salt of [Cu(phth) 2] (-) did not. Similar selectivities for stoichiometric and catalytic reactions with two different iodoarenes and faster rates for the stoichiometric reactions implied that the isolated amidate and imidate complexes are intermediates in the reactions of amides and imides with haloarenes catalyzed by copper complexes containing dative N,N ligands. These amidates and imidates reacted much more slowly with chloroarenes, including chloroarenes that possess more favorable reduction potentials than some bromoarenes and that are known to undergo fast dissociation of chloride from the chloroarene radical anion. The reaction of o-(allyloxy)iodobenzene with [(phen) 2Cu][Cu(pyrr) 2] results in formation of the C-N coupled product in high yield and no detectable amount of the 3-methyl-2,3-dihydrobenzofuran or 3-methylene-2,3-dihydrobenzofuran products that would be expected from a reaction that generated free radicals. These data and computed reaction barriers argue against mechanisms in which the haloarene reacts with a two-coordinate anionic copper species and mechanisms that start with electron transfer to generate a free iodoarene radical anion. Instead, these data are more consistent with mechanisms involving cleavage of the carbon-halogen bond within the coordination sphere of the metal.

Functional-Group-Tolerant, Silver-Catalyzed N-N Bond Formation by Nitrene Transfer to Amines.

PubMed

Maestre, Lourdes; Dorel, Ruth; Pablo, Óscar; Escofet, Imma; Sameera, W M C; Álvarez, Eleuterio; Maseras, Feliu; Díaz-Requejo, M Mar; Echavarren, Antonio M; Pérez, Pedro J

2017-02-15

Silver(I) promotes the highly chemoselective N-amidation of tertiary amines under catalytic conditions to form aminimides by nitrene transfer from PhI═NTs. Remarkably, this transformation proceeds in a selective manner in the presence of olefins and other functional groups without formation of the commonly observed aziridines or C-H insertion products. The methodology can be applied not only to rather simple tertiary amines but also to complex natural molecules such as brucine or quinine, where the products derived from N-N bond formation were exclusively formed. Theoretical mechanistic studies have shown that this selective N-amidation reaction proceeds through triplet silver nitrenes.

Oxidation of monohydric phenol substrates by tyrosinase: effect of dithiothreitol on kinetics.

PubMed

Naish-Byfield, S; Cooksey, C J; Riley, P A

1994-11-15

The effect of thiol compounds on the monophenolase activity of tyrosinase was investigated using 4-hydroxyanisole as the substrate and dithiothreitol (DTT) as the model thiol compound. We have demonstrated three actions of DTT on tyrosinase-catalysed reactions: (1) direct reduction of the copper at the active site of the enzyme; (2) generation of secondary, oxidizable species by adduct formation with the o-quinone reaction product, 4-MOB, which leads to an increase in the total oxygen utilization by the reaction system; and (3) reversible inhibition of the enzyme. We confirm our previous observation that, at approx. 10 mol of DTT/mol of enzyme, the lag phase associated with monohydric phenol oxidation by tyrosinase is abolished. We suggest that this is due to reduction of the copper at the active site of the enzyme by DTT, since (a) reduction of active-site copper in situ by DTT was demonstrated by [Cu(I)]2-carbon monoxide complex formation and (b) abolition of the lag at low DTT concentration occurs without effect on the maximum rate of reaction or on the total amount of oxygen utilized. At concentrations of DTT above that required to abolish the lag, we found that the initial velocity of the reaction increased with increasing DTT, with a concomitant increase in the total oxygen utilization. This is due to the formation of DTT-4-methoxy-o-benzoquinone (4-MOB) adducts which provide additional dihydric phenol substrate either directly or by reducing nascent 4-MOB. We present n.m.r. evidence for the formation of mono- and di-aromatic DTT adducts with 4-MOB, consistent with a suggested reoxidation scheme in the presence of tyrosinase. Inhibition of the enzyme at concentrations of DTT above 300 pmol/unit of enzyme was released on exhaustion of DTT by adduct formation with 4-MOB as it was generated.

Biomimetic syntheses of racemic natural products.

PubMed

Zask, Arie; Ellestad, George

2018-02-01

Racemic natural products are rarely produced in plants and microorganisms and are thought to be the result of nonenzymatic, spontaneous reactions. These compounds are often highly complex with multiple contiguous chiral centers that present a challenge to organic synthesis. Formation of these racemates often occurs by cyclization reactions that can generate multiple stereocenters from achiral precursors. Biomimetic synthesis of these racemic natural products provides support for their proposed nonenzymatic spontaneous biosynthesis. These elegant syntheses also provide scalable and efficient routes to these complex natural products. Although the number of reported racemic natural products is relatively low, an isolated natural product that has a very small optical rotation has been shown to be a true racemate. Thus, the occurrence of racemic natural products could be more common than thought. © 2017 Wiley Periodicals, Inc.

Formation of uniform carrot-like Cu31S16-CuInS2 heteronanostructures assisted by citric acid at the oil/aqueous interface.

PubMed

Li, Yongjie; Tang, Aiwei; Liu, Zhenyang; Peng, Lan; Yuan, Yi; Shi, Xifeng; Yang, Chunhe; Teng, Feng

2018-01-07

A simple two-phase strategy was developed to prepare Cu 31 S 16 -CuInS 2 heterostructures (HNS) at the oil/aqueous interface, in which the In(OH) 3 phase was often obtained in the products due to the reaction between indium ions and hydroxyl ions in the aqueous phase. To prevent the formation of the In(OH) 3 phase, citric acid was incorporated into the aqueous phase to assist in the synthesis of uniform carrot-like Cu 31 S 16 -CuInS 2 semiconductor HNS at the oil/aqueous interface for the first time. By manipulating the dosage of citric acid and Cu/In precursor ratios, the morphology of the Cu 31 S 16 -CuInS 2 HNS could be tailored from mushroom to carrot-like, and the presence of citric acid played a critical role in the synthesis of high-quality Cu 31 S 16 -CuInS 2 HNS, which inhibited the formation of the In(OH) 3 phase due to the formation of the indium(iii)-citric acid complex. The formation mechanism was studied by monitoring the morphology and phase evolution of the Cu 31 S 16 -CuInS 2 HNS with reaction time, which revealed that the Cu 31 S 16 seeds were first formed and then the cation-exchange reaction directed the subsequent anisotropic growth of the Cu 31 S 16 -CuInS 2 HNS.

Revealing Brown Carbon Chromophores Produced in Reactions of Methylglyoxal with Ammonium Sulfate.

PubMed

Lin, Peng; Laskin, Julia; Nizkorodov, Sergey A; Laskin, Alexander

2015-12-15

Atmospheric brown carbon (BrC) is an important contributor to light absorption and climate forcing by aerosols. Reactions between small water-soluble carbonyls and ammonia or amines have been identified as one of the potential pathways of BrC formation. However, detailed chemical characterization of BrC chromophores has been challenging and their formation mechanisms are still poorly understood. Understanding BrC formation is impeded by the lack of suitable methods which can unravel the variability and complexity of BrC mixtures. This study applies high performance liquid chromatography (HPLC) coupled to photodiode array (PDA) detector and high resolution mass spectrometry (HRMS) to investigate optical properties and chemical composition of individual BrC components produced through reactions of methylglyoxal (MG) and ammonium sulfate (AS), both of which are abundant in the atmospheric environment. A direct relationship between optical properties and chemical composition of 30 major BrC chromophores is established. Nearly all of these chromophores are nitrogen-containing compounds that account for >70% of the overall light absorption by the MG+AS system in the 300-500 nm range. These results suggest that reduced-nitrogen organic compounds formed in reactions between atmospheric carbonyls and ammonia/amines are important BrC chromophores. It is also demonstrated that improved separation of BrC chromophores by HPLC will significantly advance understanding of BrC chemistry.

Revealing Brown Carbon Chromophores Produced in Reactions of Methylglyoxal with Ammonium Sulfate

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

Lin, Peng; Laskin, Julia; Nizkorodov, Sergey A.

Atmospheric brown carbon (BrC) is an important contributor to light absorption and climate forcing by aerosols. Reactions between small water-soluble carbonyls and ammonia or amines have been identified as one of the potential pathways of BrC formation. However, detailed chemical characterization of BrC chromophores has been challenging and their formation mechanisms are still poorly understood. Understanding BrC formation is impeded by the lack of suitable methods which can unravel the variability and complexity of BrC mixtures. This study applies high performance liquid chromatography (HPLC) coupled to photodiode array (PDA) detector and high resolution mass spectrometry (HRMS) to investigate optical propertiesmore » and chemical composition of individual BrC components produced through reactions of methylglyoxal (MG) and ammonium sulfate (AS), both of which are abundant in the atmospheric environment. A direct relationship between optical properties and chemical composition of 30 major BrC chromophores was established. Nearly all of these chromophores are nitrogen-containing compounds that account for >70% of the overall light absorption by the MG+AS system in the 300-500 nm range. These results suggest that reduced-nitrogen organic compounds formed in reactions between atmospheric carbonyls and ammonia/amines are important BrC chromophores. It is also demonstrated that improved separation of BrC chromophores by HPLC will significantly advance understanding of BrC chemistry.« less

Insertion reactions into Pd[bond]O and Pd[bond]N bonds: preparation of alkoxycarbonyl, carbonato, carbamato, thiocarbamate, and thioureide complexes of palladium(II).

PubMed

Ruiz, José; Martínez, M Teresa; Florenciano, Félix; Rodríguez, Venancio; López, Gregorio; Pérez, José; Chaloner, Penny A; Hitchcock, Peter B

2003-06-02

Mononuclear palladium hydroxo complexes of the type [Pd(N[bond]N)(C(6)F(5))(OH)] [(N[bond]N = 2,2'-bipyridine (bipy), 4,4'-dimethyl-2,2'-bipyridine (Me(2)bipy), 1,10-phenanthroline (phen), or N,N,N',N'-tetramethylethylenediamine (tmeda)] have been prepared by reaction of [Pd(N[bond]N)(C(6)F(5))(acetone)]ClO(4) with KOH in methanol. These hydroxo complexes react, in methanol, with CO (1 atm, room temperature) to yield the corresponding methoxycarbonyl complexes [Pd(N[bond]N)(C(6)F(5))(CO(2)Me)]. Similar alkoxycarbonyl complexes [Pd(N[bond]N)(C(6)F(5))(CO(2)R)] (N[bond]N = bis(3,5-dimethylpyrazol-1-yl)methane); R = Me, Et, or (i)Pr) are obtained when [Pd(N[bond]N)(C(6)F(5))Cl] is treated with KOH in the corresponding alcohol ROH and CO is bubbled through the solution. The reactions of [Pd(N[bond]N)(C(6)F(5))(OH)] (N[bond]N = bipy or Me(2)bipy) with CO(2), in tetrahydrofuran, lead to the formation of the binuclear carbonate complexes [(N[bond]N)(C(6)F(5))Pd(mu-eta(2)-CO(3))Pd(C(6)F(5))(N[bond]N)]. Complexes [Pd(N[bond]N)(C(6)F(5))(OH)] react in alcohol with PhNCS to yield the corresponding N-phenyl-O-alkylthiocarbamate complexes [Pd(N[bond]N)(C(6)F(5))[SC(OR)NPh

Structure, dynamics and stability of water/scCO2/mineral interfaces from ab initio molecular dynamics simulations.

PubMed

Lee, Mal-Soon; Peter McGrail, B; Rousseau, Roger; Glezakou, Vassiliki-Alexandra

2015-10-12

The boundary layer at solid-liquid interfaces is a unique reaction environment that poses significant scientific challenges to characterize and understand by experimentation alone. Using ab initio molecular dynamics (AIMD) methods, we report on the structure and dynamics of boundary layer formation, cation mobilization and carbonation under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar) on a prototypical anorthite (001) surface. At low coverage, water film formation is enthalpically favored, but entropically hindered. Simulated adsorption isotherms show that a water monolayer will form even at the low water concentrations of water-saturated scCO2. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies that readily form in the presence of a water monolayer. These results point to a carbonation mechanism that does not require prior carbonic acid formation in the bulk liquid. This work also highlights the modern capabilities of theoretical methods to address structure and reactivity at interfaces of high chemical complexity.

Complexes of horseradish peroxidase with formate, acetate, and carbon monoxide.

PubMed

Carlsson, Gunilla H; Nicholls, Peter; Svistunenko, Dimitri; Berglund, Gunnar I; Hajdu, Janos

2005-01-18

Carbon monoxide, formate, and acetate interact with horseradish peroxidase (HRP) by binding to subsites within the active site. These ligands also bind to catalases, but their interactions are different in the two types of enzymes. Formate (notionally the "hydrated" form of carbon monoxide) is oxidized to carbon dioxide by compound I in catalase, while no such reaction is reported to occur in HRP, and the CO complex of ferrocatalase can only be obtained indirectly. Here we describe high-resolution crystal structures for HRP in its complexes with carbon monoxide and with formate, and compare these with the previously determined HRP-acetate structure [Berglund, G. I., et al. (2002) Nature 417, 463-468]. A multicrystal X-ray data collection strategy preserved the correct oxidation state of the iron during the experiments. Absorption spectra of the crystals and electron paramagnetic resonance data for the acetate and formate complexes in solution correlate electronic states with the structural results. Formate in ferric HRP and CO in ferrous HRP bind directly to the heme iron with iron-ligand distances of 2.3 and 1.8 A, respectively. CO does not bind to the ferric iron in the crystal. Acetate bound to ferric HRP stacks parallel with the heme plane with its carboxylate group 3.6 A from the heme iron, and without an intervening solvent molecule between the iron and acetate. The positions of the oxygen atoms in the bound ligands outline a potential access route for hydrogen peroxide to the iron. We propose that interactions in this channel ensure deprotonation of the proximal oxygen before binding to the heme iron.

Simultaneous determination of thermodynamic and kinetic parameters of aminopolycarbonate complexes of cobalt(II) and nickel(II) based on isothermal titration calorimetry data.

PubMed

Tesmar, Aleksandra; Wyrzykowski, Dariusz; Muñoz, Eva; Pilarski, Bogusław; Pranczk, Joanna; Jacewicz, Dagmara; Chmurzyński, Lech

2017-04-01

The influence of the different side chain residues on the thermodynamic and kinetic parameters for complexation reactions of the Co 2 + and Ni 2 + ions has been investigated by using the isothermal titration calorimetry (ITC) technique supported by potentiometric titration data. The study was concerned with the 2 common tripodal aminocarboxylate ligands, namely, nitrilotriacetic acid and N-(2-hydroxyethyl) iminodiacetic acid. Calorimetric measurements (ITC) were run in the 2-(N-morpholino)ethanesulfonic acid hydrate (2-(N-morpholino) ethanesulfonic acid), piperazine-N,N'-bis(2-ethanesulfonic acid), and dimethylarsenic acid buffers (0.1 mol L -1 , pH 6) at 298.15 K. The quantification of the metal-buffer interactions and their incorporation into the ITC data analysis enabled to obtain the pH-independent and buffer-independent thermodynamic parameters (K, ΔG, ΔH, and ΔS) for the reactions under study. Furthermore, the kinITC method was applied to obtain kinetic information on complexation reactions from the ITC data. Correlations, based on kinetic and thermodynamic data, between the kinetics of formation of Co 2 + and Ni 2 + complexes and their thermodynamic stabilities are discussed. Copyright © 2016 John Wiley & Sons, Ltd.

Studying the association complex formation of atomoxetine and fluvoxamine with eosin Y and its application in their fluorimetric determination

NASA Astrophysics Data System (ADS)

Derayea, Sayed M.; Omar, Mahmoud A.; Abu-hassan, Ahmed A.

2018-03-01

A simple, sensitive and non-extractive spectrofluorimetric method has been developed and validated for the determination of two psychoanaleptic drugs, atomoxetine and fluvoxamine, in pure forms and pharmaceutical dosage forms. The proposed method is based on the formation of binary complexes between eosin Y and the studied drugs in the presence of a Teorell-Stenhagen buffer. The quenching of the native fluorescence of eosin Y due to complex formation with the studied drugs was measured spectrofluorimetrically at 545 nm after excitation at 302 nm. At the optimum reaction conditions, the fluorescence quenching values (ΔF) and concentrations were rectilinear over the concentration ranges of 0.2-2.2 and 0.3-2.2 µg ml-1 for atomoxetine and fluvoxamine, respectively. The developed method was successfully applied for the determination of the studied drugs in their pharmaceutical formulations with average percentage recoveries of 100.13 ± 0.66 and 99.69 ± 0.44 for atomoxetine and fluvoxamine, respectively (n = 5), without interference from common excipients.

Studying the association complex formation of atomoxetine and fluvoxamine with eosin Y and its application in their fluorimetric determination

PubMed Central

Omar, Mahmoud A.; Abu-hassan, Ahmed A.

2018-01-01

A simple, sensitive and non-extractive spectrofluorimetric method has been developed and validated for the determination of two psychoanaleptic drugs, atomoxetine and fluvoxamine, in pure forms and pharmaceutical dosage forms. The proposed method is based on the formation of binary complexes between eosin Y and the studied drugs in the presence of a Teorell–Stenhagen buffer. The quenching of the native fluorescence of eosin Y due to complex formation with the studied drugs was measured spectrofluorimetrically at 545 nm after excitation at 302 nm. At the optimum reaction conditions, the fluorescence quenching values (ΔF) and concentrations were rectilinear over the concentration ranges of 0.2–2.2 and 0.3–2.2 µg ml−1 for atomoxetine and fluvoxamine, respectively. The developed method was successfully applied for the determination of the studied drugs in their pharmaceutical formulations with average percentage recoveries of 100.13 ± 0.66 and 99.69 ± 0.44 for atomoxetine and fluvoxamine, respectively (n = 5), without interference from common excipients. PMID:29657744

Capture approximations beyond a statistical quantum mechanical method for atom-diatom reactions

NASA Astrophysics Data System (ADS)

Barrios, Lizandra; Rubayo-Soneira, Jesús; González-Lezana, Tomás

2016-03-01

Statistical techniques constitute useful approaches to investigate atom-diatom reactions mediated by insertion dynamics which involves complex-forming mechanisms. Different capture schemes based on energy considerations regarding the specific diatom rovibrational states are suggested to evaluate the corresponding probabilities of formation of such collision species between reactants and products in an attempt to test reliable alternatives for computationally demanding processes. These approximations are tested in combination with a statistical quantum mechanical method for the S + H2(v = 0 ,j = 1) → SH + H and Si + O2(v = 0 ,j = 1) → SiO + O reactions, where this dynamical mechanism plays a significant role, in order to probe their validity.

Oxidation kinetics and soot formation

NASA Technical Reports Server (NTRS)

Glassman, I.; Brezinsky, K.

1983-01-01

The research objective is to clarify the role of aromaticity in the soot nucleation process by determining the relative importance of phenyl radical/molecular oxygen and benzene/atomic oxygen reactions in the complex combustion of aromatic compounds. Three sets of chemical flow reactor experiments have been designed to determine the relative importance of the phenyl radical/molecular oxygen and benzene/atomic oxygen reactions. The essential elements of these experiments are 1) the use of cresols and anisole formed during the high temperature oxidation of toluene as chemical reaction indicators; 2) the in situ photolysis of molecular oxygen to provide an oxygen atom perturbation in the reacting aromatic system; and 3) the high temperature pyrolysis of phenol, the cresols and possibly anisole.

Supported rhenium complexes: almost uniform rhenium tricarbonyls synthesized from CH3Re(CO)5 and HY zeolite.

PubMed

Lobo-Lapidus, Rodrigo J; Gates, Bruce C

2010-11-02

Supported rhenium complexes were prepared from CH(3)Re(CO)(5) and dealuminated HY zeolite or NaY zeolite, each with a Si/Al atomic ratio of 30. The samples were characterized with infrared (IR) and extended X-ray absorption fine structure (EXAFS) spectroscopies. EXAFS data characterizing the sample formed by the reaction of CH(3)Re(CO)(5) with dealuminated HY zeolite show that the rhenium complexes were bonded to the zeolite frame, incorporating, on average, three carbonyl ligands per Re atom (as shown by Re-C and multiple-scattering Re-O EXAFS contributions). The IR spectra, consistent with this result, show that the supported rhenium carbonyls were bonded near aluminum sites of the zeolite, as shown by the decrease in intensity of the IR bands characterizing the acidic silanol groups resulting from the reaction of the rhenium carbonyl with the zeolite. This supported metal complex was characterized by narrow peaks in the ν(CO) region of the IR spectrum, indicating highly uniform species. In contrast, the species formed from CH(3)Re(CO)(5) on NaY zeolite lost fewer carbonyl ligands than those formed on HY zeolite and were significantly less uniform, as indicated by the greater breadth of the ν(CO) bands in the IR spectra. The results show the importance of zeolite H(+) sites for the formation of uniform supported rhenium carbonyls from CH(3)Re(CO)(5); the formation of such uniform complexes did not occur on the NaY zeolite.

Intramolecular Aza-Diels-Alder Reactions of ortho-Quinone Methide Imines: Rapid, Catalytic, and Enantioselective Assembly of Benzannulated Quinolizidines.

PubMed

Kretzschmar, Martin; Hofmann, Fabian; Moock, Daniel; Schneider, Christoph

2018-04-16

Aza-Diels-Alder reactions (ADARs) are powerful processes that furnish N-heterocycles in a straightforward fashion. Intramolecular variants offer the additional possibility of generating bi- and polycyclic systems with high stereoselectivity. We report herein a novel Brønsted acid catalyzed process in which ortho-quinone methide imines tethered to the dienophile via the N substituent react in an intramolecular ADAR to form complex quinolizidines and oxazinoquinolines in a one-step process. The reactions proceed under very mild conditions, with very good yields and good to very good diastereo- and enantioselectivities. Furthermore, the process was extended to a domino reaction that efficiently combines substrate synthesis, ortho-quinone methide imine formation, and ADAR. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evidence of preorganization in quinonoid intermediate formation from L-Trp in H463F mutant Escherichia coli tryptophan indole-lyase from effects of pressure and pH.

PubMed

Phillips, Robert S; Kalu, Ukoha; Hay, Sam

2012-08-21

The effects of pH and hydrostatic pressure on the reaction of H463F tryptophan indole-lyase (TIL) have been evaluated. The mutant TIL shows very low activity for elimination of indole but is still competent to form a quinonoid intermediate from l-tryptophan [Phillips, R. S., Johnson, N., and Kamath, A. V. (2002) Biochemistry 41, 4012-4019]. Stopped-flow measurements show that the formation of the quinonoid intermediate at 505 nm is affected by pH, with a bell-shaped dependence for the forward rate constant, k(f), and dependence on a single basic group for the reverse rate constant, k(r), with the following values: pK(a1) = 8.14 ± 0.15, pK(a2) = 7.54 ± 0.15, k(f,min) = 18.1 ± 1.3 s(-1), k(f,max) = 179 ± 46.3 s(-1), k(r,min) = 11.4 ± 1.2 s(-1), and k(r,max) = 33 ± 1.6 s(-1). The pH effects may be due to ionization of Tyr74 as the base and Cys298 as the acid influencing the rate constant for deprotonation. High-pressure stopped-flow measurements were performed at pH 8, which is the optimum for the forward reaction. The rate constants show an increase with pressure up to 100 MPa and a subsequent decrease above 100 MPa. Fitting the pressure data gives the following values: k(f,0) = 15.4 ± 0.8 s(-1), ΔV(‡) = -29.4 ± 2.9 cm(3) mol(-1), and Δβ(‡) = -0.23 ± 0.03 cm(3) mol(-1) MPa(-1) for the forward reaction, and k(r,0) = 20.7 ± 0.8 s(-1), ΔV(‡) = -9.6 ± 2.3 cm(3) mol(-1), and Δβ(‡) = -0.05 ± 0.02 cm(3) mol(-1) MPa(-1) for the reverse reaction. The primary kinetic isotope effect on quinonoid intermediate formation at pH 8 is small (~2) and is not significantly pressure-dependent, suggesting that the effect of pressure on k(f) may be due to perturbation of an active site preorganization step. The negative activation volume is also consistent with preorganization of the ES complex prior to quinonoid intermediate formation, and the negative compressibility may be due to the effect of pressure on the enzyme conformation. These results support the conclusion that the preorganization of the H463F TIL Trp complex, which is probably dominated by motion of the l-Trp indole moiety of the aldimine complex, contributes to quinonoid intermediate formation.