Methyl (4-bromo-benzene-sulfonamido)acetate.

PubMed

Arshad, Muhammad Nadeem; Tahir, M Nawaz; Khan, Islam Ullah; Ahmad, Ejaz; Shafiq, Muhammad

2008-11-20

The title compound, C(9)H(10)BrNO(4)S, is an inter-mediate for the formation of benzothia-zines. In the crystal structure, inter-molecular N-H⋯O hydrogen bonds link the mol-ecules, forming R(2) (2)(10) ring motifs, which are linked into a two-dimensional polymeric sheet through inter-molecular C-H⋯O hydrogen bonds.

C-C bond forming radical SAM enzymes involved in the construction of carbon skeletons of cofactors and natural products.

PubMed

Yokoyama, Kenichi; Lilla, Edward A

2018-04-10

Covering: up to the end of 2017C-C bond formations are frequently the key steps in cofactor and natural product biosynthesis. Historically, C-C bond formations were thought to proceed by two electron mechanisms, represented by Claisen condensation in fatty acids and polyketide biosynthesis. These types of mechanisms require activated substrates to create a nucleophile and an electrophile. More recently, increasing number of C-C bond formations catalyzed by radical SAM enzymes are being identified. These free radical mediated reactions can proceed between almost any sp3 and sp2 carbon centers, allowing introduction of C-C bonds at unconventional positions in metabolites. Therefore, free radical mediated C-C bond formations are frequently found in the construction of structurally unique and complex metabolites. This review discusses our current understanding of the functions and mechanisms of C-C bond forming radical SAM enzymes and highlights their important roles in the biosynthesis of structurally complex, naturally occurring organic molecules. Mechanistic consideration of C-C bond formation by radical SAM enzymes identifies the significance of three key mechanistic factors: radical initiation, acceptor substrate activation and radical quenching. Understanding the functions and mechanisms of these characteristic enzymes will be important not only in promoting our understanding of radical SAM enzymes, but also for understanding natural product and cofactor biosynthesis.

The effect of nitrogen incorporation on the bonding structure of hydrogenated carbon nitride films

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

Camero, M.; Buijnsters, J. G.; Gomez-Aleixandre, C.

2007-03-15

This work describes the composition and bonding structure of hydrogenated carbon nitride (a-CN{sub x}:H) films synthesized by electron cyclotron resonance chemical vapor deposition using as precursor gases argon, methane, and nitrogen. The composition of the films was derived from Rutherford backscattering and elastic recoil detection analysis and the bonding structure was examined by infrared (IR) spectroscopy and x-ray absorption near edge spectroscopy (XANES). By varying the nitrogen to methane ratio in the applied gas mixture, polymeric a-CN{sub x}:H films with N/C contents varying from 0.06 to 0.49 were obtained. Remarkably, the H content of the films ({approx}40 at. %) wasmore » rather unaffected by the nitrogenation process. The different bonding states as detected in the measured XANES C(1s) and N(1s) spectra have been correlated with those of a large number of reference samples. The XANES and IR spectroscopy results indicate that N atoms are efficiently incorporated into the amorphous carbon network and can be found in different bonding environments, such as pyridinelike, graphitelike, nitrilelike, and amino groups. The nitrogenation of the films results in the formation of N-H bonding environments at the cost of C-H structures. Also, the insertion of N induces a higher fraction of double bonds in the structure at the expense of the linear polymerlike chains, hence resulting in a more cross-linked solid. The formation of double bonds takes place through complex C=N structures and not by formation of graphitic aromatic rings. Also, the mechanical and tribological properties (hardness, friction, and wear) of the films have been studied as a function of the nitrogen content. Despite the major modifications in the bonding structure with nitrogen uptake, no significant changes in these properties are observed.« less

Role of disulfide cross-linking of mutant SOD1 in the formation of inclusion-body-like structures.

PubMed

Roberts, Brittany L T; Patel, Kinaree; Brown, Hilda H; Borchelt, David R

2012-01-01

Pathologic aggregates of superoxide dismutase 1 (SOD1) harboring mutations linked to familial amyotrophic lateral sclerosis (fALS) have been shown to contain aberrant intermolecular disulfide cross-links. In prior studies, we observed that intermolecular bonding was not necessary in the formation of detergent- insoluble SOD1 complexes by mutant SOD1, but we were unable to assess whether this type of bonding may be important for pathologic inclusion formation. In the present study, we visually assess the formation of large inclusions by fusing mutant SOD1 to yellow fluorescent protein (YFP). Experimental constructs possessing mutations at all cysteine residues in SOD1 (sites 6, 57, 111, and 146 to F,S,Y,R or G,S,Y,R, respectively) were shown to maintain a high propensity of inclusion formation despite the inability to form disulfide cross-links. Interestingly, although aggregates form when all cysteines were mutated, double mutants of the ALS mutation C6G with an experimental mutation C111S exhibited low aggregation propensity. Overall, this study is an extension of previous work demonstrating that cysteine residues in mutant SOD1 play a role in modulating aggregation and that intermolecular disulfide bonds are not required to produce large intracellular inclusion-like structures.

Drosophila vitelline membrane assembly: A critical role for an evolutionarily conserved cysteine in the “VM domain” of sV23

PubMed Central

Wu, T; Manogaran, A.L; Beauchamp, J.M.; Waring, G.L.

2010-01-01

The vitelline membrane (VM), the oocyte proximal layer of the Drosophila eggshell, contains four major proteins (VMPs) that possess a highly conserved “VM domain” which includes three precisely spaced, evolutionarily conserved, cysteines (CX7CX8C). Focusing on sV23, this study showed that the three cysteines are not functionally equivalent. While substitution mutations at the first (C123S) or third (C140S) cysteines were tolerated, females with a substitution at the second position (C131S) were sterile. Fractionation studies showed sV23 incorporates into a large disulfide linked network well after its secretion ceases, suggesting post-depositional mechanisms are in place to restrict disulfide bond formation until late oogenesis, when the oocyte no longer experiences large volume increases. Affinity chromatography utilizing histidine tagged sV23 alleles revealed small sV23 disulfide linked complexes during the early stages of eggshell formation that included other VMPs, namely sV17 and Vml. The early presence but late loss of these associations in an sV23 double cysteine mutant suggests reorganization of disulfide bonds may underlie the regulated growth of disulfide-linked networks in the vitelline membrane. Found within the context of a putative thioredoxin active site (CXXS) C131, the critical cysteine in sV23, may play an important enzymatic role in isomerizing intermolecular disulfide bonds during eggshell assembly. PMID:20832396

Regio-selectivity of the Oxidative C-S Bond Formation in Ergothioneine and Ovothiol Biosyntheses

PubMed Central

Song, Heng; Leninger, Maureen; Lee, Norman

2014-01-01

Ergothioneine (5) and ovothiol (8) are two novel thiol-containing natural products. Their C-S bonds are formed by oxidative coupling reactions catalyzed by EgtB and OvoA enzymes, respectively. In this work, it was discovered that besides catalyzing the oxidative coupling between histidine and cysteine (1 → 6 conversion), OvoA can also catalyze a direct oxidative coupling between hercynine (2) and cysteine (2 → 4 conversion), which can shorten the ergothioneine biosynthetic pathway by two steps. PMID:24016264

Ab initio computational study of –N-C and –O-C bonding formation : functional group modification reaction based chitosan

NASA Astrophysics Data System (ADS)

Siahaan, P.; Salimah, S. N. M.; Sipangkar, M. J.; Hudiyanti, D.; Djunaidi, M. C.; Laksitorini, M. D.

2018-04-01

Chitosan application in pharmaceutics and cosmeceutics industries is limited by its solubility issue. Modification of -NH2 and -OH fuctional groups of chitosan by adding carboxyl group has been shown to improve its solubility and application. Attempt to synthesize carboxymethyl chitosan (CMC) from monocloroacetic acid (MCAA) has been done prior this report. However no information is available wether –OH (-O-C bonding formation) or -NH2 (-N-C bonding formation) is the preference for - CH2COOH to attach. In the current study, the reaction mechanism between chitosan and MCAA reactants into carboxymethyl chitosan (CMC) was examined by computational approach. Dimer from of chitosan used as a molecular model in calculation All the molecular structure involved in the reaction mechanism was optimized by ab initio computational on the theory and basis set HF/6-31G(d,p). The results showed that the - N-C bonding formation via SN2 than the -O-C bonding formation via SN2 which have activation energy 469.437 kJ/mol and 533.219 kJ/mol respectively. However, the -O-C bonding formation more spontaneous than the -N-C bonding formation because ΔG the formation of O-CMC-2 reaction is more negative than ΔG of formation N-CMC-2 reaction is -4.353 kJ/mol and -1.095 kJ/mol respectively. The synthesis of N,O-CMC first forms -O-CH2COOH, then continues to form -NH-CH2COOH. This information is valuable to further optimize the reaction codition for CMC synthesis.

Modeling the archetype cysteine protease reaction using dispersion corrected density functional methods in ONIOM-type hybrid QM/MM calculations; the proteolytic reaction of papain.

PubMed

Fekete, Attila; Komáromi, István

2016-12-07

A proteolytic reaction of papain with a simple peptide model substrate N-methylacetamide has been studied. Our aim was twofold: (i) we proposed a plausible reaction mechanism with the aid of potential energy surface scans and second geometrical derivatives calculated at the stationary points, and (ii) we investigated the applicability of the dispersion corrected density functional methods in comparison with the popular hybrid generalized gradient approximations (GGA) method (B3LYP) without such a correction in the QM/MM calculations for this particular problem. In the resting state of papain the ion pair and neutral forms of the Cys-His catalytic dyad have approximately the same energy and they are separated by only a small barrier. Zero point vibrational energy correction shifted this equilibrium slightly to the neutral form. On the other hand, the electrostatic solvation free energy corrections, calculated using the Poisson-Boltzmann method for the structures sampled from molecular dynamics simulation trajectories, resulted in a more stable ion-pair form. All methods we applied predicted at least a two elementary step acylation process via a zwitterionic tetrahedral intermediate. Using dispersion corrected DFT methods the thioester S-C bond formation and the proton transfer from histidine occur in the same elementary step, although not synchronously. The proton transfer lags behind (or at least does not precede) the S-C bond formation. The predicted transition state corresponds mainly to the S-C bond formation while the proton is still on the histidine Nδ atom. In contrast, the B3LYP method using larger basis sets predicts a transition state in which the S-C bond is almost fully formed and the transition state can be mainly featured by the Nδ(histidine) to N(amid) proton transfer. Considerably lower activation energy was predicted (especially by the B3LYP method) for the next amide bond breaking elementary step of acyl-enzyme formation. Deacylation appeared to be a single elementary step process in all the methods we applied.

Microwave-assisted Ullmann C-S bond formation: synthesis of the P38alpha MAPK clinical candidate VX-745.

PubMed

Bagley, Mark C; Davis, Terence; Dix, Matthew C; Fusillo, Vincenzo; Pigeaux, Morgane; Rokicki, Michal J; Kipling, David

2009-11-06

Microwave irradiation promotes the rapid and efficient reaction of a thiophenol and aryl or heteroaryl halide using a copper or palladium catalyst and a range of ligands, depending upon substrate. Of particular utility is the use of copper(I) iodide (5 mol %) and trans-cyclohexane-1,2-diol as ligand under basic conditions and microwave irradiation to give the corresponding sulfide in high yield. This method for C-S bond formation is applied in the four-step synthesis of the clinical candidate VX-745 in 38% overall yield. The inhibitory activity of VX-745 against p38alpha MAPK is confirmed in Werner syndrome dermal fibroblasts at 1.0 microM concentration by immunoblot assay.

Reductive Elimination Leading to C-C Bond Formation in Gold(III) Complexes: A Mechanistic and Computational Study.

PubMed

Rocchigiani, Luca; Fernandez-Cestau, Julio; Budzelaar, Peter H M; Bochmann, Manfred

2018-06-21

The factors affecting the rates of reductive C-C cross-coupling reactions in gold(III) aryls were studied by using complexes that allow easy access to a series of electronically modified aryl ligands, as well as to gold methyl and vinyl complexes, by using the pincer compounds [(C^N^C)AuR] (R=C 6 F 5 , CH=CMe 2 , Me and p-C 6 H 4 X, where X=OMe, F, H, tBu, Cl, CF 3 , or NO 2 ) as starting materials (C^N^C=2,6-(4'-tBuC 6 H 3 ) 2 pyridine dianion). Protodeauration followed by addition of one equivalent SMe 2 leads to the quantitative generation of the thioether complexes [(C^N-CH)AuR(SMe 2 )] + . Upon addition of a second SMe 2 pyridine is displaced, which triggers the reductive aryl-R elimination. The rates for these cross-couplings increase in the sequence k(vinyl)>k(aryl)≫k(C 6 F 5 )>k(Me). Vinyl-aryl coupling is particularly fast, 1.15×10 -3  L mol -1  s -1 at 221 K, whereas both C 6 F 5 and Me couplings encountered higher barriers for the C-C bond forming step. The use of P(p-tol) 3 in place of SMe 2 greatly accelerates the C-C couplings. Computational modelling shows that in the C^N-bonded compounds displacement of N by a donor L is required before the aryl ligands can adopt a conformation suitable for C-C bond formation, so that elimination takes place from a four-coordinate intermediate. The C-C bond formation is the rate-limiting step. In the non-chelating case, reductive C(sp 2 )-C(sp 2 ) elimination from three-coordinate ions [(Ar 1 )(Ar 2 )AuL] + is almost barrier-free, particularly if L=phosphine. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Yazdani, Ahmad, E-mail: Yazdania@modares.ac.ir; Shadrokh, Zohreh; Department of Physics, University of Shahrood, P.O. Box 316-36155, Shahrood

Highlights: • Opto-crystalline character of the composition of Cu{sub 2}S and S{sub 2}Sn was considered. • The formation Cu{sub 2}SnS{sub 3} is strongly related to phase separation at interface. • The entanglement of phases is strongly due to the chemical bond competition. • The suggested fluctuation region is approved by PL spectra. • Reconstruction and cluster formation is evident by formation of flat-spiral flowers. - Abstract: Optical character of crystal structure of the composition of two different semiconducting metallic sulfides, Cu{sub 2}S and S{sub 2}Sn, in pure phase formation of the ternary chalcogenide Cu{sub 2}SnS{sub 3} was considered. Because ofmore » the difficulties related to the phase separation at the definite Eutectic temperature for the composite formation, which is evident in optical absorption fluctuations, solvothermal synthesis in the intermediate temperature range 180–220 °C seems convenient where tetragonal crystal structure is investigated by XRD. Absorption fluctuations below E = E{sub g} were more pronounced for the lower limit case (180 °C) reflected in a sharp peak located at 1.48 eV on S1 as seen in UV-PL measurement. The characteristic behavior of the interface, resulting in the reconstruction and cluster formation due to the offset of bond rupturing displacement of atomic positions, is in favor of aggregation instead of agglomeration, which is evident by formation of small flat-spiral flowers in SEM images.« less

The adsorption of methyl, acetylide, chlorine and phosphorus trifluoride on zinc oxide: A quantum-chemical study

NASA Astrophysics Data System (ADS)

Rodriguez, JoséA.

1989-11-01

The chemisorptions of methyl (CH 3), acetylide (H-CC), chlorine (Cl) and phosphorus trifluoride (PF 3) on ZnO(0001) and of Cl on ZnO(101¯0) have been examined employing semi-em- pirical quantum-chemical calculations (INDO/S) and neutral clusters of limited size (Zn 13O 13). CH 3, H-CC and Cl appear as strong electron acceptors when adsorbed on Zn sites of ZnO. The chemisorption bonds of these molecules are almost pure σ-bonds and are largely localized on the adsorption site. An increase in the work function of ZnO surfaces upon adsorption of CH 3, H-CC and Cl is predicted. The PF 3 molecule is a very weak acceptor of electrons when adsorbed on a-top sites of ZnO(0001). The bonding mechanism of CH 3, H-CC, Cl and PF 3 on the ZnO(0001) surface involves primarily the HOMO and LUMO of the adsorbate and the Zn(4s,4p) orbitals of the substrate. The effects of chemisorption on the C-H bonds of CH 3 and H-CC, the C-C bond of H-CC, and the P-F bonds of PF 3 are examined. On the basis of these INDO/S results, the possible UPS spectra for CH 3, H-CC and PF 3 adsorbed on ZnO(0001) are discussed and compared with results for adsorption on transition-metal surfaces. A general picture of the chemisorption bond of alkyls, acetylides, alkoxides, carboxylates and halogens on a-top sites of ZnO(0001) is obtained by comparing our results for adsorption of CH 3, H-CC and Cl with those previously reported for adsorption of methoxy, OH and formate.

Formation of {Co(dppe)}2{μ2-η(2):η(2)-η(2):η(2)-[(C60)2]} Dimers Bonded by Single C-C Bonds and Bridging η(2)-Coordinated Cobalt Atoms.

PubMed

Konarev, Dmitri V; Troyanov, Sergey I; Ustimenko, Kseniya A; Nakano, Yoshiaki; Shestakov, Alexander F; Otsuka, Akihiro; Yamochi, Hideki; Saito, Gunzi; Lyubovskaya, Rimma N

2015-05-18

Coordination of two bridging cobalt atoms to fullerenes by the η(2) type in {Co(dppe)}2{μ2-η(2):η(2)-η(2):η(2)-[(C60)2]}·3C6H4Cl2 [1; dppe = 1,2-bis(diphenylphosphino)ethane] triggers fullerene dimerization with the formation of two intercage C-C bonds of 1.571(4) Å length. Coordination-induced fullerene dimerization opens a path to the design of fullerene structures bonded by both covalent C-C bonds and η(2)-coordination-bridged metal atoms.

Identification of the formation of metal-vinylidene interfacial bonds of alkyne-capped platinum nanoparticles by isotopic labeling.

PubMed

Hu, Peiguang; Chen, Limei; Deming, Christopher P; Bonny, Lewis W; Lee, Hsiau-Wei; Chen, Shaowei

2016-10-07

Stable platinum nanoparticles were prepared by the self-assembly of 1-dodecyne and dodec-1-deuteroyne onto bare platinum colloid surfaces. The nanoparticles exhibited consistent core size and optical properties. FTIR and NMR measurements confirmed the formation of Pt-vinylidene (Pt[double bond, length as m-dash]C[double bond, length as m-dash]CH-) interfacial linkages rather than Pt-acetylide (Pt-C[triple bond, length as m-dash]C-) and platinum-hydride (Pt-H) bonds.

Lanthanum-mediated dehydrogenation of butenes: Spectroscopy and formation of La(C4H6) isomers

NASA Astrophysics Data System (ADS)

Cao, Wenjin; Hewage, Dilrukshi; Yang, Dong-Sheng

2018-01-01

La atom reactions with 1-butene, 2-butene, and isobutene are carried out in a laser-vaporization molecular beam source. The three reactions yield the same La-hydrocarbon products from the dehydrogenation and carbon-carbon bond cleavage and coupling of the butenes. The dehydrogenated species La(C4H6) is the major product, which is characterized with mass-analyzed threshold ionization (MATI) spectroscopy and quantum chemical computations. The MATI spectrum of La(C4H6) produced from the La+1-butene reaction exhibits two band systems, whereas the MATI spectra produced from the La+2-butene and isobutene reactions display only a single band system. Each of these spectra shows a strong origin band and several vibrational progressions. The two band systems from the spectrum of the 1-butene reaction are assigned to the ionization of two isomers: La[C(CH2)3] (Iso A) and La(CH2CHCHCH2) (Iso B), and the single band system from the spectra of the 2-butene and isobutene reactions is attributed to Iso B and Iso A, respectively. The ground electronic states are 2A1 (C3v) for Iso A and 2A' (Cs) for Iso B. The ionization of the doublet state of each isomer removes a La 6s-based electron and leads to the 1A1 ion of Iso A and the 1A' ion of Iso B. The formation of both isomers consists of La addition to the C=C double bond, La insertion into two C(sp3)—H bonds, and H2 elimination. In addition to these steps, the formation of Iso A from the La+1-butene reaction may involve the isomerization of 1-butene to isobutene prior to the C—H bond activation, whereas the formation of Iso B from the La+trans-2-butene reaction may include the trans- to cis-butene isomerization after the C—H bond activation.

Snapshots of C-S Cleavage in Egt2 Reveals Substrate Specificity and Reaction Mechanism.

PubMed

Irani, Seema; Naowarojna, Nathchar; Tang, Yang; Kathuria, Karan R; Wang, Shu; Dhembi, Anxhela; Lee, Norman; Yan, Wupeng; Lyu, Huijue; Costello, Catherine E; Liu, Pinghua; Zhang, Yan Jessie

2018-05-17

Sulfur incorporation in the biosynthesis of ergothioneine, a histidine thiol derivative, differs from other well-characterized transsulfurations. A combination of a mononuclear non-heme iron enzyme-catalyzed oxidative C-S bond formation and a subsequent pyridoxal 5'-phosphate (PLP)-mediated C-S lyase reaction leads to the net transfer of a sulfur atom from a cysteine to a histidine. In this study, we structurally and mechanistically characterized a PLP-dependent C-S lyase Egt2, which mediates the sulfoxide C-S bond cleavage in ergothioneine biosynthesis. A cation-π interaction between substrate and enzyme accounts for Egt2's preference of sulfoxide over thioether as a substrate. Using mutagenesis and structural biology, we captured three distinct states of the Egt2 C-S lyase reaction cycle, including a labile sulfenic intermediate captured in Egt2 crystals. Chemical trapping and high-resolution mass spectrometry were used to confirm the involvement of the sulfenic acid intermediate in Egt2 catalysis. Copyright © 2018 Elsevier Ltd. All rights reserved.

Low-temperature formation of Ga-oxide/GaN interface with remote oxygen plasma and its interface properties

NASA Astrophysics Data System (ADS)

Yamamoto, Taishi; Taoka, Noriyuki; Ohta, Akio; Truyen, Nguyen Xuan; Yamada, Hisashi; Takahashi, Tokio; Ikeda, Mitsuhisa; Makihara, Katsunori; Shimizu, Mitsuaki; Miyazaki, Seiichi

2018-06-01

The Ga-oxide/GaN structures formed by remote oxygen plasma (ROP) exposure at various temperatures (T s) and times have been systematically investigated. X-ray photoelectron spectroscopy clarified the formation of Ga2O3 layers with close-to-stoichiometric composition and a slight N incorporation of ∼6 at. %. Also, we found that a high T s increases the intensity of a signal related to the N–O bond, which is located near the Ga-oxide/GaN interfaces. Total photoelectron yield spectroscopy (PYS) also revealed that the ROP exposure at T s of 300 °C produces fewer filled defect states in the bandgap of GaN than at 500 °C. This difference in the filled defect states could be attributable to the amount of N–O bonds at the interface.

Reactivity of triruthenium thiophyne and furyne clusters: competitive S-C and P-C bond cleavage reactions and the generation of highly unsymmetrical alkyne ligands.

PubMed

Uddin, Md Nazim; Begum, Noorjahan; Hassan, Mohammad R; Hogarth, Graeme; Kabir, Shariff E; Miah, Md Arzu; Nordlander, Ebbe; Tocher, Derek A

2008-11-28

The synthesis and reactivity of the thiophyne and furyne clusters [Ru3(CO)7(mu-dppm)(mu3-eta2-C4H2E)(mu-P(C4H3E)2)(mu-H)] (E = S, O) is reported. Addition of P(C4H3E)3 to [Ru3(CO)10(mu-dppm)] (1) at room temperature in the presence of Me3NO gives simple substitution products [Ru3(CO)9(mu-dppm)(P(C4H3E)3)] (E = S, 2; E = O, 3). Mild thermolysis in the presence of further Me3NO affords the thiophyne and furyne complexes [Ru3(CO)7(mu-dppm)(mu3-eta2-C4H2E)(mu-P(C4H3E)2)(mu-H)] (E = S, 4; E = O, 6) resulting from both carbon-hydrogen and carbon-phosphorus bond activation. In each the C4H2E (E = S, O) ligand donates 4-electrons to the cluster and the rings are tilted with respect to the mu-dppm and the phosphido-bridged open triruthenium unit. Heating 4 at 80 degrees C leads to the formation of the ring-opened cluster [Ru3(CO)5(mu-CO)(mu-dppm)(mu3-eta3-SC4H3)(mu-P(C4H3S)2)] (5) resulting from carbon-sulfur bond scission and carbon-hydrogen bond formation and containing a ring-opened mu3-eta3-1-thia-1,3-butadiene ligand. In contrast, a similar thermolysis of 3 affords the phosphinidene cluster [Ru3(CO)7(mu-dppm)(mu3-eta2-C4H2O)(mu3-P(C4H3O))] (7) resulting from a second phosphorus-carbon bond cleavage and (presumably) elimination of furan. Treatment of 4 and 6 with PPh3 affords the simple phosphine-substituted products [Ru3(CO)6(PPh3)(mu-dppm)(mu3-eta2-C4H2E)(mu-P(C4H3E)2)(mu-H)] (E = S, 8; E = O, 9). Both thiophyne and furyne clusters 4 and 6 readily react with hydrogen bromide to give [Ru3(CO)6Br(mu-Br)(mu-dppm)(mu3-eta2-eta1-C4H2E)(mu-P(C4H3E)2)(mu-H)] (E = S, 10; E = O, 11) containing both terminal and bridging bromides. Here the alkynes bind in a highly unsymmetrical manner with one carbon acting as a bridging alkylidene and the second as a terminally bonded Fisher carbene. As far as we are aware, this binding mode has only previously been noted in ynamine complexes or those with metals in different oxidation states. The crystal structures of seven of these new triruthenium clusters have been carried out, allowing a detailed analysis of the relative orientations of coordinated ligands.

Methyl-coenzyme M reductase from methanogenic archaea: isotope effects on label exchange and ethane formation with the homologous substrate ethyl-coenzyme M.

PubMed

Scheller, Silvan; Goenrich, Meike; Thauer, Rudolf K; Jaun, Bernhard

2013-10-09

Ethyl-coenzyme M (CH3CH2-S-CH2CH2-SO3(-), Et-S-CoM) serves as a homologous substrate for the enzyme methyl-coenzyme M reductase (MCR) resulting in the product ethane instead of methane. The catalytic reaction proceeds via an intermediate that already contains all six C-H bonds of the product. Because product release occurs after a second, rate-limiting step, many cycles of intermediate formation and reconversion to substrate occur before a substantial amount of ethane is released. In deuterated buffer, the intermediate becomes labeled, and C-H activation in the back reaction rapidly leads to labeled Et-S-CoM, which enables intermediate formation to be detected. Here, we present a comprehensive analysis of this pre-equilibrium. (2)H- and (13)C-labeled isotopologues of Et-S-CoM were used as the substrates, and the time course of each isotopologue was followed by NMR spectroscopy. A kinetic simulation including kinetic isotope effects allowed determination of the primary and α- and β-secondary isotope effects for intermediate formation and for the C-H/C-D bond activation in the ethane-containing intermediate. The values obtained are in accordance with those found for the native substrate Me-S-CoM (see preceding publication, Scheller, S.; Goenrich, M.; Thauer, R. K.; Jaun, B. J. Am. Chem. Soc. 2013, 135, DOI: 10.1021/ja406485z) and thus imply the same catalytic mechanism for both substrates. The experiment by Floss and co-workers, demonstrating a net inversion of configuration to chiral ethane with CH3CDT-S-CoM as the substrate, is compatible with the observed rapid isotope exchange if the isotope effects measured here are taken into account.

Ammonolysis of ketene as a potential source of acetamide in the troposphere: a quantum chemical investigation.

PubMed

Sarkar, Saptarshi; Mallick, Subhasish; Kumar, Pradeep; Bandyopadhyay, Biman

2018-05-16

Quantum chemical calculations at the CCSD(T)/CBS//MP2/aug-cc-pVTZ levels of theory have been carried out to investigate a potential new source of acetamide in Earth's atmosphere through the ammonolysis of the simplest ketene. It was found that the reaction can occur via the addition of ammonia at either the C[double bond, length as m-dash]C or C[double bond, length as m-dash]O bond of ketene. The potential energy surface as well as calculated rate coefficients indicate that under tropospheric conditions, ammonolysis would occur almost exclusively via ammonia addition at the C[double bond, length as m-dash]O bond with negligible contribution from addition at the C[double bond, length as m-dash]C bond. The reaction of ketene with water has also been investigated in order to compare between hydrolysis and ammonolysis, as the former is known to be responsible for the formation of acetic acid. The rate coefficient for the formation of acetamide was found to be ∼106 to 109 times higher than that for the formation of acetic acid from the same ketene source in the troposphere. By means of the relative rate of ammonolysis with respect to hydrolysis, it was shown that acetamide formation would dominate over acetic acid formation at various altitudes in the troposphere.

A blue corrinoid from partial degradation of vitamin B12 in aqueous bicarbonate: spectra, structure, and interaction with proteins of B12 transport.

PubMed

Fedosov, Sergey N; Ruetz, Markus; Gruber, Karl; Fedosova, Natalya U; Kräutler, Bernhard

2011-09-20

Cobalamin (Cbl) is a complex cofactor produced only by bacteria but used by all animals and humans. Cyanocobalamin (vitamin B(12), CNCbl) is one commonly isolated form of cobalamin. B(12) belongs to a large group of corrinoids, which are characterized by a distinct red color conferred by the system of conjugated double bonds of the corrin ring retaining a Co(III) ion. A unique blue Cbl derivative was produced by hydrolysis of CNCbl in a weakly alkaline aqueous solution of bicarbonate. This corrinoid was purified and isolated as dark blue crystals. Its spectroscopic analysis and X-ray crystallography revealed B-ring opening with formation of 7,8-seco-cyanocobalamin (7,8-sCNCbl). The unprecedented structural change was caused by cleavage of the peripheral C-C bond between saturated carbons 7 and 8 of the corrin macrocycle accompanied by formation of a C═C bond at C7 and a carbonyl group at C8. Additionally, the C-amide was hydrolyzed to a carboxylic acid. The extended conjugation of the π-system caused a considerable red shift of the absorbance spectrum. Formation and degradation of 7,8-sCNCbl were analyzed qualitatively. Its interaction with the proteins of mammalian Cbl transport revealed both a slow binding kinetics and a low overall affinity. The binding data were compared to those of other monocarboxylic derivatives and agreed with the earlier proposed scheme for two-step ligand recognition. The obtained results are consistent with the structural models of 7,8-sCNCbl and the transport proteins intrinsic factor and transcobalamin. Potential applications of the novel derivative for drug conjugation are discussed. © 2011 American Chemical Society

An intramolecular disulfide bridge between Cys-7 and Cys61 determines the structure of the secretory core gene product (e antigen) of hepatitis B virus.

PubMed Central

Nassal, M; Rieger, A

1993-01-01

Hepatitis B virus, the prototypic member of the Hepadnaviridae, is a small enveloped DNA virus that replicates via reverse transcription. Efficient usage of its compact 3.2-kb genome is exemplified by the pre-C/C gene from which two proteins with largely overlapping primary sequences but distinctly different properties are synthesized: the self-assembling core protein p21c (hepatitis B core antigen [HbcAg]) and the secretory, nonparticulate protein p17e (hepatitis B e antigen [HbeAg]). Mature p17e carries a 10-amino-acid N-terminal extension with a Cys residue (Cys-7). Using transient transfection of a human liver cell line with constructs expressing wild-type p17 or a series of Cys mutants of p17, we show that Cys-7 forms an intramolecular S-S bond to Cys61, which in assembly-competent core proteins is available for intermolecular disulfide bonds between two neighboring subunits. Removal of the Cys-7/Cys61 bond by mutating either residue has differential effects: in the absence of Cys-7, secretion is relatively efficient and independent of Cys61; however, the molecules are exported as homodimers exhibiting both HBe and HBc antigenicity. In the absence of Cys61, the nonpaired Cys-7 interferes with secretion efficiency. The amino acid sequence flanking Cys-7 also contributes to the formation of the proper intramolecular S-S bond. These results suggest that the Cys-7/Cys61 bond imposes on p17e a conformation that is critical for its secretion and distinct biophysical and antigenic properties. This mechanism adds selective disulfide formation to the repertoire of hepatitis B virus for efficient use of its tiny genome. Images PMID:8510224

Amavadin and other vanadium complexes as remarkably efficient catalysts for one-pot conversion of ethane to propionic and acetic acids.

PubMed

Kirillova, Marina V; Kuznetsov, Maxim L; da Silva, José A L; Guedes da Silva, Maria Fátima C; Fraústo da Silva, João J R; Pombeiro, Armando J L

2008-01-01

Synthetic amavadin Ca[V{ON[CH(CH(3))COO](2)}(2)] and its models Ca[V{ON(CH(2)COO)(2)}(2)] and [VO{N(CH(2)CH(2)O)(3)}], in the presence of K(2)S(2)O(8) in trifluoroacetic acid (TFA), exhibit remarkable catalytic activity for the one-pot carboxylation of ethane to propionic and acetic acids with the former as the main product (overall yields up to 93 %, catalyst turnover numbers (TONs) up to 2.0 x 10(4)). The simpler V complexes [VO(CF(3)SO(3))(2)], [VO(acac)(2)] and VOSO(4) are less active. The effects of various factors, namely, C(2)H(6) and CO pressures, time, temperature, and amounts of catalyst, TFA and K(2)S(2)O(8), have been investigated, and this allowed optimisation of the process and control of selectivity. (13)C-labelling experiments indicated that the formation of acetic acid follows two pathways, the dominant one via oxidation of ethane with preservation of the C--C bond, and the other via rupture of this bond and carbonylation of the methyl group by CO; the C--C bond is retained in the formation of propionic acid upon carbonylation of ethane. The reactions proceed via both C- and O-centred radicals, as shown by experiments with radical traps. On the basis of detailed DFT calculations, plausible reaction mechanisms are discussed. The carboxylation of ethane in the presence of CO follows the sequential formation of C(2)H(5) (*), C(2)H(5)CO(*), C(2)H(5)COO(*) and C(2)H(5)COOH. The C(2)H(5)COO(*) radical is easily formed on reaction of C(2)H(5)CO(*) with a peroxo V catalyst via a V{eta(1)-OOC(O)C(2)H(5)} intermediate. In the absence of CO, carboxylation proceeds by reaction of C(2)H(5) (*) with TFA. For the oxidation of ethane to acetic acid, either with preservation or cleavage of the C-C bond, metal-assisted and purely organic pathways are also proposed and discussed.

Extended reaction scope of thiamine diphosphate dependent cyclohexane-1,2-dione hydrolase: from C-C bond cleavage to C-C bond ligation.

PubMed

Loschonsky, Sabrina; Wacker, Tobias; Waltzer, Simon; Giovannini, Pier Paolo; McLeish, Michael J; Andrade, Susana L A; Müller, Michael

2014-12-22

ThDP-dependent cyclohexane-1,2-dione hydrolase (CDH) catalyzes the CC bond cleavage of cyclohexane-1,2-dione to 6-oxohexanoate, and the asymmetric benzoin condensation between benzaldehyde and pyruvate. One of the two reactivities of CDH was selectively knocked down by mutation experiments. CDH-H28A is much less able to catalyze the CC bond formation, while the ability for CC bond cleavage is still intact. The double variant CDH-H28A/N484A shows the opposite behavior and catalyzes the addition of pyruvate to cyclohexane-1,2-dione, resulting in the formation of a tertiary alcohol. Several acyloins of tertiary alcohols are formed with 54-94 % enantiomeric excess. In addition to pyruvate, methyl pyruvate and butane-2,3-dione are alternative donor substrates for CC bond formation. Thus, the very rare aldehyde-ketone cross-benzoin reaction has been solved by design of an enzyme variant. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The role of tachysterol in vitamin D photosynthesis - a non-adiabatic molecular dynamics study

NASA Astrophysics Data System (ADS)

Cisneros, Cecilia; Thompson, Travis; Baluyot, Noel; Smith, Adam C.; Tapavicza, Enrico

To investigate the role of tachysterol in the photophysical/chemical regulation of vitamin D photosynthesis, we studied its electronic absorption properties and excited state dynamics using time-dependent density functional theory (TDDFT), coupled cluster theory (CC2), and non-adiabatic molecular dynamics. In excellent agreement with experiments, the simulated electronic spectrum shows a broad absorption band covering the spectra of the other vitamin D photoisomers. The broad band stems from the spectral overlap of four different ground state rotamers. After photoexcitation, the first excited singlet state (S1) decays within 882 fs. The S1 dynamics is characterized by a strong twisting of the central double bond. 96% of all trajectories relax without chemical transformation to the ground state. In 2.3 % of the trajectories we observed [1,5]-sigmatropic hydrogen shift forming the partly deconjugated toxisterol D1. 1.4 % previtamin D formation is observed via hula-twist double bond isomerization. We find a strong dependence between photoreactivity and dihedral angle conformation: hydrogen shift only occurs in cEc and cEt rotamers and double bond isomerization occurs mainly in cEc rotamers. Our study confirms the hypothesis that cEc rotamers are more prone to previtamin D formation than other isomers. We also observe the formation of a cyclobutene-toxisterol in the hot ground state (0.7 %). Due to its strong absorption and unreactive behavior, tachysterol acts mainly as a sun shield suppressing previtamin D formation. Tachysterol shows stronger toxisterol formation than previtamin D. Absorption of low energy UV light by the cEc rotamer can lead to previtamin D formation. Our study reinforces a recent hypothesis that tachysterol can act as a previtamin D source when only low energy ultraviolet light is available, as it is the case in winter or in the morning and evening hours of the day.

Template-directed synthesis using the heterogeneous templates produced by montmorillonite catalysis. A possible bridge between the prebiotic and RNA worlds

NASA Technical Reports Server (NTRS)

Ertem, G.; Ferris, J. P.

1997-01-01

The synthesis of oligoguanylates [oligo(G)s] is catalyzed by a template of oligocytidylates [oligo(C)s] containing 2',5'- and 3',5'-linked phosphodiester bonds with and without incorporated C5'ppC groupings. An oligo(C) template containing exclusively 2',5'-phosphodiester bonds also serves as a template for the synthesis of complementary oligo(G)s. The oligo(C) template was prepared by the condensation of the 5'-phosphorimidazolide of cytidine on montmorillonite clay. These studies establish that RNA oligomers prepared by mineral catalysis, or other routes on the primitive earth, did not have to be exclusively 3',5'-linked to catalyze template-directed synthesis, since oligo(C)s containing a variety of linkage isomers serve as templates for the formation of complementary oligo(G)s. These findings support the postulate that origin of the RNA world was initiated by the RNA oligomers produced by polymerization of activated monomers formed by prebiotic processes.

Unexpected formation of (E)-4-alkene 1,3-diketones from the three-component reaction of lithium selenolates with 1-(1-alkynyl)cyclopropyl ketones and aldehydes.

PubMed

Xu, Jianfeng; Wu, Luling; Huang, Xian

2011-07-15

A novel three-component stereoselective synthesis of (E)-4-alkene 1,3-diketones from lithium selenolates, 1-(1-alkynyl)cyclopropyl ketones, and aldehydes is reported. This reaction afforded the products in moderate to good yields with the formation of a new C-Se single bond, a new C-C double bond, and a new C-O double bond.

In situ studies of surface of NiFe 2O 4 catalyst during complete oxidation of methane

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

Zhang, Shiran; Shan, Junjun; Nie, Longhui

2015-12-21

Here, NiFe 2O 4 with an inverse spinel structure exhibits high activity for a complete oxidation of methane at 400 °C–425 °C and a higher temperature. The surface of the catalyst and its adsorbates were well characterized with ambient pressure X-ray photoelectron spectroscopy (AP-XPS) and in situ infrared spectroscopy (IR). In situ studies of the surface of NiFe 2O 4 using AP-XPS suggest the formation of methoxy-like and formate-like intermediates at a temperature lower than 200 °C, supported by the observed vibrational signatures in in situ IR studies. Evolutions of C1s photoemission features and the nominal atomic ratios of C/(Nimore » + Fe) of the catalyst surface suggest that the formate-like intermediate is transformed to product molecules CO 2 and H 2O in the temperature range of 250–300 °C. In situ studies suggest the formation of a spectator, – O lattice – CH 2 – O lattice –. It strongly bonds to surface through C–O bonds and cannot be activated even at 400 °C.« less

Preparation and Electrocatalytic Activity of Gold Nanoparticles Immobilized on the Surface of 4-Mercaptobenzoyl-Functionalized Multiwalled Carbon Nanotubes

DTIC Science & Technology

2010-12-20

thiolate -Au bonds,30 and so GNP/MB-MWCNT hybrids were synthesized using a modified literature procedure.31 The SEM images show sequential...4 The electrocatalytic stability of GNP/MB-MWCNT supposes to be originated from the formation of stable thiolate -Au bonds that prevent aggregation of...Moon, K.-S.; Wong, C. P. Carbon 2007, 45, 655–661. (19) Sandler, J.; Shaffer, M. S. P.; Prasse, T.; Bauhofer, W.; Schulte, K.; Windle, A. H. Polymer

(Z)-5-(4-Fluoro­benzyl­idene)-1,3-thia­zolidine-2,4-dione

PubMed Central

Sun, Hong-Shun; Xu, Ye-Ming; He, Wei; Tang, Shi-Gui; Guo, Cheng

2008-01-01

In the title compound, C10H6FNO2S, the benzene and thia­zolidine rings make a dihedral angle of 7.52 (3)°. Intra­molecular C—H⋯O and C—H⋯S hydrogen bonds result in the formation of nearly planar five- and six-membered rings; the adjacent rings are nearly coplanar. In the crystal structure, inter­molecular N—H⋯O hydrogen bonds link the mol­ecules. PMID:21201543

Conformational and spectroscopic study of xanthogen ethyl formates, ROC(S)SC(O)OCH₂CH₃. Isolation of CH₃CH₂OC(O)SH.

PubMed

Juncal, Luciana C; Cozzarín, Melina V; Romano, Rosana M

2015-03-15

ROC(S)SC(O)OCH2CH3, with R=CH3-, (CH3)2CH- and CH3(CH2)2-, were obtained through the reaction between potassium xanthate salts, ROC(S)SK, and ethyl chloroformate, ClC(O)OCH2CH3. The liquid compounds were identified and characterized by (1)H and (13)C NMR and mass spectrometry. The conformations adopted by the molecules were studied by DFT methods. 6 conformers were theoretically predicted for R=CH3- and (CH3)2CH-, while the conformational flexibility of the n-propyl substituent increases the total number of feasible rotamers to 21. For the three molecules, the conformers can be associated in 3 groups, being the most stable the AS forms - the C=S double bond anti (A) with respect to the C-S single bond and the S-C single bond syn (S) with respect to the C=O double bond - followed by AA and SS conformers. The vibrational spectra were interpreted in terms of the predicted conformational equilibrium, presenting the ν(C=O) spectral region signals corresponding to the three groups of conformers. A moderated pre-resonance Raman enhancement of the ν(C=S) vibrational mode of CH3(CH2)2OC(S)SC(O)OCH2CH3 was detected, when the excitation radiation approaches the energy of a n→π∗ electronic transition associated with the C=S chromophore. UV-visible spectra in different solvents were measured and interpreted in terms of TD-DFT calculations. The unknown molecule CH3CH2OC(O)SH was isolated by the UV-visible photolysis of CH3OC(S)SC(O)OCH2CH3 isolated in Ar matrix, and also obtained as a side-product of the reaction between potassium xanthate salts, ROC(S)SK, and ethyl chloroformate, ClC(O)OCH2CH3. Copyright © 2014 Elsevier B.V. All rights reserved.

Methyl (4-bromo­benzene­sulfonamido)acetate

PubMed Central

Arshad, Muhammad Nadeem; Tahir, M. Nawaz; Khan, Islam Ullah; Ahmad, Ejaz; Shafiq, Muhammad

2008-01-01

The title compound, C9H10BrNO4S, is an inter­mediate for the formation of benzothia­zines. In the crystal structure, inter­molecular N—H⋯O hydrogen bonds link the mol­ecules, forming R 2 2(10) ring motifs, which are linked into a two-dimensional polymeric sheet through inter­molecular C—H⋯O hydrogen bonds. PMID:21581352

TDDFT study of twisted intramolecular charge transfer and intermolecular double proton transfer in the excited state of 4‧-dimethylaminoflavonol in ethanol solvent

NASA Astrophysics Data System (ADS)

Wang, Ye; Shi, Ying; Cong, Lin; Li, Hui

2015-02-01

Time-dependent density functional theory method at the def-TZVP/B3LYP level was employed to investigate the intramolecular and intermolecular hydrogen bonding dynamics in the first excited (S1) state of 4‧-dimethylaminoflavonol (DMAF) monomer and in ethanol solution. In the DMAF monomer, we demonstrated that the intramolecular charge transfer (ICT) takes place in the S1 state. This excited state ICT process was followed by intramolecular proton transfer. Our calculated results are in good agreement with the mechanism proposed in experimental work. For the hydrogen-bonded DMAF-EtOH complex, it was demonstrated that the intermolecular hydrogen bonds can induce the formation of the twisted intramolecular charge transfer (TICT) state and the conformational twisting is along the C3-C4 bond. Moreover, the intermolecular hydrogen bonds can also facilitate the intermolecular double proton transfer in the TICT state. A stepwise intermolecular double proton transfer process was revealed. Therefore, the intermolecular hydrogen bonds can alter the mechanism of intramolecular charge transfer and proton transfer in the excited state for the DMAF molecule.

Real-time Monitoring of Intermediates Reveals the Reaction Pathway in the Thiol-Disulfide Exchange between Disulfide Bond Formation Protein A (DsbA) and B (DsbB) on a Membrane-immobilized Quartz Crystal Microbalance (QCM) System*

PubMed Central

Yazawa, Kenjiro; Furusawa, Hiroyuki; Okahata, Yoshio

2013-01-01

Disulfide bond formation protein B (DsbBS-S,S-S) is an inner membrane protein in Escherichia coli that has two disulfide bonds (S-S, S-S) that play a role in oxidization of a pair of cysteine residues (SH, SH) in disulfide bond formation protein A (DsbASH,SH). The oxidized DsbAS-S, with one disulfide bond (S-S), can oxidize proteins with SH groups for maturation of a folding preprotein. Here, we have described the transient kinetics of the oxidation reaction between DsbASH,SH and DsbBS-S,S-S. We immobilized DsbBS-S,S-S embedded in lipid bilayers on the surface of a 27-MHz quartz crystal microbalance (QCM) device to detect both formation and degradation of the reaction intermediate (DsbA-DsbB), formed via intermolecular disulfide bonds, as a mass change in real time. The obtained kinetic parameters (intermediate formation, reverse, and oxidation rate constants (kf, kr, and kcat, respectively) indicated that the two pairs of cysteine residues in DsbBS-S,S-S were more important for the stability of the DsbA-DsbB intermediate than ubiquinone, an electron acceptor for DsbBS-S,S-S. Our data suggested that the reaction pathway of almost all DsbASH,SH oxidation processes would proceed through this stable intermediate, avoiding the requirement for ubiquinone. PMID:24145032

Cleavage of Sn-C and S-C(alkyl) bonds on an organotin scaffold: synthesis and characterization of a novel organotin-sulfite cluster bearing methyltin- and dimethyltin fragments.

PubMed

Shankar, Ravi; Jain, Archana; Kociok-Köhn, Gabriele; Mahon, Mary F; Molloy, Kieran C

2010-05-17

Hydrolysis of the mixed-ligand dimethyltin(ethoxy)ethanesulfonate, [Me(2)Sn(OEt)(OSO(2)Et)](n) (1a) in moist hexane proceeds via disproportionation and partial cleavage of Sn-C and S-C bonds to afford a novel oxo-/hydroxo- organotin cluster of the composition [(Me(2)Sn)(MeSn)(4)(OSO(2)Et)(2)(OH)(4)(O)(2)(SO(3))(2)] (1) bearing both mono- and dimethyltin fragments and in situ generated sulfite (SO(3)(2-)) anion in the structural framework. On the other hand, similar reactions with analogous mixed ligand diorganotin precursors, [R(2)Sn(OR(1))(OSO(2)R(1))](n) (R = n-Bu, R(1) = Et (2a); R = Et, R(1) = Me (3a)), result in the formation of tetranuclear diorganotin clusters, [{(n-Bu(2)Sn)(2)(OH)(OSO(2)Et)}O](2) (2) and [(Et(2)Sn)(4)(OH)(O)(2)(OSO(2)Me)(3)] (3), respectively. The activation of the Sn-C or S-C bond is not observed in these cases. These findings provide a preliminary insight into the unusual reactivity of 1a under hydrolytic conditions.

Cross-dehydrogenative coupling and oxidative-amination reactions of ethers and alcohols with aromatics and heteroaromatics

PubMed Central

Vuram, Prasanna K.

2017-01-01

Cross-dehydrogenative coupling (CDC) is a process in which, typically, a C–C bond is formed at the expense of two C–H bonds, either catalyzed by metals or other organic compounds, or via uncatalyzed processes. In this perspective, we present various modes of C–H bond-activation at sp3 centers adjacent to ether oxygen atoms, followed by C–C bond formation with aromatic systems as well as with heteroaromatic systems. C–N bond-formation with NH-containing heteroaromatics, leading to hemiaminal ethers, is also an event that can occur analogously to C–C bond formation, but at the expense of C–H and N–H bonds. A large variety of hemiaminal ether-forming reactions have recently appeared in the literature and this perspective also includes this complementary chemistry. In addition, the participation of C–H bonds in alcohols in such processes is also described. Facile access to a wide range of compounds can be attained through these processes, rendering such reactions useful for synthetic applications via Csp3 bond activations. PMID:28970941

Concentration-dependent multiple chirality transition in halogen-bond-driven 2D self-assembly process

NASA Astrophysics Data System (ADS)

Miao, Xinrui; Li, Jinxing; Zha, Bao; Miao, Kai; Dong, Meiqiu; Wu, Juntian; Deng, Wenli

2018-03-01

The concentration-dependent self-assembly of iodine substituted thienophenanthrene derivative (5,10-DITD) is investigated at the 1-octanic acid/graphite interface using scanning tunneling microscopy. Three kinds of chiral arrangement and transition of 2D molecular assembly mainly driven by halogen bonding is clearly revealed. At high concentration the molecules self-assembled into a honeycomb-like chiral network. Except for the interchain van der Waals forces, this pattern is stabilized by intermolecular continuous Cdbnd O⋯I⋯S halogen bonds in each zigzag line. At moderate concentration, a chiral kite-like nanoarchitecture are observed, in which the Cdbnd O⋯I⋯S and I⋯Odbnd C halogen bonds, along with the molecule-solvent Cdbnd O⋯I⋯H halogen bonds are the dominated forces to determine the structural formation. At low concentration, the molecules form a chiral cyclic network resulting from the solvent coadsorption mainly by molecule-molecule Cdbnd O⋯I⋯S halogen bonds and molecule-solvent Cdbnd O⋯I⋯H halogen bonds. The density of molecular packing becomes lower with the decreasing of the solution concentration. The solution-concentration dependent self-assembly of thienophenanthrene derivative with iodine and ester chain moieties reveals that the type of intermolecular halogen bond and the number of the co-adsorbing 1-octanic acids by molecule-solvent Cdbnd O⋯I⋯H halogen bonds determine the formation and transformation of chirality. This research emphasizes the role of different types of halogen (I) bonds in the controllable supramolecular structures and provides an approach for the fabrication of chirality.

Reusable ionic liquid-catalyzed oxidative coupling of azoles and benzylic compounds via sp(3) C-N bond formation under metal-free conditions.

PubMed

Liu, Wenbo; Liu, Chenjiang; Zhang, Yonghong; Sun, Yadong; Abdukadera, Ablimit; Wang, Bin; Li, He; Ma, Xuecheng; Zhang, Zengpeng

2015-07-14

The heterocyclic ionic liquid-catalyzed direct oxidative amination of benzylic sp(3) C-H bonds via intermolecular sp(3) C-N bond formation for the synthesis of N-alkylated azoles under metal-free conditions is reported for the first time. The catalyst 1-butylpyridinium iodide can be recycled and reused with similar efficacies for at least eight cycles.

Carbon-fluorine bond activation coupled with carbon-hydrogen bond formation alpha to iridium: kinetics, mechanism, and diastereoselectivity.

PubMed

Garratt, Shaun A; Hughes, Russell P; Kovacik, Ivan; Ward, Antony J; Willemsen, Stefan; Zhang, Donghui

2005-11-09

Reactions of iridium(fluoroalkyl)hydride complexes CpIr(PMe(3))(CF(2)R(F))Y (R(F) = F, CF(3); Y = H, D) with LutHX (Lut = 2,6-dimethylpyridine; X = Cl, I) results in C-F activation coupled with hydride migration to give CpIr(PMe(3))(CYFR(F))X as variable mixtures of diastereomers. Solution conformations and relative diastereomer configurations of the products have been determined by (19)F{(1)H}HOESY NMR to be (S(C), S(Ir))(R(C), R(Ir)) for the kinetic diastereomer and (R(C), S(Ir))(S(C), R(Ir)) for its thermodynamic counterpart. Isotope labeling experiments using LutDCl/CpIr(PMe(3))(CF(2)R(F))H and CpIr(PMe(3))(CF(2)R(F))D/LutHCl) showed that, unlike a previously studied system, H/D exchange is faster than protonation of the alpha-CF bond, giving an identical mixture of product isotopologues from both reaction mixtures. The kinetic rate law shows a first-order dependence on the concentration of iridium substrate, but a half-order dependence on that of LutHCl; this is interpreted to mean that LutHCl dissociates to give HCl as the active protic source for C-F bond activation. Detailed kinetic studies are reported, which demonstrate that lack of complete diastereoselectivity is not a function of the C-F bond activation/H migration steps but that a cationic intermediate plays a double role in loss of diastereoselectivity; the intermediate can undergo epimerization at iridium before being trapped by halide and can also catalyze the epimerization of kinetic diastereomer product to thermodynamic product. A detailed mechanism is proposed and simulations performed to fit the kinetic data.

CuO nanoparticles catalyzed C-N, C-O, and C-S cross-coupling reactions: scope and mechanism.

PubMed

Jammi, Suribabu; Sakthivel, Sekarpandi; Rout, Laxmidhar; Mukherjee, Tathagata; Mandal, Santu; Mitra, Raja; Saha, Prasenjit; Punniyamurthy, Tharmalingam

2009-03-06

CuO nanoparticles have been studied for C-N, C-O, and C-S bond formations via cross-coupling reactions of nitrogen, oxygen, and sulfur nucleophiles with aryl halides. Amides, amines, imidazoles, phenols, alcohols and thiols undergo reactions with aryl iodides in the presence of a base such as KOH, Cs(2)CO(3), and K(2)CO(3) at moderate temperature. The procedure is simple, general, ligand-free, and efficient to afford the cross-coupled products in high yield.

Catalytic hydrolysis of carbonyl sulphide and carbon disulphide over Fe2O3 cluster: Competitive adsorption and reaction mechanism.

PubMed

Ning, Ping; Song, Xin; Li, Kai; Wang, Chi; Tang, Lihong; Sun, Xin

2017-10-31

The competitive adsorption and reaction mechanism for the catalytic hydrolysis of carbonyl sulphide (COS) and carbon disulphide (CS 2 ) over Fe 2 O 3 cluster was investigated. Compared with experimental results, the theoretical study was used to further investigate the competitive adsorption and effect of H 2 S in the hydrolysis reaction of COS and CS 2 . Experimental results showed that Fe 2 O 3 cluster enhanced the catalytic hydrolysis effect. Meanwhile, H 2 S was not conducive to the hydrolysis of COS and CS 2 . Theoretical calculations indicated that the order of competitive adsorption on Fe 2 O 3 is as follows: H 2 O (strong) >CS 2 (medium) >COS (weak). In the hydrolysis process, the C=S bond cleavage occurs easier than C=O bond cleavage. The hydrolysis reaction is initiated via the migration of an H-atom, which triggers C=S bond cleavage and S-H bond formation. Additionally, we find the first step of CS 2 hydrolysis to be rate limiting. The presence of H 2 S increases the reaction energy barrier, which is not favourable for COS hydrolysis. Fe 2 O 3 can greatly decrease the maximum energy barrier, which decreases the minimum energy required for hydrolysis, making it relatively facile to occur. In general, the theoretical results were consistent with experimental results, which proved that the theoretical study was reliable.

Secondary organic aerosol formation from in situ OH, O3, and NO3 oxidation of ambient forest air in an oxidation flow reactor

NASA Astrophysics Data System (ADS)

Palm, Brett B.; Campuzano-Jost, Pedro; Day, Douglas A.; Ortega, Amber M.; Fry, Juliane L.; Brown, Steven S.; Zarzana, Kyle J.; Dube, William; Wagner, Nicholas L.; Draper, Danielle C.; Kaser, Lisa; Jud, Werner; Karl, Thomas; Hansel, Armin; Gutiérrez-Montes, Cándido; Jimenez, Jose L.

2017-04-01

Ambient pine forest air was oxidized by OH, O3, or NO3 radicals using an oxidation flow reactor (OFR) during the BEACHON-RoMBAS (Bio-hydro-atmosphere interactions of Energy, Aerosols, Carbon, H2O, Organics and Nitrogen - Rocky Mountain Biogenic Aerosol Study) campaign to study biogenic secondary organic aerosol (SOA) formation and organic aerosol (OA) aging. A wide range of equivalent atmospheric photochemical ages was sampled, from hours up to days (for O3 and NO3) or weeks (for OH). Ambient air processed by the OFR was typically sampled every 20-30 min, in order to determine how the availability of SOA precursor gases in ambient air changed with diurnal and synoptic conditions, for each of the three oxidants. More SOA was formed during nighttime than daytime for all three oxidants, indicating that SOA precursor concentrations were higher at night. At all times of day, OH oxidation led to approximately 4 times more SOA formation than either O3 or NO3 oxidation. This is likely because O3 and NO3 will only react with gases containing C = C bonds (e.g., terpenes) to form SOA but will not react appreciably with many of their oxidation products or any species in the gas phase that lacks a C = C bond (e.g., pinonic acid, alkanes). In contrast, OH can continue to react with compounds that lack C = C bonds to produce SOA. Closure was achieved between the amount of SOA formed from O3 and NO3 oxidation in the OFR and the SOA predicted to form from measured concentrations of ambient monoterpenes and sesquiterpenes using published chamber yields. This is in contrast to previous work at this site (Palm et al., 2016), which has shown that a source of SOA from semi- and intermediate-volatility organic compounds (S/IVOCs) 3.4 times larger than the source from measured VOCs is needed to explain the measured SOA formation from OH oxidation. This work suggests that those S/IVOCs typically do not contain C = C bonds. O3 and NO3 oxidation produced SOA with elemental O : C and H : C similar to the least-oxidized OA observed in local ambient air, and neither oxidant led to net mass loss at the highest exposures, in contrast to OH oxidation. An OH exposure in the OFR equivalent to several hours of atmospheric aging also produced SOA with O : C and H : C values similar to ambient OA, while higher aging (days-weeks) led to formation of SOA with progressively higher O : C and lower H : C (and net mass loss at the highest exposures). NO3 oxidation led to the production of particulate organic nitrates (pRONO2), while OH and O3 oxidation (under low NO) did not, as expected. These measurements of SOA formation provide the first direct comparison of SOA formation potential and chemical evolution from OH, O3, and NO3 oxidation in the real atmosphere and help to clarify the oxidation processes that lead to SOA formation from biogenic hydrocarbons.

2,2′-(Carbono­thio­yldisulfanedi­yl)bis­(2-methyl­propanoic acid)

PubMed Central

Moreno-Fuquen, Rodolfo; Grande, Carlos; Advincula, Rigoberto C.; Tenorio, Juan C.; Ellena, Javier

2013-01-01

The mol­ecular structure of the title compound, C9H14O4S3, exhibits intra­molecular C—H⋯S hydrogen bonds. In the crystal, pairs of O—H⋯O hydrogen bonds lead to the formation of centrosymmetric dimers, which are in turn connected by weak C—H⋯O inter­actions. The combination of these inter­actions generates edge-fused R 2 2(8) and R 2 2(20) rings running along [211]. PMID:23723918

Selective Hydrogen Atom Abstraction through Induced Bond Polarization: Direct α-Arylation of Alcohols through Photoredox, HAT, and Nickel Catalysis.

PubMed

Twilton, Jack; Christensen, Melodie; DiRocco, Daniel A; Ruck, Rebecca T; Davies, Ian W; MacMillan, David W C

2018-05-04

The combination of nickel metallaphotoredox catalysis, hydrogen atom transfer catalysis, and a Lewis acid activation mode, has led to the development of an arylation method for the selective functionalization of alcohol α-hydroxy C-H bonds. This approach employs zinc-mediated alcohol deprotonation to activate α-hydroxy C-H bonds while simultaneously suppressing C-O bond formation by inhibiting the formation of nickel alkoxide species. The use of Zn-based Lewis acids also deactivates other hydridic bonds such as α-amino and α-oxy C-H bonds. This approach facilitates rapid access to benzylic alcohols, an important motif in drug discovery. A 3-step synthesis of the drug Prozac exemplifies the utility of this new method. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Copper-catalyzed transformation of ketones to amides via C(CO)-C(alkyl) bond cleavage directed by picolinamide.

PubMed

Ma, Haojie; Zhou, Xiaoqiang; Zhan, Zhenzhen; Wei, Daidong; Shi, Chong; Liu, Xingxing; Huang, Guosheng

2017-09-13

Copper catalyzed chemoselective cleavage of the C(CO)-C(alkyl) bond leading to C-N bond formation with chelation assistance of N-containing directing groups is described. Inexpensive Cu(ii)-acetate serves as a convenient catalyst for this transformation. This method highlights the emerging strategy to transform unactivated alkyl ketones into amides in organic synthesis and provides a new strategy for C-C bond cleavage.

Alkali metal mediated C-C bond coupling reaction

NASA Astrophysics Data System (ADS)

Tachikawa, Hiroto

2015-02-01

Metal catalyzed carbon-carbon (C-C) bond formation is one of the important reactions in pharmacy and in organic chemistry. In the present study, the electron and hole capture dynamics of a lithium-benzene sandwich complex, expressed by Li(Bz)2, have been investigated by means of direct ab-initio molecular dynamics method. Following the electron capture of Li(Bz)2, the structure of [Li(Bz)2]- was drastically changed: Bz-Bz parallel form was rapidly fluctuated as a function of time, and a new C-C single bond was formed in the C1-C1' position of Bz-Bz interaction system. In the hole capture, the intermolecular vibration between Bz-Bz rings was only enhanced. The mechanism of C-C bond formation in the electron capture was discussed on the basis of theoretical results.

The promotional effects of cesium promoter on higher alcohol synthesis from syngas over cesium-promoted Cu/ZnO/Al2O3 catalysts

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

Sun, Jie; Cai, Qiuxia; Wan, Yan

In this study, the promotional effects of cesium promoter on higher alcohol (C2+OH) synthesis from syngas over Cs-Cu/ZnO/Al2O3 catalysts were investigated using a combined experimental and theoretical density functional theory (DFT) calculation method. In the presence of cesium, the C2+OH productivity increases from 77.1 g•kgcat-1•h-1 to 157.3 g•kgcat-1•h-1 at 583 K due to the enhancement of the initial C–C bond formation. Detailed analysis of chain growth probabilities (CGPs) confirms that initial C–C bond formation is the rate-determining step in the temperature range of 543-583 K. Addition of cesium promoter significantly increases the productivities of 2-methyl-1-propanol, while the CGPs values (C3*more » to 2-methyl-C3*) is almost unaffected. With the assistance of cesium promoter, the CGPs of the initial C–C bond formation step (C1* to C2*) could be increased from 0.13 to 0.25 at 583 K. DFT calculations indicate that the initial C–C bond formation is mainly contributed by the HCO+HCO coupling reaction over the ZnCu(211) model surface. In the presence of the Cs2O, the stabilities of key reaction intermediates such as HCO and H2CO are enhanced which facilitates both HCO+HCO and HCO+H2CO coupling reaction steps with lower activation barriers over the Cs2O-ZnCu(211) surface. The promotional effects of cesium on the C2+OH productivity are also benefited from the competitive CH+HCO coupling reaction over CH hydrogenation that leads to lower alkane formation. In addition, Bader charge analysis suggests that the presence of cesium ions would facilitate the nucleophilic reaction between HCO and H2CO for initial C–C bond formation. This work was supported by the National Natural Science Foundation of China (No. 91545114 and No. 91545203). We appreciate the joint PhD scholarship support from the China Scholarship Council. The authors would also like to thank the support from Collaborative Innovation Center of Chemistry for Energy Materials (2011-iChEM). DM was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences. Computing time was granted by the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL). EMSL is a national scientific user facility located at Pacific Northwest National Laboratory (PNNL) and sponsored by DOE’s Office of Biological and Environmental Research. PNNL is a multiprogram national laboratory operated for DOE by Battelle Memorial Institute. We also appreciate the support from Sinochem Quanzhou Petrochemical Co. Ltd.« less

Diffusion Bonding of Silicon Carbide Ceramics using Titanium Interlayers

NASA Technical Reports Server (NTRS)

Halbig, Michael C.; Singh, Mrityunjay; Shpargel, Tarah P.; Kiser, James D.

2006-01-01

Robust joining approaches for silicon carbide ceramics are critically needed to fabricate leak free joints with high temperature mechanical capability. In this study, titanium foils and physical vapor deposited (PVD) titanium coatings were used to form diffusion bonds between SiC ceramics using hot pressing. Silicon carbide substrate materials used for bonding include sintered SiC and two types of CVD SiC. Microscopy results show the formation of well adhered diffusion bonds. The bond strengths as determined from pull tests are on the order of several ksi, which is much higher than required for a proposed application. Microprobe results show the distribution of silicon, carbon, titanium, and other minor elements across the diffusion bond. Compositions of several phases formed in the joint region were identified. Potential issues of material compatibility and optimal bond formation will also be discussed.

Comparing Ullmann Coupling on Noble Metal Surfaces: On-Surface Polymerization of 1,3,6,8-Tetrabromopyrene on Cu(111) and Au(111).

PubMed

Pham, Tuan Anh; Song, Fei; Nguyen, Manh-Thuong; Li, Zheshen; Studener, Florian; Stöhr, Meike

2016-04-18

The on-surface polymerization of 1,3,6,8-tetrabromopyrene (Br4 Py) on Cu(111) and Au(111) surfaces under ultrahigh vacuum conditions was investigated by a combination of scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS) and density functional theory (DFT) calculations. Deposition of Br4 Py on Cu(111) held at 300 K resulted in a spontaneous debromination reaction, generating the formation of a branched coordination polymer network stabilized by C-Cu-C bonds. After annealing at 473 K, the C-Cu-C bonds were converted to covalent C-C bonds, leading to the formation of a covalently linked molecular network of short oligomers. In contrast, highly ordered self-assembled two-dimensional (2D) patterns stabilized by both Br-Br halogen and Br-H hydrogen bonds were observed upon deposition of Br4 Py on Au(111) held at 300 K. Subsequent annealing of the sample at 473 K led to a dissociation of the C-Br bonds and the formation of disordered metal-coordinated molecular networks. Further annealing at 573 K resulted in the formation of covalently linked disordered networks. Importantly, we found that the chosen substrate not only plays an important role as catalyst for the Ullmann reaction, but also influences the formation of different types of intermolecular bonds and thus, determines the final polymer network morphology. DFT calculations further support our experimental findings obtained by STM and XPS and add complementary information on the reaction pathway of Br4 Py on the different substrates. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multiple C-H Bond Activations and Ring-Opening C-S Bond Cleavage of Thiophene by Dirhenium Carbonyl Complexes.

PubMed

Adams, Richard D; Dhull, Poonam; Tedder, Jonathan D

2018-06-14

The reaction of Re 2 (CO) 8 (μ-C 6 H 5 )(μ-H) (1) with thiophene in CH 2 Cl 2 at 40 °C yielded the new compound Re 2 (CO) 8 (μ-η 2 -SC 4 H 3 )(μ-H) (2), which contains a bridging σ-π-coordinated thienyl ligand formed by the activation of the C-H bond at the 2 position of the thiophene. Compound 2 exhibits dynamical activity on the NMR time scale involving rearrangements of the bridging thienyl ligand. The reaction of compound 2 with a second 1 equiv of 1 at 45 °C yielded the doubly metalated product [Re 2 (CO) 8 (μ-H)] 2 (μ-η 2 -2,3-μ-η 2 -4,5-C 4 H 2 S) (3), formed by the activation of the C-H bond at the 5 position of the thienyl ligand in 2. Heating 3 in a hexane solvent to reflux transformed it into the ring-opened compound Re(CO) 4 [μ-η 5 -η 2 -SCC(H)C(H)C(H)][Re(CO) 3 ][Re 2 (CO) 8 (μ-H)] (4) by the loss of one CO ligand. Compound 4 contains a doubly metalated 1-thiapentadienyl ligand formed by the cleavage of one of the C-S bonds. When heated to reflux (125 °C) in an octane solvent in the presence of H 2 O, the new compound Re(CO) 4 [η 5 -μ-η 2 -SC(H)C(H)C(H)C(H)]Re(CO) 3 (5) was obtained by cleavage of the Re 2 (CO) 8 (μ-H) group from 4 with formation of the known coproduct [Re(CO) 3 (μ 3 -OH)] 4 . All new products were characterized by single-crystal X-ray diffraction analyses.

Hydrophilicity of dentin bonding systems influences in vitro Streptococcus mutans biofilm formation

PubMed Central

Brambilla, Eugenio; Ionescu, Andrei; Mazzoni, Annalisa; Cadenaro, Milena; Gagliani, Massimo; Ferraroni, Monica; Tay, Franklin; Pashley, David; Breschi, Lorenzo

2014-01-01

Objectives To evaluate in vitro Streptococcus mutans (S. mutans) biofilm formation on the surface of five light-curing experimental dental bonding systems (DBS) with increasing hydrophilicity. The null hypothesis tested was that resin chemical composition and hydrophilicity does not affect S. mutans biofilm formation. Methods Five light-curing versions of experimental resin blends with increasing hydrophilicity were investigated (R1, R2, R3, R4 and R5). R1 and R2 contained ethoxylated BisGMA/TEGDMA or BisGMA/TEGDMA, respectively, and were very hydrophobic, were representative of pit-and-fissure bonding agents. R3 was representative of a typical two-step etch- and-rinse adhesive, while R4 and R5 were very hydrophilic resins analogous to self-etching adhesives. Twenty-eight disks were prepared for each resin blend. After a 24 h-incubation at 37 °C, a multilayer monospecific biofilm of S. mutans was obtained on the surface of each disk. The adherent biomass was determined using the MTT assay and evaluated morphologically with confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM). Results R2 and R3 surfaces showed the highest biofilm formation while R1 and R4 showed a similar intermediate biofilm formation. R5 was more hydrophilic and acidic and was significantly less colonized than all the other resins. A significant quadratic relationship between biofilm formation and hydrophilicity of the resin blends was found. CLSM and SEM evaluation confirmed MTT assay results. Conclusions The null hypothesis was rejected since S. mutans biofilm formation was influenced by hydrophilicity, surface acidity and chemical composition of the experimental resins. Further studies using a bioreactor are needed to confirm the results and clarify the role of the single factors. PMID:24954666

Nanometre-scale 3D defects in Cr2AlC thin films.

PubMed

Chen, Y T; Music, D; Shang, L; Mayer, J; Schneider, J M

2017-04-20

MAX-phase Cr 2 AlC containing thin films were synthesized by magnetron sputtering in an industrial system. Nanometre-scale 3D defects are observed near the boundary between regions of Cr 2 AlC and of the disordered solid solution (CrAl) x C y . Shrinkage of the Cr-Cr interplanar distance and elongation of the Cr-Al distance in the vicinity of the defects are detected using transmission electron microscopy. The here observed deformation surrounding the defects was described using density functional theory by comparing the DOS of bulk Cr 2 AlC with the DOS of a strained and unstrained Cr 2 AlC(0001) surface. From the partial density of states analysis, it can be learned that Cr-C bonds are stronger than Cr-Al bonds in bulk Cr 2 AlC. Upon Cr 2 AlC(0001) surface formation, both bonds are weakened. While the Cr-C bonds recover their bulk strength as Cr 2 AlC(0001) is strained, the Cr-Al bonds experience only a partial recovery, still being weaker than their bulk counterparts. Hence, the strain induced bond strengthening in Cr 2 AlC(0001) is larger for Cr d - C p bonds than for Cr d - Al p bonds. The here observed changes in bonding due to the formation of a strained surface are consistent with the experimentally observed elongation of the Cr-Al distance in the vicinity of nm-scale 3D defects in Cr 2 AlC thin films.

Acetic Acid Can Catalyze Succinimide Formation from Aspartic Acid Residues by a Concerted Bond Reorganization Mechanism: A Computational Study

PubMed Central

Takahashi, Ohgi; Kirikoshi, Ryota; Manabe, Noriyoshi

2015-01-01

Succinimide formation from aspartic acid (Asp) residues is a concern in the formulation of protein drugs. Based on density functional theory calculations using Ace-Asp-Nme (Ace = acetyl, Nme = NHMe) as a model compound, we propose the possibility that acetic acid (AA), which is often used in protein drug formulation for mildly acidic buffer solutions, catalyzes the succinimide formation from Asp residues by acting as a proton-transfer mediator. The proposed mechanism comprises two steps: cyclization (intramolecular addition) to form a gem-diol tetrahedral intermediate and dehydration of the intermediate. Both steps are catalyzed by an AA molecule, and the first step was predicted to be rate-determining. The cyclization results from a bond formation between the amide nitrogen on the C-terminal side and the side-chain carboxyl carbon, which is part of an extensive bond reorganization (formation and breaking of single bonds and the interchange of single and double bonds) occurring concertedly in a cyclic structure formed by the amide NH bond, the AA molecule and the side-chain C=O group and involving a double proton transfer. The second step also involves an AA-mediated bond reorganization. Carboxylic acids other than AA are also expected to catalyze the succinimide formation by a similar mechanism. PMID:25588215

Acetic acid can catalyze succinimide formation from aspartic acid residues by a concerted bond reorganization mechanism: a computational study.

PubMed

Takahashi, Ohgi; Kirikoshi, Ryota; Manabe, Noriyoshi

2015-01-12

Succinimide formation from aspartic acid (Asp) residues is a concern in the formulation of protein drugs. Based on density functional theory calculations using Ace-Asp-Nme (Ace = acetyl, Nme = NHMe) as a model compound, we propose the possibility that acetic acid (AA), which is often used in protein drug formulation for mildly acidic buffer solutions, catalyzes the succinimide formation from Asp residues by acting as a proton-transfer mediator. The proposed mechanism comprises two steps: cyclization (intramolecular addition) to form a gem-diol tetrahedral intermediate and dehydration of the intermediate. Both steps are catalyzed by an AA molecule, and the first step was predicted to be rate-determining. The cyclization results from a bond formation between the amide nitrogen on the C-terminal side and the side-chain carboxyl carbon, which is part of an extensive bond reorganization (formation and breaking of single bonds and the interchange of single and double bonds) occurring concertedly in a cyclic structure formed by the amide NH bond, the AA molecule and the side-chain C=O group and involving a double proton transfer. The second step also involves an AA-mediated bond reorganization. Carboxylic acids other than AA are also expected to catalyze the succinimide formation by a similar mechanism.

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.

5-Chloro-2-nitro-phenol.

PubMed

Ren, Dong-Mei

2012-05-01

The asymmetric unit of the title compound, C(6)H(4)ClNO(3), contains two independent mol-ecules in which the dihedral angles between the benzene ring and the nitro groups are 2.5 (1) and 8.5 (1)°. Intra-molecular O-H⋯O hydrogen bonds involving the hy-droxy and nitro substituents result in the formation of S(6) six-membered rings. In the crystal, O-H⋯O, O-H⋯Cl and C-H⋯O hydrogen bonds together with Cl⋯O contacts [3.238 (3) and 3.207 (3) Å] generate a three-dimensional network.

Boron-Based Catalysts for C-C Bond-Formation Reactions.

PubMed

Rao, Bin; Kinjo, Rei

2018-05-02

Because the construction of the C-C bond is one of the most significant reactions in organic chemistry, the development of an efficient strategy has attracted much attention throughout the synthetic community. Among various protocols to form C-C bonds, organoboron compounds are not just limited to stoichiometric reagents, but have also made great achievements as catalysts because of the easy modification of the electronic and steric impacts on the boron center. This review presents recent developments of boron-based catalysts applied in the field of C-C bond-formation reactions, which are classified into four kinds on the basis of the type of boron catalyst: 1) highly Lewis acidic borane, B(C 6 F 5 ) 3 ; 2) organoboron acids, RB(OH) 2 , and their ester derivatives; 3) borenium ions, (R 2 BL)X; and 4) other miscellaneous kinds. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Oxidation of Half-Lantern Pt2(II,II) Compounds by Halocarbons. Evidence of Dioxygen Insertion into a Pt(III)-CH3 Bond.

PubMed

Sicilia, V; Baya, M; Borja, P; Martín, A

2015-08-03

The half-lantern compound [{Pt(bzq)(μ-N^S)}2] (1) [bzq = benzo[h]quinoline, HN^S = 2-mercaptopyrimidine (C4H3N2HS)] reacts with CH3I and haloforms CHX3 (X = Cl, Br, I) to give the corresponding oxidized diplatinum(III) derivatives [{Pt(bzq)(μ-N^S)X}2] (X = Cl 2a, Br 2b, I 2c). These compounds exhibit half-lantern structures with short intermetallic distances (∼2.6 Å) due to Pt-Pt bond formation. The halogen abstraction mechanisms from the halocarbon molecules by the Pt2(II,II) compound 1 were investigated. NMR spectroscopic evidence using labeled reagents support that in the case of (13)CH3I the reaction initiates with an oxidative addition through an SN2 mechanism giving rise to the intermediate species [I(bzq)Pt(μ-N^S)2Pt(bzq)((13)CH3)}]. However, with haloforms the reactions proceed through a radical-like mechanism, thermally (CHBr3, CHI3) or photochemically (CHCl3) activated, giving rise to mixtures of species [X(bzq)Pt(μ-N^S)2Pt(bzq)R] (3a-c) and [X(bzq)Pt(μ-N^S)2Pt(bzq)X] (2a-c). In these cases the presence of O2 favors the formation of species 2 over 3. Transformation of 3 into 2 was possible upon irradiation with UV light. In the case of [I(bzq)Pt(μ-N^S)2Pt(bzq)((13)CH3)}] (3d), in the presence of O2 the formation of the unusual methylperoxo derivative [I(bzq)Pt(μ-N^S)2Pt(bzq)(O-O(13)CH3)}] (4d) was detected, which in the presence of (13)CH3I rendered the final product [{Pt(bzq)(μ-N^S)I}2] (2c) and (13)CH3OH.

Clumped isotope thermometry in deeply buried sedimentary carbonates: The effects of C-O bond reordering and recrystallization

NASA Astrophysics Data System (ADS)

Passey, B. H.; Shenton, B.; Grossman, E. L.; Henkes, G. A.; Laya, J. C.; Perez-Huerta, A.

2014-12-01

Constraining the thermal histories of sedimentary basins is fundamental to a range of geologic applications including tectonics, petroleum system analysis, and the genesis of ore deposits. Carbonate rocks can serve as archives of basin thermal histories through solid-state reordering of their 13C-18O, or 'clumped isotope', bonds at elevated burial temperatures. Here we present one of the first applied studies of carbonate clumped isotope reordering to explore the diagenetic and thermal histories of exhumed brachiopods, crinoids, cements, and host rock in the Permian Palmarito Formation, Venezuela and the Carboniferous Bird Spring Formation, Nevada, USA. Carbonate components in the Palmarito Formation, buried to ~4 km depth, yield statistically indistinguishable clumped isotope temperatures (T(Δ47)) ranging from 86 to 122 °C. Clumped isotope temperatures of components in the more deeply buried Bird Spring Formation (>5 km), range from ~100 to 165 °C and differ by component type, with brachiopods and pore-filling cements yielding the highest T(Δ47) (mean = 153 and 141 °C, respectively) and crinoids and host rock yielding significantly cooler T(Δ47) (mean = 103 and 114 °C). New high-resolution thermal histories are coupled with kinetic models to predict the extent of solid-state C-O bond reordering during burial and exhumation for both sites. Application of these models suggests that brachiopods in the Palmarito Formation experienced partial bond reordering without complete equilibration of clumped isotopes at maximum burial temperature. In contrast, clumped isotope bonds of brachiopods from the Bird Spring Formation appear to have completely equilibrated at maximum burial temperature, and now reflect blocking temperatures 'locked-in' during cooling. The 40-50 °C cooler clumped isotope temperatures measured in Bird Spring Formation crinoids and host rock can be explained by both recrystallization and cementation during shallow burial and a greater inherent resistance to solid-state reordering than brachiopods.

Chemoselective Radical Dehalogenation and C-C Bond Formation on Aryl Halide Substrates Using Organic Photoredox Catalysts.

PubMed

Poelma, Saemi O; Burnett, G Leslie; Discekici, Emre H; Mattson, Kaila M; Treat, Nicolas J; Luo, Yingdong; Hudson, Zachary M; Shankel, Shelby L; Clark, Paul G; Kramer, John W; Hawker, Craig J; Read de Alaniz, Javier

2016-08-19

Despite the number of methods available for dehalogenation and carbon-carbon bond formation using aryl halides, strategies that provide chemoselectivity for systems bearing multiple carbon-halogen bonds are still needed. Herein, we report the ability to tune the reduction potential of metal-free phenothiazine-based photoredox catalysts and demonstrate the application of these catalysts for chemoselective carbon-halogen bond activation to achieve C-C cross-coupling reactions as well as reductive dehalogenations. This procedure works both for conjugated polyhalides as well as unconjugated substrates. We further illustrate the usefulness of this protocol by intramolecular cyclization of a pyrrole substrate, an advanced building block for a family of natural products known to exhibit biological activity.

A single Watson-Crick G x C base pair in water: aqueous hydrogen bonds in hydrophobic cavities.

PubMed

Sawada, Tomohisa; Fujita, Makoto

2010-05-26

Hydrogen bond (H-bond) formation in water has been a challenging task because water molecules are constant competitors. In biological systems, however, stable H-bonds are formed by shielding the H-bonding sites from the competing water molecules within hydrophobic pockets. Inspired by the nature's elaborated way, we found that even mononucleotides (G and C) can form the minimal G x C Watson-Crick pair in water by simply providing a synthetic cavity that efficiently shields the Watson-Crick H-bonding sites. The minimal Watson-Crick structure in water was elucidated by NMR study and firmly characterized by crystallographic analysis. The crystal structure also displays that, within the cavity, coencapsulated anions and solvents efficiently mediate the minimal G x C Watson-Crick pair formation. Furthermore, the competition experiments with the other nucleobases clearly revealed the evident selectivity for the G x C base pairing in water. These results show the fact that a H-bonded nucleobase pair was effectively induced and stabilized in the local environment of an artificial hydrophobic cavity.

Tracing the Fingerprint of Chemical Bonds within the Electron Densities of Hydrocarbons: A Comparative Analysis of the Optimized and the Promolecule Densities.

PubMed

Keyvani, Zahra Alimohammadi; Shahbazian, Shant; Zahedi, Mansour

2016-10-18

The equivalence of the molecular graphs emerging from the comparative analysis of the optimized and the promolecule electron densities in two hundred and twenty five unsubstituted hydrocarbons was recently demonstrated [Keyvani et al. Chem. Eur. J. 2016, 22, 5003]. Thus, the molecular graph of an optimized molecular electron density is not shaped by the formation of the C-H and C-C bonds. In the present study, to trace the fingerprint of the C-H and C-C bonds in the electron densities of the same set of hydrocarbons, the amount of electron density and its Laplacian at the (3, -1) critical points associated with these bonds are derived from both optimized and promolecule densities, and compared in a newly proposed comparative analysis. The analysis not only conforms to the qualitative picture of the electron density build up between two atoms upon formation of a bond in between, but also quantifies the resulting accumulation of the electron density at the (3, -1) critical points. The comparative analysis also reveals a unified mode of density accumulation in the case of 2318 studied C-H bonds, but various modes of density accumulation are observed in the case of 1509 studied C-C bonds and they are classified into four groups. The four emerging groups do not always conform to the traditional classification based on the bond orders. Furthermore, four C-C bonds described as exotic bonds in previous studies, for example the inverted C-C bond in 1,1,1-propellane, are naturally distinguished from the analysis. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

S-glutathionylation of glyceraldehyde-3-phosphate dehydrogenase induces formation of C150-C154 intrasubunit disulfide bond in the active site of the enzyme.

PubMed

Barinova, K V; Serebryakova, M V; Muronetz, V I; Schmalhausen, E V

2017-12-01

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a glycolytic protein involved in numerous non-glycolytic functions. S-glutathionylated GAPDH was revealed in plant and animal tissues. The role of GAPDH S-glutathionylation is not fully understood. Rabbit muscle GAPDH was S-glutathionylated in the presence of H 2 O 2 and reduced glutathione (GSH). The modified protein was assayed by MALDI-MS analysis, differential scanning calorimetry, dynamic light scattering, and ultracentrifugation. Incubation of GAPDH in the presence of H 2 O 2 together with GSH resulted in the complete inactivation of the enzyme. In contrast to irreversible oxidation of GAPDH by H 2 O 2 , this modification could be reversed in the excess of GSH or dithiothreitol. By data of MALDI-MS analysis, the modified protein contained both mixed disulfide between Cys150 and GSH and the intrasubunit disulfide bond between Cys150 and Cys154 (different subunits of tetrameric GAPDH may contain different products). S-glutathionylation results in loosening of the tertiary structure of GAPDH, decreases its affinity to NAD + and thermal stability. The mixed disulfide between Cys150 and GSH is an intermediate product of S-glutathionylation: its subsequent reaction with Cys154 results in the intrasubunit disulfide bond in the active site of GAPDH. The mixed disulfide and the C150-C154 disulfide bond protect GAPDH from irreversible oxidation and can be reduced in the excess of thiols. Conformational changes that were observed in S-glutathionylated GAPDH may affect interactions between GAPDH and other proteins (ligands), suggesting the role of S-glutathionylation in the redox signaling. The manuscript considers one of the possible mechanisms of redox regulation of cell functions. Copyright © 2017 Elsevier B.V. All rights reserved.

Room-Temperature Synthesis of Thiostannates from {[Ni(tren)]2[Sn2S6]}n.

PubMed

Hilbert, Jessica; Näther, Christian; Weihrich, Richard; Bensch, Wolfgang

2016-08-15

The compound {[Ni(tren)]2[Sn2S6]}n (1) (tren = tris(2-aminoethyl)amine, C6H18N4) was successfully applied as source for the room-temperature synthesis of the new thiostannates [Ni(tren)(ma)(H2O)]2[Sn2S6]·4H2O (2) (ma = methylamine, CH5N) and [Ni(tren)(1,2-dap)]2[Sn2S6]·2H2O (3) (1,2-dap = 1,2-diaminopropane, C3H10N2). The Ni-S bonds in the Ni2S2N8 bioctahedron in the structure of 1 are analyzed with density functional theory calculations demonstrating significantly differing Ni-S bond strengths. Because of this asymmetry they are easily broken in the presence of an excess of ma or 1,2-dap immediately followed by Ni-N bond formation to N donor atoms of the amine ligands thus generating [Ni(tren)(amine)](2+) complexes. The chemical reactions are fast, and compounds 2 and 3 are formed within 1 h. The synthesis concept presented here opens hitherto unknown possibilities for preparation of new thiostannates.

Secondary organic aerosol formation from in situ OH, O 3, and NO 3 oxidation of ambient forest air in an oxidation flow reactor

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

Palm, Brett B.; Campuzano-Jost, Pedro; Day, Douglas A.

Ambient pine forest air was oxidized by OH, O 3, or NO 3 radicals using an oxidation flow reactor (OFR) during the BEACHON-RoMBAS (Bio–hydro–atmosphere interactions of Energy, Aerosols, Carbon, H 2O, Organics and Nitrogen – Rocky Mountain Biogenic Aerosol Study) campaign to study biogenic secondary organic aerosol (SOA) formation and organic aerosol (OA) aging. A wide range of equivalent atmospheric photochemical ages was sampled, from hours up to days (for O 3 and NO 3) or weeks (for OH). Ambient air processed by the OFR was typically sampled every 20–30 min, in order to determine how the availability of SOAmore » precursor gases in ambient air changed with diurnal and synoptic conditions, for each of the three oxidants. More SOA was formed during nighttime than daytime for all three oxidants, indicating that SOA precursor concentrations were higher at night. At all times of day, OH oxidation led to approximately 4 times more SOA formation than either O 3 or NO 3 oxidation. This is likely because O 3 and NO 3 will only react with gases containing C = C bonds (e.g., terpenes) to form SOA but will not react appreciably with many of their oxidation products or any species in the gas phase that lacks a C = C bond (e.g., pinonic acid, alkanes). In contrast, OH can continue to react with compounds that lack C = C bonds to produce SOA. Closure was achieved between the amount of SOA formed from O 3 and NO 3 oxidation in the OFR and the SOA predicted to form from measured concentrations of ambient monoterpenes and sesquiterpenes using published chamber yields. This is in contrast to previous work at this site (Palm et al., 2016), which has shown that a source of SOA from semi- and intermediate-volatility organic compounds (S/IVOCs) 3.4 times larger than the source from measured VOCs is needed to explain the measured SOA formation from OH oxidation. This work suggests that those S/IVOCs typically do not contain C = C bonds. O 3 and NO 3 oxidation produced SOA with elemental O : C and H : C similar to the least-oxidized OA observed in local ambient air, and neither oxidant led to net mass loss at the highest exposures, in contrast to OH oxidation. An OH exposure in the OFR equivalent to several hours of atmospheric aging also produced SOA with O : C and H : C values similar to ambient OA, while higher aging (days–weeks) led to formation of SOA with progressively higher O : C and lower H : C (and net mass loss at the highest exposures). NO 3 oxidation led to the production of particulate organic nitrates (pRONO 2), while OH and O 3 oxidation (under low NO) did not, as expected. As a result, these measurements of SOA formation provide the first direct comparison of SOA formation potential and chemical evolution from OH, O 3, and NO 3 oxidation in the real atmosphere and help to clarify the oxidation processes that lead to SOA formation from biogenic hydrocarbons.« less

Secondary organic aerosol formation from in situ OH, O 3, and NO 3 oxidation of ambient forest air in an oxidation flow reactor

DOE PAGES

Palm, Brett B.; Campuzano-Jost, Pedro; Day, Douglas A.; ...

2017-04-25

Ambient pine forest air was oxidized by OH, O 3, or NO 3 radicals using an oxidation flow reactor (OFR) during the BEACHON-RoMBAS (Bio–hydro–atmosphere interactions of Energy, Aerosols, Carbon, H 2O, Organics and Nitrogen – Rocky Mountain Biogenic Aerosol Study) campaign to study biogenic secondary organic aerosol (SOA) formation and organic aerosol (OA) aging. A wide range of equivalent atmospheric photochemical ages was sampled, from hours up to days (for O 3 and NO 3) or weeks (for OH). Ambient air processed by the OFR was typically sampled every 20–30 min, in order to determine how the availability of SOAmore » precursor gases in ambient air changed with diurnal and synoptic conditions, for each of the three oxidants. More SOA was formed during nighttime than daytime for all three oxidants, indicating that SOA precursor concentrations were higher at night. At all times of day, OH oxidation led to approximately 4 times more SOA formation than either O 3 or NO 3 oxidation. This is likely because O 3 and NO 3 will only react with gases containing C = C bonds (e.g., terpenes) to form SOA but will not react appreciably with many of their oxidation products or any species in the gas phase that lacks a C = C bond (e.g., pinonic acid, alkanes). In contrast, OH can continue to react with compounds that lack C = C bonds to produce SOA. Closure was achieved between the amount of SOA formed from O 3 and NO 3 oxidation in the OFR and the SOA predicted to form from measured concentrations of ambient monoterpenes and sesquiterpenes using published chamber yields. This is in contrast to previous work at this site (Palm et al., 2016), which has shown that a source of SOA from semi- and intermediate-volatility organic compounds (S/IVOCs) 3.4 times larger than the source from measured VOCs is needed to explain the measured SOA formation from OH oxidation. This work suggests that those S/IVOCs typically do not contain C = C bonds. O 3 and NO 3 oxidation produced SOA with elemental O : C and H : C similar to the least-oxidized OA observed in local ambient air, and neither oxidant led to net mass loss at the highest exposures, in contrast to OH oxidation. An OH exposure in the OFR equivalent to several hours of atmospheric aging also produced SOA with O : C and H : C values similar to ambient OA, while higher aging (days–weeks) led to formation of SOA with progressively higher O : C and lower H : C (and net mass loss at the highest exposures). NO 3 oxidation led to the production of particulate organic nitrates (pRONO 2), while OH and O 3 oxidation (under low NO) did not, as expected. As a result, these measurements of SOA formation provide the first direct comparison of SOA formation potential and chemical evolution from OH, O 3, and NO 3 oxidation in the real atmosphere and help to clarify the oxidation processes that lead to SOA formation from biogenic hydrocarbons.« less

Epitaxial growth of ReS2(001) thin film via deposited-Re sulfurization

NASA Astrophysics Data System (ADS)

Urakami, Noriyuki; Okuda, Tetsuya; Hashimoto, Yoshio

2018-02-01

In this paper, we present the formation of large-size rhenium disulfide (ReS2) films via the sulfurization of Re films deposited on sapphire substrates. The effects of sulfurization temperature and pressure on the crystal quality were investigated. A [001]-oriented single crystal of ReS2 films with 6 × 10 mm2 area was realized. By sulfurizing Re films at 1100 °C, ReS2 films with well-defined sharp interfaces to c-plane sapphire substrates could be formed. Below and above the sulfurization temperature of 1100 °C, incomplete sulfurization and film degradation were observed. The twofold symmetry of the monocrystalline in-plane structure composed of Re-Re bonds along with Re-S bonds pointed to a distorted 1T structure, indicating that this structure is the most stable atomic arrangement for ReS2. For a S/Re compositional ratio equal to or slightly lower than 2.0, characteristic Raman vibrational modes with the narrowest line widths were observed. The typical absorption peak of ReS2 can be detected at 1.5 eV.

Theoretical investigation of the reaction of Mn+ with ethylene oxide.

PubMed

Li, Yuanyuan; Guo, Wenyue; Zhao, Lianming; Liu, Zhaochun; Lu, Xiaoqing; Shan, Honghong

2012-01-12

The potential energy surfaces of Mn(+) reaction with ethylene oxide in both the septet and quintet states are investigated at the B3LYP/DZVP level of theory. The reaction paths leading to the products of MnO(+), MnO, MnCH(2)(+), MnCH(3), and MnH(+) are described in detail. Two types of encounter complexes of Mn(+) with ethylene oxide are formed because of attachments of the metal at different sites of ethylene oxide, i.e., the O atom and the CC bond. Mn(+) would insert into a C-O bond or the C-C bond of ethylene oxide to form two different intermediates prior to forming various products. MnO(+)/MnO and MnH(+) are formed in the C-O activation mechanism, while both C-O and C-C activations account for the MnCH(2)(+)/MnCH(3) formation. Products MnO(+), MnCH(2)(+), and MnH(+) could be formed adiabatically on the quintet surface, while formation of MnO and MnCH(3) is endothermic on the PESs with both spins. In agreement with the experimental observations, the excited state a(5)D is calculated to be more reactive than the ground state a(7)S. This theoretical work sheds new light on the experimental observations and provides fundamental understanding of the reaction mechanism of ethylene oxide with transition metal cations.

Copper(I)-Catalyzed Chemoselective Coupling of Cyclopropanols with Diazoesters: Ring-Opening C-C Bond Formations.

PubMed

Zhang, Hang; Wu, Guojiao; Yi, Heng; Sun, Tong; Wang, Bo; Zhang, Yan; Dong, Guangbin; Wang, Jianbo

2017-03-27

Reported herein is an exceptional chemoselective ring-opening/C(sp 3 )-C(sp 3 ) bond formation in the copper(I)-catalyzed reaction of cyclopropanols with diazo esters. The conventional O-H insertion product is essentially suppressed by judicious choice of reaction conditions. DFT calculations provide insights into the reaction mechanism and the rationale for this unusual chemoselectivity. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Controlling formation of single-molecule junctions by electrochemical reduction of diazonium terminal groups.

PubMed

Hines, Thomas; Díez-Pérez, Ismael; Nakamura, Hisao; Shimazaki, Tomomi; Asai, Yoshihiro; Tao, Nongjian

2013-03-06

We report controlling the formation of single-molecule junctions by means of electrochemically reducing two axialdiazonium terminal groups on a molecule, thereby producing direct Au-C covalent bonds in situ between the molecule and gold electrodes. We report a yield enhancement in molecular junction formation as the electrochemical potential of both junction electrodes approach the reduction potential of the diazonium terminal groups. Step length analysis shows that the molecular junction is significantly more stable, and can be pulled over a longer distance than a comparable junction created with amine anchoring bonds. The stability of the junction is explained by the calculated lower binding energy associated with the direct Au-C bond compared with the Au-N bond.

Nano-Welding of Multi-Walled Carbon Nanotubes on Silicon and Silica Surface by Laser Irradiation.

PubMed

Yuan, Yanping; Chen, Jimin

2016-02-24

In this study, a continuous fiber laser (1064 nm wavelength, 30 W/cm²) is used to irradiate multi-walled carbon nanotubes (MWCNTs) on different substrate surfaces. Effects of substrates on nano-welding of MWCNTs are investigated by scanning electron microscope (SEM). For MWCNTs on silica, after 3 s irradiation, nanoscale welding with good quality can be achieved due to breaking C-C bonds and formation of new graphene layers. While welding junctions can be formed until 10 s for the MWCNTs on silicon, the difference of irradiation time to achieve welding is attributed to the difference of thermal conductivity for silica and silicon. As the irradiation time is prolonged up to 12.5 s, most of the MWCNTs are welded to a silicon substrate, which leads to their frameworks of tube walls on the silicon surface. This is because the accumulation of absorbed energy makes the temperature rise. Then chemical reactions among silicon, carbon and nitrogen occur. New chemical bonds of Si-N and Si-C achieve the welding between the MWCNTs and silicon. Vibration modes of Si₃N₄ appear at peaks of 363 cm -1 and 663 cm -1 . There are vibration modes of SiC at peaks of 618 cm -1 , 779 cm -1 and 973 cm -1 . The experimental observation proves chemical reactions and the formation of Si₃N₄ and SiC by laser irradiation.

Structural requirements for thioester bond formation in human complement component C3. Reassessment of the role of thioester bond integrity on the conformation of C3.

PubMed

Isaac, L; Isenman, D E

1992-05-15

A unique thioester bond, formed between the side chains of neighboring C and Q residues, is present in complement components C3 and C4 and the protease inhibitor alpha 2-macroglobulin. This structure is essential for mediating covalent attachment to target acceptors and also for maintaining these proteins in their native conformation. An examination of the residues in the immediate vicinity of the C and Q reveals a very high degree of sequence similarity among the three proteins which crosses species barriers. The following is the sequence flanking the thioester residues in C3, the highly conserved amino acids being underlined and the the thioester-forming residues being indicated by italics: 1005V-T-P-S-G-C-G-E-Q-N-M-I-G-M-T-P-T1021. Through a site-directed mutagenesis and cDNA expression approach, we have examined the importance of the conserved amino acids in the formation, stability, and function of the thioester bond in C3. The behavior of the mutants fell into three categories. The potential loss in peptide backbone flexibility by the replacement of G1009 by A or S was permissive to thioester formation and function as was replacement of M1015 by the still fairly bulky residue F. In contrast, replacement of M1015 by A resulted in an alpha-chain which was highly unstable toward proteolytic degradation. The third category, which included mutant molecules P1007G, P1020G, E1012Q, and Q1013N, displayed an unusual phenotype in which both the autolytic fragmentation and the hemolytic activity characteristics of thioester-intact molecules were absent. However, like their wildtype counterpart, these molecules retained the ability to be cleaved by C3 convertase (C4b2a), a conformation-dependent property that is normally lost in the conversion of native C3 to thioester-hydrolyzed C3(H2O). Since an identical functional profile was obtained when the thioester was deliberately prevented from forming in the mutant C1010A, we conclude that if a stable thioester fails to form during biosynthesis, at least parts of the mature protein can adopt a more native-like conformation than is the case when the thioester is first formed and then hydrolyzed in the mature protein. In view of these new findings, the interpretation of the previously observed correlation between the loss of thioester integrity and the adoption of a C3b-like conformation must be reassessed.

Model studies of hydrogen atom addition and abstraction processes involving ortho-, meta-, and para-benzynes.

PubMed

Clark, A E; Davidson, E R

2001-10-31

H-atom addition and abstraction processes involving ortho-, meta-, and para-benzyne have been investigated by multiconfigurational self-consistent field methods. The H(A) + H(B)...H(C) reaction (where r(BC) is adjusted to mimic the appropriate singlet-triplet energy gap) is shown to effectively model H-atom addition to benzyne. The doublet multiconfiguration wave functions are shown to mix the "singlet" and "triplet" valence bond structures of H(B)...H(C) along the reaction coordinate; however, the extent of mixing is dependent on the singlet-triplet energy gap (DeltaE(ST)) of the H(B)...H(C) diradical. Early in the reaction, the ground-state wave function is essentially the "singlet" VB function, yet it gains significant "triplet" VB character along the reaction coordinate that allows H(A)-H(B) bond formation. Conversely, the wave function of the first excited state is predominantly the "triplet" VB configuration early in the reaction coordinate, but gains "singlet" VB character when the H-atom is close to a radical center. As a result, the potential energy surface (PES) for H-atom addition to triplet H(B)...H(C) diradical is repulsive! The H3 model predicts, in agreement with the actual calculations on benzyne, that the singlet diradical electrons are not coupled strongly enough to give rise to an activation barrier associated with C-H bond formation. Moreover, this model predicts that the PES for H-atom addition to triplet benzyne will be characterized by a repulsive curve early in the reaction coordinate, followed by a potential avoided crossing with the (pi)1(sigma*)1 state of the phenyl radical. In contrast to H-atom addition, large activation barriers characterize the abstraction process in both the singlet ground state and first triplet state. In the ground state, this barrier results from the weakly avoided crossing of the dominant VB configurations in the ground-state singlet (S0) and first excited singlet (S1) because of the large energy gap between S0 and S1 early in the reaction coordinate. Because the S1 state is best described as the combination of the triplet X-H bond and the triplet H(B)...H(C) spin couplings, the activation barrier along the S0 abstraction PES will have much less dependence on the DeltaE(ST) of H(B)...H(C) than previously speculated. For similar reasons, the T1 potential surface is quite comparable to the S0 PES.

X-ray Absorption Spectroscopic Characterization of the Synthesis Process: Revealing the Interactions in Cetyltrimethylammonium Bromide-Modified Sulfur–Graphene Oxide Nanocomposites

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

Ye, Yifan; Kawase, Ayako; Song, Min-Kyu

In this paper, we have investigated the chemical bonding interaction of S in a CTAB (cetyltrimethylammonium bromide, CH 3(CH 2) 15N +(CH 3) 3Br –)-modified sulfur–graphene oxide (S–GO) nanocomposite used as the cathode material for Li/S cells by S K-edge X-ray absorption spectroscopy (XAS). The results show that the introduction of CTAB to the S–GO nanocomposite and changes in the synthesis recipe including alteration of the S precursor ratios and the sequence of mixing ingredients lead to the formation of different S species. CTAB modifies the cathode materials through bonding with Na 2S x in the precursor solution, which ismore » subsequently converted to C–S bonds during the heat treatment at 155 °C. Moreover, GO bonds with CTAB and acts as the nucleation center for S precipitation. Finally, all these interactions among S, CTAB, and GO help to immobilize the sulfur in the cathode and may be responsible for the enhanced cell cycle life of CTAB–S–GO nanocomposite-based Li/S cells.« less

X-ray Absorption Spectroscopic Characterization of the Synthesis Process: Revealing the Interactions in Cetyltrimethylammonium Bromide-Modified Sulfur–Graphene Oxide Nanocomposites

DOE PAGES

Ye, Yifan; Kawase, Ayako; Song, Min-Kyu; ...

2016-04-22

In this paper, we have investigated the chemical bonding interaction of S in a CTAB (cetyltrimethylammonium bromide, CH 3(CH 2) 15N +(CH 3) 3Br –)-modified sulfur–graphene oxide (S–GO) nanocomposite used as the cathode material for Li/S cells by S K-edge X-ray absorption spectroscopy (XAS). The results show that the introduction of CTAB to the S–GO nanocomposite and changes in the synthesis recipe including alteration of the S precursor ratios and the sequence of mixing ingredients lead to the formation of different S species. CTAB modifies the cathode materials through bonding with Na 2S x in the precursor solution, which ismore » subsequently converted to C–S bonds during the heat treatment at 155 °C. Moreover, GO bonds with CTAB and acts as the nucleation center for S precipitation. Finally, all these interactions among S, CTAB, and GO help to immobilize the sulfur in the cathode and may be responsible for the enhanced cell cycle life of CTAB–S–GO nanocomposite-based Li/S cells.« less

Alkali metal mediated C–C bond coupling reaction

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

Tachikawa, Hiroto, E-mail: hiroto@eng.hokudai.ac.jp

2015-02-14

Metal catalyzed carbon-carbon (C–C) bond formation is one of the important reactions in pharmacy and in organic chemistry. In the present study, the electron and hole capture dynamics of a lithium-benzene sandwich complex, expressed by Li(Bz){sub 2}, have been investigated by means of direct ab-initio molecular dynamics method. Following the electron capture of Li(Bz){sub 2}, the structure of [Li(Bz){sub 2}]{sup −} was drastically changed: Bz–Bz parallel form was rapidly fluctuated as a function of time, and a new C–C single bond was formed in the C{sub 1}–C{sub 1}′ position of Bz–Bz interaction system. In the hole capture, the intermolecular vibrationmore » between Bz–Bz rings was only enhanced. The mechanism of C–C bond formation in the electron capture was discussed on the basis of theoretical results.« less

Oxidation of p53 through DNA Charge Transport Involves a Network of Disulfides within the DNA-Binding Domain

PubMed Central

2016-01-01

Transcription factor p53 plays a critical role in the cellular response to stress stimuli. We have seen that p53 dissociates selectively from various promoter sites as a result of oxidation at long-range through DNA-mediated charge transport (CT). Here, we examine this chemical oxidation and determine the residues in p53 that are essential for oxidative dissociation, focusing on the network of cysteine residues adjacent to the DNA-binding site. Of the eight mutants studied, only the C275S mutation shows decreased affinity for the Gadd45 promoter site. However, both mutations C275S and C277S result in substantial attenuation of oxidative dissociation, with C275S causing the most severe attenuation. Differential thiol labeling was used to determine the oxidation states of cysteine residues within p53 after DNA-mediated oxidation. Reduced cysteines were iodoacetamide-labeled, whereas oxidized cysteines participating in disulfide bonds were 13C2D2-iodoacetamide-labeled. Intensities of respective iodoacetamide-modified peptide fragments were analyzed by mass spectrometry. A distinct shift in peptide labeling toward 13C2D2-iodoacetamide-labeled cysteines is observed in oxidized samples, confirming that chemical oxidation of p53 occurs at long range. All observable cysteine residues trend toward the heavy label under conditions of DNA CT, indicating the formation of multiple disulfide bonds among the cysteine network. On the basis of these data, it is proposed that disulfide formation involving C275 is critical for inducing oxidative dissociation of p53 from DNA. PMID:25584637

On the correlation between bond-length change and vibrational frequency shift in halogen-bonded complexes

NASA Astrophysics Data System (ADS)

Wang, Weizhou; Zhang, Yu; Ji, Baoming; Tian, Anmin

2011-06-01

The C-Hal (Hal = Cl, Br, or I) bond-length change and the corresponding vibrational frequency shift of the C-Hal stretch upon the C-Hal ⋯Y (Y is the electron donor) halogen bond formation have been determined by using density functional theory computations. Plots of the C-Hal bond-length change versus the corresponding vibrational frequency shift of the C-Hal stretch all give straight lines. The coefficients of determination range from 0.94366 to 0.99219, showing that the correlation between the C-Hal bond-length change and the corresponding frequency shift is very good in the halogen-bonded complexes. The possible effects of vibrational coupling, computational method, and anharmonicity on the bond-length change-frequency shift correlation are discussed in detail.

An unusual cysteine VL87 affects the antibody fragment conformations without interfering with the disulfide bond formation.

PubMed

Attallah, Carolina; Aguilar, María Fernanda; Garay, A Sergio; Herrera, Fernando E; Etcheverrigaray, Marina; Oggero, Marcos; Rodrigues, Daniel E

2017-10-01

The Cys residues are almost perfectly conserved in all antibodies. They contribute significantly to the antibody fragment stability. The relevance of two natural contiguous Cys residues of an anti-recombinant human-follicle stimulation hormone (rhFSH) in a format of single-chain variable fragment (scFv) was studied. This scFv contains 5 Cys residues: V H 22 and V H 92 in the variable heavy chain (V H ) and V L 23, V L 87 and V L 88 in the variable light chain (V L ). The influence of two unusual contiguous Cys at positions V L 87 and V L 88 was studied by considering the wild type fragment and mutant variants: V L -C88S, V L -C87S, V L -C87Y. The analysis was carried out using antigen-binding ability measurement by indirect specific ELISA and a detailed molecular modeling that comprises homology methods, long molecular dynamics simulations and docking. We found that V L -C87 affected the antibody fragment stability without interfering with the disulfide bond formation. The effect of mutating the V L -C87 by a usual residue at this position like Tyr caused distant structural changes at the V H region that confers a higher mobility to the V H -CDR2 and V H -CDR3 loops improving the scFv binding to the antigen. Copyright © 2017 Elsevier Ltd. All rights reserved.

Influence of heat-pretreatments on the microstructural and mechanical properties of galfan-coated metal bonds

NASA Astrophysics Data System (ADS)

Hordych, Illia; Rodman, Dmytro; Nürnberger, Florian; Schmidt, Hans Christian; Orive, Alejandro Gonzalez; Homberg, Werner; Grundmeier, Guido; Maier, Hans Jürgen

2018-05-01

In the present study, heat-treatment assisted bonding of galfan-coated low-carbon steel sheets was investigated. Steel sheets were bonded by cold rolling subsequently to a heat treatment in the temperature range from 400 °C to 550°C. The reduction ratio during cold rolling was varied in the range from 50% to 80%. Such high reduction ratios were achieved by splitting the bonding process into three stages. By employing heat-treatments, the mechanical properties of the bonds were improved. The heat-pretreatment allowed the formation of brittle intermetallic phases that were easily fractured in the rolling gap during the bonding process. Thus, juvenile non-oxidized surfaces were formed, which facilitated the bonding between the steel layers, and thus increased the bond strength. The intermetallic phases were actively formed at temperatures of 450 °C and above; however increasing temperatures resulted in decreasing mechanical properties due to oxidation processes. The local microstructure was analyzed by scanning electron microscopy in order to characterize the contact zone on the micro level with a focus on the formation of intermetallic phases. The mechanical properties were determined in tensile shear tests. Interestingly, it was found that the galfan coating allowed for bonding at room temperature, and the aluminum fraction was primarily responsible for the enhanced oxide formation during the heat-pretreatment.

Montmorillonite, Oligonucleotides, RNA and Origin of Life

NASA Astrophysics Data System (ADS)

Ertem, Gözen

2004-12-01

Na-montmorillonite prepared from Volclay by the titration method facilitates the self-condensation of ImpA, the 5'-phosphorimidazolide derivative of adenosine. As was shown by AE-HPLC analysis and selective enzymatic hydrolysis of products, oligo(A)s formed in this reaction are 10 monomer units long and contain 67% 3',5'-phosphodiester bonds (Ferris and Ertem, 1992a). Under the same reaction conditions, 5'-phosphorimidazolide derivatives of cytidine, uridine and guanosine also undergo self-condensation producing oligomers containing up to 12-14 monomer units for oligo(C)s to 6 monomer units for oligo(G)s. In oligo(C)s and oligo(U)s, 75-80% of the monomers are linked by 2',5'-phosphodiester bonds. Hexamer and higher oligomers isolated from synthetic oligo(C)s formed by montmorillonite catalysis, which contain both 3',5'- and 2',5'-linkages, serve as catalysts for the non-enzymatic template directed synthesis of oligo(G)s from activated monomer 2-MeImpG, guanosine 5'-phospho-2-methylimidazolide (Ertem and Ferris, 1996). Pentamer and higher oligomers containing exclusively 2',5'-linkages, which were isolated from the synthetic oligo(C)s, also serve as templates and produce oligo(G)s with both 2',5'- and 3',5'-phosphodiester bonds. Kinetic studies on montmorillonite catalyzed elongation rates of oligomers using the computer program SIMFIT demonstrated that the rate constants for the formation of oligo(A)s increased in the order of 2-mer <3-mer <4-mer ... <7-mer (Kawamura and Ferris, 1994). A decameric primer, dA(pdA)8pA bound to montmorillonite was elongated to contain up to 50 monomer units by daily addition of activated monomer ImpA to the reaction mixture (Ferris, Hill and Orgel, 1996). Analysis of dimer fractions formed in the montmorillonite catalyzed reaction of binary and quaternary mixtures of ImpA, ImpC, 2-MeImpG and ImpU suggested that only a limited number of oligomers could have formed on the primitive Earth rather than equal amounts of all possible isomers (Ertem and Ferris, 2000). Formation of phosphodiester bonds between mononucleotides by montmorillonite catalysis is a fascinating discovery, and a significant step forward in efforts to find out how the first RNA-like oligomers might have formed in the course of chemical evolution. However, as has been pointed out in several publications, these systems should be regarded as models rather than a literal representation of prebiotic chemistry (Orgel, 1998; Joyce and Orgel, 1999; Schwartz, 1999).

Montmorillonite, oligonucleotides, RNA and origin of life

NASA Technical Reports Server (NTRS)

Ertem, Gozen

2004-01-01

Na-montmorillonite prepared from Volclay by the titration method facilitates the self-condensation of ImpA, the 5'-phosphorimidazolide derivative of adenosine. As was shown by AE-HPLC analysis and selective enzymatic hydrolysis of products, oligo(A)s formed in this reaction are 10 monomer units long and contain 67% 3',5'-phosphodiester bonds (Ferris and Ertem, 1992a). Under the same reaction conditions, 5'-phosphorimidazolide derivatives of cytidine, uridine and guanosine also undergo self-condensation producing oligomers containing up to 12-14 monomer units for oligo(C)s to 6 monomer units for oligo(G)s. In oligo(C)s and oligo(U)s, 75-80% of the monomers are linked by 2',5'-phosphodiester bonds. Hexamer and higher oligomers isolated from synthetic oligo(C)s formed by montmorillonite catalysis, which contain both 3',5'- and 2',5'-linkages, serve as catalysts for the non-enzymatic template directed synthesis of oligo(G)s from activated monomer 2-MeImpG, guanosine 5'-phospho-2-methylimidazolide (Ertem and Ferris, 1996). Pentamer and higher oligomers containing exclusively 2',5'-linkages, which were isolated from the synthetic oligo(C)s, also serve as templates and produce oligo(G)s with both 2',5'- and 3',5'-phosphodiester bonds. Kinetic studies on montmorillonite catalyzed elongation rates of oligomers using the computer program SIMFIT demonstrated that the rate constants for the formation of oligo(A)s increased in the order of 2-mer < 3-mer < 4-mer ... < 7-mer (Kawamura and Ferris, 1994). A decameric primer, dA(pdA)8pA bound to montmorillonite was elongated to contain up to 50 monomer units by daily addition of activated monomer ImpA to the reaction mixture (Ferris, Hill and Orgel, 1996). Analysis of dimer fractions formed in the montmorillonite catalyzed reaction of binary and quaternary mixtures of ImpA, ImpC, 2-MeImpG and ImpU suggested that only a limited number of oligomers could have formed on the primitive Earth rather than equal amounts of all possible isomers (Ertem and Ferris, 2000). Formation of phosphodiester bonds between mononucleotides by montmorillonite catalysis is a fascinating discovery, and a significant step forward in efforts to find out how the first RNA-like oligomers might have formed in the course of chemical evolution. However, as has been pointed out in several publications, these systems should be regarded as models rather than a literal representation of prebiotic chemistry (Orgel, 1998; Joyce and Orgel, 1999; Schwartz, 1999).

Accounting for the differences in the structures and relative energies of the highly homoatomic np pi-np pi (n > or = 3)-bonded S2I4 2+, the Se-I pi-bonded Se2I4 2+, and their higher-energy isomers by AIM, MO, NBO, and VB methodologies.

PubMed

Brownridge, Scott; Crawford, Margaret-Jane; Du, Hongbin; Harcourt, Richard D; Knapp, Carsten; Laitinen, Risto S; Passmore, Jack; Rautiainen, J Mikko; Suontamo, Reijo J; Valkonen, Jussi

2007-02-05

The bonding in the highly homoatomic np pi-np pi (n > or = 3)-bonded S2I42+ (three sigma + two pi bonds), the Se-I pi-bonded Se2I42+ (four sigma + one pi bonds), and their higher-energy isomers have been studied using modern DFT and ab initio calculations and theoretical analysis methods: atoms in molecules (AIM), molecular orbital (MO), natural bond orbital (NBO), and valence bond (VB) analyses, giving their relative energies, theoretical bond orders, and atomic charges. The aim of this work was to seek theory-based answers to four main questions: (1) Are the previously proposed simple pi*-pi* bonding models valid for S2I42+ and Se2I42+? (2) What accounts for the difference in the structures of S2I42+ and Se2I42+? (3) Why are the classically bonded isolobal P2I4 and As2I4 structures not adopted? (4) Is the high experimentally observed S-S bond order supported by theoretical bond orders, and how does it relate to high bond orders between other heavier main group elements? The AIM analysis confirmed the high bond orders and established that the weak bonds observed in S2I42+ and Se2I42+ are real and the bonding in these cations is covalent in nature. The full MO analysis confirmed that S2I42+ contains three sigma and two pi bonds, that the positive charge is essentially equally distributed over all atoms, that the bonding between S2 and two I2+ units in S2I42+ is best described by two mutually perpendicular 4c2e pi*-pi* bonds, and that in Se2I42+, two SeI2+ moieties are joined by a 6c2e pi*-pi* bond, both in agreement with previously suggested models. The VB treatment provided a complementary approach to MO analysis and provided insight how the formation of the weak bonds affects the other bonds. The NBO analysis and the calculated AIM charges showed that the minimization of the electrostatic repulsion between EI2+ units (E = S, Se) and the delocalization of the positive charge are the main factors that explain why the nonclassical structures are favored for S2I42+ and Se2I42+. The difference in the structures of S2I42+ and Se2I42+ is related to the high strength of the S-S pi bond compared to the weak S-I sigma bond and the additional stabilization from increased delocalization of positive charge in the structure of S2I42+ compared to the structure of Se2I42+. The investigation of the E2X42+ series (E = S, Se, Te; X = Cl, Br, I) revealed that only S2I42+ adopts the highly np pi-np pi (n > or = 3)-bonded structure, while all other dications favor the pi-bonded Se2I42+ structure. Theoretical bond order calculations for S2I42+ confirm the previously presented experimentally based bond orders for S-S (2.1-2.3) and I-I (1.3-1.5) bonds. The S-S bond is determined to have the highest reported S-S bond order in an isolated compound and has a bond order that is either similar to or slightly less than the Si-Si bond order in the proposed triply bonded [(Me3Si)2CH]2(iPr)SiSi triple bond SiSi(iPr)[CH(SiMe3)2]2 depending on the definition of bond orders used.

5-Ethynyl-2'-deoxycytidine: a DNA building block with a 'clickable' side chain.

PubMed

Seela, Frank; Mei, Hui; Xiong, Hai; Budow, Simone; Eickmeier, Henning; Reuter, Hans

2012-10-01

The title compound [systematic name: 4-amino-1-(2-deoxy-β-D-erythro-pentofuranosyl)-5-ethynylpyrimidin-2(1H)-one], C(11)H(13)N(3)O(4), shows two conformations in the crystalline state. The N-glycosylic bonds of both conformers adopt similar conformations, with χ = -149.2 (1)° for conformer (I-1) and -151.4 (1)° for conformer (I-2), both in the anti range. The sugar residue of (I-1) shows a C2'-endo envelope conformation ((2)E, S-type), with P = 164.7 (1)° and τ(m) = 36.9 (1)°, while (I-2) shows a major C3'-exo sugar pucker (C3'-exo-C2'-endo, (3)T(2), S-type), with P = 189.2 (1)° and τ(m) = 33.3 (1)°. Both conformers participate in the formation of a layered three-dimensional crystal structure with a chain-like arrangement of the conformers. The ethynyl groups do not participate in hydrogen bonding, but are arranged in proximal positions.

MALDI In-Source Decay of Protein: The Mechanism of c-Ion Formation

PubMed Central

Takayama, Mitsuo

2016-01-01

The in-source decay (ISD) phenomenon, the fragmentation at an N–Cα bond of a peptide backbone that occurs within several tens of nanoseconds in the ion-source in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS), is discussed from the standpoints of the discovery and early publications dealing with MALDI-ISD, the formation of c-ions in energy-sudden desorption/ionization methods, the formation of radical species in a MALDI, model construction for ISD, and matrix materials that are suitable for use in MALDI-ISD. The formation of c-ions derived from peptides and proteins in MALDI-ISD can be rationalized by a mechanism involving intermolecular hydrogen transfer, denoted as the “Takayama’s model” by De Pauw’s group (Anal. Chem. 79: 8678–8685, 2007). It should be emphasized that the model for MALDI-ISD was constructed on the basis of X-ray crystallography and scanning probe microscopy (SPM) analyses of matrix crystals, as well as the use of isotopically-labelled peptides. PMID:27162707

Probing the Watson-Crick, wobble, and sugar-edge hydrogen bond sites of uracil and thymine.

PubMed

Müller, Andreas; Frey, Jann A; Leutwyler, Samuel

2005-06-16

The nucleobases uracil (U) and thymine (T) offer three hydrogen-bonding sites for double H-bond formation via neighboring N-H and C=O groups, giving rise to the Watson-Crick, wobble and sugar-edge hydrogen bond isomers. We probe the hydrogen bond properties of all three sites by forming hydrogen bonded dimers of U, 1-methyluracil (1MU), 3-methyluracil (3MU), and T with 2-pyridone (2PY). The mass- and isomer-specific S1 <-- S0 vibronic spectra of 2PY.U, 2PY.3MU, 2PY.1MU, and 2PY.T were measured using UV laser resonant two-photon ionization (R2PI). The spectra of the Watson-Crick and wobble isomers of 2PY.1MU were separated using UV-UV spectral hole-burning. We identify the different isomers by combining three different diagnostic tools: (1) Selective methylation of the uracil N3-H group, which allows formation of the sugar-edge isomer only, and methylation of the N1-H group, which leads to formation of the Watson-Crick and wobble isomers. (2) The experimental S1 <-- S0 origins exhibit large spectral blue shifts relative to the 2PY monomer. Ab initio CIS calculations of the spectral shifts of the different hydrogen-bonded dimers show a linear correlation with experiment. This correlation allows us to identify the R2PI spectra of the weakly populated Watson-Crick and wobble isomers of both 2PY.U and 2PY.T. (3) PW91 density functional calculation of the ground-state binding and dissociation energies De and D0 are in agreement with the assignment of the dominant hydrogen bond isomers of 2PY.U, 2PY.3MU and 2PY.T as the sugar-edge form. For 2PY.U, 2PY.T and 2PY.1MU the measured wobble:Watson-Crick:sugar-edge isomer ratios are in good agreement with the calculated ratios, based on the ab initio dissociation energies and gas-phase statistical mechanics. The Watson-Crick and wobble isomers are thereby determined to be several kcal/mol less strongly bound than the sugar-edge isomers. The 36 observed intermolecular frequencies of the nine different H-bonded isomers give detailed insight into the intermolecular force field.

Drazenka Svedruzic | NREL

Science.gov Websites

intrinsically and extrinsically strained materials Electrochemical and biochemical CO2 reduction and C-C bond reduction, and C-C bond formation. Svedruzic started her career at NREL as a postdoctoral researcher working -electrochemistry and fuel-forming mechano-electrocatalysis on spring electrodes," J. Phys. Chem. C. (2014

Characterization of Disulfide-Linked Peptides Using Tandem Mass Spectrometry Coupled with Automated Data Analysis Software

NASA Astrophysics Data System (ADS)

Liang, Zhidan; McGuinness, Kenneth N.; Crespo, Alejandro; Zhong, Wendy

2018-05-01

Disulfide bond formation is critical for maintaining structure stability and function of many peptides and proteins. Mass spectrometry has become an important tool for the elucidation of molecular connectivity. However, the interpretation of the tandem mass spectral data of disulfide-linked peptides has been a major challenge due to the lack of appropriate tools. Developing proper data analysis software is essential to quickly characterize disulfide-linked peptides. A thorough and in-depth understanding of how disulfide-linked peptides fragment in mass spectrometer is a key in developing software to interpret the tandem mass spectra of these peptides. Two model peptides with inter- and intra-chain disulfide linkages were used to study fragmentation behavior in both collisional-activated dissociation (CAD) and electron-based dissociation (ExD) experiments. Fragments generated from CAD and ExD can be categorized into three major types, which result from different S-S and C-S bond cleavage patterns. DiSulFinder is a computer algorithm that was newly developed based on the fragmentation observed in these peptides. The software is vendor neutral and capable of quickly and accurately identifying a variety of fragments generated from disulfide-linked peptides. DiSulFinder identifies peptide backbone fragments with S-S and C-S bond cleavages and, more importantly, can also identify fragments with the S-S bond still intact to aid disulfide linkage determination. With the assistance of this software, more comprehensive disulfide connectivity characterization can be achieved. [Figure not available: see fulltext.

Characterization of Disulfide-Linked Peptides Using Tandem Mass Spectrometry Coupled with Automated Data Analysis Software

NASA Astrophysics Data System (ADS)

Liang, Zhidan; McGuinness, Kenneth N.; Crespo, Alejandro; Zhong, Wendy

2018-01-01

Disulfide bond formation is critical for maintaining structure stability and function of many peptides and proteins. Mass spectrometry has become an important tool for the elucidation of molecular connectivity. However, the interpretation of the tandem mass spectral data of disulfide-linked peptides has been a major challenge due to the lack of appropriate tools. Developing proper data analysis software is essential to quickly characterize disulfide-linked peptides. A thorough and in-depth understanding of how disulfide-linked peptides fragment in mass spectrometer is a key in developing software to interpret the tandem mass spectra of these peptides. Two model peptides with inter- and intra-chain disulfide linkages were used to study fragmentation behavior in both collisional-activated dissociation (CAD) and electron-based dissociation (ExD) experiments. Fragments generated from CAD and ExD can be categorized into three major types, which result from different S-S and C-S bond cleavage patterns. DiSulFinder is a computer algorithm that was newly developed based on the fragmentation observed in these peptides. The software is vendor neutral and capable of quickly and accurately identifying a variety of fragments generated from disulfide-linked peptides. DiSulFinder identifies peptide backbone fragments with S-S and C-S bond cleavages and, more importantly, can also identify fragments with the S-S bond still intact to aid disulfide linkage determination. With the assistance of this software, more comprehensive disulfide connectivity characterization can be achieved. [Figure not available: see fulltext.

Thermochemistry of Hydroxyl and Hydroperoxide Substituted Furan, Methylfuran, and Methoxyfuran.

PubMed

Hudzik, Jason M; Bozzelli, Joseph W

2017-06-15

Reaction pathways are influenced by thermochemical properties, species stability, and chemical kinetics. Understanding these factors allows for an understanding of the reaction paths and formation of intermediate species. Enthalpies of formation (ΔH f,298 ° ), entropies (S 298 ° ), heat capacities (C p (T)), oxygen-hydrogen (O-H), oxygen-oxygen (O-O), and (R-O) bond dissociation energies (BDEs) are reported for hydroxyl and hydroperoxide substituted furan, methylfuran, and methoxyfuran species. Standard enthalpies of formation for parent and radical species have been determined using density functional theory B3LYP/6-31G(d,p), B3LYP/6-311G(2d,2p), and M06-2X/6-31G(d,p) along with higher-level CBS-QB3 and CBS-APNO composite methods. Isodesmic work reactions were employed to improve accuracy by canceling error and show consistency between the levels of theory. Corresponding O-H and O-O BDEs are determined and compared to other similar structures. The stability of the furan moiety coupled with the double-bond-forming capability of the oxygen moiety results in a number of bond energies significantly lower than one might have expected. Substituted hydroperoxides are calculated to have ROO-H BDEs between 86.9 and 94.2 kcal mol -1 , and their RO-OH BDEs show a large 49 kcal mol -1 range of -2.3-46.8 kcal mol -1 . Substituted alcohols also show a wide 48 kcal mol -1 range with RO-H BDEs, ranging from 59.3 to 106.9 kcal mol -1 . Bond lengths of parent and radical species are presented to highlight potential bonds of interest leading to furan ring opening. Group additivity is discussed, and groups for substituted furan, methylfuran, and methoxyfuran species are derived. Structures, moments of inertia, vibrational frequencies, and internal rotor potentials are calculated at the B3LYP/6-31G(d,p) density functional level and are used to determine the S 298 ° and C p (T) values.

Rhodium-Catalyzed Asymmetric Conjugate Alkynylation/Aldol Cyclization Cascade for the Formation of α-Propargyl-β-hydroxyketones.

PubMed

Choo, Ken-Loon; Lautens, Mark

2018-03-02

A rhodium-catalyzed conjugate alkynylation/aldol cyclization cascade was developed. Densely functionalized cyclic α-propargyl-β-hydroxyketones were synthesized with simultaneous formation of a C(sp)-C(sp 3 ) bond, a C(sp 3 )-C(sp 3 ) bond, as well as three new contiguous stereocenters. The transformation was achieved with excellent enantio- and diastereoselectivities using BINAP as the ligand. The synthetic utility of the newly installed alkynyl moiety was exhibited by subjecting the products to an array of derivatizations.

Oxidative cleavage of the octyl side chain of 1-(3,4-dichlorobenzyl)-5-octylbiguanide (OPB-2045) in rat and dog liver preparations.

PubMed

Umehara, K; Kudo, S; Hirao, Y; Morita, S; Uchida, M; Odomi, M; Miyamoto, G

2000-08-01

The metabolism of 1-(3,4-dichlorobenzyl)-5-octylbiguanide (OPB-2045), a new potent biguanide antiseptic, was investigated using rat and dog liver preparations to elucidate the mechanism of OPB-2045 metabolite formation, in which the octyl side chain is reduced to four, five, or six carbon atoms. Chemical structures of metabolites were characterized by 1H NMR, fast atom bombardment/mass spectrometry, and liquid chromatography/electrospray ionization-tandem mass spectrometry. Three main metabolites were observed during incubation of OPB-2045 with rat liver S9: 2-octanol (M-1), 3-octanol (M-2), and 4-octanol (M-3). In the incubation of OPB-2045 with dog liver S9, eight metabolites were observed, seven of which being M-1, M-2, M-3, 2-octanone (M-4), threo-2,3-octandiol (M-5), erythro-2,3-octandiol (M-6), and 1,2-octandiol (M-7). M-5 and M-6 were further biotransformed to a ketol derivative and C-C bond cleavage metabolite (hexanoic acid derivative), an in vivo end product, in the incubation with dog liver microsomes. The reactions required NADPH as a cofactor and were significantly inhibited by the various inhibitors of cytochrome P450 (i.e., CO, n-octylamine, SKF 525-A, metyrapone, and alpha-naphthoflavone). The results indicate that the degraded products of OPB-2045 are produced by C-C bond cleavage after monohydroxylation, dihydroxylation, and ketol formation at the site of the octyl side chain with possible involvement of cytochrome P450 systems. This aliphatic C-C bond cleavage by sequential oxidative reactions may play an important role in the metabolism of other drugs or endogenous compounds that possess aliphatic chains.

Correlation between bonding structure and microstructure in fullerenelike carbon nitride thin films

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

Gago, R.; Abendroth, B.; Moeller, W.

2005-03-15

The bonding structure of highly ordered fullerenelike (FL) carbon nitride (CN{sub x}) thin films has been assessed by x-ray absorption near-edge spectroscopy (XANES). Samples with different degrees of FL character have been analyzed to discern spectral signatures related to the FL microstructure. The XANES spectra of FL-CN{sub x} films resemble that of graphitic CN{sub x}, evidencing the sp{sup 2} hybridization of both C and N atoms. The FL structure is achieved with the promotion of N in threefold positions over pyridinelike and cyanidelike bonding environments. In addition, the relative {pi}{sup *}/{sigma}* XANES intensity ratio at the C(1s) edge is independentmore » of the FL character, while it decreases {approx}40% at the N(1s) edge with the formation of FL arrangements. This result indicates that there is no appreciable introduction of C-sp{sup 3} hybrids with the development of FL structures and, additionally, that a different spatial localization of {pi} electrons at C and N sites takes place in curved graphitic structures. The latter has implications for the elastic properties of graphene sheets and could, as such, explain the outstanding elastic properties of FL-CN{sub x}.« less

Conformational and spectroscopic study of xanthogen ethyl formates, ROC(S)SC(O)OCH2CH3. Isolation of CH3CH2OC(O)SH

NASA Astrophysics Data System (ADS)

Juncal, Luciana C.; Cozzarín, Melina V.; Romano, Rosana M.

2015-03-01

ROC(S)SC(O)OCH2CH3, with R = CH3sbnd , (CH3)2CHsbnd and CH3(CH2)2sbnd , were obtained through the reaction between potassium xanthate salts, ROC(S)SK, and ethyl chloroformate, ClC(O)OCH2CH3. The liquid compounds were identified and characterized by 1H and 13C NMR and mass spectrometry. The conformations adopted by the molecules were studied by DFT methods. 6 conformers were theoretically predicted for R = CH3sbnd and (CH3)2CHsbnd , while the conformational flexibility of the n-propyl substituent increases the total number of feasible rotamers to 21. For the three molecules, the conformers can be associated in 3 groups, being the most stable the AS forms - the Cdbnd S double bond anti (A) with respect to the Csbnd S single bond and the Ssbnd C single bond syn (S) with respect to the Cdbnd O double bond - followed by AA and SS conformers. The vibrational spectra were interpreted in terms of the predicted conformational equilibrium, presenting the ν(Cdbnd O) spectral region signals corresponding to the three groups of conformers. A moderated pre-resonance Raman enhancement of the ν(Cdbnd S) vibrational mode of CH3(CH2)2OC(S)SC(O)OCH2CH3 was detected, when the excitation radiation approaches the energy of a n → π∗ electronic transition associated with the Cdbnd S chromophore. UV-visible spectra in different solvents were measured and interpreted in terms of TD-DFT calculations. The unknown molecule CH3CH2OC(O)SH was isolated by the UV-visible photolysis of CH3OC(S)SC(O)OCH2CH3 isolated in Ar matrix, and also obtained as a side-product of the reaction between potassium xanthate salts, ROC(S)SK, and ethyl chloroformate, ClC(O)OCH2CH3.

High sensitivity of tunneling spin polarization to chemical bonding of transition metal ferromagnetic alloys at interface with insulating barrier

NASA Astrophysics Data System (ADS)

Yang, See-Hun; Yang, Hyunsoo; Kaiser, Christian; Parkin, Stuart

2006-03-01

We report that the tunneling spin polarization (TSP) is found to be strongly influenced by the amount of oxygen used in the deposition of the tunnel barrier itself that chemical bonding at the interface between Al2O3 and ferromagnetic Co and Co-Pt alloys. For reactive sputter (RS) deposition of alumina using an argon-oxygen gas mixture with a low concentration of oxygen (˜0.1 mTorr), much lower TSP values are found than when the alumina barrier is formed by post-plasma oxidation (PO) with ˜100mTorr oxygen of Al layers. X-ray absorption spectroscopy (XAS) has been used to characterize the chemical bonding at the Co or Co-Pt/Al2O3 interface. These studies show that Co-O bonds are much more formed for the barrier fromed by PO of Al than for that formed by RS deposition. We attribute the changes in TSP to changes in the relative tunneling probabilities from Co and Pt which are strongly influenced by oxygen bond formation.^1 ^1C. Kaiser, S. van Dijken, S.-H. Yang, H. Yang, and S. S. P. Parkin, Phys. Rev. Lett. 94, 247203 (2005).

Radical SAM catalysis via an organometallic intermediate with an Fe-[5'-C]-deoxyadenosyl bond.

PubMed

Horitani, Masaki; Shisler, Krista; Broderick, William E; Hutcheson, Rachel U; Duschene, Kaitlin S; Marts, Amy R; Hoffman, Brian M; Broderick, Joan B

2016-05-13

Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to cleave SAM to initiate diverse radical reactions. These reactions are thought to involve the 5'-deoxyadenosyl radical intermediate, which has not yet been detected. We used rapid freeze-quenching to trap a catalytically competent intermediate in the reaction catalyzed by the radical SAM enzyme pyruvate formate-lyase activating enzyme. Characterization of the intermediate by electron paramagnetic resonance and (13)C, (57)Fe electron nuclear double-resonance spectroscopies reveals that it contains an organometallic center in which the 5' carbon of a SAM-derived deoxyadenosyl moiety forms a bond with the unique iron site of the [4Fe-4S] cluster. Discovery of this intermediate extends the list of enzymatic bioorganometallic centers to the radical SAM enzymes, the largest enzyme superfamily known, and reveals intriguing parallels to B12 radical enzymes. Copyright © 2016, American Association for the Advancement of Science.

Renewable Formate from C-H Bond Formation with CO2: Using Iron Carbonyl Clusters as Electrocatalysts.

PubMed

Loewen, Natalia D; Neelakantan, Taruna V; Berben, Louise A

2017-09-19

As a society, we are heavily dependent on nonrenewable petroleum-derived fuels and chemical feedstocks. Rapid depletion of these resources and the increasingly evident negative effects of excess atmospheric CO 2 drive our efforts to discover ways of converting excess CO 2 into energy dense chemical fuels through selective C-H bond formation and using renewable energy sources to supply electrons. In this way, a carbon-neutral fuel economy might be realized. To develop a molecular or heterogeneous catalyst for C-H bond formation with CO 2 requires a fundamental understanding of how to generate metal hydrides that selectively donate H - to CO 2 , rather than recombining with H + to liberate H 2 . Our work with a unique series of water-soluble and -stable, low-valent iron electrocatalysts offers mechanistic and thermochemical insights into formate production from CO 2 . Of particular interest are the nitride- and carbide-containing clusters: [Fe 4 N(CO) 12 ] - and its derivatives and [Fe 4 C(CO) 12 ] 2- . In both aqueous and mixed solvent conditions, [Fe 4 N(CO) 12 ] - forms a reduced hydride intermediate, [H-Fe 4 N(CO) 12 ] - , through stepwise electron and proton transfers. This hydride selectively reacts with CO 2 and generates formate with >95% efficiency. The mechanism for this transformation is supported by crystallographic, cyclic voltammetry, and spectroelectrochemical (SEC) evidence. Furthermore, installation of a proton shuttle onto [Fe 4 N(CO) 12 ] - facilitates proton transfer to the active site, successfully intercepting the hydride intermediate before it reacts with CO 2 ; only H 2 is observed in this case. In contrast, isoelectronic [Fe 4 C(CO) 12 ] 2- features a concerted proton-electron transfer mechanism to form [H-Fe 4 C(CO) 12 ] 2- , which is selective for H 2 production even in the presence of CO 2 , in both aqueous and mixed solvent systems. Higher nuclearity clusters were also studied, and all are proton reduction electrocatalysts, but none promote C-H bond formation. Thermochemical insights into the disparate reactivities of these clusters were achieved through hydricity measurements using SEC. We found that only [H-Fe 4 N(CO) 12 ] - and its derivative [H-Fe 4 N(CO) 11 (PPh 3 )] - have hydricities modest enough to avoid H 2 production but strong enough to make formate. [H-Fe 4 C(CO) 12 ] 2- is a stronger hydride donor, theoretically capable of making formate, but due to an overwhelming thermodynamic driving force and the increased electrostatic attraction between the more negative cluster and H + , only H 2 is observed experimentally. This illustrates the fundamental importance of controlling thermochemistry when designing new catalysts selective for C-H bond formation and establishes a hydricity range of 15.5-24.1 or 44-49 kcal mol -1 where C-H bond formation may be favored in water or MeCN, respectively.

Involvement of DPP-IV Catalytic Residues in Enzyme-Saxagliptin Complex Formation

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

Metzler,W.; Yanchunas, J.; Weigelt, C.

The inhibition of DPP-IV by saxagliptin has been proposed to occur through formation of a covalent but reversible complex. To evaluate further the mechanism of inhibition, we determined the X-ray crystal structure of the DPP-IV:saxagliptin complex. This structure reveals covalent attachment between S630 and the inhibitor nitrile carbon (C-O distance <1.3 Angstroms). To investigate whether this serine addition is assisted by the catalytic His-Asp dyad, we generated two mutants of DPP-IV, S630A and H740Q, and assayed them for ability to bind inhibitor. DPP-IVH740Q bound saxagliptin with an {approx}1000-fold reduction in affinity relative to DPP-IVWT, while DPP-IVS630A showed no evidence formore » binding inhibitor. An analog of saxagliptin lacking the nitrile group showed unchanged binding properties to the both mutant proteins, highlighting the essential role S630 and H740 play in covalent bond formation between S630 and saxagliptin. Further supporting mechanism-based inhibition by saxagliptin, NMR spectra of enzyme-saxagliptin complexes revealed the presence of three downfield resonances with low fractionation factors characteristic of short and strong hydrogen bonds (SSHB). Comparison of the NMR spectra of various wild-type and mutant DPP-IV:ligand complexes enabled assignment of a resonance at {approx}14 ppm to H740. Two additional DPP-IV mutants, Y547F and Y547Q, generated to probe potential stabilization of the enzyme-inhibitor complex by this residue, did not show any differences in inhibitor binding either by ITC or NMR. Together with the previously published enzymatic data, the structural and binding data presented here strongly support a histidine-assisted covalent bond formation between S630 hydroxyl oxygen and the nitrile group of saxagliptin.« less

Reactive Landing of Gramicidin S and Ubiquitin Ions onto Activated Self-Assembled Monolayer Surfaces

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

Laskin, Julia; Hu, Qichi

2017-03-13

Using mass-selected ion deposition combined with in situ infrared reflection absorption spectroscopy (IRRAS), we examined the reactive landing of gramicidin S and ubiquitin ions onto activated self-assembled monolayer (SAM) surfaces terminated with N-hydroxysuccinimidyl ester (NHS-SAM) and acyl fluoride (COF-SAM) groups. Doubly protonated gramicidin S, [GS+2H]2+, and two charge states of ubiquitin, [U+5H]5+ and [U+13H]13+, were used as model systems, allowing us to explore the effect of the number of free amino groups and the secondary structure on the efficiency of covalent bond formation between the projectile ion and the surface. For all projectile ions, ion deposition resulted in the depletionmore » of IRRAS bands corresponding to the terminal groups on the SAM and the appearance of several new bands not associated with the deposited species. These new bands were assigned to the C=O stretching vibrations of COOH and COO- groups formed on the surface as a result of ion deposition. The presence of these bands was attributed to an alternative reactive landing pathway that competes with covalent bond formation. This pathway with similar yields for both gramicidin S and ubiquitin ions is analogous to the hydrolysis of the NHS ester bond in solution. The covalent bond formation efficiency increased linearly with the number of free amino groups and was found to be lower for the more compact conformation of ubiquitin compared with the fully unfolded conformation. This observation was attributed to the limited availability of amino groups on the surface of the folded conformation. Our results have provided new insights on the efficiency and mechanism of reactive landing of peptides and proteins onto activated SAMs« less

Reactive Landing of Gramicidin S and Ubiquitin Ions onto Activated Self-Assembled Monolayer Surfaces

NASA Astrophysics Data System (ADS)

Laskin, Julia; Hu, Qichi

2017-07-01

Using mass-selected ion deposition combined with in situ infrared reflection absorption spectroscopy (IRRAS), we examined the reactive landing of gramicidin S and ubiquitin ions onto activated self-assembled monolayer (SAM) surfaces terminated with N-hydroxysuccinimidyl ester (NHS-SAM) and acyl fluoride (COF-SAM) groups. Doubly protonated gramicidin S, [GS + 2H]2+, and two charge states of ubiquitin, [U + 5H]5+ and [U + 13H]13+, were used as model systems, allowing us to explore the effect of the number of free amino groups and the secondary structure on the efficiency of covalent bond formation between the projectile ion and the surface. For all projectile ions, ion deposition resulted in the depletion of IRRAS bands corresponding to the terminal groups on the SAM and the appearance of several new bands not associated with the deposited species. These new bands were assigned to the C=O stretching vibrations of COOH and COO- groups formed on the surface as a result of ion deposition. The presence of these bands was attributed to an alternative reactive landing pathway that competes with covalent bond formation. This pathway with similar yields for both gramicidin S and ubiquitin ions is analogous to the hydrolysis of the NHS ester bond in solution. The covalent bond formation efficiency increased linearly with the number of free amino groups and was found to be lower for the more compact conformation of ubiquitin compared with the fully unfolded conformation. This observation was attributed to the limited availability of amino groups on the surface of the folded conformation. Our results have provided new insights on the efficiency and mechanism of reactive landing of peptides and proteins onto activated SAMs.

Disulfide Bond Formation and ToxR Activity in Vibrio cholerae

PubMed Central

Fengler, Vera H. I.; Boritsch, Eva C.; Tutz, Sarah; Seper, Andrea; Ebner, Hanna; Roier, Sandro; Schild, Stefan; Reidl, Joachim

2012-01-01

Virulence factor production in Vibrio cholerae is complex, with ToxRS being an important part of the regulatory cascade. Additionally, ToxR is the transcriptional regulator for the genes encoding the major outer membrane porins OmpU and OmpT. ToxR is a transmembrane protein and contains two cysteine residues in the periplasmic domain. This study addresses the influence of the thiol-disulfide oxidoreductase system DsbAB, ToxR cysteine residues and ToxR/ToxS interaction on ToxR activity. The results show that porin production correlates with ToxR intrachain disulfide bond formation, which depends on DsbAB. In contrast, formation of ToxR intrachain or interchain disulfide bonds is dispensable for virulence factor production and in vivo colonization. This study further reveals that in the absence of ToxS, ToxR interchain disulfide bond formation is facilitated, whereat cysteinyl dependent homo- and oligomerization of ToxR is suppressed if ToxS is coexpressed. In summary, new insights into gene regulation by ToxR are presented, demonstrating a mechanism by which ToxR activity is linked to a DsbAB dependent intrachain disulfide bond formation. PMID:23144706

A Dynamic Pathway for Stone-Wales Bond Rotation on Carbon Nanotubes through Diamond-Like Bonds

NASA Technical Reports Server (NTRS)

Wei, Chen-Yu; Srivastava, Deepak; Cho, Kyeong-Jae; Menon, Madhu

2003-01-01

A new lower energy barrier with a two-step pathway of Stone-Wales (SW) ,ond rotation on carbon nanotubes (CNTs) is found through molecular dynamics (MD) simulations of CNTs under tension. The first step involves going over to a stable sp3-like metastable configuration with half rotated and partially tilted C-C bond. The second step involves going over to the fully rotated C-C bond with the formation of a SW defect in the nanotube. The energy barrier for this two-step dynamic pathway is significantly lower than the previously known static barrier for in-plane rotation of the C-C bond on a tensile strained (> 4%) CNT.

Synthesis of Polyheteroaromatic Compounds via Rhodium-Catalyzed Multiple C-H Bond Activation and Oxidative Annulation.

PubMed

Peng, Shiyong; Liu, Suna; Zhang, Sai; Cao, Shengyu; Sun, Jiangtao

2015-10-16

Polyheteroaromatic compounds are potential optoelectronic conjugated materials due to their electro- and photochemical properties. Transition-metal-catalyzed multiple C-H activation and sequential oxidative annulation allows rapidly assembling of those compounds from readily available starting materials. A rhodium-catalyzed cascade oxidative annulation of β-enamino esters or 4-aminocoumarins with internal alkynes is described to access those compounds, featuring multiple C-H/N-H bond cleavages and sequential C-C/C-N bond formations in one pot.

Copper-catalyzed, C-C coupling-based one-pot tandem reactions for the synthesis of benzofurans using o-iodophenols, acyl chlorides, and phosphorus ylides.

PubMed

Liu, Yunyun; Wang, Hang; Wan, Jie-Ping

2014-11-07

One-pot reactions involving acyl chlorides, phosphorus ylides, and o-iodophenols with copper catalysis have been established for the rapid synthesis of functionalized benzofurans. With all of these easily available and stable reactants, the construction of the target products has been accomplished via tandem transformations involving a key C-C coupling, leading to the formation of one C(sp(2))-C bond, one C(sp(2))-O bond, and one C ═ C bond.

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.

Ethylene decomposition over Pt(100): A mechanism study from first principle calculation

NASA Astrophysics Data System (ADS)

Wang, Yuchun; Dong, Xiuqin; Yu, Yingzhe; Zhang, Minhua

2016-12-01

First principle based density functional theory was used to calculate the complete step-by-step decomposition network of ethylene (C2H4) over Pt(100) as a model for understanding the carbon deposition of olefin hydrocarbon over transition metal surface. We discussed the structural and energetic properties of all the Csbnd H and Csbnd C bond cleavage reactions in order to fully understand the formation pathway of carbon monomer. It is easier for Csbnd H bond cleavage reactions to take place, as the activation barrier of these reactions is relatively lower than that of Csbnd C bond cleavage as a whole. However, vinyl (CH2CH) is likely to be the precursor of Csbnd C bond scission, as the activation barrier of Csbnd C bond cleavage reaction of CH2CH is much lower than that of CH2CH dehydrogenation and the reaction is exothermic by 0.15 eV. CC was another form of depositional carbon on Pt(100), as it is easy to form but difficult to decompose. Finally we proposed six possible routes of carbon monomer formation.

Solvent/oxidant-switchable synthesis of multisubstituted quinazolines and benzimidazoles via metal-free selective oxidative annulation of arylamidines.

PubMed

Lin, Jian-Ping; Zhang, Feng-Hua; Long, Ya-Qiu

2014-06-06

A fast and simple divergent synthesis of multisubstituted quinazolines and benzimidazoles was developed from readily available amidines, via iodine(III)-promoted oxidative C(sp(3))-C(sp(2)) and C(sp(2))-N bond formation in nonpolar and polar solvents, respectively. Further selective synthesis of quinazolines in polar solvent was realized by TEMPO-catalyzed sp(3)C-H/sp(2)C-H direct coupling of the amidine with K2S2O8 as the oxidant. No metal, base, or other additives were needed.

Diphthamide biosynthesis requires an organic radical generated by an iron-sulphur enzyme

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

Zhang, Yang; Zhu, Xuling; Torelli, Andrew T

2010-08-30

Archaeal and eukaryotic translation elongation factor 2 contain a unique post-translationally modified histidine residue called diphthamide, which is the target of diphtheria toxin. The biosynthesis of diphthamide was proposed to involve three steps, with the first being the formation of a C-C bond between the histidine residue and the 3-amino-3-carboxypropyl group of S-adenosyl-l-methionine (SAM). However, further details of the biosynthesis remain unknown. Here we present structural and biochemical evidence showing that the first step of diphthamide biosynthesis in the archaeon Pyrococcus horikoshii uses a novel iron-sulphur-cluster enzyme, Dph2. Dph2 is a homodimer and each of its monomers can bind amore » [4Fe-4S] cluster. Biochemical data suggest that unlike the enzymes in the radical SAM superfamily, Dph2 does not form the canonical 5'-deoxyadenosyl radical. Instead, it breaks the C γ,Met-S bond of SAM and generates a 3-amino-3-carboxypropyl radical. Our results suggest that P. horikoshii Dph2 represents a previously unknown, SAM-dependent, [4Fe-4S]-containing enzyme that catalyses unprecedented chemistry.« less

Comparison of carbon-sulfur and carbon-amine bond in therapeutic drug: 4β-S-aromatic heterocyclic podophyllum derivatives display antitumor activity

PubMed Central

Li, Jian-Long; Zhao, Wei; Zhou, Chen; Zhang, Ya-Xuan; Li, Hong-Mei; Tang, Ya-Ling; Liang, Xin-Hua; Chen, Tao; Tang, Ya-Jie

2015-01-01

Herein is a first effort to systematically study the significance of carbon-sulfur (C-S) and carbon-amine (C-NH) bonds on the antitumor proliferation activity of podophyllum derivatives and their precise mechanism of apoptosis. Compared with the derivative modified by a C-NH bond, the derivative modified by a C-S bond exhibited superior antitumor activity, the inhibition activity of target proteins tubulin or Topo II, cell cycle arrest, and apoptosis induction. Antitumor mechanistic studies showed that the death receptor and the mitochondrial apoptotic pathways were simultaneously activated by the C-S bond modified aromatic heterocyclic podophyllum derivatives with a higher cellular uptake percentage of 60–90% and induction of a higher level of reactive oxygen species (ROS). Only the mitochondrial apoptotic pathway was activated by the C-NH bond modified aromatic heterocyclic podophyllum derivatives, with a lower cellular uptake percentage of 40–50%. This study provided insight into effects of the C-S and C-NH bond modification on the improvement of the antitumor activity of Podophyllum derivatives. PMID:26443888

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.

Enantioselective Copper-Catalyzed Carboetherification of Unactivated Alkenes**

PubMed Central

Bovino, Michael T.; Liwosz, Timothy W.; Kendel, Nicole E.; Miller, Yan; Tyminska, Nina

2014-01-01

Chiral saturated oxygen heterocycles are important components of bioactive compounds. Cyclization of alcohols onto pendant alkenes is a direct route to their synthesis, but few catalytic enantioselective methods enabling cyclization onto unactivated alkenes exist. Herein is reported a highly efficient copper-catalyzed cyclization of γ-unsaturated pentenols that terminates in C-C bond formation, a net alkene carboetherification. Both intra- and intermolecular C-C bond formations are demonstrated, yielding functionalized chiral tetrahydrofurans as well as fused-ring and bridged-ring oxabicyclic products. Transition state calculations support a cis-oxycupration stereochemistry-determining step. PMID:24798697

Rhodium-Catalyzed C-C Bond Formation via Heteroatom-Directed C-H Bond Activation

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

Colby, Denise; Bergman, Robert; Ellman, Jonathan

2010-05-13

Once considered the 'holy grail' of organometallic chemistry, synthetically useful reactions employing C-H bond activation have increasingly been developed and applied to natural product and drug synthesis over the past decade. The ubiquity and relative low cost of hydrocarbons makes C-H bond functionalization an attractive alternative to classical C-C bond forming reactions such as cross-coupling, which require organohalides and organometallic reagents. In addition to providing an atom economical alternative to standard cross - coupling strategies, C-H bond functionalization also reduces the production of toxic by-products, thereby contributing to the growing field of reactions with decreased environmental impact. In the areamore » of C-C bond forming reactions that proceed via a C-H activation mechanism, rhodium catalysts stand out for their functional group tolerance and wide range of synthetic utility. Over the course of the last decade, many Rh-catalyzed methods for heteroatom-directed C-H bond functionalization have been reported and will be the focus of this review. Material appearing in the literature prior to 2001 has been reviewed previously and will only be introduced as background when necessary. The synthesis of complex molecules from relatively simple precursors has long been a goal for many organic chemists. The ability to selectively functionalize a molecule with minimal pre-activation can streamline syntheses and expand the opportunities to explore the utility of complex molecules in areas ranging from the pharmaceutical industry to materials science. Indeed, the issue of selectivity is paramount in the development of all C-H bond functionalization methods. Several groups have developed elegant approaches towards achieving selectivity in molecules that possess many sterically and electronically similar C-H bonds. Many of these approaches are discussed in detail in the accompanying articles in this special issue of Chemical Reviews. One approach that has seen widespread success involves the use of a proximal heteroatom that serves as a directing group for the selective functionalization of a specific C-H bond. In a survey of examples of heteroatom-directed Rh catalysis, two mechanistically distinct reaction pathways are revealed. In one case, the heteroatom acts as a chelator to bind the Rh catalyst, facilitating reactivity at a proximal site. In this case, the formation of a five-membered metallacycle provides a favorable driving force in inducing reactivity at the desired location. In the other case, the heteroatom initially coordinates the Rh catalyst and then acts to stabilize the formation of a metal-carbon bond at a proximal site. A true test of the utility of a synthetic method is in its application to the synthesis of natural products or complex molecules. Several groups have demonstrated the applicability of C-H bond functionalization reactions towards complex molecule synthesis. Target-oriented synthesis provides a platform to test the effectiveness of a method in unique chemical and steric environments. In this respect, Rh-catalyzed methods for C-H bond functionalization stand out, with several syntheses being described in the literature that utilize C-H bond functionalization in a key step. These syntheses are highlighted following the discussion of the method they employ.« less

Photochemically Induced Intramolecular Radical Cyclization Reactions with Imines.

PubMed

Lefebvre, Corentin; Michelin, Clément; Martzel, Thomas; Djou'ou Mvondo, Vaneck; Bulach, Véronique; Abe, Manabu; Hoffmann, Norbert

2018-02-16

The photochemically induced intramolecular hydrogen abstraction or hydrogen atom transfer in cyclic imines 8a,b followed by a cyclization is investigated. Two types of products are observed, one resulting from the formation of a C-C bond, the other from the formation of a C-N bond. A computational study reveals that hydrogen is exclusively transferred to the imine nitrogen leading to a triplet diradical intermediate. After intersystem crossing, the resulting zwitterionic intermediate undergoes cyclization leading to the final product.

Raney Ni-Sn catalyst for H2 production from biomass-derived hydrocarbons.

PubMed

Huber, G W; Shabaker, J W; Dumesic, J A

2003-06-27

Hydrogen (H2) was produced by aqueous-phase reforming of biomass-derived oxygenated hydrocarbons at temperatures near 500 kelvin over a tin-promoted Raney-nickel catalyst. The performance of this non-precious metal catalyst compares favorably with that of platinum-based catalysts for production of hydrogen from ethylene glycol, glycerol, and sorbitol. The addition of tin to nickel decreases the rate of methane formation from C-O bond cleavage while maintaining the high rates of C-C bond cleavage required for hydrogen formation.

An oxidative cross-coupling reaction of 4-hydroxydithiocoumarin and amines/thiols using a combination of I2 and TBHP: access to lead molecules for biomedical applications.

PubMed

Mahato, Karuna; Arora, Neha; Ray Bagdi, Prasanta; Gattu, Radhakrishna; Ghosh, Siddhartha Sankar; Khan, Abu T

2018-02-06

A metal-free I 2 /TBHP induced highly atom economic and operationally simple oxidative cross-coupling reaction has been developed for the direct synthesis of sulfenamides/sulfanes/disulfides from the reaction of 4-hydroxydithiocoumarin and amines/thiols. The novelties of the present protocol are unprecedented S-C bond formation in addition to S-N and S-S bonds, shorter reaction time, mild and environmentally benign reaction conditions, functional group tolerance and moderate to excellent yields. Moreover, the four newly synthesized compounds namely 4q, 6d, 6e and 7a exhibit anti-proliferative activity against the breast cancer cell line MCF7, and may be lead molecules for future drug development.

Engineering out motion: introduction of a de novo disulfide bond and a salt bridge designed to close a dynamic cleft on the surface of cytochrome b5.

PubMed

Storch, E M; Daggett, V; Atkins, W M

1999-04-20

A previous molecular dynamics (MD) simulation of cytochrome b5 (cyt b5) at 25 degrees C displayed localized dynamics on the surface of the protein giving rise to the periodic formation of a cleft that provides access to the heme through a protected hydrophobic channel [Storch and Daggett (1995) Biochemistry 34, 9682]. Here we describe the production and testing of mutants designed to prevent the cleft from opening using a combination of experimental and theoretical techniques. Two mutants have been designed to close the surface cleft: S18D to introduce a salt bridge and S18C:R47C to incorporate a disulfide bond. The putative cleft forms between two separate cores of the protein: one is structural in nature and can be monitored through the fluorescence of Trp 22, and the other binds the heme prosthetic group and can be tracked via heme absorbance. An increase in motion localized to the cleft region was observed for each protein, except for the disulfide-containing variant, in MD simulations at 50 degrees C compared to simulations at 25 degrees C. For the disulfide-containing variant, the cleft remained closed. Both urea and temperature denaturation curves were nearly identical for wild-type and mutant proteins when heme absorbance was monitored. In contrast, fluorescence studies revealed oxidized S18C:R47C to be considerably more stable based on the midpoints of the denaturation transitions, Tm and U1/2. Moreover, the fluorescence changes for each protein were complete at approximately 50 degrees C and a urea concentration of approximately 3.9 M, significantly below the temperature and urea concentration (62 degrees C, 5 M urea) required to observe heme release. In addition, solvent accessibility based on acrylamide quenching of Trp 22 was lower in the S18C:R47C mutant, particularly at 50 degrees C, before heme release [presented in the accompanying paper (58)]. The results suggest that a constraining disulfide bond can be designed to inhibit dynamic cleft formation on the surface of cyt b5. Located near the heme, the native dynamics of the cleft may be functionally important for protein-protein recognition and/or complex stabilization.

A chiral BINOL-based Gemini amphiphilic gelator and its specific discrimination of native arginine by gelation in water.

PubMed

Jia, Lihua; Yin, Jianxin; Guo, Xiangfeng; Cao, Guangzhou; Tian, Xuhua; Zhu, Bo; Pu, Lin

2017-08-16

A novel axially chiral cationic Gemini amphiphile gelator (S1) derived from (S)-BINOL has been synthesized and characterized by 1 H NMR, 13 C NMR, ESI-MS and FT-IR analyses. The critical micelle concentration (CMC) of S1 was determined to be 0.21 mM in water at room temperature. A transparent hydrogel with S1 at 43 mM was obtained at room temperature and characterized using various methods including SEM, CD, fluorescence, 1 H NMR, FT-IR, and XRD. The results indicate that the hydrophobic effect of long alkyl chains, π-π stacking of naphthalene rings, and intermolecular hydrogen-bonding of the amide groups of S1 should be responsible for the hydrogel formation. Moreover, an 8.5 mM aqueous solution of S1 could gel by the addition of l-arginine, whereas it failed to gel in the presence of other 15 amino acids, respectively. It is suggested that S1 could discriminate native arginine by hydrogel formation, mainly due to the electrostatic interaction and hydrogen bonding effects between S1 and l-arginine molecules.

Crystal structure of a looped-chain CoII coordination polymer: catena-poly[[bis-(nitrato-κO)cobalt(II)]bis-[μ-bis-(pyridin-3-ylmeth-yl)sulfane-κ2N:N'

PubMed

Moon, Suk-Hee; Seo, Joobeom; Park, Ki-Min

2017-11-01

The asymmetric unit of the title compound, [Co(NO 3 ) 2 (C 12 H 12 N 2 S) 2 ] n , contains a bis-(pyridin-3-ylmeth-yl)sulfane ( L ) ligand, an NO 3 - anion and half a Co II cation, which lies on an inversion centre. The Co II cation is six-coordinated, being bound to four pyridine N atoms from four symmetry-related L ligands. The remaining coordination sites are occupied by two O atoms from two symmetry-related nitrate anions in a monodentate manner. Thus, the Co II centre adopts a distorted octa-hedral geometry. Two symmetry-related L ligands are connected by two symmetry-related Co II cations, forming a 20-membered cyclic dimer, in which the Co II atoms are separated by 10.2922 (7) Å. The cyclic dimers are connected to each other by sharing Co II atoms, giving rise to the formation of an infinite looped chain propagating along the [101] direction. Inter-molecular C-H⋯π (H⋯ring centroid = 2.89 Å) inter-actions between one pair of corresponding L ligands and C-H⋯O hydrogen bonds between the L ligands and the nitrate anions occur in the looped chain. In the crystal, adjacent looped chains are connected by inter-molecular π-π stacking inter-actions [centroid-to-centroid distance = 3.8859 (14) Å] and C-H⋯π hydrogen bonds (H⋯ring centroid = 2.65 Å), leading to the formation of layers parallel to (101). These layers are further connected through C-H⋯O hydrogen bonds between the layers, resulting in the formation of a three-dimensional supra-molecular architecture.

Transition Metal-Mediated and -Catalyzed C-F Bond Activation via Fluorine Elimination.

PubMed

Fujita, Takeshi; Fuchibe, Kohei; Ichikawa, Junji

2018-06-28

Activation of carbon-fluorine (C-F) bonds is an important topic in synthetic organic chemistry recently. Among the methods for C-F bond cleavage, metal mediated and catalyzed β- or α-fluorine elimination proceeds under mild conditions compared with oxidative addition of C-F bond. The β- or α-fluorine elimination is initiated from organometallic intermediates having fluorine substituents on carbon atoms β or α to metal centers, respectively. Transformations via these elimination processes (C-F bond cleavage), which are typically preceded by carbon-carbon (or carbon-heteroatom) bond formation, have been remarkably developed as C-F bond activation methods in the past five years. In this minireview, we summarize the applications of transition metal-mediated and -catalyzed fluorine elimination to synthetic organic chemistry from a historical perspective for early studies and from a systematic perspective for recent studies. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Salt-Induced Universal Slowing Down of the Short-Time Self-Diffusion of a Globular Protein in Aqueous Solution

DOE PAGES

Grimaldo, Marco; Roosen-Runge, Felix; Hennig, Marcus; ...

2015-06-17

The short-time self-diffusion D of the globular model protein bovine serum albumin in aqueous (D 2O) solutions has been measured comprehensively as a function of the protein and trivalent salt (YCl 3) concentration, noted c p and c s, respectively. We observe that D follows a universal master curve D(c s,c p) = D(c s = 0,c p) g(c s/c p), where D(c s= 0,c p) is the diffusion coefficient in the absence of salt and g(c s/c p) is a scalar function solely depending on the ratio of the salt and protein concentration. This observation is consistent with amore » universal scaling of the bonding probability in a picture of cluster formation of patchy particles. In conclusion, the finding corroborates the predictive power of the description of proteins as colloids with distinct attractive ion-activated surface patches.« less

Distinct hydroxy-radical-induced damage of 3'-uridine monophosphate in RNA: a theoretical study.

PubMed

Zhang, Ru bo; Eriksson, Leif A

2009-01-01

RNA strand scission and base release in 3'-uridine monophosphate (UMP), induced by OH radical addition to uracil, is studied at the DFT B3LYP/6-31+G(d,p) level in the gas phase and in solution. In particular, the mechanism of hydrogen-atom transfer subsequent to radical formation, from C2' on the sugar to the C6 site on the base, is explored. The barriers of (C2'-)H2'(a) abstraction by the C6 radical site range from 11.2 to 20.0 kcal mol(-1) in the gas phase and 14.1 to 21.0 kcal mol(-1) in aqueous solution, indicating that the local surrounding governs the hydrogen-abstraction reaction in a stereoselective way. The calculated N1-C1' (N1-glycosidic bond) and beta-phosphate bond strengths show that homolytic and heterolytic bond-breaking processes are largely favored in each case, respectively. The barrier for beta-phosphate bond rupture is approximately 3.2-4.0 kcal mol(-1) and is preferred by 8-12 kcal mol(-1) over N1-glycosidic bond cleavage in both the gas phase and solution. The beta-phosphate bond-rupture reactions are exothermal in the gas phase and solution, whereas N1-C1' bond-rupture reactions require both solvation and thermal corrections at 298 K to be energetically favored. The presence of the ribose 2'-OH group and its formation of low-barrier hydrogen bonds with oxygen atoms of the 3'-phosphate linkage are highly important for hydrogen transfer and the subsequent bond-breakage reactions.

Electronic communication in phosphine substituted bridged dirhenium complexes - clarifying ambiguities raised by the redox non-innocence of the C4H2- and C4-bridges.

PubMed

Li, Yan; Blacque, Olivier; Fox, Thomas; Luber, Sandra; Polit, Walther; Winter, Rainer F; Venkatesan, Koushik; Berke, Heinz

2016-04-07

The mononuclear rhenium carbyne complex trans-[Re(C[triple bond, length as m-dash]CSiMe3)([triple bond, length as m-dash]C-Me)(PMe3)4][PF6] (2) was prepared in 90% yield by heating a mixture of the dinitrogen complex trans-[ReCl(N2)(PMe3)4] (1), TlPF6, and an excess of HC[triple bond, length as m-dash]CSiMe3. 2 could be deprotonated with KOtBu to the vinylidene complex trans-[Re(C[triple bond, length as m-dash]CSiMe3)([double bond, length as m-dash]C[double bond, length as m-dash]CH2)(PMe3)4] (3) in 98% yield. Oxidation of 3 with 1.2 equiv. of [Cp2Fe][PF6] at -78 °C gave the Cβ-C'β coupled dinuclear rhenium biscarbyne complex trans-[(Me3SiC[triple bond, length as m-dash]C)(PMe3)4Re[triple bond, length as m-dash]C-CH2-CH2-C[triple bond, length as m-dash]Re(PMe3)4(C[triple bond, length as m-dash]CSiMe3)][PF6]2 (5) in 92% yield. Deprotonation of 5 with an excess of KOtBu in THF produced the diamagnetic trans-[(Me3SiC[triple bond, length as m-dash]C)(PMe3)4Re[double bond, length as m-dash]C[double bond, length as m-dash]CH-CH[double bond, length as m-dash]C[double bond, length as m-dash]Re(PMe3)4(C[triple bond, length as m-dash]CSiMe3)] complex (E-6(S)) in 87% yield with an E-butadienediylidene bridge. Density functional theory (DFT) calculations of E-6(S) confirmed its singlet ground state. The Z-form of 6 (Z-6(S)) could not be observed, which is in accord with its DFT calculated 17.8 kJ mol(-1) higher energy. Oxidation of E-6 with 2 equiv. of [Cp2Fe][PF6] resulted in the stable diamagnetic dicationic trans-[(Me3SiC[triple bond, length as m-dash]C)(PMe3)4Re[triple bond, length as m-dash]C-CH[double bond, length as m-dash]CH-C[triple bond, length as m-dash]Re(PMe3)4(C[triple bond, length as m-dash]CSiMe3)][PF6]2 complex (E-6[PF6]2) with an ethylenylidene dicarbyne structure of the bridge. The paramagnetic mixed-valence (MV) complex E-6[PF6] was obtained by comproportionation of E-6(S) and E-6[PF6]2 or by oxidation of E-6(S) with 1 equiv. of [Cp2Fe][PF6]. The dicationic trans-[(Me3SiC[triple bond, length as m-dash]C)(PMe3)4Re[triple bond, length as m-dash]C-C[triple bond, length as m-dash]C-C[triple bond, length as m-dash]Re(PMe3)4(C[triple bond, length as m-dash]CSiMe3)][PF6]2 (7[PF6]2) complex, attributed a butynedi(triyl) bridge structure, was obtained by deprotonation of E-6[PF6]2 with KOtBu followed by oxidation with 2 equiv. of [Cp2Fe][PF6]. The neutral complex 7 could be accessed best by reduction of 7[PF6]2 with KH in the presence of 18-crown-6. According to DFT calculations 7 possesses two equilibrating electronic states: diamagnetic 7(S) and triplet 7(F) with ferromagnetically coupled spins. The latter is calculated to be 5.2 kcal mol(-1) lower in energy than 7(S). There is experimental evidence that 7(S) prevails in solution. 7 could not be isolated in the crystalline state and is unstable transforming mainly by H-abstraction to give E-6(S). UV-Vis-NIR spectroscopy for the dinuclear rhenium complexes E-6(S), E-6[PF6] and E-6[PF6]2, as well as EPR spectroscopic and variable-temperature magnetization measurements for the MV complex E-6[PF6] were also conducted. Spectro-electrochemical reduction studies on 7[PF6]2 allowed the characterization of the mono- and direduced forms of 7(+) and 7 by means of IR- and UV-Vis-NIR-spectroscopy and revealed the chemical fate of the higher reduced form.

On the origin of red and blue shifts of X-H and C-H stretching vibrations in formic acid (formate ion) and proton donor complexes.

PubMed

Tâme Parreira, Renato Luis; Galembeck, Sérgio Emanuel; Hobza, Pavel

2007-01-08

Complexes between formic acid or formate anion and various proton donors (HF, H(2)O, NH(3), and CH(4)) are studied by the MP2 and B3LYP methods with the 6-311++G(3df,3pd) basis set. Formation of a complex is characterized by electron-density transfer from electron donor to ligands. This transfer is much larger with the formate anion, for which it exceeds 0.1 e. Electron-density transfer from electron lone pairs of the electron donor is directed into sigma* antibonding orbitals of X--H bonds of the electron acceptor and leads to elongation of the bond and a red shift of the X--H stretching frequency (standard H-bonding). However, pronounced electron-density transfer from electron lone pairs of the electron donor also leads to reorganization of the electron density in the electron donor, which results in changes in geometry and vibrational frequency. These changes are largest for the C--H bonds of formic acid and formate anion, which do not participate in H-bonding. The resulting blue shift of this stretching frequency is substantial and amounts to almost 35 and 170 cm(-1), respectively.

Nano-Welding of Multi-Walled Carbon Nanotubes on Silicon and Silica Surface by Laser Irradiation

PubMed Central

Yuan, Yanping; Chen, Jimin

2016-01-01

In this study, a continuous fiber laser (1064 nm wavelength, 30 W/cm2) is used to irradiate multi-walled carbon nanotubes (MWCNTs) on different substrate surfaces. Effects of substrates on nano-welding of MWCNTs are investigated by scanning electron microscope (SEM). For MWCNTs on silica, after 3 s irradiation, nanoscale welding with good quality can be achieved due to breaking C–C bonds and formation of new graphene layers. While welding junctions can be formed until 10 s for the MWCNTs on silicon, the difference of irradiation time to achieve welding is attributed to the difference of thermal conductivity for silica and silicon. As the irradiation time is prolonged up to 12.5 s, most of the MWCNTs are welded to a silicon substrate, which leads to their frameworks of tube walls on the silicon surface. This is because the accumulation of absorbed energy makes the temperature rise. Then chemical reactions among silicon, carbon and nitrogen occur. New chemical bonds of Si–N and Si–C achieve the welding between the MWCNTs and silicon. Vibration modes of Si3N4 appear at peaks of 363 cm−1 and 663 cm−1. There are vibration modes of SiC at peaks of 618 cm−1, 779 cm−1 and 973 cm−1. The experimental observation proves chemical reactions and the formation of Si3N4 and SiC by laser irradiation. PMID:28344293

Carbon-sulfur bond-forming reaction catalysed by the radical SAM enzyme HydE.

PubMed

Rohac, Roman; Amara, Patricia; Benjdia, Alhosna; Martin, Lydie; Ruffié, Pauline; Favier, Adrien; Berteau, Olivier; Mouesca, Jean-Marie; Fontecilla-Camps, Juan C; Nicolet, Yvain

2016-05-01

Carbon-sulfur bond formation at aliphatic positions is a challenging reaction that is performed efficiently by radical S-adenosyl-L-methionine (SAM) enzymes. Here we report that 1,3-thiazolidines can act as ligands and substrates for the radical SAM enzyme HydE, which is involved in the assembly of the active site of [FeFe]-hydrogenase. Using X-ray crystallography, in vitro assays and NMR spectroscopy we identified a radical-based reaction mechanism that is best described as the formation of a C-centred radical that concomitantly attacks the sulfur atom of a thioether. To the best of our knowledge, this is the first example of a radical SAM enzyme that reacts directly on a sulfur atom instead of abstracting a hydrogen atom. Using theoretical calculations based on our high-resolution structures we followed the evolution of the electronic structure from SAM through to the formation of S-adenosyl-L-cysteine. Our results suggest that, at least in this case, the widely proposed and highly reactive 5'-deoxyadenosyl radical species that triggers the reaction in radical SAM enzymes is not an isolable intermediate.

Carbon-sulfur bond-forming reaction catalysed by the radical SAM enzyme HydE

NASA Astrophysics Data System (ADS)

Rohac, Roman; Amara, Patricia; Benjdia, Alhosna; Martin, Lydie; Ruffié, Pauline; Favier, Adrien; Berteau, Olivier; Mouesca, Jean-Marie; Fontecilla-Camps, Juan C.; Nicolet, Yvain

2016-05-01

Carbon-sulfur bond formation at aliphatic positions is a challenging reaction that is performed efficiently by radical S-adenosyl-L-methionine (SAM) enzymes. Here we report that 1,3-thiazolidines can act as ligands and substrates for the radical SAM enzyme HydE, which is involved in the assembly of the active site of [FeFe]-hydrogenase. Using X-ray crystallography, in vitro assays and NMR spectroscopy we identified a radical-based reaction mechanism that is best described as the formation of a C-centred radical that concomitantly attacks the sulfur atom of a thioether. To the best of our knowledge, this is the first example of a radical SAM enzyme that reacts directly on a sulfur atom instead of abstracting a hydrogen atom. Using theoretical calculations based on our high-resolution structures we followed the evolution of the electronic structure from SAM through to the formation of S-adenosyl-L-cysteine. Our results suggest that, at least in this case, the widely proposed and highly reactive 5‧-deoxyadenosyl radical species that triggers the reaction in radical SAM enzymes is not an isolable intermediate.

Cocrystals of 6-propyl-2-thiouracil: N-H···O versus N-H···S hydrogen bonds.

PubMed

Tutughamiarso, Maya; Egert, Ernst

2011-11-01

In order to investigate the relative stability of N-H···O and N-H···S hydrogen bonds, we cocrystallized the antithyroid drug 6-propyl-2-thiouracil with two complementary heterocycles. In the cocrystal pyrimidin-2-amine-6-propyl-2-thiouracil (1/2), C(4)H(5)N(3)·2C(7)H(10)N(2)OS, (I), the `base pair' is connected by one N-H···S and one N-H···N hydrogen bond. Homodimers of 6-propyl-2-thiouracil linked by two N-H···S hydrogen bonds are observed in the cocrystal N-(6-acetamidopyridin-2-yl)acetamide-6-propyl-2-thiouracil (1/2), C(9)H(11)N(3)O(2)·2C(7)H(10)N(2)OS, (II). The crystal structure of 6-propyl-2-thiouracil itself, C(7)H(10)N(2)OS, (III), is stabilized by pairwise N-H···O and N-H···S hydrogen bonds. In all three structures, N-H···S hydrogen bonds occur only within R(2)(2)(8) patterns, whereas N-H···O hydrogen bonds tend to connect the homo- and heterodimers into extended networks. In agreement with related structures, the hydrogen-bonding capability of C=O and C=S groups seems to be comparable.

Highly enantioselective rhodium(I)-catalyzed carbonyl carboacylations initiated by C-C bond activation.

PubMed

Souillart, Laetitia; Cramer, Nicolai

2014-09-01

The lactone motif is ubiquitous in natural products and pharmaceuticals. The Tishchenko disproportionation of two aldehydes, a carbonyl hydroacylation, is an efficient and atom-economic access to lactones. However, these reaction types are limited to the transfer of a hydride to the accepting carbonyl group. The transfer of alkyl groups enabling the formation of CC bonds during the ester formation would be of significant interest. Reported herein is such asymmetric carbonyl carboacylation of aldehydes and ketones, thus affording complex bicyclic lactones in excellent enantioselectivities. The rhodium(I)-catalyzed transformation is induced by an enantiotopic CC bond activation of a cyclobutanone and the formed rhodacyclic intermediate reacts with aldehyde or ketone groups to give highly functionalized lactones. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

XANES mapping of organic sulfate in three scleractinian coral skeletons

NASA Astrophysics Data System (ADS)

Cuif, Jean-Pierre; Dauphin, Yannicke; Doucet, Jean; Salome, Murielle; Susini, Jean

2003-01-01

The presence and localization of organic sulfate within coral skeletons are studied by using X-ray absorption near edge structure spectroscopy (XANES) fluorescence. XANES spectra are recorded from four reference sulfur-bearing organic molecules: three amino acids (H-S-C bonds in cysteine; C-S-C bonds in methionine; one disulfide bond C-S-S-C bonds in cystine) and a sulfated sugar (C-SO 4 bonds in chondroitin sulfate). Spectral responses of three coral skeletons show that the sulfated form is extremely dominant in coral aragonite, and practically exclusive within both centres of calcification and the surrounding fibrous tissues of coral septa. Mapping of S-sulfate concentrations in centres and fibres gives us direct evidence of high concentration of organic sulfate in centres of calcification. Additionally, a banding pattern of S-sulfate is visible in fibrous part of the coral septa, evidencing a biochemical zonation that corresponds to the step-by-step growth of fibres.

Deciphering the chemoselectivity of nickel-dependent quercetin 2,4-dioxygenase.

PubMed

Wang, Wen-Juan; Wei, Wen-Jie; Liao, Rong-Zhen

2018-06-13

The reaction mechanism and chemoselectivity of nickel-dependent quercetin 2,4-dioxygenase (2,4-QueD) have been investigated using the QM/MM approach. The protonation state of the Glu74 residue, a first-shell ligand of Ni, has been considered to be either neutral or deprotonated. QM/MM calculations predict that Glu74 must be deprotonated to rationalize the chemoselectivity and steer the 2,4-dioxygenolytic cleavage of quercetin, which harvests the experimentally-observed product, 2-protocatechuoylphloroglucinol carboxylic acid, coupled with the release of carbon monoxide. If the enzyme has a neutral Glu74 residue, the undesired 2,3-dioxygenolytic cleavage of quercetin becomes the dominant pathway, leading to the formation of α-keto acid. The calculations suggest that the reaction takes place via three major steps: (1) attack of the superoxide on the C2 of the substrate pyrone ring to generate a NiII-peroxide intermediate; (2) formation of the second C-O bond between C4 and the peroxide to produce a peroxide bridge; (3) simultaneous cleavage of the C2-C3, C3-C4, and O1-O2 bonds with the formation of 2-protocatechuoylphloroglucinol carboxylic acid and carbon monoxide. The third step was found to be rate-limiting, with a barrier of 17.4 kcal mol-1, which is in very good agreement with the experimental kinetic data. For the second C-O bond formation, an alternative pathway is that the peroxide attacks the C3 of the substrate pyrone ring, leading to the formation of a four-membered ring intermediate, which then undergoes concerted C2-C3 and O1-O2 bond cleavages to produce an α-keto acid. This pathway is associated with a barrier of 30.6 kcal mol-1, which is much higher than the major pathway. When Glu74 is protonated, the 2,3-dioxygenolytic pathway, however, has a lower barrier (21.8 kcal mol-1) than the 2,4-dioxygenolytic pathway.

Microstructural Evolution of Ni-Sn Transient Liquid Phase Sintering Bond during High-Temperature Aging

NASA Astrophysics Data System (ADS)

Feng, Hongliang; Huang, Jihua; Peng, Xianwen; Lv, Zhiwei; Wang, Yue; Yang, Jian; Chen, Shuhai; Zhao, Xingke

2018-05-01

For high-temperature-resistant packaging of new generation power chip, a chip packaging simulation structure of Ni/Ni-Sn/Ni was bonded by a transient liquid-phase sintering process. High-temperature aging experiments were carried out to investigate joint heat stability. The microstructural evolution and mechanism during aging, and mechanical properties after aging were analyzed. The results show that the 30Ni-70Sn bonding layer as-bonded at 340°C for 240 min is mainly composed of Ni3Sn4 and residual Ni particles. When aged at 350°C, because of the difficulty of nucleation for Ni3Sn and quite slow growth of Ni3Sn2, the bonding layer is stable and the strength of that doesn't change obviously with aging time. When aging temperature increased to 500°C, however, the residual Ni particles were gradually dissolved and the bonding layer formed a stable structure with dominated Ni3Sn2 after 36 h. Meanwhile, due to the volume shrinkage (4.43%) from Ni3Sn2 formation, a number of voids were formed. The shear strength shows an increase, resulting from Ni3Sn2 formation, but then it decreases slightly caused by voids. After aging at 500°C for 100 h, shear strength is still maintained at 29.6 MPa. In addition, the mechanism of void formation was analyzed and microstructural evolution model was also established.

Gas-phase ozonolysis of β-ocimene: Temperature dependent rate coefficients and product distribution

NASA Astrophysics Data System (ADS)

Gaona-Colmán, Elizabeth; Blanco, María B.; Barnes, Ian; Teruel, Mariano A.

2016-12-01

Rate coefficients for the reaction of β-ocimene with O3 molecules have been determined over the temperature range 288-311 K at 750 Torr total pressure of nitrogen using the relative rate technique. The investigations were performed in a large volume reaction vessel using long-path in-situ Fourier transformed infrared (FTIR) spectroscopy to monitor the reactants and products. A value of k(β-ocimene + O3) = (3.74 ± 0.92) × 10-16 cm3 molecule-1 s-1 has been obtained for the reaction at 298 K. The temperature dependence of the reaction is best described by the Arrhenius expression k = (1.94 ± 0.02) × 10-14 exp [(-1181 ± 51)/T] cm3 molecule-1 s-1. In addition, a product study has been carried out at 298 K in 750 Torr of synthetic air and the following products with yields in molar % were observed: formaldehyde (36 ± 2), acetone (15 ± 1), methylglyoxal (9.5 ± 0.4) and hydroxyacetone (19 ± 1). The formation of formaldehyde can be explained by the addition of O3 to the C1sbnd C2 double bond of the β-ocimene. Addition of O3 to the C6sbnd C7 double bond leads to the formation of acetone and the CH3C·(OO·)CH3 biradical, which can through isomerization/stabilization form methylglyoxal (hydroperoxide channel) and hydroxyacetone. The formed products will contribute to the formation of PAN and derivatives in polluted environments and also the oxidation capacity of the atmosphere.

Enantioselective copper-catalyzed carboetherification of unactivated alkenes.

PubMed

Bovino, Michael T; Liwosz, Timothy W; Kendel, Nicole E; Miller, Yan; Tyminska, Nina; Zurek, Eva; Chemler, Sherry R

2014-06-16

Chiral saturated oxygen heterocycles are important components of bioactive compounds. Cyclization of alcohols onto pendant alkenes is a direct route to their synthesis, but few catalytic enantioselective methods enabling cyclization onto unactivated alkenes exist. Herein reported is a highly efficient copper-catalyzed cyclization of γ-unsaturated pentenols which terminates in C-C bond formation, a net alkene carboetherification. Both intra- and intermolecular C-C bond formations are demonstrated, thus yielding functionalized chiral tetrahydrofurans as well as fused-ring and bridged-ring oxabicyclic products. Transition-state calculations support a cis-oxycupration stereochemistry-determining step. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Platinum(II) 1,10-phenanthroline complexes of acetylides containing redox-active groups.

PubMed

Siemeling, Ulrich; Bausch, Kirstin; Fink, Heinrich; Bruhn, Clemens; Baldus, Marc; Angerstein, Brigitta; Plessow, Regina; Brockhinke, Andreas

2005-07-21

The new diimine ligand 3,8-di-n-pentyl-4,7-di(phenylethynyl)-1,10-phenanthroline (1) was used for the synthesis of a range of Pt(II) complexes, viz.[Pt(1)Cl2], [Pt(1)(C triple bond C-Ph)2], [Pt(1)(C triple bond C-Fc)2] and [Pt(1)(C triple bond C-p-C6H4-C triple bond C-Fc)2](Fc = ferrocenyl). Crystal structure analyses were performed for [Pt(1)Cl2] and [Pt(1)(C triple bond C-Ph)2] and revealed that the di(acetylide)pi-tweezer of the latter binds a molecule of chloroform through C-H...pi hydrogen bonds. The redox and optical properties of 1 and its complexes were investigated by (spectro-)electrochemistry, UV-Vis and luminescence spectroscopy, and an energy level diagram was derived for [Pt(1)(C triple bond C-Fc)2] and related compounds on the basis of the data collected. The ferrocenyl-substituted Pt(II) complexes are donor-sensitiser assemblies. Intramolecular quenching of the photoexcited Pt(II) diimine unit leads to very short luminescence lifetimes for [Pt(1)(C triple bond C-p-C(6)H(4)-C triple bond C-Fc)2](2 ns) and [Pt(1)(C triple bond C-Fc)2](0.3 ns), as opposed to [Pt(1)(C triple bond C-Ph)2](0.7 micros). Excimer formation has been observed for [Pt(1)(C triple bond C-Ph)(2)] at room temperature in dichloromethane and at low temperatures in frozen glassy dichloromethane and 2-methyltetrahydrofuran solution, but not in the solid state.

Crystal structures of two 6-(2-hy-droxy-benzo-yl)-5H-thia-zolo[3,2-a]pyrimidin-5-ones.

PubMed

Gomes, Ligia R; Low, John Nicolson; Cagide, Fernando; Borges, Fernanda

2015-07-01

The title compounds, 6-(2-hy-droxy-benz-yl)-5H-thia-zolo[3,2-a]pyrimidin-5-one, C13H8N2O3S, (1), and 6-(2-hy-droxy-benz-yl)-3-methyl-5H-thia-zolo[3,2-a]pyrimidin-5-one, C14H10N2O3S, (2), were synthesized when a chromone-3-carb-oxy-lic acid, activated with (benzotriazol-1-yl-oxy)tripyrrolidinyl-phospho-nium hexa-fluorido-phosphate (PyBOP), was reacted with a primary heteromamine. Instead of the expected amidation, the unusual title thia-zolo-pyrimidine-5-one derivatives were obtained serendipitously and a mechanism of formation is proposed. Both compounds present an intra-molecular O-H⋯O hydrogen bond, which generates an S(6) ring. The dihedral angles between the heterocyclic moiety and the 2-hydroxybenzoyl ring are 55.22 (5) and 46.83 (6)° for (1) and (2), respectively. In the crystals, the mol-ecules are linked by weak C-H⋯O hydrogen bonds and π-π stacking inter-actions.

Ionic liquid syntheses via click chemistry: expeditious routes toward versatile functional materials.

PubMed

Mirjafari, Arsalan

2018-03-25

Since the introduction of click chemistry by K. B. Sharpless in 2001, its exploration and exploitation has occurred in countless fields of materials sciences in both academic and industrial spheres. Click chemistry is defined as an efficient, robust, and orthogonal synthetic platform for the facile formation of new carbon-heteroatom bonds, using readily available starting materials. Premier examples of click reactions are copper(i)-catalyzed azide-alkyne Huisgen cycloaddition (CuAAC) and the thiol-X (X = ene and yne) coupling reactions to form C-N and C-S bonds, respectively. The emphasis of this review is centered on the rapidly expanding area of click chemistry-mediated synthesis of functional ionic liquids via CuAAC, thiol-X and oxime formation, and selected examples of nucleophilic ring-opening reactions, while offering some thoughts on emerging challenges, opportunities and ultimately the evolution of this field. Click chemistry offers tremendous opportunities, and introduces intriguing perspectives for efficient and robust generation of tailored task-specific ionic liquids - an important class of soft materials.

{bold {ital Ab initio}} studies of the structural and electronic properties of solid cubane

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

Richardson, S.L.; Martins, J.L.

1998-12-01

In this paper, we report {ital ab initio} calculation of the structural and electronic properties of solid cubane (s-C{sub 8}H{sub 8}) in the local-density approximation. By using an {ital ab initio} constant pressure extended molecular dynamics method with variable cell shape proposed by Wentzcovitch, Martins, and Price, we compute a lattice parameter {ital a} and a bond angle {alpha} for the rhombohedral Bravais lattice and compare it with experimental x-ray data. We obtain bond lengths for the mononuclear C{sub 8}H{sub 8} unit of basis atoms, as well as a density of states and heat of formation. {copyright} {ital 1998} {italmore » The American Physical Society}« less

Insights into the catalysis of a lysine-tryptophan bond in bacterial peptides by a SPASM domain radical S-adenosylmethionine (SAM) peptide cyclase.

PubMed

Benjdia, Alhosna; Decamps, Laure; Guillot, Alain; Kubiak, Xavier; Ruffié, Pauline; Sandström, Corine; Berteau, Olivier

2017-06-30

Radical S -adenosylmethionine (SAM) enzymes are emerging as a major superfamily of biological catalysts involved in the biosynthesis of the broad family of bioactive peptides called ribosomally synthesized and post-translationally modified peptides (RiPPs). These enzymes have been shown to catalyze unconventional reactions, such as methyl transfer to electrophilic carbon atoms, sulfur to C α atom thioether bonds, or carbon-carbon bond formation. Recently, a novel radical SAM enzyme catalyzing the formation of a lysine-tryptophan bond has been identified in Streptococcus thermophilus , and a reaction mechanism has been proposed. By combining site-directed mutagenesis, biochemical assays, and spectroscopic analyses, we show here that this enzyme, belonging to the emerging family of SPASM domain radical SAM enzymes, likely contains three [4Fe-4S] clusters. Notably, our data support that the seven conserved cysteine residues, present within the SPASM domain, are critical for enzyme activity. In addition, we uncovered the minimum substrate requirements and demonstrate that KW cyclic peptides are more widespread than anticipated, notably in pathogenic bacteria. Finally, we show a strict specificity of the enzyme for lysine and tryptophan residues and the dependence of an eight-amino acid leader peptide for activity. Altogether, our study suggests novel mechanistic links among SPASM domain radical SAM enzymes and supports the involvement of non-cysteinyl ligands in the coordination of auxiliary clusters. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Effect of the Anion Activity on the Stability of Li Metal Anodes in Lithium-Sulfur Batteries

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

Cao, Ruiguo; Chen, Junzheng; Han, Kee Sung

2016-03-29

With the significant progress made in the development of cathodes in lithium-sulfur (Li-S) batteries, the stability of Li metal anodes becomes a more urgent challenge in these batteries. Here we report the systematic investigation of the stability of the anode/electrolyte interface in Li-S batteries with concentrated electrolytes containing various lithium salts. It is found that Li-S batteries using LiTFSI-based electrolytes are more stable than those using LiFSI-based electrolytes. The decreased stability is because the N-S bond in the FSI- anion is fairly weak and the scission of this bond leads to the formation of lithium sulfate (LiSOx) in the presencemore » of polysulfide species. In contrast, even the weakest bond (C-S) in the TFSI- anion is stronger than the N-S bond in the FSI- anion. In the LiTFSI-based electrolyte, the lithium metal anode tends to react with polysulfide to form lithium sulfide (LiSx) which is more reversible than LiSOx formed in the LiTFSI-based electrolyte. This fundamental difference in the bond strength of the salt anions in the presence of polysulfide species leads to a large difference in the stability of the anode-electrolyte interface and performance of the Li-S batteries with electrolytes composed of these salts. Therefore, anion selection is one of the key parameters in the search for new electrolytes for stable operation of Li-S batteries.« less

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.

On the Reaction Mechanism of Acetaldehyde Decomposition on Mo(110)

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

Mei, Donghai; Karim, Ayman M.; Wang, Yong

2012-02-16

The strong Mo-O bond strength provides promising reactivity of Mo-based catalysts for the deoxygenation of biomass-derived oxygenates. Combining the novel dimer saddle point searching method with periodic spin-polarized density functional theory calculations, we investigated the reaction pathways of a acetaldehyde decomposition on the clean Mo(110) surface. Two reaction pathways were identified, a selective deoxygenation and a nonselective fragmentation pathways. We found that acetaldehyde preferentially adsorbs at the pseudo 3-fold hollow site in the η2(C,O) configuration on Mo(110). Among four possible bond (β-C-H, γ-C-H, C-O and C-C) cleavages, the initial decomposition of the adsorbed acetaldehyde produces either ethylidene via the C-Omore » bond scission or acetyl via the β-C-H bond scission while the C-C and the γ-C-H bond cleavages of acetaldehyde leading to the formation of methyl (and formyl) and formylmethyl are unlikely. Further dehydrogenations of ethylidene into either ethylidyne or vinyl are competing and very facile with low activation barriers of 0.24 and 0.31 eV, respectively. Concurrently, the formed acetyl would deoxygenate into ethylidyne via the C-O cleavage rather than breaking the C-C or the C-H bonds. The selective deoxygenation of acetaldehyde forming ethylene is inhibited by relatively weaker hydrogenation capability of the Mo(110) surface. Instead, the nonselective pathway via vinyl and vinylidene dehydrogenations to ethynyl as the final hydrocarbon fragment is kinetically favorable. On the other hand, the strong interaction between ethylene and the Mo(110) surface also leads to ethylene decomposition instead of desorption into the gas phase. This work was financially supported by the National Advanced Biofuels Consortium (NABC). Computing time was granted by a user project (emsl42292) at the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL). This work was financially supported by the National Advanced Biofuels Consortium (NABC). Computing time was granted by a user project (emsl42292) at the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL). The EMSL is a U.S. Department of Energy (DOE) national scientific user facility located at Pacific Northwest National Laboratory (PNNL) and supported by the DOE Office of Biological and Environmental Research. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.« less

Influences of the molecular fuel structure on combustion reactions towards soot precursors in selected alkane and alkene flames.

PubMed

Ruwe, Lena; Moshammer, Kai; Hansen, Nils; Kohse-Höinghaus, Katharina

2018-04-25

In this study, we experimentally investigate the high-temperature oxidation kinetics of n-pentane, 1-pentene and 2-methyl-2-butene (2M2B) in a combustion environment using flame-sampling molecular beam mass spectrometry. The selected C5 fuels are prototypes for linear and branched, saturated and unsaturated fuel components, featuring different C-C and C-H bond structures. It is shown that the formation tendency of species, such as polycyclic aromatic hydrocarbons (PAHs), yielded through mass growth reactions increases drastically in the sequence n-pentane < 1-pentene < 2M2B. This comparative study enables valuable insights into fuel-dependent reaction sequences of the gas-phase combustion mechanism that provide explanations for the observed difference in the PAH formation tendency. First, we investigate the fuel-structure-dependent formation of small hydrocarbon species that are yielded as intermediate species during the fuel decomposition, because these species are at the origin of the subsequent mass growth reaction pathways. Second, we review typical PAH formation reactions inspecting repetitive growth sequences in dependence of the molecular fuel structure. Third, we discuss how differences in the intermediate species pool influence the formation reactions of key aromatic ring species that are important for the PAH growth process underlying soot formation. As a main result it was found that for the fuels featuring a C[double bond, length as m-dash]C double bond, the chemistry of their allylic fuel radicals and their decomposition products strongly influences the combination reactions to the initially formed aromatic ring species and as a consequence, the PAH formation tendency.

MICROWAVE-ASSISTED CHEMISTRY: SYNTHESIS OF AMINES AND HETEROCYCLES VIA CARBON-NITROGEN BOND FORMATION IN AQUEOUS MEDIA

EPA Science Inventory

Improved C-N bond formation under MW influence is demonstrated by a) solventless three-component coupling reaction to generate propargyl amines that uses only Cu (I); b) aqueous N-alkylation of amines by alkyl halides that proceeds expeditiously in the presence of NaOH to deliver...

Three new enantiomerically pure ferrocenylphosphole compounds.

PubMed

López Cortés, José Guadalupe; Vincendeau, Sandrine; Daran, Jean Claude; Manoury, Eric; Gouygou, Maryse

2006-05-01

The absolute configurations of three new enantiomerically pure ferrocenylphosphole compounds, namely (2S,4S,S(Fc))-4-methoxymethyl-2-[2-(9-thioxo-9lambda5-phosphafluoren-9-yl)ferrocenyl]-1,3-dioxane, [Fe(C5H5)(C23H22O3PS)], (III), (S(Fc))-[2-(9-thioxo-9lambda5-phosphafluoren-9-yl)ferrocenyl]methanol, [Fe(C5H5)(C18H14OPS)], (V), and (S(Fc))-diphenyl[2-(9-thioxo-9lambda5-phosphafluoren-9-yl]ferrocenylmethyl]phosphine, [Fe(C5H5)(C30H23P2)], (VIII), have been unambiguously established. All three ligands contain a planar chiral ferrocene group, bearing a dibenzophosphole and either a dioxane, a methanol or a diphenylphosphinomethane group on the same cyclopentadienyl. In compound (V), the occurrence of O-H...S and C-H...S hydrogen bonds results in the formation of a two-dimensional network parallel to (001). The geometry of the ferrocene frameworks agrees with related reported structures.

Cross-dehydrogenative coupling for the intermolecular C–O bond formation

PubMed Central

Krylov, Igor B; Vil’, Vera A

2015-01-01

Summary The present review summarizes primary publications on the cross-dehydrogenative C–O coupling, with special emphasis on the studies published after 2000. The starting compound, which donates a carbon atom for the formation of a new C–O bond, is called the CH-reagent or the C-reagent, and the compound, an oxygen atom of which is involved in the new bond, is called the OH-reagent or the O-reagent. Alcohols and carboxylic acids are most commonly used as O-reagents; hydroxylamine derivatives, hydroperoxides, and sulfonic acids are employed less often. The cross-dehydrogenative C–O coupling reactions are carried out using different C-reagents, such as compounds containing directing functional groups (amide, heteroaromatic, oxime, and so on) and compounds with activated C–H bonds (aldehydes, alcohols, ketones, ethers, amines, amides, compounds containing the benzyl, allyl, or propargyl moiety). An analysis of the published data showed that the principles at the basis of a particular cross-dehydrogenative C–O coupling reaction are dictated mainly by the nature of the C-reagent. Hence, in the present review the data are classified according to the structures of C-reagents, and, in the second place, according to the type of oxidative systems. Besides the typical cross-dehydrogenative coupling reactions of CH- and OH-reagents, closely related C–H activation processes involving intermolecular C–O bond formation are discussed: acyloxylation reactions with ArI(O2CR)2 reagents and generation of O-reagents in situ from C-reagents (methylarenes, aldehydes, etc.). PMID:25670997

Statistical analysis of native contact formation in the folding of designed model proteins

NASA Astrophysics Data System (ADS)

Tiana, Guido; Broglia, Ricardo A.

2001-02-01

The time evolution of the formation probability of native bonds has been studied for designed sequences which fold fast into the native conformation. From this analysis a clear hierarchy of bonds emerge: (a) local, fast forming highly stable native bonds built by some of the most strongly interacting amino acids of the protein; (b) nonlocal bonds formed late in the folding process, in coincidence with the folding nucleus, and involving essentially the same strongly interacting amino acids already participating in the fast bonds; (c) the rest of the native bonds whose behavior is subordinated, to a large extent, to that of the strong local and nonlocal native contacts.

A new approach to construct a fused 2-ylidene chromene ring: highly regioselective synthesis of novel chromeno quinoxalines.

PubMed

Kumar, K Shiva; Rambabu, D; Prasad, Bagineni; Mujahid, Mohammad; Krishna, G Rama; Rao, M V Basaveswara; Reddy, C Malla; Vanaja, G R; Kalle, Arunasree M; Pal, Manojit

2012-06-28

Regioselective construction of a fused 2-ylidene chromene ring was achieved for the first time by using AlCl(3)-induced C-C bond formation followed by Pd/C-Cu mediate coupling-cyclization strategy. A number of chromeno[4,3-b]quinoxaline derivatives were prepared by using this strategy. Single crystal X-ray diffraction study of a representative compound e.g. 6-(2,2-dimethylpropylidene)-4-methyl-6H-chromeno[4,3-b]quinoxalin-3-ol confirmed the presence of an exocyclic C-C double bond with Z-geometry. The crystal structure analysis and hydrogen bonding patterns of the same compound along with its structure elaboration via propargylation followed by Sonogashira coupling of the resulting terminal alkyne is presented. A probable mechanism for the formation of 2-ylidene chromene ring is discussed. Some of the compounds synthesized showed anticancer properties when tested in vitro.

Palladium-Catalyzed Carbon-Fluorine and Carbon-Hydrogen Bond Alumination of Fluoroarenes and Heteroarenes.

PubMed

Chen, Wenyi; Hooper, Thomas N; Ng, Jamues; White, Andrew J P; Crimmin, Mark R

2017-10-02

Through serendipitous discovery, a palladium bis(phosphine) complex was identified as a catalyst for the selective transformation of sp 2 C-F and sp 2 C-H bonds of fluoroarenes and heteroarenes to sp 2 C-Al bonds (19 examples, 1 mol % Pd loading). The carbon-fluorine bond functionalization reaction is highly selective for the formation of organoaluminium products in preference to hydrodefluorination products (selectivity=4.4:1 to 27:1). Evidence is presented for a tandem catalytic process in which hydrodefluorination is followed by sp 2 C-H alumination. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mini-Review: Ergothioneine and Ovothiol Biosyntheses, an Unprecedented Trans-Sulfur Strategy in Natural Product Biosynthesis.

PubMed

Naowarojna, Nathchar; Cheng, Ronghai; Chen, Li; Quill, Melissa; Xu, Meiling; Zhao, Changming; Liu, Pinghua

2018-06-19

As one of the most abundant elements on earth, sulfur is part of many small molecular metabolites and is key to their biological activities. Over the past few decades, some general strategies have been discovered for the incorporation of sulfur into natural products. In this review, we summarize recent efforts in elucidating the biosynthetic details for two sulfur-containing metabolites, ergothioneine and ovothiol. Their biosyntheses involve an unprecedented trans-sulfur strategy, a combination of a mononuclear non-heme iron enzyme-catalyzed oxidative C-S bond formation reaction and a PLP enzyme-mediated C-S lyase reaction.

Crystal structures of 5-amino-N-phenyl-3H-1,2,4-di-thia-zol-3-iminium chloride and 5-amino-N-(4-chloro-phen-yl)-3H-1,2,4-di-thia-zol-3-iminium chloride monohydrate.

PubMed

Yeo, Chien Ing; Tan, Yee Seng; Tiekink, Edward R T

2015-10-01

The crystal and mol-ecular structures of the title salt, C8H8N3S2 (+)·Cl(-), (I), and salt hydrate, C8H7ClN3S2 (+)·Cl(-)·H2O, (II), are described. The heterocyclic ring in (I) is statistically planar and forms a dihedral angle of 9.05 (12)° with the pendant phenyl ring. The comparable angle in (II) is 15.60 (12)°, indicating a greater twist in this cation. An evaluation of the bond lengths in the H2N-C-N-C-N sequence of each cation indicates significant delocalization of π-electron density over these atoms. The common feature of the crystal packing in (I) and (II) is the formation of charge-assisted amino-N-H⋯Cl(-) hydrogen bonds, leading to helical chains in (I) and zigzag chains in (II). In (I), these are linked by chains mediated by charge-assisted iminium-N(+)-H⋯Cl(-) hydrogen bonds into a three-dimensional architecture. In (II), the chains are linked into a layer by charge-assisted water-O-H⋯Cl(-) and water-O-H⋯O(water) hydrogen bonds with charge-assisted iminium-N(+)-H⋯O(water) hydrogen bonds providing the connections between the layers to generate the three-dimensional packing. In (II), the chloride anion and water mol-ecules are resolved into two proximate sites with the major component being present with a site occupancy factor of 0.9327 (18).

Two-Center/Three-Electron Sigma Half-Bonds in Main Group and Transition Metal Chemistry.

PubMed

Berry, John F

2016-01-19

First proposed in a classic Linus Pauling paper, the two-center/three-electron (2c/3e) σ half-bond challenges the extremes of what may or may not be considered a chemical bond. Two electrons occupying a σ bonding orbital and one electron occupying the antibonding σ* orbital results in bond orders of ∼0.5 that are characteristic of metastable and exotic species, epitomized in the fleetingly stable He2(+) ion. In this Account, I describe the use of coordination chemistry to stabilize such fugacious three-electron bonded species at disparate ends of the periodic table. A recent emphasis in the chemistry of metal-metal bonds has been to prepare compounds with extremely short metal-metal distances and high metal-metal bond orders. But similar chemistry can be used to explore metal-metal bond orders less than one, including 2c/3e half-bonds. Bimetallic compounds in the Ni2(II,III) and Pd2(II,III) oxidation states were originally examined in the 1980s, but the evidence collected at that time suggested that they did not contain 2c/3e σ bonds. Both classes of compounds have been re-examined using EPR spectroscopy and modern computational methods that show the unpaired electron of each compound to occupy a M-M σ* orbital, consistent with 2c/3e Ni-Ni and Pd-Pd σ half-bonds. Elsewhere on the periodic table, a seemingly unrelated compound containing a trigonal bipyramidal Cu3S2 core caused a stir, leaving prominent theorists at odds with one another as to whether the compound contains a S-S bond. Due to my previous experience with 2c/3e metal-metal bonds, I suggested that the Cu3S2 compound could contain a 2c/3e S-S σ half-bond in the previously unknown oxidation state of S2(3-). By use of the Cambridge Database, a number of other known compounds were identified as potentially containing S2(3-) ligands, including a noteworthy set of cyclopentadienyl-supported compounds possessing diamond-shaped Ni2E2 units with E = S, Se, and Te. These compounds were subjected to extensive studies using X-ray absorption spectroscopy, X-ray photoelectron spectroscopy, density functional theory, and wave function-based computational methods, as well as chemical oxidation and reduction. The compounds contain E-E 2c/3e σ half-bonds and unprecedented E2(3-) "subchalcogenide" ligands, ushering in a new oxidation state paradigm for transition metal-chalcogen chemistry.

Cocrystal assembled by 1,4-diiodotetrafluorobenzene and phenothiazine based on C-I...π/N/S halogen bond and other assisting interactions.

PubMed

Wang, Hui; Jin, Wei Jun

2017-04-01

The halogen-bonded cocrystal of 1,4-diiodotetrafluorobenzene (1,4-DITFB) with the butterfly-shape non-planar heterocyclic compound phenothiazine (PHT) was successfully assembled by the conventional solution-based method. X-ray single-crystal diffraction analysis reveals a 3:2 stoichiometric ratio for the cocrystal (1,4-DITFB/PHT), and the cocrystal structure is constructed via C-I...π, C-I...N and C-I...S halogen bonds as well as other assisting interactions (e.g. C-H...F/S hydrogen bond, C-H...H-C and C-F...F-C bonds). The small shift of the 1,4-DITFB vibrational band to lower frequencies in FT-IR and Raman spectroscopies provide evidence to confirm the existence of the halogen bond. In addition, the non-planarity of the PHT molecule in the cocrystal results in PHT emitting weak phosphorescence and relatively strong delayed fluorescence. Thus, a wide range of delayed fluorescence and weak phosphorescence could play a significant role in selecting a proper π-conjugated system to engineer functional cocrystal and luminescent materials by halogen bonds.

1,1,1-tris(hydroxymethyl)ethane as a new, efficient, and versatile tripod ligand for copper-catalyzed cross-coupling reactions of aryl iodides with amides, thiols, and phenols.

PubMed

Chen, Yao-Jung; Chen, Hsin-Hung

2006-11-23

1,1,1-tris(hydroxymethyl)ethane was presented as a new, efficient, and versatile tridentate O-donor ligand suitable for the copper-catalyzed formation of C-N, C-S, and C-O bonds. This inexpensive and commercially available tripod ligand has been demonstrated to facilitate the copper-catalyzed cross-coupling reactions of aryl iodides with amides, thiols, and phenols to afford the corresponding desired products in good to excellent yields. [reaction: see text].

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

Catalytic RNA and synthesis of the peptide bond

NASA Technical Reports Server (NTRS)

Usher, D. A.; Kozlowski, M.; Zou, X.

1991-01-01

We are studying whether the L-19 IVS ribozyme from Tetrahymena thermophila can catalyze the formation of the peptide bond when it is supplied with synthetic aminoacyl oligonucleotides. If this reaction works, it could give us some insight into the mechanism of peptide bond formation and the origin of coded protein synthesis. Two short oligoribonucleotides, CCCCC and a protected form of CCCCU were prepared; the former was made by the controlled hydrolysis of Poly(C), and the later by multistep chemical synthesis from the protected monomers. The homopentamer was then aminocylated using C-14 labelled Boc-protected glycine imidazolide. This aminoacylated oligo-nucleotide has now been shown to enter the active site of the L-19 IVS, and aminoacyl transfer, and peptide bond formation reactions are being sought. Our synthesis of CCCCU made us aware of the inadequacy of many of the 2'- hydroxyl protecting groups that are in use today and we therefore designed a new 2'- protecting group that is presently being tested.

Analysis of the vibronic structure of the trans-stilbene fluorescence and excitation spectra: the S0 and S1 PES along the Ce[double bond, length as m-dash]Ce and Ce-Cph torsions.

PubMed

Orlandi, Giorgio; Garavelli, Marco; Zerbetto, Francesco

2017-09-20

We analyze the highly resolved vibronic structure of the low energy (≤200 cm -1 ) region of the fluorescence and fluorescence excitation spectra of trans-stilbene in supersonic beams. In this spectral region the vibronic structure is associated mainly with vibrational levels of the C e -C e torsion (τ) and the a u combination of the two C e -C ph bond twisting (ϕ). We base this analysis on the well-established S 0 (τ, ϕ) two-dimensional potential energy surface (PES) and on a newly refined S 1 (τ, ϕ) PES. We obtain vibrational eigenvalues and eigenvectors of the anharmonic S 0 (τ, ϕ) and S 1 (τ, ϕ) PES using a numerical procedure based on the Meyer's flexible model [R. Meyer, J. Mol. Spectrosc., 1979, 76, 266]. Then we derive Franck-Condon factors and therefore intensities of the relevant vibronic bands for the S 0 → S 1 excitation and S 1 → S 0 fluorescence spectra. Furthermore, we assess the role of the b g combination of the two C e -C ph bond twisting (ν 48 ) in the structure of the S 1 → S 0 fluorescence spectra. By the use of these results we are able to assign most of the low energy vibrational levels of the S 0 → S 1 excitation spectra and of the fluorescence spectra of the emission from several low energy S 1 vibronic levels. The good agreement between the observed and the computed vibrational structure of the S 0 → S 1 and S 1 → S 0 spectra suggests that the proposed picture of the E 1 (τ, ϕ) and E 0 (τ, ϕ) PES, in particular along the coordinate τ governing trans-cis photo-isomerization in S 1 , is accurate. In S 0 , the barriers for the C e [double bond, length as m-dash]C e torsion and for the a u type C e -C ph bond twisting are 16 080 cm -1 and 3125 cm -1 , respectively, while in S 1 , where the bond orders of the C e [double bond, length as m-dash]C e and C e -C ph bonds are reversed, the two barriers become 1350 cm -1 and 8780 cm -1 , respectively.

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.

Recent advances in copper-catalyzed asymmetric coupling reactions

PubMed Central

2015-01-01

Summary Copper-catalyzed (or -mediated) asymmetric coupling reactions have received significant attention over the past few years. Especially the coupling reactions of aryl or alkyl halides with nucleophiles became a very powerful tool for the formation of C–C, C–N, C–O and other carbon–heteroatom bonds as well as for the construction of heteroatom-containing ring systems. This review summarizes the recent progress in copper-catalyzed asymmetric coupling reactions for the formation of C–C and carbon–heteroatom bonds. PMID:26734106

The bond of different post materials to a resin composite cement and a resin composite core material.

PubMed

Stewardson, D; Shortall, A; Marquis, P

2012-01-01

To investigate the bond of endodontic post materials, with and without grit blasting, to a resin composite cement and a core material using push-out bond strength tests. Fiber-reinforced composite (FRC) posts containing carbon (C) or glass (A) fiber and a steel (S) post were cemented into cylinders of polymerized restorative composite without surface treatment (as controls) and after grit blasting for 8, 16, and 32 seconds. Additional steel post samples were sputter-coated with gold before cementation to prevent chemical interaction with the cement. Cylindrical composite cores were bonded to other samples. After sectioning into discs, bond strengths were determined using push-out testing. Profilometry and electron microscopy were used to assess the effect of grit blasting on surface topography. Mean (standard deviation) bond strength values (MPa) for untreated posts to resin cement were 8.41 (2.80) for C, 9.61(1.88) for A, and 19.90 (3.61) for S. Prolonged grit blasting increased bond strength for FRC posts but produced only a minimal increase for S. After 32 seconds, mean values were 20.65 (4.91) for C, 20.41 (2.93) for A, and 22.97 (2.87) for S. Gold-coated steel samples produced the lowest bond strength value, 7.84 (1.40). Mean bond strengths for untreated posts bonded to composite cores were 6.19 (0.95) for C, 13.22 (1.61) for A, and 8.82 (1.18) for S, and after 32 seconds of grit blasting the values were 17.30 (2.02) for C, 26.47 (3.09) for A, and 20.61 (2.67) for S. FRC materials recorded higher roughness values before and after grit blasting than S. With prolonged grit blasting, roughness increased for A and C, but not for S. There was no evidence of significant bonding to untreated FRC posts, but significant bonding occurred between untreated steel posts and the resin cement. Increases in the roughness of FRC samples were material dependent and roughening significantly increased bond strength values (p<0.05). Surface roughening of the tested FRC posts is required for effective bonding.

Development of a QSAR model for predicting aqueous reaction rate constants of organic chemicals with hydroxyl radicals.

PubMed

Luo, Xiang; Yang, Xianhai; Qiao, Xianliang; Wang, Ya; Chen, Jingwen; Wei, Xiaoxuan; Peijnenburg, Willie J G M

2017-03-22

Reaction with hydroxyl radicals (˙OH) is an important removal pathway for organic pollutants in the aquatic environment. The aqueous reaction rate constant (k OH ) is therefore an important parameter for fate assessment of aquatic pollutants. Since experimental determination fails to meet the requirement of being able to efficiently handle numerous organic chemicals at limited cost and within a relatively short period of time, in silico methods such as quantitative structure-activity relationship (QSAR) models are needed to predict k OH . In this study, a QSAR model with a larger and wider applicability domain as compared with existing models was developed. Following the guidelines for the development and validation of QSAR models proposed by the Organization for Economic Co-operation and Development (OECD), the model shows satisfactory performance. The applicability domain of the model has been extended and contained chemicals that have rarely been covered in most previous studies. The chemicals covered in the current model contain functional groups including [double bond splayed left]C[double bond, length as m-dash]C[double bond splayed right], -C[triple bond, length as m-dash]C-, -C 6 H 5 , -OH, -CHO, -O-, [double bond splayed left]C[double bond, length as m-dash]O, -C[double bond, length as m-dash]O(O)-, -COOH, -C[triple bond, length as m-dash]N, [double bond splayed left]N-, -NH 2 , -NH-C(O)-, -NO 2 , -N[double bond, length as m-dash]C-N[double bond splayed right], [double bond splayed left]N-N[double bond splayed right], -N[double bond, length as m-dash]N-, -S-, -S-S-, -SH, -SO 3 , -SO 4 , -PO 4 , and -X (F, Cl, Br, and I).

A novel disulfide bond in the SH2 Domain of the C-terminal Src kinase controls catalytic activity.

PubMed

Mills, Jamie E; Whitford, Paul C; Shaffer, Jennifer; Onuchic, Jose N; Adams, Joseph A; Jennings, Patricia A

2007-02-02

The SH2 domain of the C-terminal Src kinase [Csk] contains a unique disulfide bond that is not present in other known SH2 domains. To investigate whether this unusual disulfide bond serves a novel function, the effects of disulfide bond formation on catalytic activity of the full-length protein and on the structure of the SH2 domain were investigated. The kinase activity of full-length Csk decreases by an order of magnitude upon formation of the disulfide bond in the distal SH2 domain. NMR spectra of the fully oxidized and fully reduced SH2 domains exhibit similar chemical shift patterns and are indicative of similar, well-defined tertiary structures. The solvent-accessible disulfide bond in the isolated SH2 domain is highly stable and far from the small lobe of the kinase domain. However, reduction of this bond results in chemical shift changes of resonances that map to a cluster of residues that extend from the disulfide bond across the molecule to a surface that is in direct contact with the small lobe of the kinase domain in the intact molecule. Normal mode analyses and molecular dynamics calculations suggest that disulfide bond formation has large effects on residues within the kinase domain, most notably within the active-site cleft. Overall, the data indicate that reversible cross-linking of two cysteine residues in the SH2 domain greatly impacts catalytic function and interdomain communication in Csk.

Laboratory spectroscopic analyses of electron irradiated alkanes and alkenes in solar system ices

NASA Astrophysics Data System (ADS)

Hand, K. P.; Carlson, R. W.

2012-03-01

We report results from laboratory experiments of 10 keV electron irradiation of thin ice films of water and short-chain hydrocarbons at ˜10-8 Torr and temperatures ranging from 70-100 K. Hydrocarbon mixtures include water with C3H8, C3H6, C4H10 (butane and isobutane), and C4H8, (1-butene and cis/trans-2-butene). The double bonds of the alkenes in our initial mixtures were rapidly destroyed or converted to single carbon bonds, covalent bonds with hydrogen, bonds with -OH (hydroxyl), bonds with oxygen (C-O), or double bonds with oxygen (carbonyl). Spectra resulting from irradiation of alkane and alkene ices are largely indistinguishable; the initial differences in film composition are destroyed and the resulting mixture includes long-chain, branched aliphatics, aldehydes, ketones, esters, and alcohols. Methane was observed as a product during radiolysis but CO was largely absent. We find that while some of the carbon is oxidized and lost to CO2 formation, some carbon is sequestered into highly refractory, long-chain aliphatic compounds that remain as a thin residue even after the ice film has been raised to standard temperature and pressure. We conclude that the high availability of hydrogen in our experiments leads to the formation of the formyl radical which then serves as the precursor for formaldehyde and polymerization of longer hydrocarbon chains.

Structural and Biochemical Analyses Reveal the Mechanism of Glutathione S-Transferase Pi 1 Inhibition by the Anti-cancer Compound Piperlongumine.

PubMed

Harshbarger, Wayne; Gondi, Sudershan; Ficarro, Scott B; Hunter, John; Udayakumar, Durga; Gurbani, Deepak; Singer, William D; Liu, Yan; Li, Lianbo; Marto, Jarrod A; Westover, Kenneth D

2017-01-06

Glutathione S-transferase pi 1 (GSTP1) is frequently overexpressed in cancerous tumors and is a putative target of the plant compound piperlongumine (PL), which contains two reactive olefins and inhibits proliferation in cancer cells but not normal cells. PL exposure of cancer cells results in increased reactive oxygen species and decreased GSH. These data in tandem with other information led to the conclusion that PL inhibits GSTP1, which forms covalent bonds between GSH and various electrophilic compounds, through covalent adduct formation at the C7-C8 olefin of PL, whereas the C2-C3 olefin of PL was postulated to react with GSH. However, direct evidence for this mechanism has been lacking. To investigate, we solved the X-ray crystal structure of GSTP1 bound to PL and GSH at 1.1 Å resolution to rationalize previously reported structure activity relationship studies. Surprisingly, the structure showed that a hydrolysis product of PL (hPL) was conjugated to glutathione at the C7-C8 olefin, and this complex was bound to the active site of GSTP1; no covalent bond formation between hPL and GSTP1 was observed. Mass spectrometry (MS) analysis of the reactions between PL and GSTP1 confirmed that PL does not label GSTP1. Moreover, MS data also indicated that nucleophilic attack on PL at the C2-C3 olefin led to PL hydrolysis. Although hPL inhibits GSTP1 enzymatic activity in vitro, treatment of cells susceptible to PL with hPL did not have significant anti-proliferative effects, suggesting that hPL is not membrane-permeable. Altogether, our data suggest a model wherein PL is a prodrug whose intracellular hydrolysis initiates the formation of the hPL-GSH conjugate, which blocks the active site of and inhibits GSTP1 and thereby cancer cell proliferation. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Structural and Biochemical Analyses Reveal the Mechanism of Glutathione S-Transferase Pi 1 Inhibition by the Anti-cancer Compound Piperlongumine*

PubMed Central

Harshbarger, Wayne; Gondi, Sudershan; Ficarro, Scott B.; Hunter, John; Udayakumar, Durga; Gurbani, Deepak; Singer, William D.; Liu, Yan; Li, Lianbo; Marto, Jarrod A.; Westover, Kenneth D.

2017-01-01

Glutathione S-transferase pi 1 (GSTP1) is frequently overexpressed in cancerous tumors and is a putative target of the plant compound piperlongumine (PL), which contains two reactive olefins and inhibits proliferation in cancer cells but not normal cells. PL exposure of cancer cells results in increased reactive oxygen species and decreased GSH. These data in tandem with other information led to the conclusion that PL inhibits GSTP1, which forms covalent bonds between GSH and various electrophilic compounds, through covalent adduct formation at the C7-C8 olefin of PL, whereas the C2-C3 olefin of PL was postulated to react with GSH. However, direct evidence for this mechanism has been lacking. To investigate, we solved the X-ray crystal structure of GSTP1 bound to PL and GSH at 1.1 Å resolution to rationalize previously reported structure activity relationship studies. Surprisingly, the structure showed that a hydrolysis product of PL (hPL) was conjugated to glutathione at the C7-C8 olefin, and this complex was bound to the active site of GSTP1; no covalent bond formation between hPL and GSTP1 was observed. Mass spectrometry (MS) analysis of the reactions between PL and GSTP1 confirmed that PL does not label GSTP1. Moreover, MS data also indicated that nucleophilic attack on PL at the C2-C3 olefin led to PL hydrolysis. Although hPL inhibits GSTP1 enzymatic activity in vitro, treatment of cells susceptible to PL with hPL did not have significant anti-proliferative effects, suggesting that hPL is not membrane-permeable. Altogether, our data suggest a model wherein PL is a prodrug whose intracellular hydrolysis initiates the formation of the hPL-GSH conjugate, which blocks the active site of and inhibits GSTP1 and thereby cancer cell proliferation. PMID:27872191

Biocatalytic organic synthesis of optically pure (S)-scoulerine and berbine and benzylisoquinoline alkaloids.

PubMed

Schrittwieser, Joerg H; Resch, Verena; Wallner, Silvia; Lienhart, Wolf-Dieter; Sattler, Johann H; Resch, Jasmin; Macheroux, Peter; Kroutil, Wolfgang

2011-08-19

A chemoenzymatic approach for the asymmetric total synthesis of the title compounds is described that employs an enantioselective oxidative C-C bond formation catalyzed by berberine bridge enzyme (BBE) in the asymmetric key step. This unique reaction yielded enantiomerically pure (R)-benzylisoquinoline derivatives and (S)-berbines such as the natural product (S)-scoulerine, a sedative and muscle relaxing agent. The racemic substrates rac-1 required for the biotransformation were prepared in 4-8 linear steps using either a Bischler-Napieralski cyclization or a C1-Cα alkylation approach. The chemoenzymatic synthesis was applied to the preparation of fourteen enantiomerically pure alkaloids, including the natural products (S)-scoulerine and (R)-reticuline, and gave overall yields of up to 20% over 5-9 linear steps.

NMR Spectroscopy and Structural Characterization of Dithiophosphinates Relevant to Minor Actinide Extraction Processes

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

Scott R. Daly; Kevin S. Boland; John R. Klaehn

2012-02-01

Synthetic routes to alkyl and aryl substituted dithiophosphinate salts that contain non-coordinating PPh{sub 4}{sup 1+} counter cations are reported. In general, these compounds can be prepared via a multi-step procedure that starts with reacting secondary phosphines, i.e. HPR{sub 2}, with two equivalents elemental S. This transformation proceeds in two steps - first oxidation of the phosphine and second insertion of S into the H-P bond - and has been used to synthesize a series of dithiophoshinic acids, which were fully characterized, namely HS{sub 2}P(p-CF{sub 3}C{sub 6}H{sub 4}){sub 2}, HS{sub 2}P(m-CF{sub 3}C{sub 6}H{sub 4}){sub 2}, HS{sub 2}P(o-MeC{sub 6}H{sub 4}){sub 2}, andmore » HS{sub 2}P(o-MeOC{sub 6}H{sub 4}){sub 2}. Although the insertion step was found to be much slower than the oxidation reaction, the formation of (NH{sub 4})S{sub 2}PR{sub 2} from HPSR{sub 2} occurs almost instantaneous upon addition of NH{sub 4}OH. Subsequent cation exchange reactions proceed readily with PPh{sub 4}Cl in water, under air, and at ambient conditions to provide analytically pure samples of [PPh{sub 4}][S{sub 2}PR{sub 2}] (R = p-CF{sub 3}C{sub 6}H{sub 4}, m-CF{sub 3}C{sub 6}H{sub 4}, o-CF{sub 3}C{sub 6}H{sub 4}, o-MeC{sub 6}H{sub 4}, o-MeOC{sub 6}H{sub 4}, Ph, and Me, 1b-7b, respectively), which were characterized by elemental analysis, multinuclear NMR, and IR spectroscopy. In addition the S{sub 2}PMe{sub 2}{sup 1-}, S{sub 2}PPh{sub 2}{sup 1-}, and dithiophosphinates with ortho-substituted arene rings were characterized by X-ray crystallography. Structural analysis show that, as opposed to the acids which have short P=S double bonds and long P-SH single bonds, the metric parameters for the S atoms in S{sub 2}PR{sub 2}{sup 1-} are equivalent. In addition, the presence of large non-coordinating PPh{sub 4}{sup 1+} cations guard against intermolecular P-S {hor_ellipsis} X interactions and insure that the P-S bond is isolated. Overall, this synthetic procedure provides high-purity S{sub 2}PR{sub 2}{sup 1-} compounds necessary for subsequent spectroscopic and theoretical studies.« less

In search of efficient 5-endo-dig cyclization of a carbon-centered radical: 40 years from a prediction to another success for the Baldwin rules.

PubMed

Alabugin, Igor V; Timokhin, Vitaliy I; Abrams, Jason N; Manoharan, Mariappan; Abrams, Rachel; Ghiviriga, Ion

2008-08-20

Despite being predicted to be stereoelectronically favorable by the Baldwin rules, efficient formation of a C-C bond through a 5-endo-dig radical cyclization remained unknown for more than 40 years. This work reports a remarkable increase in the efficiency of this process upon beta-Ts substitution, which led to the development of an expedient approach to densely functionalized cyclic 1,3-dienes. Good qualitative agreement between the increased efficiency and stereoselectivity for the 5-endo-dig cyclization of Ts-substituted vinyl radicals and the results of density functional theory analysis further confirms the utility of computational methods in the design of new radical processes. Although reactions of Br atoms generated through photochemical Ts-Br bond homolysis lead to the formation of cyclic dibromide side products, the yields of target bromosulfones in the photochemically induced reactions can be increased by recycling the dibromide byproduct into the target bromosulfones through a sequence of addition/elimination reactions at the exocyclic double bond. Discovery of a relatively efficient radical 5-endo-dig closure, accompanied by a C-C bond formation, provides further support to stereoelectronic considerations at the heart of the Baldwin rules and fills one of the last remaining gaps in the arsenal of radical cyclizations.

Ethylene Glycol Adsorption and Reaction over CeOX(111) Thin Films

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

Mullins, David R; Chen, Tsung-Liang

2011-01-01

This study reports the interaction of ethylene glycol with well-ordered CeO{sub x}(111) thin film surfaces. Ethylene glycol initially adsorbs on fully oxidized CeO{sub 2}(111) and reduced CeO{sub 2-x}(111) through the formation of one C-O-Ce bond and then forms a second alkoxy bond after annealing. On fully oxidized CeO{sub 2}(111) both recombination of ethylene glycol and water desorption occur at low temperature leaving stable -OCH{sub 2}CH{sub 2}O- (ethylenedioxy) intermediates and oxygen vacancies on the surface. This ethylenedioxy intermediate goes through C-C bond scission to produce formate species which then react to produce CO and CO{sub 2}. The formation of water resultsmore » in the reduction of the ceria. On a reduced CeO{sub 2-x}(111) surface the reaction selectivity shifts toward a dehydration process. The ethylenedioxy intermediate decomposes by breaking a C-O bond and converts into an enolate species. Similar to the reaction of acetaldehyde on reduced CeO{sub 2-x}(111), the enolate reacts to produce acetaldehyde, acetylene, and ethylene. The loss of O from ethylene glycol leads to a small amount of oxidation of the reduced ceria.« less

Ethylene Glycol Adsorption and Reaction over CeOX(111) Thin Films

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

T Chen; D Mullins

2011-12-31

This study reports the interaction of ethylene glycol with well-ordered CeO{sub x}(111) thin film surfaces. Ethylene glycol initially adsorbs on fully oxidized CeO{sub 2}(111) and reduced CeO{sub 2-x}(111) through the formation of one C-O-Ce bond and then forms a second alkoxy bond after annealing. On fully oxidized CeO{sub 2}(111) both recombination of ethylene glycol and water desorption occur at low temperature leaving stable -OCH{sub 2}CH{sub 2}O- (ethylenedioxy) intermediates and oxygen vacancies on the surface. This ethylenedioxy intermediate goes through C-C bond scission to produce formate species which then react to produce CO and CO{sub 2}. The formation of water resultsmore » in the reduction of the ceria. On a reduced CeO{sub 2-x}(111) surface the reaction selectivity shifts toward a dehydration process. The ethylenedioxy intermediate decomposes by breaking a C-O bond and converts into an enolate species. Similar to the reaction of acetaldehyde on reduced CeO{sub 2-x}(111), the enolate reacts to produce acetaldehyde, acetylene, and ethylene. The loss of O from ethylene glycol leads to a small amount of oxidation of the reduced ceria.« less

Role of disulphide bonds in a thermophilic serine protease aqualysin I from Thermus aquaticus YT-1.

PubMed

Sakaguchi, Masayoshi; Takezawa, Makoto; Nakazawa, Rie; Nozawa, Kazutaka; Kusakawa, Taro; Nagasawa, Takeshi; Sugahara, Yasusato; Kawakita, Masao

2008-05-01

A thermophilic serine protease, Aqualysin I, from Thermus aquaticus YT-1 has two disulphide bonds, which are also found in a psychrophilic serine protease from Vibrio sp. PA-44 and a proteinase K-like enzyme from Serratia sp. at corresponding positions. To understand the significance of these disulphide bonds in aqualysin I, we prepared mutants C99S, C194S and C99S/C194S (WSS), in which Cys69-Cys99, Cys163-Cys194 and both of these disulphide bonds, respectively, were disrupted by replacing Cys residues with Ser residues. All mutants were expressed stably in Escherichia coli. The C99S mutant was 68% as active as the wild-type enzyme at 40 degrees C in terms of k(cat) value, while C194S and WSS were only 6 and 3%, respectively, as active, indicating that disulphide bond Cys163-Cys194 is critically important for maintaining proper catalytic site conformation. Mutants C194S and WSS were less thermostable than wild-type enzyme, with a half-life at 90 degrees C of 10 min as compared to 45 min of the latter and with transition temperatures on differential scanning calorimetry of 86.7 degrees C and 86.9 degrees C, respectively. Mutant C99S was almost as stable as the wild-type aqualysin I. These results indicate that the disulphide bond Cys163-Cys194 is more important for catalytic activity and conformational stability of aqualysin I than Cys67-Cys99.

Erosion and strength degradation of biomorphic SiC.

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

Martinez-Fernandez, J.; de Arellano-Lopez, A. R; Varela-Feria, F. M.

2004-05-01

Solid-particle-erosion studies were conducted on biomorphic SiC based on eucalyptus and pine, reaction-bonded (RB) SiC, and hot-pressed (HP) SiC. The erodents were angular SiC abrasives of average diameter 63, 143, or 390 {mu}m and the impact velocity was 100 m s{sup -1}. Impact occurred at normal incidence. Material loss in all targets occurred by brittle fracture. The biomorphic specimens eroded by formation of both lateral and radial cracks and their erosion rates were higher than both conventional SiCs. The RB SiC eroded as a classic brittle material, by formation and propagation of lateral cracks. The HP SiC, the hardest target,more » was the most erosion resistant. In erosion of the HP SiC, the abrasive particles, especially the largest ones, fragmented upon impact. The resulting dissipation of energy led to relatively low erosion rates. Flexural strength before and after erosion was measured for the biomorphic eucalyptus, RB SiC, and HP SiC. Erosion damage reduced the flexural strengths of all of the specimens. The relative strength reductions were lowest for the biomorphic eucalyptus and highest for the HP SiC. The hot-pressed SiC responded as predicted by accepted models of impact damage in brittle solids. The responses of the biomorphic and reaction-bonded SiC specimens were modeled as if they consisted of only SiC and porosity. This approximation agreed reasonably well with observed degradations of strength.« less

Blue- and Red-Shifting Hydrogen Bonding: A Gas Phase FTIR and Ab Initio Study of RR'CO···DCCl3 and RR'S···DCCl3 Complexes.

PubMed

Behera, B; Das, Puspendu K

2018-05-10

Blue-shifting H-bonded (C-D···O) complexes between CDCl 3 and CH 3 HCO, (CH 3 ) 2 CO, and C 2 H 5 (CH 3 )CO, and red-shifting H-bonded (C-D···S) complexes between CDCl 3 with (CH 3 ) 2 S and (C 2 H 5 ) 2 S have been identified by Fourier transform infrared spectroscopy in the gas phase at room temperature. With increasing partial pressure of the components, a new band appears in the C-D stretching region of the vibrational spectra. The intensity of this band decreases with an increase in temperature at constant pressure, which provides the basis for identification of the H-bonded bands in the spectrum. The C-D stretching frequency of CDCl 3 is blue-shifted by +7.1, +4, and +3.2 cm -1 upon complexation with CH 3 HCO, (CH 3 ) 2 CO, and C 2 H 5 (CH 3 )CO, respectively, and red-shifted by -14 and -19.2 cm -1 upon complexation with (CH 3 ) 2 S and (C 2 H 5 ) 2 S, respectively. By using quantum chemical calculations at the MP2/6-311++G** level, we predict the geometry, electronic structural parameters, binding energy, and spectral shift of H-bonded complexes between CDCl 3 and two series of compounds named RCOR' (H 2 CO, CH 3 HCO, (CH 3 ) 2 CO, and C 2 H 5 (CH 3 )CO) and RSR' (H 2 S, CH 3 HS, (CH 3 ) 2 S, and (C 2 H 5 ) 2 S) series. The calculated and observed spectral shifts follow the same trends. With an increase in basicity of the H-bond acceptor, the C-D bond length increases, force constant decreases, and the frequency shifts to the red from the blue. The potential energy scans of the above complexes are done, which show that electrostatic attraction between electropositive D and electron-rich O/S causes bond elongation and red shift, and the electronic and nuclear repulsions lead to bond contraction and blue shifts. The dominance of the two opposing forces at the equilibrium geometry of the complex determines the nature of the shift, which changes both in magnitude and in direction with the basicity of the hydrogen-bond acceptor.

Formation and Characterization of Silver Nanoparticle Composite with Poly(p-Br/F-phenylsilane).

PubMed

Roh, Sung-Hee; Noh, Ji Eun; Woo, Hee-Gweon; Cho, Myong-Shik; Sohn, Honglae

2015-02-01

The one-pot production and structural characterization of composites of silver nanoparticles with poly(p-Br/F-phenylsilane), Br/F-PPS, have been performed. The conversion of Ag+ ions to stable Ag0 nanoparticles is mediated by the copolymer Br/F-PPS having both possibly reactive Si-H bonds in the polymer backbone and C-Br bonds in the substituents along with relatively inert C-F bonds. Transmission electron microscopy and field emission scanning electron microscopy analyses show the formation of the composites where silver nanoparticles (less than 30 nm of size) are well dispersed over the Br/F-PPS matrix. X-ray diffraction patterns are consistent with that for face-centered-cubic typed silver. The polymer solubility in toluene implys that the cleavage of C-Br bond and the Si-F dative bonding may not be occurred appreciably at ambient temperature. Nonetheless, thermogravimetric analysis data suggest that some sort of cross-linking could take place at high temperature. Most of the silver particles undergo macroscopic aggregation without Br/F-PPS, which indicates that the polysilane is necessary for stabilizing the silver nanoparticles.

Influence of drying time and temperature on bond strength of contemporary adhesives to dentine.

PubMed

Garcia, Fernanda C P; Almeida, Júlio C F; Osorio, Raquel; Carvalho, Ricardo M; Toledano, Manuel

2009-04-01

To evaluate the bond strength (microTBS) of self-etching adhesives in different solvent evaporation conditions. Flat dentine surfaces from extracted human third molars were bonded with: (1) 2 two-steps self-etching adhesives (Clearfil SE Bond-CSEB); (Protect Bond-PB) and (2) 2 one-step self-etch systems (Adper Prompt L Pop-ADPLP); (Xeno III-XIII). Bonded dentine surfaces were air-dried for 5s, 20s, 30s or 40s at either 21 degrees C or 38 degrees C. Composite build-ups were constructed incrementally. After storage in water for 24h at 37 degrees C, the specimens were prepared for microtensile bond strength testing. Data were analyzed by two-way ANOVA and Student-Newman-Keuls at alpha=0.05. CSEB and PB performed better at warm temperature with only 20s of air-blowing. The bond strength increased when XIII was performed at warm temperature at 40s air-blowing. Extended air-blowing not affect the performance of ADPLP, except at 30s air-blowing time at warm temperature. The use of a warm air-dry stream seems to be a clinical tool to improve the bond strength to self-etching adhesives.

The mechanism of the formation of the hemiaminal and Schiff base from the benzaldehyde and triazole studied by means of the topological analysis of electron localisation function and catastrophe theory

NASA Astrophysics Data System (ADS)

Berski, Slawomir; Zbigniew Ciunik, Leszek

2015-04-01

The mechanisms of reaction of benzaldehyde (ald) with 4-amine-4H-1,2,4-triazole (4at), leading to Schiff base (Sch) and water, were investigated using topological analysis of the electron localisation function and catastrophe theory. Two reactions (synthesis of hemiaminal and synthesis of Schiff base) are represented by one catastrophe sequence: ald+4at: 1-14-[FF†F†FFTS1FF†F†FF†F†CF†]-2-9-[C†FFTS3F†F†FFF]-0:Sch+H2O with only fold (F) and cusp (C) catastrophes. The first reaction, in which a molecule of the hemiaminal is formed, consists of 14 steps separated by 13 catastrophes. The mechanism is non-concerted. The covalent bond C-N is formed after the formation of the O-H bond is terminated. The Schiff base formation through the water molecule elimination in the second reaction requires nine steps with eight catastrophes. The mechanism is non-concerted because first the C-O bond is broken and then the proton transfer occurs that results in the O-H bond creation.

New Redox Polymers that Exhibit Reversible Cleavage of Sulfur Bonds as Cathode Materials.

PubMed

Baloch, Marya; Ben Youcef, Hicham; Li, Chunmei; Garcia-Calvo, Oihane; Rodriguez, Lide M; Shanmukaraj, Devaraj; Rojo, Teofilo; Armand, Michel

2016-11-23

Two new cathode materials based on redox organosulfur polymers were synthesized and investigated for rechargeable lithium batteries as a proof-of-concept study. These cathodes offered good cycling performance owing to the absence of polysulfide solubility, which plagues Li/S systems. Herein, an aliphatic polyamine or a conjugated polyazomethine was used as the base to tether the redox-active species. The activity comes from the cleavage and formation of S-S or N-S bonds, which is made possible by the rigid conjugated backbone. The synthesized polymers were characterized through FTIR spectroscopy and thermogravimetric analysis (TGA). Galvanostatic measurements were performed to evaluate the discharge/charge cycles and characterize the performance of the lithium-based cells, which displayed initial discharge capacities of approximately 300 mA h g -1 at C/5 over 100 cycles with approximately 98 % Coulombic efficiency. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A frequent, GxxxG-mediated, transmembrane association motif is optimized for the formation of interhelical Cα–H hydrogen bonds

PubMed Central

Mueller, Benjamin K.; Subramaniam, Sabareesh; Senes, Alessandro

2014-01-01

Carbon hydrogen bonds between Cα–H donors and carbonyl acceptors are frequently observed between transmembrane helices (Cα–H···O=C). Networks of these interactions occur often at helix−helix interfaces mediated by GxxxG and similar patterns. Cα–H hydrogen bonds have been hypothesized to be important in membrane protein folding and association, but evidence that they are major determinants of helix association is still lacking. Here we present a comprehensive geometric analysis of homodimeric helices that demonstrates the existence of a single region in conformational space with high propensity for Cα–H···O=C hydrogen bond formation. This region corresponds to the most frequent motif for parallel dimers, GASright, whose best-known example is glycophorin A. The finding suggests a causal link between the high frequency of occurrence of GASright and its propensity for carbon hydrogen bond formation. Investigation of the sequence dependency of the motif determined that Gly residues are required at specific positions where only Gly can act as a donor with its “side chain” Hα. Gly also reduces the steric barrier for non-Gly amino acids at other positions to act as Cα donors, promoting the formation of cooperative hydrogen bonding networks. These findings offer a structural rationale for the occurrence of GxxxG patterns at the GASright interface. The analysis identified the conformational space and the sequence requirement of Cα–H···O=C mediated motifs; we took advantage of these results to develop a structural prediction method. The resulting program, CATM, predicts ab initio the known high-resolution structures of homodimeric GASright motifs at near-atomic level. PMID:24569864

A DFT investigation of a bulky biomimetic model catalyzing the 5'-outer ring deiodination of thyroxine.

PubMed

Fortino, Mariagrazia; Marino, Tiziana; Russo, Nino; Sicilia, Emilia

2016-12-01

This paper illustrates the outcomes of a density functional theory investigation aimed at unraveling mechanistic aspects of the 5'-outer ring deiodination process of thyroxine (T4) assisted by the sterically protected organoselenol compound BpqSeH. BpqSeH, which was previously synthesized and tested for its deiodinase activity, is able to afford the active hormone 3,5,3'-tetraiodothyronine (T3) by selective outer-ring deiodination of T4, and to protect the SeH moiety inside the nano-sized molecular cavity from further reactivity, allowing its isolation and characterization. Calculations were also performed including an imidazole ring that, mimicking a His residue in the active site of the original enzyme, plays an crucial role in deprotonating the selenol moiety. Both the suggested enol/keto tautomerization and the previously proven formation of an intermediate whose main characteristic is the presence of a Se⋯I⋯C halogen bond, were examined along the pathway leading to 5'-outer ring deiodination. The calculated potential energy surface showed that neither the pathway encompassing enol/keto tautomerism nor the formation of a halogen bond paving the way to C-I bond breaking and chalcogen-I bond forming is viable. The exergonic formation of the final selenenyl iodide product confirms the stabilization effect of the molecular cavity. Graphical Abstract Computed free energy profile describing the 5'-outer deiodination of thyroxine assisted by the steric hindered organoselenol BpqSH compound. The molecular electrostatic potential map reoported for the INT1 intermediate shows the non-covalent Se-I interaction, due to the attraction between charges of opposite sign, that weakens the C-I bond and prepares the formation of the new Se-I bond.

Microbial cleavage of organic C-S bonds

DOEpatents

Kilbane, J.J. II.

1994-10-25

A microbial process is described for selective cleavage of organic C-S bonds which may be used for reducing the sulfur content of sulfur-containing organic carbonaceous materials. Microorganisms of Rhodococcus rhodochrous and Bacillus sphaericus have been found which have the ability of selective cleavage of organic C-S bonds. Particularly preferred microorganisms are Rhodococcus rhodochrous strain ATCC 53968 and Bacillus sphaericus strain ATCC 53969 and their derivatives.

Microbial cleavage of organic C-S bonds

DOEpatents

Kilbane, II, John J.

1994-01-01

A microbial process for selective cleavage of organic C--S bonds which may be used for reducing the sulfur content of sulfur-containing organic carbonaceous materials, Microorganisms of Rhodococcus rhodochrous and Bacillus sphaericus have been found which have the ability of selective cleavage of organic C--S bonds. Particularly preferred microorganisms are Rhodococcus rhodochrous strain ATCC 53968 and Bacillus sphaericus strain ATCC 53969 and their derivatives.

Chemisorbed monolayers of corannulene penta-thioethers on gold.

PubMed

Angelova, Polina; Solel, Ephrath; Parvari, Galit; Turchanin, Andrey; Botoshansky, Mark; Gölzhäuser, Armin; Keinan, Ehud

2013-02-19

Penta(tert-butylthio)corannulene and penta(4-dimethylaminophenylthio)corannulene form highly stable monolayers on gold surfaces, as indicated by X-ray photoelectron spectroscopy (XPS). Formation of these homogeneous monolayers involves multivalent coordination of the five sulfur atoms to gold with the peripheral alkyl or aryl substituents pointing away from the surface. No dissociation of C-S bonds upon binding could be observed at room temperature. Yet, the XPS experiments reveal strong chemical bonding between the thioether groups and gold. Temperature-dependent XPS study shows that the thermal stability of the monolayers is higher than the typical stability of self-assembled monolayers (SAMs) of thiolates on gold.

Titanium Insertion into CO Bonds in Anionic Ti-CO2 Complexes.

PubMed

Dodson, Leah G; Thompson, Michael C; Weber, J Mathias

2018-03-22

We explore the structures of [Ti(CO 2 ) y ] - cluster anions using infrared photodissociation spectroscopy and quantum chemistry calculations. The existence of spectral signatures of metal carbonyl CO stretching modes shows that insertion of titanium atoms into C-O bonds represents an important reaction during the formation of these clusters. In addition to carbonyl groups, the infrared spectra show that the titanium center is coordinated to oxalato, carbonato, and oxo ligands, which form along with the metal carbonyls. The presence of a metal oxalato ligand promotes C-O bond insertion in these systems. These results highlight the affinity of titanium for C-O bond insertion processes.

Silica, Alumina and Clay Catalyzed Peptide Bond Formation: Enhanced Efficiency of Alumina Catalyst

NASA Astrophysics Data System (ADS)

Bujdák, Juraj; Rode, Bernd M.

1999-10-01

Catalytic efficiencies of clay (hectorite), silica and alumina were tested in peptide bond formation reactions of glycine (Gly), alanine (Ala), proline (Pro), valine (Val) and leucine (Leu). The reactions were performed as drying/wetting (hectorite) and temperature fluctuation (silica and alumina) experiments at 85 °C. The reactivity of amino acids decreased in order Gly > Ala > Pro ~ Val ~ Leu. The highest catalytic efficiency was observed for alumina, the only catalyst producing oligopeptides in all investigated reaction systems. The peptide bond formation on alumina is probably catalyzed by the same sites and via similar reaction mechanisms as some alumina-catalyzed dehydration reactions used in industrial chemistry.

The electronic donation and frequency shifts on the YCCH⋯BH4- boron-bonded complexes (Y = H, CH3, CF3 and CCl3)

NASA Astrophysics Data System (ADS)

Pordeus, Renato Q.; Rego, Danilo G.; Oliveira, Boaz G.

2015-06-01

In this theoretical work, the tetrahydroborate ion (BH4-) was used as proton acceptor in the formation of the YCC-H⋯BH4- complexes (Y = H, CH3, CCl3 and CF3). Using B3LYP/6-311++G(d,p) level of theory, the results of structure corroborate with the analyses of infrared spectra showing that the changes in the bond lengths are in good agreement with the frequency shifts of the HCC-H, H3CCC-H, Cl3CCC-H and F3CCC-H proton donors. Based on the calculations carried out by the Quantum Theory of Atoms in Molecules (QTAIM), the reductions of electronic density corroborate with the red shifts in the frequencies of the C-H bonds. In addition to that, the C-H bonds are polarized because the contributions of s orbital diminish whereas of p increase. In line with this, the variations on the atomic radii computed via QTAIM calculations show that carbon outweigh hydrogen as follows (ΔrC > ΔrH). This scenario is indirectly supported by the Bent's rule of the chemical bonding. Although the interaction energies (corrected with BSSE and ZPE) vary between -19 and -67 kJ mol-1, these complexes interact without covalent character.

The electronic donation and frequency shifts on the YCCH⋯BH₄⁻ boron-bonded complexes (Y=H, CH₃, CF₃ and CCl₃).

PubMed

Pordeus, Renato Q; Rego, Danilo G; Oliveira, Boaz G

2015-06-15

In this theoretical work, the tetrahydroborate ion (BH4(-)) was used as proton acceptor in the formation of the YCC-H⋯BH4(-) complexes (Y=H, CH3, CCl3 and CF3). Using B3LYP/6-311++G(d,p) level of theory, the results of structure corroborate with the analyses of infrared spectra showing that the changes in the bond lengths are in good agreement with the frequency shifts of the HCC-H, H3CCC-H, Cl3CCC-H and F3CCC-H proton donors. Based on the calculations carried out by the Quantum Theory of Atoms in Molecules (QTAIM), the reductions of electronic density corroborate with the red shifts in the frequencies of the C-H bonds. In addition to that, the C-H bonds are polarized because the contributions of s orbital diminish whereas of p increase. In line with this, the variations on the atomic radii computed via QTAIM calculations show that carbon outweigh hydrogen as follows (ΔrC>ΔrH). This scenario is indirectly supported by the Bent's rule of the chemical bonding. Although the interaction energies (corrected with BSSE and ZPE) vary between -19 and -67 kJ mol(-1), these complexes interact without covalent character. Copyright © 2015 Elsevier B.V. All rights reserved.

Un-catalyzed peptide bond formation between two monomers of glycine, alanine, serine, threonine, and aspartic acid in gas phase: a density functional theory study

NASA Astrophysics Data System (ADS)

Bhunia, Snehasis; Singh, Ajeet; Ojha, Animesh K.

2016-05-01

In the present report, un-catalyzed peptide bond formation between two monomers of glycine (Gly), alanine (Ala), serine (Ser), threonine (Thr), and aspartic acid (Asp) has been investigated in gas phase via two steps reaction mechanism and concerted mechanism at B3LYP/6-31G(d,p) and M062X/6-31G(d,p) level of theories. The peptide bond is formed through a nucleophilic reaction via transition states, TS1 and TS2 in stepwise mechanism. The TS1 reveals formation of a new C-N bond while TS2 illustrate the formation of C=O bond. In case of concerted mechanism, C-N bond is formed by a single four-centre transition state (TS3). The energy barrier is used to explain the involvement of energy at each step of the reaction. The energy barrier (20-48 kcal/mol) is required for the transformation of reactant state R1 to TS1 state and intermediate state I1 to TS2 state. The large value of energy barrier is explained in terms of distortion and interaction energies for stepwise mechanism. The energy barrier of TS3 in concerted mechanism is very close to the energy barrier of the first transition state (TS1) of the stepwise mechanism for the formation of Gly-Gly and Ala-Ala di- peptide. However, in case of Ser-Ser, Thr-Thr and Asp-Asp di-peptide, the energy barrier of TS3 is relatively high than that of the energy barrier of TS1 calculated at B3LYP/6-31G(d,p) and M062X/6-31G(d,p) level of theories. In both the mechanisms, the value of energy barrier calculated at B3LYP/6-31G(d,p) level of theory is greater than that of the value calculated at M062X/6-31G(d,p) level of theory.

C–C Bond formation catalyzed by natural gelatin and collagen proteins

PubMed Central

Kühbeck, Dennis; Bijayi Dhar, Basab; Schön, Eva-Maria; Cativiela, Carlos; Gotor-Fernández, Vicente

2013-01-01

Summary The activity of gelatin and collagen proteins towards C–C bond formation via Henry (nitroaldol) reaction between aldehydes and nitroalkanes is demonstrated for the first time. Among other variables, protein source, physical state and chemical modification influence product yield and kinetics, affording the nitroaldol products in both aqueous and organic media under mild conditions. Significantly, the scale-up of the process between 4-nitrobenzaldehyde and nitromethane is successfully achieved at 1 g scale and in good yield. A comparative kinetic study with other biocatalysts shows an increase of the first-order rate constant in the order chitosan < gelatin < bovine serum albumin (BSA) < collagen. The results of this study indicate that simple edible gelatin can promote C–C bond forming reactions under physiological conditions, which may have important implications from a metabolic perspective. PMID:23843902

A four-component coupling reaction of carbon dioxide, amines, cyclic ethers and 3-triflyloxybenzynes for the synthesis of functionalized carbamates.

PubMed

Xiong, Wenfang; Qi, Chaorong; Cheng, Ruixiang; Zhang, Hao; Wang, Lu; Yan, Donghao; Jiang, Huanfeng

2018-04-27

A novel four-component coupling reaction of carbon dioxide, amines, cyclic ethers and 3-triflyloxybenzynes has been developed for the first time, providing an efficient method for the synthesis of a series of functionalized carbamate derivatives in moderate to high yields. The process proceeds under mild, transition metal-free and fluoride-free conditions, leading to the formation of two new C-O bonds, one new C-N bond and one C-H bond in a single step.

Sol-gel dip coating of yttria-stabilized tetragonal zirconia dental ceramic by aluminosilicate nanocomposite as a novel technique to improve the bonding of veneering porcelain.

PubMed

Madani, Azamsadat; Nakhaei, Mohammadreza; Karami, Parisa; Rajabzadeh, Ghadir; Salehi, Sahar; Bagheri, Hossein

2016-01-01

The aim of this in vitro study was to evaluate the effect of silica and aluminosilicate nanocomposite coating of zirconia-based dental ceramic by a sol-gel dip-coating technique on the bond strength of veneering porcelain to the yttria-stabilized tetragonal zirconia polycrystal (Y-TZP) in vitro. Thirty Y-TZP blocks (10 mm ×10 mm ×3 mm) were prepared and were assigned to four experimental groups (n=10/group): C, without any further surface treatment as the control group; S, sandblasted using 110 μm alumina powder; Si, silica sol dip coating + calcination; and Si/Al, aluminosilicate sol dip coating + calcination. After preparing Y-TZP samples, a 3 mm thick layer of the recommended porcelain was fired on the coated Y-TZP surface. Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), scanning electron microscopy (SEM), and energy-dispersive X-ray analysis were used to characterize the coating and the nature of the bonding between the coating and zirconia. To examine the zirconia-porcelain bond strength, a microtensile bond strength (μTBS) approach was chosen. FT-IR study showed the formation of silica and aluminosilicate materials. XRD pattern showed the formation of new phases consisting of Si, Al, and Zr in coated samples. SEM showed the formation of a uniform coating on Y-TZP samples. Maximum μTBS values were obtained in aluminosilicate samples, which were significantly increased compared to control and sandblasted groups (P=0.013 and P<0.001, respectively). This study showed that aluminosilicate sol-gel dip coating can be considered as a convenient, less expensive reliable method for improving the bond strength between dental Y-TZP ceramics and veneering porcelain.

Sol–gel dip coating of yttria-stabilized tetragonal zirconia dental ceramic by aluminosilicate nanocomposite as a novel technique to improve the bonding of veneering porcelain

PubMed Central

Madani, Azamsadat; Nakhaei, Mohammadreza; Karami, Parisa; Rajabzadeh, Ghadir; Salehi, Sahar; Bagheri, Hossein

2016-01-01

The aim of this in vitro study was to evaluate the effect of silica and aluminosilicate nanocomposite coating of zirconia-based dental ceramic by a sol–gel dip-coating technique on the bond strength of veneering porcelain to the yttria-stabilized tetragonal zirconia polycrystal (Y-TZP) in vitro. Thirty Y-TZP blocks (10 mm ×10 mm ×3 mm) were prepared and were assigned to four experimental groups (n=10/group): C, without any further surface treatment as the control group; S, sandblasted using 110 μm alumina powder; Si, silica sol dip coating + calcination; and Si/Al, aluminosilicate sol dip coating + calcination. After preparing Y-TZP samples, a 3 mm thick layer of the recommended porcelain was fired on the coated Y-TZP surface. Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), scanning electron microscopy (SEM), and energy-dispersive X-ray analysis were used to characterize the coating and the nature of the bonding between the coating and zirconia. To examine the zirconia–porcelain bond strength, a microtensile bond strength (μTBS) approach was chosen. FT-IR study showed the formation of silica and aluminosilicate materials. XRD pattern showed the formation of new phases consisting of Si, Al, and Zr in coated samples. SEM showed the formation of a uniform coating on Y-TZP samples. Maximum μTBS values were obtained in aluminosilicate samples, which were significantly increased compared to control and sandblasted groups (P=0.013 and P<0.001, respectively). This study showed that aluminosilicate sol–gel dip coating can be considered as a convenient, less expensive reliable method for improving the bond strength between dental Y-TZP ceramics and veneering porcelain. PMID:27478376

(Z)-N,N-Dimethyl-2-[phen­yl(pyridin-2-yl)methyl­idene]hydrazinecarbothio­amide

PubMed Central

Jayakumar, K.; Sithambaresan, M.; Prathapachandra Kurup, M. R.

2011-01-01

The title compound, C15H16N4S, exists in the Z conformation with the thionyl S atom lying cis to the azomethine N atom. The shortening of the N—N distance [1.3697 (17) Å] is due to extensive delocalization with the pyridine ring. The hydrazine–carbothio­amide unit is almost planar, with a maximum deviation of 0.013 (2) Å for the amide N atom. The stability of this conformation is favoured by the formation of an intra­molecular N—H⋯N hydrogen bond. The packing of the mol­ecules involves no classical inter­molecular hydrogen-bonding inter­actions; however, a C—H⋯π inter­action occurs. PMID:22199715

Site-Specific Imaging of Elemental Steps in Dehydration of Diols on TiO 2(110)

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

Acharya, Danda P.; Yoon, Yeohoon; Li, Zhenjun

2013-11-26

The conversion of diols on partially reduced TiO 2(110) at low coverage was studied using variable-temperature scanning tunneling microscopy, temperature programmed desorption and density functional theory calculations. We find, that below ~230 K, ethane-1,2-diol and propane-1,3-diol molecules adsorb predominantly on five-fold coordinated Ti5c atoms. The dynamic equilibrium between molecularly bound and dissociated species resulting from O-H bond scission and reformation is observed. As the diols start to diffuse on the Ti5c rows above ~230 K, they dissociate irreversibly upon encountering bridging oxygen (O b) vacancy (VO’s) defects. Two dissociation pathways, one via O-H and the other via C-O bond scissionmore » leading to identical surface intermediates, hydroxyalkoxy, O b-(CH 2)n-OH (n = 2, 3) and bridging hydroxyl, HO b, are seen. For O-H bond scission, the O b-(CH 2)n-OH is found on the position of the original VO, while for C-O scission it is found on the adjacent Ob site. Theoretical calculations suggest that the observed mixture of C-O/O-H bond breaking processes are a result of the steric factors enforced upon the diols by the second OH group that is bound to a Ti5c site. At room temperature, rich dissociation/reformation dynamics of the second, Ti5c-bound O-H leads to the formation of dioxo, Ob-(CH 2)n-OTi, species. Above ~400 K, both O b-(CH 2)n-OH and Ob-(CH 2)n-OTi species convert into a new intermediate, that is centered on Ob row. Combined experimental and theoretical evidence shows that this intermediate is most likely a new dioxo, O b-(CH 2) 2-Ob, species. Further annealing leads to sequential C-Ob bond cleavage and alkene desorption above ~ 500 K. Simulations find that the sequential C-O bond breaking process follows a homolytic diradical pathway with the first C-O bond breaking event accompanied by a non-adiabatic electron transfer within the TiO 2(110) substrate.« less

Structural requirements of cholesterol for binding to Vibrio cholerae hemolysin.

PubMed

Ikigai, Hajime; Otsuru, Hiroshi; Yamamoto, Koichiro; Shimamura, Tadakatsu

2006-01-01

Cholesterol is necessary for the conversion of Vibrio cholerae hemolysin (VCH) monomers into oligomers in liposome membranes. Using different sterols, we determined the stereochemical structures of the VCH-binding active groups present in cholesterol. The VCH monomers are bound to cholesterol, diosgenin, campesterol, and ergosterol, which have a hydroxyl group at position C-3 (3betaOH) in the A ring and a C-C double bond between positions C-5 and C-6 (C-C Delta(5)) in the B ring. They are not bound to epicholesterol and dihydrocholesterol, which form a covalent link with a 3alphaOH group and a C-C single bond between positions C-5 and C-6, respectively. This result suggests that the 3betaOH group and the C-CDelta(5) bond in cholesterol are required for VCH monomer binding. We further examined VCH oligomer binding to cholesterol. However, this oligomer did not bind to cholesterol, suggesting that the disappearance of the cholesterol-binding potential of the VCH oligomer might be a result of the conformational change caused by the conversion of the monomer into the oligomer. VCH oligomer formation was observed in liposomes containing sterols with the 3betaOH group and the C-C Delta(5) bond, and it correlated with the binding affinity of the monomer to each sterol. Therefore, it seems likely that monomer binding to membrane sterol leads to the assembly of the monomer. However, since oligomer formation was induced by liposomes containing either epicholesterol or dihydrocholesterol, the 3betaOH group and the C-C Delta(5) bond were not essential for conversion into the oligomer.

Splitting of the O–O bond at the heme-copper catalytic site of respiratory oxidases

PubMed Central

Poiana, Federica; von Ballmoos, Christoph; Gonska, Nathalie; Blomberg, Margareta R. A.; Ädelroth, Pia; Brzezinski, Peter

2017-01-01

Heme-copper oxidases catalyze the four-electron reduction of O2 to H2O at a catalytic site that is composed of a heme group, a copper ion (CuB), and a tyrosine residue. Results from earlier experimental studies have shown that the O–O bond is cleaved simultaneously with electron transfer from a low-spin heme (heme a/b), forming a ferryl state (PR; Fe4+=O2−, CuB2+–OH−). We show that with the Thermus thermophilus ba3 oxidase, at low temperature (10°C, pH 7), electron transfer from the low-spin heme b to the catalytic site is faster by a factor of ~10 (τ ≅ 11 μs) than the formation of the PR ferryl (τ ≅110 μs), which indicates that O2 is reduced before the splitting of the O–O bond. Application of density functional theory indicates that the electron acceptor at the catalytic site is a high-energy peroxy state [Fe3+–O−–O−(H+)], which is formed before the PR ferryl. The rates of heme b oxidation and PR ferryl formation were more similar at pH 10, indicating that the formation of the high-energy peroxy state involves proton transfer within the catalytic site, consistent with theory. The combined experimental and theoretical data suggest a general mechanism for O2 reduction by heme-copper oxidases. PMID:28630929

On the mechanism of nitrosoarene-alkyne cycloaddition.

PubMed

Penoni, Andrea; Palmisano, Giovanni; Zhao, Yi-Lei; Houk, Kendall N; Volkman, Jerome; Nicholas, Kenneth M

2009-01-21

The thermal reaction between nitrosoarenes and alkynes produces N-hydroxyindoles as the major products. The mechanism of these novel reactions has been probed using a combination of experimental and computational methods. The reaction of nitrosobenzene (NB) with an excess of phenyl acetylene (PA) is determined to be first order in each reactant in benzene at 75 degrees C. The reaction rates have been determined for reactions between phenyl acetylene with a set of p-substituted nitrosoarenes, 4-X-C(6)H(4)NO, and of 4-O(2)N-C(6)H(4)NO with a set of p-substituted arylalkynes, 4-Y-C(6)H(4)C[triple bond]CH. The former reactions are accelerated by electron-withdrawing X groups (rho = +0.4), while the latter are faster with electron-donating Y groups (rho = -0.9). The kinetic isotope effect for the reaction of C(6)H(5)NO/C(6)D(5)NO with PhC[triple bond]CH is found to be 1.1 (+/-0.1) while that between PhC[triple bond]CH/PhC[triple bond]CD with PhNO is also 1.1 (+/-0.1). The reaction between nitrosobenzene and the radical clock probe cyclopropylacetylene affords 3-cyclopropyl indole in low yield. In addition to 3-carbomethoxy-N-hydroxyindole, the reaction between PA and o-carbomethoxy-nitrosobenzene also affords a tricyclic indole derivative, 3, likely derived from trapping of an intermediate indoline nitrone with PA and subsequent rearrangement. Computational studies of the reaction mechanism were carried out with density functional theory at the (U)B3LYP/6-31+G(d) level. The lowest energy pathway of the reaction of PhNO with alkynes was found to be stepwise; the N-C bond between nitrosoarene and acetylene is formed first, the resulting vinyl diradical undergoes cis-trans isomerization, and then the C-C bond forms. Conjugating substituents Z on the alkyne, Z-C[triple bond]CH, lower the calculated (and observed) activation barrier, Z = -H (19 kcal/mol), -Ph (15.8 kcal/mol), and -C(O)H (13 kcal/mol). The regioselectivity of the reaction, with formation of the 3-substituted indole, was reproduced by the calculations of PhNO + PhC[triple bond]CH; the rate-limiting step for formation of the 2-substituted indole is higher in energy by 11.6 kcal/mol. The effects of -NO(2), -CN, -Cl, -Br, -Me, and -OMe substituents were computed for the reactions of p-X-C(6)H(4)NO with PhC[triple bond]CH and of PhNO and/or p-NO(2)-C(6)H(4)NO with p-Y-C(6)H(4)C[triple bond]CH. The activation energies for the set of p-X-C(6)H(4)NO vary by 4.3 kcal/mol and follow the trend found experimentally, with electron-withdrawing X groups accelerating the reactions. The range of barriers for the p-Y-C(6)H(4)C[triple bond]CH reactions is smaller, about 1.5 and 1.8 kcal/mol in the cases of PhNO and p-NO(2)-PhNO, respectively. In agreement with the experiments, electron-donating Y groups on the alkyne accelerate the reactions with p-NO(2)-C(6)H(4)NO, while both ED and EW groups are predicted to facilitate the reaction. The calculated kinetic isotope effect for the reaction of C(6)H(5)NO/C(6)D(5)NO with PhC[triple bond]CH is negligible (as found experimentally) while that for PhC[triple bond]CH/PhC[triple bond]CD with PhNO (0.7) differs somewhat from the experiment (1.1). Taken together the experimental and computational results point to the operation of a stepwise diradical cycloaddition, with rate-limiting N-C bond formation and rapid C-C connection to form a bicyclic cyclohexadienyl-N-oxyl diradical, followed by fast tautomerization to the N-hydroxyindole product.

Rhenium(V) Oxo Complexes of Novel N(2)S(2) Dithiourea (DTU) Chelate Ligands: Synthesis and Structural Characterization.

PubMed

Lipowska, Malgorzata; Hayes, Brittany L.; Hansen, Lory; Taylor, Andrew; Marzilli, Luigi G.

1996-07-03

The compounds RNHC(=S)NH(CH(2))(n)()NHC(=S)NHR were prepared in a search for new, relatively small N(2)S(2) ligands. These dithiourea (DTU) ligands are the first chelates containing two potentially bidentate thiourea moieties. A one-step reaction of 1,3-diaminopropane (1) with aryl or alkyl isothiocyanates or of 1,2-diaminoethane (2) with phenyl isothiocyanate afforded the target ligands in excellent yields (95-98%). The Re(V)=O complexes of RNHC(=S)NH(CH(2))(3)NHC(=S)NHR ligands were obtained through ligand exchange reactions with Re(V) precursors. The chemistry required neither protection of the sulfur atoms for ligand synthesis nor deprotection prior to metal complexation. The structure of (1-phenyl-3-(3-phenylthioureido)propyl]thioureato)oxorhenium(V) (7a), determined by X-ray diffraction methods, revealed the expected pseudo-square-pyramidal geometry with an N(2)S(2) basal and an apical oxo donor set. Both coordinated N's (N(c)) were deprotonated. One uncoordinated N (N(u)) was deprotonated, producing a neutral complex containing an unexpected new type of dianionic, four-membered N,S chelate. In the crystal, the N(u) atoms, N(3)H and N(4), of one complex each formed an H-bond with N(4) and N(3)H, respectively, of a symmetry-related complex. The N(c)-C-S bond angles (106.1(6) and 101.5(6) degrees ) were severely distorted from the 120 degrees expected for an sp(2)-hybridized C. However, these small bite angles and the large N-Re-N bond angle (86.1(3) degrees ) allowed for the formation of two four-membered chelate rings with normal Re-N and Re-S bond distances. Attempts to prepare complexes with the PhNHC(=S)NH(CH(2))(2)NHC(=S)NHPh ligand were unsuccessful. These results suggest that a central five-membered chelate ring is too small to accommodate bidentate coordination of both thiourea moieties. NMR studies in methanol established that the neutral complex with one uncoordinated N deprotonated was the favored form in neutral and basic solutions. However, under acidic conditions, a cationic form with both uncoordinated N's protonated was favored.

A new face of phenalenyl-based radicals in the transition metal-free C-H arylation of heteroarenes at room temperature: trapping the radical initiator via C-C σ-bond formation.

PubMed

Ahmed, Jasimuddin; P, Sreejyothi; Vijaykumar, Gonela; Jose, Anex; Raj, Manthan; Mandal, Swadhin K

2017-11-01

The radical-mediated transition metal-free approach for the direct C-H bond functionalization of arenes is considered as a cost effective alternative to transition metal-based catalysis. An organic ligand-based radical plays a key role by generating an aryl radical which undergoes a subsequent functionalization process. The design principle of the present study takes advantage of a relatively stable odd alternant hydrocarbon-based phenalenyl (PLY) radical. In this study, the first transition metal-free catalyzed direct C-H arylation of a variety of heteroarenes such as azoles, furan, thiophene and pyridine at room temperature has been reported using a phenalenyl-based radical without employing any photoactivation step. This protocol has been successfully applied to the gram scale synthesis of core moieties of bioactive molecules. The phenalenyl-based radical initiator has been characterized crystallographically by trapping it via the formation of a C-C σ-bond between the phenalenyl radical and solvent-based radical species.

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.

Reliable aluminum contact formation by electrostatic bonding

NASA Astrophysics Data System (ADS)

Kárpáti, T.; Pap, A. E.; Radnóczi, Gy; Beke, B.; Bársony, I.; Fürjes, P.

2015-07-01

The paper presents a detailed study of a reliable method developed for aluminum fusion wafer bonding assisted by the electrostatic force evolving during the anodic bonding process. The IC-compatible procedure described allows the parallel formation of electrical and mechanical contacts, facilitating a reliable packaging of electromechanical systems with backside electrical contacts. This fusion bonding method supports the fabrication of complex microelectromechanical systems (MEMS) and micro-opto-electromechanical systems (MOEMS) structures with enhanced temperature stability, which is crucial in mechanical sensor applications such as pressure or force sensors. Due to the applied electrical potential of  -1000 V the Al metal layers are compressed by electrostatic force, and at the bonding temperature of 450 °C intermetallic diffusion causes aluminum ions to migrate between metal layers.

Spectroscopy and formation of lanthanum-hydrocarbon radicals formed by association and carbon-carbon bond cleavage of isoprene

NASA Astrophysics Data System (ADS)

Cao, Wenjin; Hewage, Dilrukshi; Yang, Dong-Sheng

2018-05-01

La atom reaction with isoprene is carried out in a laser-vaporization molecular beam source. The reaction yields an adduct as the major product and C—C cleaved and dehydrogenated species as the minor ones. La(C5H8), La(C2H2), and La(C3H4) are characterized with mass-analyzed threshold ionization (MATI) spectroscopy and quantum chemical computations. The MATI spectra of all three species exhibit a strong origin band and several weak vibronic bands corresponding to La-ligand stretch and ligand-based bend excitations. La(C5H8) is a five-membered metallacycle, whereas La(C2H2) and La(C3H4) are three-membered rings. All three metallacycles prefer a doublet ground state with a La 6s1-based valence electron configuration and a singlet ion. The five-membered metallacycle is formed through La addition and isoprene isomerization, whereas the two three-membered rings are produced by La addition and insertion, hydrogen migration, and carbon-carbon bond cleavage.

Ultrafast forward and backward electron transfer dynamics of coumarin 337 in hydrogen-bonded anilines as studied with femtosecond UV-pump/IR-probe spectroscopy.

PubMed

Ghosh, Hirendra N; Verma, Sandeep; Nibbering, Erik T J

2011-02-10

Femtosecond infrared spectroscopy is used to study both forward and backward electron transfer (ET) dynamics between coumarin 337 (C337) and the aromatic amine solvents aniline (AN), N-methylaniline (MAN), and N,N-dimethylaniline (DMAN), where all the aniline solvents can donate an electron but only AN and MAN can form hydrogen bonds with C337. The formation of a hydrogen bond with AN and MAN is confirmed with steady state FT-IR spectroscopy, where the C═O stretching vibration is a direct marker mode for hydrogen bond formation. Transient IR absorption measurements in all solvents show an absorption band at 2166 cm(-1), which has been attributed to the C≡N stretching vibration of the C337 radical anion formed after ET. Forward electron transfer dynamics is found to be biexponential with time constants τ(ET)(1) = 500 fs, τ(ET)(2) = 7 ps in all solvents. Despite the presence of hydrogen bonds of C337 with the solvents AN and MAN, no effect has been found on the forward electron transfer step. Because of the absence of an H/D isotope effect on the forward electron transfer reaction of C337 in AN, hydrogen bonds are understood to play a minor role in mediating electron transfer. In contrast, direct π-orbital overlap between C337 and the aromatic amine solvents causes ultrafast forward electron transfer dynamics. Backward electron transfer dynamics, in contrast, is dependent on the solvent used. Standard Marcus theory explains the observed backward electron transfer rates.

Mechanisms of Bond Cleavage during Manganese Oxide and UV Degradation of Glyphosate: Results from Phosphate Oxygen Isotopes and Molecular Simulations.

PubMed

Jaisi, Deb P; Li, Hui; Wallace, Adam F; Paudel, Prajwal; Sun, Mingjing; Balakrishna, Avula; Lerch, Robert N

2016-11-16

Degradation of glyphosate in the presence of manganese oxide and UV light was analyzed using phosphate oxygen isotope ratios and density function theory (DFT). The preference of C-P or C-N bond cleavage was found to vary with changing glyphosate/manganese oxide ratios, indicating the potential role of sorption-induced conformational changes on the composition of intermediate degradation products. Isotope data confirmed that one oxygen atom derived solely from water was incorporated into the released phosphate during glyphosate degradation, and this might suggest similar nucleophilic substitution at P centers and C-P bond cleavage both in manganese oxide- and UV light-mediated degradation. The DFT results reveal that the C-P bond could be cleaved by water, OH - or • OH, with the energy barrier opposing bond dissociation being lowest in the presence of the radical species, and that C-N bond cleavage is favored by the formation of both nitrogen- and carbon-centered radicals. Overall, these results highlight the factors controlling the dominance of C-P or C-N bond cleavage that determines the composition of intermediate/final products and ultimately the degradation pathway.

Mechanistic studies of a novel C-S lyase in ergothioneine biosynthesis: the involvement of a sulfenic acid intermediate

PubMed Central

Song, Heng; Hu, Wen; Naowarojna, Nathchar; Her, Ampon Sae; Wang, Shu; Desai, Rushil; Qin, Li; Chen, Xiaoping; Liu, Pinghua

2015-01-01

Ergothioneine is a histidine thio-derivative isolated in 1909. In ergothioneine biosynthesis, the combination of a mononuclear non-heme iron enzyme catalyzed oxidative C-S bond formation reaction and a PLP-mediated C-S lyase (EgtE) reaction results in a net sulfur transfer from cysteine to histidine side-chain. This demonstrates a new sulfur transfer strategy in the biosynthesis of sulfur-containing natural products. Due to difficulties associated with the overexpression of Mycobacterium smegmatis EgtE protein, the proposed EgtE functionality remained to be verified biochemically. In this study, we have successfully overexpressed and purified M. smegmatis EgtE enzyme and evaluated its activities under different in vitro conditions: C-S lyase reaction using either thioether or sulfoxide as a substrate in the presence or absence of reductants. Results from our biochemical characterizations support the assignment of sulfoxide 4 as the native EgtE substrate and the involvement of a sulfenic acid intermediate in the ergothioneine C-S lyase reaction. PMID:26149121

A Theoretical Study of the Photodissociation Mechanism of Cyanoacetylene in Its Lowest Singlet and Triplet Excited States

NASA Astrophysics Data System (ADS)

Luo, Cheng; Du, Wei-Na; Duan, Xue-Mei; Li, Ze-Sheng

2008-11-01

Cyanoacetylene (H5-C4 ≡ C3-C2 ≡ N1) is a minor constituent of the atmosphere of Titan, and its photochemistry plays an important role in the formation of the haze surrounding the satellite. In this paper, the complete active space self-consistent field (CASSCF) and multiconfigurational second-order perturbation (CASPT2) approaches are employed to investigate the photochemical processes for cyanoacetylene in its first singlet and triplet excited states with the cc-pVTZ basis set. Fissions of the C4-H5 and C2-C3 bonds in S1 yield H(2S) + CCCN(A2Π) and HCC(A2Π) + CN(X2Σ+), respectively. In T1, the corresponding dissociation products are H(2S) + CCCN(X2Σ+) and HCC(X2Σ) + CN(X2Σ+). At the CASPT2(14,13)//CASSCF(14,13) + ZPE level, the barriers for the adiabatic dissociation of the C4-H5 and C2-C3 bonds are 6.11 and 6.94 eV in S1 and 5.71 and 6.39 eV in T1, respectively, taking the energy of S0 minimum as reference. Based on the calculated potential energy surfaces, the existence of a metastable excited molecule is anticipated upon 260-230 nm photoexcitation, which provides a probable approach for cyanoacetylene to polymerize. The internal conversion (IC) process through vibronic interaction followed by C4-H5 fission in the ground state is found to account for the observed diffuse character in the UV absorption spectrum below 240 nm.

Synthesis and reaction of [[HC(CMeNAr)2]Mn]2 (Ar = 2,6-iPr2C6H3): the complex containing three-coordinate manganese(I) with a Mn-Mn bond exhibiting unusual magnetic properties and electronic structure.

PubMed

Chai, Jianfang; Zhu, Hongping; Stückl, A Claudia; Roesky, Herbert W; Magull, Jörg; Bencini, Alessandro; Caneschi, Andrea; Gatteschi, Dante

2005-06-29

This paper reports on the synthesis, X-ray structure, magnetic properties, and DFT calculations of [[HC(CMeNAr)2]Mn]2 (Ar = 2,6-iPr2C6H3) (2), the first complex with three-coordinate manganese(I). Reduction of the iodide [[HC(CMeNAr)2]Mn(mu-I)]2 (1) with Na/K in toluene afforded 2 as dark-red crystals. The molecule of 2 contains a Mn2(2+) core with a Mn-Mn bond. The magnetic investigations show a rare example of a high-spin manganese(I) complex with an antiferromagnetic interaction between the two Mn(I) centers. The DFT calculations indicate a strong s-s interaction of the two Mn(I) ions with the open shell configuration (3d54s1). This suggests that the magnetic behavior of 2 could be correctly described as the coupling between two S1 = S2 = 5/2 spin centers. The Mn-Mn bond energy is estimated at 44 kcal mol(-1) by first principle calculations with the B3LYP functional. The further oxidative reaction of 2 with KMnO4 or O2 resulted in the formation of manganese(III) oxide [[HC(CMeNAr)2]Mn(mu-O)]2 (3). Compound 3 shows an antiferromagnetic coupling between the two oxo-bridged manganese(III) centers by magnetic measurements.

Methods of using ionic liquids having a fluoride anion as solvents

DOEpatents

Pagoria, Philip [Livermore, CA; Maiti, Amitesh [San Ramon, CA; Gash, Alexander [Brentwood, CA; Han, Thomas Yong [Pleasanton, CA; Orme, Christine [Oakland, CA; Fried, Laurence [Livermore, CA

2011-12-06

A method in one embodiment includes contacting a strongly hydrogen bonded organic material with an ionic liquid having a fluoride anion for solubilizing the strongly hydrogen bonded organic material; and maintaining the ionic liquid at a temperature of about 90.degree. C. or less during the contacting. A method in another embodiment includes contacting a strongly hydrogen bonded organic material with an ionic liquid having an acetate or formate anion for solubilizing the strongly hydrogen bonded organic material; and maintaining the ionic liquid at a temperature of less than about 90.degree. C. during the contacting.

Hydroalumination of Ketenimines and Subsequent Reactions with Heterocumulenes: Synthesis of Unsaturated Amide Derivatives and 1,3-Diimines.

PubMed

Jin, Xing; Willeke, Matthias; Lucchesi, Ralph; Daniliuc, Constantin-Gabriel; Fröhlich, Roland; Wibbeling, Birgit; Uhl, Werner; Würthwein, Ernst-Ulrich

2015-06-19

The series of differently substituted ketenimines 1 was hydroluminated using di-iso-butyl aluminum hydride. For the sterically congested ketenimine 1a, preferred hydroalumination of the C═N-bond was proven by X-ray crystallography (compound 5a). In situ treatment of the hydroaluminated ketenimines 5 with various heterocumulenes like carbodiimides, isocycanates, isothiocyanates and ketenimines as electrophiles and subsequent hydrolytic workup resulted in novel enamine derived amide species in case of N-attack (sterically less hindered ketenimines) under formation of a new C-N-bond or in 1,3-diimines by C-C-bond-formation in case of bulky substituents at the ketenimine-nitrogen atom. Furthermore, domino reactions with more than 1 equiv of the electrophile or by subsequent addition of two different electrophiles are possible and lead to polyfunctional amide derivatives of the biuret type which are otherwise not easily accessible.

Experimental and theoretical study on activation of the C-H bond in pyridine by [M(m)]- (M = Cu, Ag, Au, m = 1-3).

PubMed

Liu, Xiao-Jing; Hamilton, I P; Han, Ke-Li; Tang, Zi-Chao

2010-09-21

Activation of the C-H bond of pyridine by [M(m)](-) (M = Cu, Ag, Au, m = 1-3) is investigated by experiment and theory. Complexes of coinage metal clusters and the pyridyl group, [M(m)-C(5)H(4)N](-), are produced from reactions between metal clusters formed by laser ablation of coinage metal samples and pyridine molecules seeded in argon carrier gas. We examine the structure and formation mechanism of these pyridyl-coinage metal complexes. Our study shows that C(5)H(4)N bonds to the metal clusters through a M-C sigma bond and [M(m)-C(5)H(4)N](-) is produced via a stepwise mechanism. The first step is a direct insertion reaction between [M(m)](-) and C(5)H(5)N with activation of the C-H bond to yield the intermediate [HM(m)-C(5)H(4)N](-). The second step is H atom abstraction by a neutral metal atom to yield [M(m)-C(5)H(4)N](-).

Oxidative 1,2-carboamination of alkenes with alkyl nitriles and amines toward γ-amino alkyl nitriles

NASA Astrophysics Data System (ADS)

Liu, Yan-Yun; Yang, Xu-Heng; Song, Ren-Jie; Luo, Shenglian; Li, Jin-Heng

2017-04-01

Difunctionalization of alkenes has become a powerful tool for quickly increasing molecular complexity in synthesis. Despite significant progress in the area of alkene difunctionalization involving the incorporation of a nitrogen atom across the C-C double bonds, approaches for the direct 1,2-carboamination of alkenes to produce linear N-containing molecules are scarce and remain a formidable challenge. Here we describe a radical-mediated oxidative intermolecular 1,2-alkylamination of alkenes with alkyl nitriles and amines involving C(sp3)-H oxidative functionalization catalysed by a combination of Ag2CO3 with iron Lewis acids. This three-component alkene 1,2-alkylamination method is initiated by the C(sp3)-H oxidative radical functionalization, which enables one-step formation of two new chemical bonds, a C-C bond and a C-N bond, to selectively produce γ-amino alkyl nitriles.

Insertion of terminal alkyne into Pt-N bond of the square planar [PtI2(Me2phen)] complex.

PubMed

Benedetti, Michele; De Castro, Federica; Lamacchia, Vincenza; Pacifico, Concetta; Natile, Giovanni; Fanizzi, Francesco P

2017-11-21

The reactivity of [PtX 2 (Me 2 phen)] complexes (X = Cl, Br, I; Me 2 phen = 2,9-dimethyl-1,10-phenanthroline) with terminal alkynes has been investigated. Although the dichlorido species [PtCl 2 (Me 2 phen)] exhibits negligible reactivity, the bromido and iodido derivatives lead in short time to the formation of five-coordinate Pt(ii) complexes of the type [PtX 2 (Me 2 phen)(η 2 -CH[triple bond, length as m-dash]CR)] (X = Br, I; R = Ph, n-Bu), in equilibrium with the starting reagents. Similar to analogous complexes with simple acetylene, the five coordinate species can also undergo dissociation of an halido ligand and formation of the transient square-planar cationic species [PtX(Me 2 phen)(η 2 -CH[triple bond, length as m-dash]CR)] + . This latter can further evolve to give an unusual, sparingly soluble square planar product where the former terminal alkyne is converted into a :C[double bond, length as m-dash]C(H)(R) moiety with the α-carbon bridging the Pt(ii) core with one of the two N-donors of coordinated Me 2 phen. The final product [PtX 2 {κ 2 -N,C-(Z)-N[combining low line]1-N10-C[combining low line][double bond, length as m-dash]C(H)(R)}] (N1-N10 = 2,9-dimethyl-1,10-phenanthroline; X = Br, I) contains a Pt-N-C-C-N-C six-membered chelate ring in a square planar Pt(ii) coordination environment.

BF3·Et2O-promoted cleavage of the Csp-Csp2 bond of 2-propynolphenols/anilines: route to C2-alkenylated benzoxazoles and benzimidazoles.

PubMed

Song, Xian-Rong; Qiu, Yi-Feng; Song, Bo; Hao, Xin-Hua; Han, Ya-Ping; Gao, Pin; Liu, Xue-Yuan; Liang, Yong-Min

2015-02-20

A novel BF3·Et2O-promoted tandem reaction of easily prepared 2-propynolphenols/anilines and trimethylsilyl azide is developed to give C2-alkenylated benzoxazoles and benzimidazoles in moderate to good yields. Most reactions could be accomplished in 30 min at room temperature. This tandem process involves a Csp-Csp2 bond cleavage and a C-N bond formation. Moreover, both tertiary and secondary propargylic alcohols with diverse functional groups were tolerated under the mild conditions.

A homogeneous, recyclable polymer support for Rh(I)-catalyzed C-C bond formation.

PubMed

Jana, Ranjan; Tunge, Jon A

2011-10-21

A robust and practical polymer-supported, homogeneous, recyclable biphephos rhodium(I) catalyst has been developed for C-C bond formation reactions. Control of polymer molecular weight allowed tuning of the polymer solubility such that the polymer-supported catalyst is soluble in nonpolar solvents and insoluble in polar solvents. Using the supported rhodium catalysts, addition of aryl and vinylboronic acids to the electrophiles such as enones, aldehydes, N-sulfonyl aldimines, and alkynes occurs smoothly to provide products in high yields. Additions of terminal alkynes to enones and industrially relevant hydroformylation reactions have also been successfully carried out. Studies show that the leaching of Rh from the polymer support is low and catalyst recycle can be achieved by simple precipitation and filtration.

A Homogeneous, Recyclable Polymer Support for Rh(I)-Catalyzed C-C Bond Formation

PubMed Central

Jana, Ranjan; Tunge, Jon A.

2011-01-01

A robust and practical polymer-supported, homogeneous, recyclable biphephos rhodium(I) catalyst has been developed for C-C bond formation reactions. Control of polymer molecular weight allowed tuning of the polymer solubility such that the polymer-supported catalyst is soluble in nonpolar solvents and insoluble in polar solvents. Using the supported rhodium catalysts, addition of aryl and vinylboronic acids to the electrophiles such as enones, aldehydes, N-sulfonyl aldimines, and alkynes occurs smoothly to provide products in high yields. Additions of terminal alkynes to enones and industrially relevant hydroformylation reactions have also been successfully carried out. Studies show that the leaching of Rh from the polymer support is low and catalyst recycle can be achieved by simple precipitation and filtration. PMID:21895010

Photoinduced reactions of both 2-formyl-2H-azirine and isoxazole: A theoretical study based on electronic structure calculations and nonadiabatic dynamics simulations.

PubMed

Cao, Jun

2015-06-28

In the present work, the combined electronic structure calculations and dynamics simulations have been performed to explore photocleavages of 2-formyl-2H-azirine and isoxazole in the gas phase and the subsequent rearrangement reactions. The carbonyl n → π(*) transition induces a cleavage of the C-N single bond of 2-formyl-2H-azirine to yield β-formylvinylnitrene in open-shell singlet state. However, the n → π(*) excitation of the imine chromophore results in a cleavage of the C-C single bond, producing a nitrile ylide intermediate through an internal conversion to the ground state. β-formylvinylnitrene and nitrile ylide with the carbonyl group are easily transformed into 2-formyl-2H-azirine and oxazole, respectively. The N-O bond cleavages on both S1((1)ππ(*)) and S2((1)nNπ(*)) of isoxazole are ultrafast processes, and they give products of 2-formyl-2H-azirine, 3-formylketenimine, HCN + CHCHO, and HCO + CHCHN. Both 2H-azirines and ketenimines were suggested to be formed from the triplet vinylnitrenes by intersystem crossing in the previous studies. However, our calculations show that the singlet β-formylvinylnitrene is responsible for the formation of 2-formyl-2H-azirine and 3-formylketenimine, and the singlet vinylnitrenes can play a key role in the photoinduced reactions of both 2H-azirines and isoxazoles.

Formation and characterization of microcrystalline semiconductor particles on bilayer lipid membranes

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

Baral, S.; Zhao, X.K.; Rolandi, R.

Microcrystalline cadmium, indium, copper, and zinc sulfides were generated in situ on the surface of bilayer lipid membranes (BLMs) prepared from bovine-brain phosphatidylserine (PS), glyceryl monooleate (GMO), and a synthetic, polymerizable surfactant (n-C/sub 15/H/sub 31/CO/sub 2/(CH/sub 2/)/sub 2/)/sub 2/N/sup +/(CH/sub 3/)CH/sub 2/C/sub 6/H/sub 4/CH double bond CH/sub 2/, Cl/sup -/ (STYRS). Semiconductor-containing BLMs remained stable for days. Semiconductor formation on the BLM surface was monitored by optical microscopy, voltage-dependent capacitance measurements, and absorption and intracavity-laser-absorption spectroscopy. Band gap excitation of GMO- BLM-incorporated CdS resulted in the development of photovoltage. Irradiation of CdS incorporated into BLMs formed from STYRS (using amore » 350-nm cutoff filter) led to absorption losses due to the styrene moiety in the surfactant. Apparently, CdS sensitized the photopolymerization of STRYS BLMs.« less

Ethyl 2-{N-[N-(4-chloro-6-methoxy­pyrimidin-2-yl)carbamo­yl]sulfamo­yl}benzoate

PubMed Central

Lu, Chui; Li, Fang-Shi; Yu, Da-Sheng; Yao, Wei; Liu, Yin-Hong

2008-01-01

The asymmetric unit of the title compound, C15H15ClN4O6S, contains two independent mol­ecules, in which the pyrimidine and benzene rings are oriented at dihedral angles of 75.21 (3) and 86.00 (3)°. Intra­molecular N—H⋯N and C—H⋯O hydrogen bonds result in the formation of two five- and two six-membered rings. The six-membered rings have flattened-boat conformations, while the five-membered rings adopt envelope conformations. In the crystal structure, inter­molecular N—H⋯O hydrogen bonds link the mol­ecules. PMID:21202882

Reversible hydrogen transfer reactions of cysteine thiyl radicals in peptides: the conversion of cysteine into dehydroalanine and alanine, and of alanine into dehydroalanine

PubMed Central

Mozziconacci, Olivier; Kerwin, Bruce A.; Schöneich, Christian

2013-01-01

The photodissociation of disulfide bonds in model peptides containing Ala and Ala-d3 generates a series of photoproducts following the generation of a CysS• thiyl radical pair. These photoproducts include transformations of Cys to dehydroalanine (Dha) and Ala, as well as Ala to Dha. Intramolecular Michael addition of an intact Cys with a photolytically generated Dha results in the formation of cyclic thioethers. The conversion of Cys into Dha likely involves a 1,3-H-shift from the Cys αC-H bond to the thiyl radical, followed by elimination of HS•. The conversion of Dha into Ala most likely involves hydrated electrons, which are generated through the photolysis of Cys, the photoproduct of disulfide photolysis. Prior to stable product formation, CysS• radicals engage in reversible hydrogen transfer reactions with αC-H and βC-H bonds of the surrounding amino acids. Especially for the βC-H bonds of Ala such hydrogen transfer reactions are unexpected based on thermodynamic grounds; however, the replacement of deuterons in Ala-d3 by hydrogens in H2O provides strong experimental evidence for such reactions. PMID:21895001

Gas production in the radiolysis of Poly(dimethysiloxanes)

NASA Astrophysics Data System (ADS)

LaVerne, Jay A.; Tratnik, Nicole A. I.; Sasgen, Andrea

2018-01-01

A variety of small poly(dimethyl siloxanes) were irradiated with γ-rays followed by the determination of the production of methane and molecular hydrogen and characterization of spectroscopic changes in the medium. The yields of methane was found to be about twice that of molecular hydrogen indicating that breakage of the C-Si bond occurs at a frequency comparable to the breakage of the C-H bond. Both yields slowly decrease with increasing molecular weight of the medium. The presence of oxygen decreases the yield of both gases suggesting radical precursors to methane and molecular hydrogen, presumably the methyl radical and H atom, respectively. Temperature gravimetric analysis and UV-visible spectroscopy both suggest the formation of higher molecular weight compounds with radiolysis, which agrees with bond loss and formation observed in infrared spectroscopy.

Dual Roles of β-Oxodithioesters in the Copper-Catalyzed Synthesis of Benzo[e]pyrazolo[1,5-c][1,3]thiazine Derivatives.

PubMed

Wen, Li-Rong; Yuan, Wen-Kui; Li, Ming

2015-05-15

A facile and efficient method for the chemoselective synthesis of benzo[e]pyrazolo[1,5-c][1,3]thiazine derivatives has been developed by tandem Ullmann coupling reactions of β-oxodithioesters (ODEs) with 3-(2-bromoaryl)-1H-pyrazoles in C-S bond formation manner, in which ODEs play dual roles as both a substrate and a ligand. A series of benzo[e]pyrazolo[1,5-c][1,3]thiazine derivatives were provided in good to excellent yields with CuI as the copper source in the presence of NaOH in CH3CN at 80 °C under a N2 atmosphere.

Contributions of a disulfide bond and a reduced cysteine side chain to the intrinsic activity of the HDL receptor SR-BI

PubMed Central

Yu, Miao; Lau, Thomas Y.; Carr, Steven A.; Krieger, Monty

2013-01-01

The high density lipoprotein (HDL) receptor, scavenger receptor class B, type I (SR-BI), binds HDL and mediates selective cholesteryl ester uptake. SR-BI's structure and mechanism are poorly understood. We used mass spectrometry to assign the two disulfide bonds in SR-BI that connect cysteines within the conserved Cys321-Pro322-Cys323 (CPC) motif and connect Cys280 to Cys334. We used site-specific mutagenesis to evaluate the contributions of the CPC motif and the side chain of extracellular Cys384 to HDL binding and lipid uptake. The effects of CPC mutations on activity were context dependent. Full wild-type (WT) activity required Pro322 and Cys323 only when Cys321 was present. Reduced intrinsic activities were observed for CXC and CPX, but not XXC, XPX or XXX mutants (X≠WT residue). Apparently, a free thiol side chain at position 321 that cannot form an intra-CPC disulfide bond with Cys323 is deleterious, perhaps because of aberrant disulfide bond formation. Pro322 may stabilize an otherwise strained CPC disulfide bond, thus supporting WT activity, but this disulfide bond is not absolutely required for activity. C384X (X=S,T,L,Y,G,A) mutants exhibited altered activities that varied with the side chain's size: larger side chains phenocopied WT SR-BI treated with its thiosemicarbazone inhibitor BLT-1 (increased binding, decreased uptake); smaller side chains produced almost inverse effects (increased uptake:binding ratio). C384X mutants were BLT-1 resistant, supporting the proposal that Cys384's thiol interacts with BLT-1. We discuss the implications of our findings on the functions of the extracellular loop cysteines in SR-BI and compare our results to those presented by other laboratories. PMID:23205738

Functionalization of P4 through Direct P-C Bond Formation.

PubMed

Borger, Jaap E; Ehlers, Andreas W; Slootweg, J Chris; Lammertsma, Koop

2017-09-04

Research on chlorine-free conversions of P 4 into organophosphorus compounds (OPCs) has a long track record, but methods that allow desirable, direct P-C bond formations have only recently emerged. These include the use of metal organyls, carbenes, carboradicals, and photochemical approaches. The versatile product scope enables the preparation of both industrially relevant organophosphorus compounds, as well as a broad range of intriguing new compound classes. Herein we provide a concise overview of recent breakthroughs and outline the acquired fundamental insights to aid future developments. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Formation of conjugated delta8,delta10-double bonds by delta12-oleic-acid desaturase-related enzymes: biosynthetic origin of calendic acid.

PubMed

Cahoon, E B; Ripp, K G; Hall, S E; Kinney, A J

2001-01-26

Divergent forms of the plant Delta(12)-oleic-acid desaturase (FAD2) have previously been shown to catalyze the formation of acetylenic bonds, epoxy groups, and conjugated Delta(11),Delta(13)-double bonds by modification of an existing Delta(12)-double bond in C(18) fatty acids. Here, we report a class of FAD2-related enzymes that modifies a Delta(9)-double bond to produce the conjugated trans-Delta(8),trans-Delta(10)-double bonds found in calendic acid (18:3Delta(8trans,10trans,12cis)), the major component of the seed oil of Calendula officinalis. Using an expressed sequence tag approach, cDNAs for two closely related FAD2-like enzymes, designated CoFADX-1 and CoFADX-2, were identified from a C. officinalis developing seed cDNA library. The deduced amino acid sequences of these polypeptides share 40-50% identity with those of other FAD2 and FAD2-related enzymes. Expression of either CoFADX-1 or CoFADX-2 in somatic soybean embryos resulted in the production of calendic acid. In embryos expressing CoFADX-2, calendic acid accumulated to as high as 22% (w/w) of the total fatty acids. In addition, expression of CoFADX-1 and CoFADX-2 in Saccharomyces cerevisiae was accompanied by calendic acid accumulation when induced cells were supplied exogenous linoleic acid (18:2Delta(9cis,12cis)). These results are thus consistent with a route of calendic acid synthesis involving modification of the Delta(9)-double bond of linoleic acid. Regiospecificity for Delta(9)-double bonds is unprecedented among FAD2-related enzymes and further expands the functional diversity found in this family of enzymes.

Characterization and antioxidant activity of gallic acid derivative

NASA Astrophysics Data System (ADS)

Malinda, Krissan; Sutanto, Hery; Darmawan, Akhmad

2017-11-01

Peroxidase enzyme was used to catalyze the dimerization process of gallic acid. The structure of the dimerization product was characterized by 1H NMR and LC-MS-MS. The mechanism of gallic acid dimerization was also discussed. It was proposed that ellagic acid was formed through an oxidative coupling mechanism that lead to the formation of a C-C bond and followed by an intramolecular Fischer esterification mechanism that lead to the formation of two C-O bonds. Moreover, the antioxidant activity of gallic acid and ellagic acid were also studied. Gallic acid and ellagic acid exhibited the DPPH radical scavenging activity with IC50 values of 13.2 μM and 15.9 μM, respectively.

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

Kinetics and Mechanism of Bioactivation via S-Oxygenation of Anti-Tubercular Agent Ethionamide by Peracetic Acid.

PubMed

Chipiso, Kudzanai; Logan, Isabelle E; Eskew, Matthew W; Omondi, Benard; Simoyi, Reuben H

2016-10-11

The kinetics and mechanism of the oxidation of the important antitubercular agent, ethionamide, ETA (2-ethylthioisonicotinamide), by peracetic acid (PAA) have been studied. It is effectively a biphasic reaction with an initial rapid first phase of the reaction which is over in about 5 s and a second slower phase of the reaction which can run up to an hour. The first phase involves the addition of a single oxygen atom to ethionamide to form the S-oxide. The second phase involves further oxidation of the S-oxide to desulfurization of ETA to give 2-ethylisonicotinamide. In contrast to the stability of most organosulfur compounds, the S-oxide of ETA is relatively stable and can be isolated. In conditions of excess ETA, the stoichiometry of the reaction was strictly 1:1: CH 3 CO 3 H + Et(C 5 H 4 )C(═S)NH 2 → CH 3 CO 2 H + Et(C 5 H 4 )C(═NH)SOH. In this oxidation, it was apparent that only the sulfur center was the reactive site. Though ETA was ultimately desulfurized, only the S-oxide was stable. Electrospray ionization (ESI) spectral analysis did not detect any substantial formation of the sulfinic and sulfonic acids. This suggests that cleavage of the carbon-sulfur bond occurs at the sulfenic acid stage, resulting in the formation of an unstable sulfur species that can react further to form more stable sulfur species. In this oxidation, no sulfate formation was observed. ESI spectral analysis data showed a final sulfur species in the form of a dimeric sulfur monoxide species, H 3 S 2 O 2 . We derived a bimolecular rate constant for the formation of the S-oxide of (3.08 ± 0.72) × 10 2 M -1 s -1 . Oxidation of the S-oxide further to give 2-ethylisonicotinamide gave zero order kinetics.

Glass formation and short-range order structures in the BaS + La 2S 3 + GeS 2 system

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

Roth, Josh R.; Martin, Steve W.; Ballato, John

Here, infrared (IR) optical materials have enabled a broad range of optical sensing and measurement applications in the mid-wave and long-wave IR. Many IR transmitting glasses are based on covalently-bonded selenides and tellurides, such as As 2Se 3 and GeTe 2, which typically have relatively low glass transition temperatures ( T g) on the order of 200 to 350 °C. Many applications have working temperatures above the T g of these materials, which compels the development of new IR materials. This work studies the underlying short-range order (SRO) structure and glass formability of a new family of ionically-bonded sulfide glasses,more » xBaS + yLa 2S 3 + (1 – x – y)GeS 2, to develop high T g optical materials with a broad IR transmission range. These sulfide glasses were produced by melting sulfide materials inside evacuated and sealed carbon-coated silica ampoules at 1150 °C for 12 h and quenching to room temperature to form glass. Glass samples were then characterized by IR and Raman spectroscopies and differential thermal analysis (DTA). It was found that by increasing the modifier concentration, the predominantly Ge 4 SRO units, the superscript defines the number of bridging sulfur (BS) ions in the tetrahedral network found in GeS 2 glasses, are ultimately converted to Ge 0 units at >40 mol% network modifier content through the generation of non-bridging sulfur (NBS) ions. These molecular ionic units still form a glassy network, with some of the highest reported T g values to date for a pure sulfide glass. This suggests that this composition has strong ionic bonds between negatively-charged tetrahedral SRO units and the positively-charged modifier cations. While the glass network is depolymerized in the high modifier content glasses though the formation of a high concentration of molecular ionic Ge 0 SRO groups, they are, nevertheless, homogeneous glassy materials that exhibit the largest T g and Δ T (difference between crystallization temperature, T c, and T g) values of glasses in this system, making them the optimal glasses for high T g IR optical components, including, potentially, refractory IR optical fibers.« less

Glass formation and short-range order structures in the BaS + La 2S 3 + GeS 2 system

DOE PAGES

Roth, Josh R.; Martin, Steve W.; Ballato, John; ...

2018-06-01

Here, infrared (IR) optical materials have enabled a broad range of optical sensing and measurement applications in the mid-wave and long-wave IR. Many IR transmitting glasses are based on covalently-bonded selenides and tellurides, such as As 2Se 3 and GeTe 2, which typically have relatively low glass transition temperatures ( T g) on the order of 200 to 350 °C. Many applications have working temperatures above the T g of these materials, which compels the development of new IR materials. This work studies the underlying short-range order (SRO) structure and glass formability of a new family of ionically-bonded sulfide glasses,more » xBaS + yLa 2S 3 + (1 – x – y)GeS 2, to develop high T g optical materials with a broad IR transmission range. These sulfide glasses were produced by melting sulfide materials inside evacuated and sealed carbon-coated silica ampoules at 1150 °C for 12 h and quenching to room temperature to form glass. Glass samples were then characterized by IR and Raman spectroscopies and differential thermal analysis (DTA). It was found that by increasing the modifier concentration, the predominantly Ge 4 SRO units, the superscript defines the number of bridging sulfur (BS) ions in the tetrahedral network found in GeS 2 glasses, are ultimately converted to Ge 0 units at >40 mol% network modifier content through the generation of non-bridging sulfur (NBS) ions. These molecular ionic units still form a glassy network, with some of the highest reported T g values to date for a pure sulfide glass. This suggests that this composition has strong ionic bonds between negatively-charged tetrahedral SRO units and the positively-charged modifier cations. While the glass network is depolymerized in the high modifier content glasses though the formation of a high concentration of molecular ionic Ge 0 SRO groups, they are, nevertheless, homogeneous glassy materials that exhibit the largest T g and Δ T (difference between crystallization temperature, T c, and T g) values of glasses in this system, making them the optimal glasses for high T g IR optical components, including, potentially, refractory IR optical fibers.« less

Identification of hydrophilic group formation on polymer surface during Ar{sup +} ion irradiation in O{sub 2} environment

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

Cho, J.S.; Choi, W.K.; Jung, H.J.

1997-12-01

Ar{sup +} ion irradiation on low density polyethylene (LDPE), and polystyrene (PS) was performed in an O{sub 2} environment in order to improve wettability of polymers to water and to identify the formation of hydrophilic groups originated from chemical reactions on the surface of polymers. Doses of a broad Ar{sup +} ion beam of 1 keV energy were changed from 5 {times} 10{sup 15} to 1 {times} 10{sup 17}/cm{sup 2} and the rate of oxygen gas flowing near the sample surface was varied from 0 to 7 ml/min. The contact angle of polymers was not reduced much by Ar{sup +}more » ion irradiation without oxygen gas. However, it dropped largely to a minimum of 35{degree} and 26{degree} for Ar{sup +} ion irradiation in the presence of flowing oxygen gas on LDPE and PS, respectively. From x-ray photoelectron spectroscopy analysis, it was observed that hydrophilic groups were formed on the surface of polymers through an ion-assisted chemical reaction between the ion-induced unstable chains and oxygen. The newly formed hydrophilic group was identified as {single_bond}(C{double_bond}){single_bond} bond and {single_bond}(C{double_bond}O){single_bond}O{single_bond} bond. The contact angle of polymer was greatly dependent on the hydrophilic group formed on the surface.« less

Room-Temperature Phosphorescence in Pure Organic Materials: Halogen Bonding Switching Effects.

PubMed

Xiao, Lu; Wu, Yishi; Yu, Zhenyi; Xu, Zhenzhen; Li, Jinbiao; Liu, Yanping; Yao, Jiannian; Fu, Hongbing

2018-02-06

Organic room-temperature phosphorescence (ORTP), when combined with external stimuli-responsive capability, is very attractive for sensors and bio-imaging devices, but remains challenging. Herein, by doping two β-iminoenamine-BF 2 derivatives (S-2CN and S-2I) into a 4-iodoaniline (I-Ph-NH 2 ) crystalline matrix, the formation of S-2CN⋅⋅⋅I-Ph-NH 2 and S-2I⋅⋅⋅I-Ph-NH 2 halogen bonds leads to bright-red RTP emissions from these two host-guest doped crystals (hgDCs) with quantum efficiencies up to 13.43 % and 15.96 %, respectively. Upon treatment with HCl, the competition of I-Ph-NH 2 ⋅HCl formation against S-2I⋅⋅⋅I-Ph-NH 2 halogen bonding switches off the red RTP from S-2I/I-Ph-NH 2 hgDCs, whereas the stable halogen-bonded S-2CN⋅⋅⋅I-Ph-NH 2 ensures red RTP from S-2CN/I-Ph-NH 2 hgDCs remains unchanged. A security protection luminescence pattern by using these different HCl-responsive RTP behaviors was designed. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Electrochemical Cobalt-Catalyzed C-H Activation.

PubMed

Sauermann, Nicolas; Meyer, Tjark H; Ackermann, Lutz

2018-06-19

Carbon-heteroatom bonds represent omnipresent structural motifs of the vast majority of functionalized materials and bioactive compounds. C-H activation has emerged as arguably the most efficient strategy to construct C-Het bonds. Despite of major advances, these C-H transformations were largely dominated by precious transition metal catalysts, in combination with stoichiometric, toxic metal oxidants. Herein, we discuss the recent evolution of cobalt-catalyzed C-H activations that enable C-Het formations with electricity as the sole sustainable oxidant until May 2018. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

From Ruthenium to Copper: A la carte Tools for the Synthesis of Molecules of Interest.

PubMed

Monnier, Florian; Taillefer, Marc

2016-01-01

Well-defined ruthenium complexes and simple copper-ligand systems proved to be powerful catalysts for the construction of complex molecules from simple and abundant organic sources. In this account, chosen examples of reactions involving C-C bond formation catalyzed by [Ru(η(5)-C(5)H(5))-(CH(3)CN)(3)][PF(6)] will be presented. A practical synthesis of the versatile catalyst [Ru(η(5)-C(5)H(5))-(CH(3)CN)(3)][PF(6)] is also described via a simple and easy-handled procedure discovered in Geneva ten years ago. The second part of this review is focused on methodologies catalyzed by an association of a copper salt and a simple ligand for the formation of C-N, C-O and C-C bonds developed in our group in Montpellier. A brief overview of applications in life sciences and materials will conclude this article.

Bodipy-C60 triple hydrogen bonding assemblies as heavy atom-free triplet photosensitizers: preparation and study of the singlet/triplet energy transfer.

PubMed

Guo, Song; Xu, Liang; Xu, Kejing; Zhao, Jianzhang; Küçüköz, Betül; Karatay, Ahmet; Yaglioglu, Halime Gul; Hayvali, Mustafa; Elmali, Ayhan

2015-07-01

Supramolecular triplet photosensitizers based on hydrogen bonding-mediated molecular assemblies were prepared. Three thymine-containing visible light-harvesting Bodipy derivatives ( B-1 , B-2 and B-3 , which show absorption at 505 nm, 630 nm and 593 nm, respectively) were used as H-bonding modules, and 1,6-diaminopyridine-appended C 60 was used as the complementary hydrogen bonding module ( C-1 ), in which the C 60 part acts as a spin converter for triplet formation. Visible light-harvesting antennae with methylated thymine were prepared as references ( B-1-Me , B-2-Me and B-3-Me ), which are unable to form strong H-bonds with C-1 . Triple H-bonds are formed between each Bodipy antenna ( B-1 , B-2 and B-3 ) and the C 60 module ( C-1 ). The photophysical properties of the H-bonding assemblies and the reference non-hydrogen bond-forming mixtures were studied using steady state UV/vis absorption spectroscopy, fluorescence emission spectroscopy, electrochemical characterization, and nanosecond transient absorption spectroscopy. Singlet energy transfer from the Bodipy antenna to the C 60 module was confirmed by fluorescence quenching studies. The intersystem crossing of the latter produced the triplet excited state. The nanosecond transient absorption spectroscopy showed that the triplet state is either localized on the C 60 module (for assembly B-1·C-1 ), or on the styryl-Bodipy antenna (for assemblies B-2·C-1 and B-3·C-1 ). Intra-assembly forward-backward (ping-pong) singlet/triplet energy transfer was proposed. In contrast to the H-bonding assemblies, slow triplet energy transfer was observed for the non-hydrogen bonding mixtures. As a proof of concept, these supramolecular assemblies were used as triplet photosensitizers for triplet-triplet annihilation upconversion.

Evidence for a novel chemisorption bond: Formate (HCO/sub 2/) on Cu(100)

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

Stoehr, J.; Outka, D.A.; Madix, R.J.

1985-03-25

Surface extended-x-ray-absorption fine-structure measurements reveal that formate (HCO/sub 2/) groups on Cu(100) chemisorb via the two oxygen atoms in adjacent fourfold hollow sites with an average O-Cu nearest-neighbor bond length of 2.38 +- 0.03 A. This distance is sig- nificantly (approx.0.4 A) longer than typical O-Cu bonds in bulk compounds and all known surface complexes. The unusually large O-Cu distance is attributed to a steric effect involving the C atom in HCO/sub 2/ and the nearest-neighbor Cu surface atoms.

Enantioselective C(sp3)‒H bond activation by chiral transition metal catalysts.

PubMed

Saint-Denis, Tyler G; Zhu, Ru-Yi; Chen, Gang; Wu, Qing-Feng; Yu, Jin-Quan

2018-02-16

Organic molecules are rich in carbon-hydrogen bonds; consequently, the transformation of C-H bonds to new functionalities (such as C-C, C-N, and C-O bonds) has garnered much attention by the synthetic chemistry community. The utility of C-H activation in organic synthesis, however, cannot be fully realized until chemists achieve stereocontrol in the modification of C-H bonds. This Review highlights recent efforts to enantioselectively functionalize C(sp 3 )-H bonds via transition metal catalysis, with an emphasis on key principles for both the development of chiral ligand scaffolds that can accelerate metalation of C(sp 3 )-H bonds and stereomodels for asymmetric metalation of prochiral C-H bonds by these catalysts. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Modeling of S-Nitrosothiol-Thiol Reactions of Biological Significance: HNO Production by S-Thiolation Requires a Proton Shuttle and Stabilization of Polar Intermediates.

PubMed

Ivanova, Lena V; Cibich, Daniel; Deye, Gregory; Talipov, Marat R; Timerghazin, Qadir K

2017-04-18

Nitroxyl (HNO), a reduced form of the important gasotransmitter nitric oxide, exhibits its own unique biological activity. A possible biological pathway of HNO formation is the S-thiolation reaction between thiols and S-nitrosothiols (RSNOs). Our density functional theory (DFT) calculations suggested that S-thiolation proceeds through a proton transfer from the thiol to the RSNO nitrogen atom, which increases electrophilicity of the RSNO sulfur, followed by nucleophilic attack by thiol, yielding a charge-separated zwitterionic intermediate structure RSS + (R)N(H)O - (Zi), which decomposes to yield HNO and disulfide RSSR. In the gas phase, the proton transfer and the S-S bond formation are asynchronous, resulting in a high activation barrier (>40 kcal mol -1 ), making the reaction infeasible. However, the barrier can decrease below the S-N bond dissociation energy in RSNOs (≈30 kcal mol -1 ) upon transition into an aqueous environment that stabilizes Zi and provides a proton shuttle to synchronize the proton transfer and the S-S bond formation. These mechanistic features suggest that S-thiolation can easily lend itself to enzymatic catalysis and thus can be a possible route of endogenous HNO production. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Tuning the oxidative power of free iron-sulfur clusters.

PubMed

Lang, Sandra M; Zhou, Shaodong; Schwarz, Helmut

2017-03-15

The gas-phase reactions between a series of di-iron sulfur clusters Fe 2 S x + (x = 1-3) and the small alkenes C 2 H 4 , C 3 H 6 , and C 4 H 8 have been investigated by means of Fourier-transform ion-cyclotron resonance mass spectrometry. For all studied alkenes, the reaction efficiency is found to increase in the order Fe 2 S + < Fe 2 S 2 + < Fe 2 S 3 + . In particular, Fe 2 S + and Fe 2 S 2 + only form simple association products, whereas the sulfur-rich Fe 2 S 3 + is able to dehydrogenate propene and 2-butene via desulfurization of the cluster and formation of H 2 S. This indicates an increased propensity to induce oxidation reactions, i.e. oxidative power, of Fe 2 S 3 + that is attributed to an increased formal oxidation state of the iron atoms. Furthermore, the ability of Fe 2 S 3 + to activate and dissociate the C-H bonds of the alkenes is observed to increase with increasing size of the alkene and thus correlates with the alkene ionization energy.

Enhancement of peptide bond formation by polyribonucleotides on clay surfaces in fluctuating environments

NASA Technical Reports Server (NTRS)

White, D. H.; Erickson, J. C.

1981-01-01

The selective effects of polyribonucleotides on the formation of glycine peptide bonds in glycine on clay surfaces are investigated as a model for a template mechanism for the effects of polynucleotides on peptide bond formation. Free oligoglycine yields were determined for the cycling reaction of glycine in the presence and absence of clay and polyribonucleotides or polydeoxyribonucleotides. The polyribonucleotides are observed to lead to increases of up to fourfold increases in oligoglycine formed, with greater enhancements for poly-G nucleotides than for poly-A, poly-U and poly-C, indicating a codonic bias. Polydeoxyribonucleotides are found to provide no enhancement in peptide formation rates, and yields were also greatly reduced in the absence of clay. A mechanism for peptide synthesis is proposed which involves the activation of glycine on the clay surface, followed by the formation of esters between glycine and the 2-prime OH groups of the polyribonucleotide and peptide bonds between adjacent amino acyl esters. It is pointed out that if this mechanism is correct, it may provide a basis for a direct template translation process, which would produce a singlet genetic code.

Thermodynamic studies of iron chelation with doxycycline in acidic medium

NASA Astrophysics Data System (ADS)

Javed, Javeria; Zahir, Erum

2017-06-01

Doxycycline (DOX) is a broad-spectrum tetracycline antibiotic synthetically derived from oxytetracycline. The complex formation of this drug with iron(III) was studied using spectrophotometry. The thermodynamic parameters of the systems were calculated using the changes in the absorption spectra which occur due to hydrogen bond or complex formation. Thermodynamic parameters of the formation of iron(III) complex with doxycycline (Δ H, Δ G, Δ S, and stability constants) were determined spectrophotometrically at a wavelength corresponding to absorption maximum (374.5 nm) at three different temperatures (22, 35, and 45°C). The obtained data show that the complex has metal to ligand molar ratio of 1: 2 at pH 2-3. The stability constants were calculated to be 13.99 × 106, 7.06 × 105, and 1.29 × 106 by mole ratio method at 22, 35, and 45°C, respectively.

Formate binding near the redox-active tyrosineD in photosystem II: consequences on the properties of tyrD.

PubMed

Hienerwadel, Rainer; Gourion-Arsiquaud, Samuel; Ballottari, Matteo; Bassi, Roberto; Diner, Bruce A; Berthomieu, Catherine

2005-06-01

Formate and phosphate affect substantially the rate of tyrosine D (TyrD) oxidation and the stability of the radical TyrD* in Photosystem II [Hienerwadel R, Boussac A, Breton J and Berthomieu C (1996) Biochemistry 35: 15447-15460]. This observation prompted us to analyze the influence of formate and phosphate on the environment of TyrD using FTIR spectroscopy. The nu (CO) IR mode of TyrD* at 1503 cm-1 remains unchanged whatever the buffer used at pH 6 and whether formate is present or not in the sample. Similarly, the main IR mode of reduced TyrD remains at approximately 1250 cm-1 in all tested conditions. We thus conclude that formate does not modify the hydrogen-bonded interactions of TyrD and TyrD* with neighbouring D2His189 and D2Gln164. In the TyrD-state, an IR mode of formate significantly different from that observed in solution, is detected using 13C-formate, showing that formate forms a strong electrostatic interaction within PS II. The presence of formate affects also IR bands that may be assigned to an arginine side chain. Upon TyrD* formation, formate does not protonate but its binding interaction weakens. A proton uptake by Mes or phosphate buffer is detected, which is not observed when BisTris is used as a buffer. In these latter conditions, IR bands characteristic of the protonation of a carboxylate group of the protein are detected instead. The present IR data and the recent structural model of the TyrD environment proposed by Ferreira KN, Iverson TM, Maghlaoui K, Barber J and Iwata S [(2004) Science 303: 1831-1838], suggest that the proton released upon TyrD* formation is shared within a hydrogen bonding network including D2Arg294, and CP47Glu364 and that perturbation of this network by formate - possibly binding near D2Arg294 - substantially affects the properties of TyrD.

Formation of Covalently Modified Folding Intermediates of Simian Virus 40 Vp1 in Large T Antigen-Expressing Cells

PubMed Central

Watanabe, Marika; Phamduong, Ellen; Huang, Chu-Han; Itoh, Noriko; Bernal, Janie; Nakanishi, Akira; Rundell, Kathleen; Gjoerup, Ole

2013-01-01

The folding and pentamer assembly of the simian virus 40 (SV40) major capsid protein Vp1, which take place in the infected cytoplasm, have been shown to progress through disulfide-bonded Vp1 folding intermediates. In this report, we further demonstrate the existence of another category of Vp1 folding or assembly intermediates: the nonreducible, covalently modified mdVp1s. These species were present in COS-7 cells that expressed a recombinant SV40 Vp1, Vp1ΔC, through plasmid transfection. The mdVp1s persisted under cell and lysate treatment and SDS-PAGE conditions that are expected to have suppressed the formation of artifactual disulfide cross-links. As shown through a pulse-chase analysis, the mdVp1s were derived from the newly synthesized Vp1ΔC in the same time frame as Vp1's folding and oligomerization. The apparent covalent modifications occurred in the cytoplasm within the core region of Vp1 and depended on the coexpression of the SV40 large T antigen (LT) in the cells. Analogous covalently modified species were found with the expression of recombinant polyomavirus Vp1s and human papillomavirus L1s in COS-7 cells. Furthermore, the mdVp1s formed multiprotein complexes with LT, Hsp70, and Hsp40, and a fraction of the largest mdVp1, md4, was disulfide linked to the unmodified Vp1ΔC. Both mdVp1 formation and most of the multiprotein complex formation were blocked by a Vp1 folding mutation, C87A-C254A. Our observations are consistent with a role for LT in facilitating the folding process of SV40 Vp1 by stimulating certain covalent modifications of Vp1 or by recruiting certain cellular proteins. PMID:23427157

IR spectroscopy as a source of data on bond strengths

NASA Astrophysics Data System (ADS)

Finkelshtein, E. I.; Shamsiev, R. S.

2018-02-01

The aim of this work is the estimation of double bond strength, namely Cdbnd O bonds in ketones and aldehydes and Cdbnd C bonds in various compounds. By the breaking of these bonds one or both fragments formed are carbenes, for which experimental data on the enthalpies of formation (ΔHf298) are scarce. Thus for the estimation of ΔHf298 of the corresponding carbenes, the empirical equations were proposed based on different approximations. In addition, a quantum chemical calculations of the ΔHf298 values of carbenes were performed, and the data obtained were compared with experimental values and the results of earlier calculations. Equations for the calculation of Cdbnd O bond strengths of different ketones and aldehydes from the corresponding stretching frequencies ν(Cdbnd O) were derived. Using the proposed equations, the strengths of Cdbnd O bonds of 25 ketones and 12 conjugated aldehydes, as well as Cdbnd C bonds of 13 hydrocarbons and 7 conjugated aldehydes were estimated for the first time. Linear correlations of Cdbnd C and Cdbnd O bond strengths with the bond lengths were established, and the equations permitting the estimation of the double bond strengths and lengths with acceptable accuracy were obtained. Also, the strength of central Cdbnd C bond of stilbene was calculated for the first time. The uncertainty of the strengths of double bonds obtained may be regarded as accurate ±10-15 kJ/mol.

Structure and Reaction Mechanism of Basil Eugenol Synthase

PubMed Central

Louie, Gordon V.; Baiga, Thomas J.; Bowman, Marianne E.; Koeduka, Takao; Taylor, John H.; Spassova, Snejina M.; Pichersky, Eran; Noel, Joseph P.

2007-01-01

Phenylpropenes, a large group of plant volatile compounds that serve in multiple roles in defense and pollinator attraction, contain a propenyl side chain. Eugenol synthase (EGS) catalyzes the reductive displacement of acetate from the propenyl side chain of the substrate coniferyl acetate to produce the allyl-phenylpropene eugenol. We report here the structure determination of EGS from basil (Ocimum basilicum) by protein x-ray crystallography. EGS is structurally related to the short-chain dehydrogenase/reductases (SDRs), and in particular, enzymes in the isoflavone-reductase-like subfamily. The structure of a ternary complex of EGS bound to the cofactor NADP(H) and a mixed competitive inhibitor EMDF ((7S,8S)-ethyl (7,8-methylene)-dihydroferulate) provides a detailed view of the binding interactions within the EGS active site and a starting point for mutagenic examination of the unusual reductive mechanism of EGS. The key interactions between EMDF and the EGS-holoenzyme include stacking of the phenyl ring of EMDF against the cofactor's nicotinamide ring and a water-mediated hydrogen-bonding interaction between the EMDF 4-hydroxy group and the side-chain amino moiety of a conserved lysine residue, Lys132. The C4 carbon of nicotinamide resides immediately adjacent to the site of hydride addition, the C7 carbon of cinnamyl acetate substrates. The inhibitor-bound EGS structure suggests a two-step reaction mechanism involving the formation of a quinone-methide prior to reduction. The formation of this intermediate is promoted by a hydrogen-bonding network that favors deprotonation of the substrate's 4-hydroxyl group and disfavors binding of the acetate moiety, akin to a push-pull catalytic mechanism. Notably, the catalytic involvement in EGS of the conserved Lys132 in preparing the phenolic substrate for quinone methide formation through the proton-relay network appears to be an adaptation of the analogous role in hydrogen bonding played by the equivalent lysine residue in other enzymes of the SDR family. PMID:17912370

Crystal structure of bis-(3-bromo-pyridine-κN)bis-(O-ethyl di-thio-carbonato-κ(2) S,S')nickel(II).

PubMed

Kant, Rajni; Kour, Gurvinder; Anthal, Sumati; Neerupama; Sachar, Renu

2015-01-01

In the title mol-ecular complex, [Ni(C3H5OS2)2(C5H4BrN)2], the Ni(2+) cation is located on a centre of inversion and has a distorted octa-hedral N2S4 environment defined by two chelating xanthate ligands and two monodentate pyridine ligands. The C-S bond lengths of the thio-carboxyl-ate group are indicative of a delocalized bond and the O-Csp (2) bond is considerably shorter than the O-Csp (3) bond, consistent with a significant contribution of one resonance form of the xanthate anion that features a formal C=O+ unit and a negative charge on each of the S atoms. The packing of the mol-ecules is stabilized by C-H⋯S and C-H⋯π inter-actions. In addition, π-π inter-actions between the pyridine rings [centroid-to-centroid distance = 3.797 (3) Å] are also present. In the crystal structure, mol-ecules are arranged in rows along [100], forming layers parallel to (010) and (001).

A conserved catalytic residue in the ubiquitin-conjugating enzyme family

PubMed Central

Wu, Pei-Ying; Hanlon, Mary; Eddins, Michael; Tsui, Colleen; Rogers, Richard S.; Jensen, Jane P.; Matunis, Michael J.; Weissman, Allan M.; Wolberger, Cynthia P.; Pickart, Cecile M.

2003-01-01

Ubiquitin (Ub) regulates diverse functions in eukaryotes through its attachment to other proteins. The defining step in this protein modification pathway is the attack of a substrate lysine residue on Ub bound through its C-terminus to the active site cysteine residue of a Ub-conjugating enzyme (E2) or certain Ub ligases (E3s). So far, these E2 and E3 cysteine residues are the only enzyme groups known to participate in the catalysis of conjugation. Here we show that a strictly conserved E2 asparagine residue is critical for catalysis of E2- and E2/RING E3-dependent isopeptide bond formation, but dispensable for upstream and downstream reactions of Ub thiol ester formation. In constrast, the strictly conserved histidine and proline residues immediately upstream of the asparagine are dispensable for catalysis of isopeptide bond formation. We propose that the conserved asparagine side chain stabilizes the oxyanion intermediate formed during lysine attack. The E2 asparagine is the first non-covalent catalytic group to be proposed in any Ub conjugation factor. PMID:14517261

Reactions between palladium and gallium arsenide: Bulk versus thin-film studies

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

Lin, J.; Hsieh, K.; Schulz, K.J.

1988-01-01

Reactions between Pd and GaAs have been studied using bulk-diffusion couples of Pd (approx.0.6 mm thick)/GaAs and thin-film Pd (50 and 160 nm)/GaAs samples. The sequence of phase formation at 600 /sup 0/C between bulk Pd and GaAs was established. Initial formation of the solution phase ..mu.. and the ternary phase T does not represent the stable configuration. The stable configuration is GaAs chemically bondepsilonchemically bondlambdachemically bond..gamma..chemically bond..nu..chemically bondPd and is termed the diffusion path between GaAs and Pd. The sequence of phase formation for the bulk-diffusion couples is similar at 500 /sup 0/C. Phase formation for the thin-film Pd/GaAsmore » specimens was studied at 180, 220, 250, 300, 350, 400, 450, 600, and 1000 /sup 0/C for various annealing times. The sequence of phase formation obtained from the thin-film experiments is rationalized readily from the known ternary phase equilibria of Ga--Pd--As and the results from the bulk-diffusion couples of Pd/GaAs. The thin-film results reported in the literature are likewise rationalized. The diffusion path concept provides a useful guide in understanding the phase formation in Pd--GaAs interface or any other M--GaAs interface. This information is important in designing a uniform, stable contact for the metallization of GaAs.« less

Photochemical formation rates of organic aerosols through time-resolved in situ laboratory measurements

NASA Astrophysics Data System (ADS)

Ádámkovics, Máté; Boering, Kristie A.

2003-08-01

The fundamental kinetics of photochemical particle formation and the mechanism(s) for polymerization of hydrocarbons to form condensable species under anoxic conditions have yet to be determined experimentally. Thus these processes remain highly parameterized in models of planetary atmospheres. We have developed instrumentation for simultaneously measuring the net production rates of complex gas-phase hydrocarbons and of organic aerosols formed from irradiating mixtures of simple precursor gases through online quadrupole mass spectrometry measurements of stable gas-phase species and in situ optical scattering detection of the particulates at 633 nm. The new technique and results for the generation of hydrocarbon aerosol from the irradiation of pure, gas-phase CH4 at a pressure of 70 Torr with 8.8 +/- 0.8 × 1015 photons s-1 of vacuum ultraviolet light (120-300nm) are reported. The net production rates for the following gaseous species are measured: H2 = 9.9 +/- 2.2 . 1011, C2H2 = 2.8 +/- 0.5 . 1010, C2H4 = 5.5 +/- 9.4 . 109, C2H6 = 8.6 +/- 2.5 . 1010, C3H4 = 2.5 +/- 1.2 . 109, C4H2 = 6.6 +/- 5.0 . 108, C4H10 = 1.3 +/- 0.5 . 1010 cm-3 s-1. The production of hydrocarbon particulates is detected by optical scattering, and the condensed phase C-C bond formation rate is inferred to be 7.5 +/- 3.1 . 1011 cm-3 s-1. Applications of this technique to the atmospheres of Titan and terrestrial-like planets, such as the early Earth before the rise of molecular oxygen, are discussed.

Activation of remote meta-C-H bonds assisted by an end-on template.

PubMed

Leow, Dasheng; Li, Gang; Mei, Tian-Sheng; Yu, Jin-Quan

2012-06-27

Functionalization of unactivated carbon-hydrogen (C-H) single bonds is an efficient strategy for rapid generation of complex molecules from simpler ones. However, it is difficult to achieve selectivity when multiple inequivalent C-H bonds are present in the target molecule. The usual approach is to use σ-chelating directing groups, which lead to ortho-selectivity through the formation of a conformationally rigid six- or seven-membered cyclic pre-transition state. Despite the broad utility of this approach, proximity-driven reactivity prevents the activation of remote C-H bonds. Here we report a class of easily removable nitrile-containing templates that direct the activation of distal meta-C-H bonds (more than ten bonds away) of a tethered arene. We attribute this new mode of C-H activation to a weak 'end-on' interaction between the linear nitrile group and the metal centre. The 'end-on' coordination geometry relieves the strain of the cyclophane-like pre-transition state of the meta-C-H activation event. In addition, this template overrides the intrinsic electronic and steric biases as well as ortho-directing effects with two broadly useful classes of arene substrates (toluene derivatives and hydrocinnamic acids).

C-Cl bond activation and catalytic hydrodechlorination of hexachlorobenzene by cobalt and nickel complexes with sodium formate as a reducing agent.

PubMed

Li, Junye; Li, Xiaoyan; Wang, Lin; Hu, Qingping; Sun, Hongjian

2014-05-14

A benzyne cobalt complex, Co(η(2)-C6Cl4)(PMe3)3 (2), was generated from the reaction of hexachlorobenzene with 2 equiv. of Co(PMe3)4 through selective activation of two C-Cl bonds of hexachlorobenzene. Meanwhile, the byproduct CoCl2(PMe3)3 was also confirmed by IR spectra. The cobalt(II) complex, CoCl(C6Cl5)(PMe3)3 (1), as an intermediate in the formation of aryne complex 2, was also isolated by the reaction of hexachlorobenzene with the stoichiometric amount of Co(PMe3)4. Complex 2 could be obtained by the reaction of 1 with Co(PMe3)4. Under similar reaction conditions, the reaction of Ni(PMe3)4 with hexachlorobenzene afforded only a mono-(C-Cl) bond activation nickel(II) complex, NiCl(C6H5)(PMe3)2 (5). The expected benzyne nickel complex was not formed. The structures of complexes 2 and 5 were determined by X-ray single crystal diffraction. Successful selective hydrodechlorinations of hexachlorobenzene were studied and in the presence of Co(PMe3)4 or Ni(PMe3)4 as catalysts and sodium formate as a reducing agent pentachlorobenzene and 1,2,4,5-tetrachlorobenzene were obtained. The catalytic hydrodechlorination mechanism is proposed and discussed.

Photosynthetic dioxygen formation studied by time-resolved delayed fluorescence measurements--method, rationale, and results on the activation energy of dioxygen formation.

PubMed

Buchta, Joachim; Grabolle, Markus; Dau, Holger

2007-06-01

The analysis of the time-resolved delayed fluorescence (DF) measurements represents an important tool to study quantitatively light-induced electron transfer as well as associated processes, e.g. proton movements, at the donor side of photosystem II (PSII). This method can provide, inter alia, insights in the functionally important inner-protein proton movements, which are hardly detectable by conventional spectroscopic approaches. The underlying rationale and experimental details of the method are described. The delayed emission of chlorophyll fluorescence of highly active PSII membrane particles was measured in the time domain from 10 mus to 60 ms after each flash of a train of nanosecond laser pulses. Focusing on the oxygen-formation step induced by the third flash, we find that the recently reported formation of an S4-intermediate prior to the onset of O-O bond formation [M. Haumann, P. Liebisch, C. Müller, M. Barra, M. Grabolle, H. Dau, Science 310, 1019-1021, 2006] is a multiphasic process, as anticipated for proton movements from the manganese complex of PSII to the aqueous bulk phase. The S4-formation involves three or more likely sequential steps; a tri-exponential fit yields time constants of 14, 65, and 200 mus (at 20 degrees C, pH 6.4). We determine that S4-formation is characterized by a sizable difference in Gibbs free energy of more than 90 meV (20 degrees C, pH 6.4). In the second part of the study, the temperature dependence (-2.7 to 27.5 degrees C) of the rate constant of dioxygen formation (600/s at 20 degrees C) was investigated by analysis of DF transients. If the activation energy is assumed to be temperature-independent, a value of 230 meV is determined. There are weak indications for a biphasicity in the Arrhenius plot, but clear-cut evidence for a temperature-dependent switch between two activation energies, which would point to the existence of two distinct rate-limiting steps, is not obtained.

Sugar Radical Formation by a Proton Coupled Hole Transfer in 2′-Deoxyguanosine Radical Cation (2′-dG•+): A Theoretical Treatment

PubMed Central

Kumar, Anil; Sevilla, Michael D.

2009-01-01

Previous experimental and theoretical work has established that electronic excitation of a guanine cation radical in nucleosides or in DNA itself leads to sugar radical formation by deprotonation from the dexoxyribose sugar. In this work we investigate a ground electronic state pathway for such sugar radical formation in a hydrated one electron oxidized 2′-deoxyguanosine (dG•+ + 7H2O), using density functional theory (DFT) with the B3LYP functional and the 6-31G* basis set. We follow the stretching of the C5′-H bond in dG•+ to gain an understanding of the energy requirements to transfer the hole from the base to sugar ring and then to deprotonate to proton acceptor sites in solution and on the guanine ring. The geometries of reactant (dG•+ + 7H2O), transition state (TS) for deprotonation of C5′ site and product (dG(•C5′, N7-H+) + 7 H2O) were fully optimized. The zero point energy (ZPE) corrected activation energy (TS) for the proton transfer (PT) from C5′ is calculated to be 9.0 kcal/mol and is achieved by stretching the C5′-H bond by 0.13 Å from its equilibrium bond distance (1.099 Å). Remarkably, this small bond stretch is sufficient to transfer the “hole” (positive charge and spin) from guanine to the C5′ site on the deoxyribose group. Beyond the TS, the proton (H+) spontaneously adds to water to form a hydronium ion (H3O+) as an intermediate. The proton subsequently transfers to the N7 site of the guanine (product). The 9 kcal/mol barrier suggests slow thermal conversion of the cation radical to the sugar radical but also suggests that localized vibrational excitations would be sufficient to induce rapid sugar radical formation in DNA base cation radicals. PMID:19754084

High NaCl- and urea-induced posttranslational modifications that increase glycerophosphocholine by inhibiting GDPD5 phosphodiesterase.

PubMed

Topanurak, Supachai; Ferraris, Joan D; Li, Jinxi; Izumi, Yuichiro; Williams, Chester K; Gucek, Marjan; Wang, Guanghui; Zhou, Xiaoming; Burg, Maurice B

2013-04-30

Glycerophosphocholine (GPC) is high in cells of the renal inner medulla where high interstitial NaCl and urea power concentration of the urine. GPC protects inner medullary cells against the perturbing effects of high NaCl and urea by stabilizing intracellular macromolecules. Degradation of GPC is catalyzed by the glycerophosphocholine phosphodiesterase activity of glycerophosphodiester phosphodiesterase domain containing 5 (GDPD5). We previously found that inhibitory posttranslational modification (PTM) of GDPD5 contributes to high NaCl- and urea-induced increase of GPC. The purpose of the present studies was to identify the PTM(s). We find at least three such PTMs in HEK293 cells: (i) Formation of a disulfide bond between C25 and C571. High NaCl and high urea increase reactive oxygen species (ROS). The ROS increase disulfide bonding between GDPD5-C25 and -C571, which inhibits GDPD5 activity, as supported by the findings that the antioxidant N-acetylcysteine prevents high NaCl- and urea-induced inhibition of GDPD5; GDPD5-C25S/C571S mutation or over expression of peroxiredoxin increases GDPD5 activity; H2O2 inhibits activity of wild type GDPD5, but not of GDPD5-C25S/C571S; and peroxiredoxin is relatively low in the renal inner medulla where GPC is high. (ii) Dephosphorylation of GDPD5-T587. GDPD5 threonine 587 is constitutively phosphorylated. High NaCl and high urea dephosphorylate GDPD5-T587. Mutation of GDPD5-T587 to alanine, which cannot be phosphorylated, decreases GPC-PDE activity of GDPD5. (iii) Alteration at an unknown site mediated by CDK1. Inhibition of CDK1 protein kinase reduces GDE-PDE activity of GDPD5 without altering phosphorylation at T587, and CDK1/5 inhibitor reduces activity of GDPD5- C25S/C571S-T587A.

High NaCl- and urea-induced posttranslational modifications that increase glycerophosphocholine by inhibiting GDPD5 phosphodiesterase

PubMed Central

Topanurak, Supachai; Ferraris, Joan D.; Li, Jinxi; Izumi, Yuichiro; Williams, Chester K.; Gucek, Marjan; Wang, Guanghui; Zhou, Xiaoming; Burg, Maurice B.

2013-01-01

Glycerophosphocholine (GPC) is high in cells of the renal inner medulla where high interstitial NaCl and urea power concentration of the urine. GPC protects inner medullary cells against the perturbing effects of high NaCl and urea by stabilizing intracellular macromolecules. Degradation of GPC is catalyzed by the glycerophosphocholine phosphodiesterase activity of glycerophosphodiester phosphodiesterase domain containing 5 (GDPD5). We previously found that inhibitory posttranslational modification (PTM) of GDPD5 contributes to high NaCl- and urea-induced increase of GPC. The purpose of the present studies was to identify the PTM(s). We find at least three such PTMs in HEK293 cells: (i) Formation of a disulfide bond between C25 and C571. High NaCl and high urea increase reactive oxygen species (ROS). The ROS increase disulfide bonding between GDPD5-C25 and -C571, which inhibits GDPD5 activity, as supported by the findings that the antioxidant N-acetylcysteine prevents high NaCl- and urea-induced inhibition of GDPD5; GDPD5-C25S/C571S mutation or over expression of peroxiredoxin increases GDPD5 activity; H2O2 inhibits activity of wild type GDPD5, but not of GDPD5-C25S/C571S; and peroxiredoxin is relatively low in the renal inner medulla where GPC is high. (ii) Dephosphorylation of GDPD5-T587. GDPD5 threonine 587 is constitutively phosphorylated. High NaCl and high urea dephosphorylate GDPD5-T587. Mutation of GDPD5-T587 to alanine, which cannot be phosphorylated, decreases GPC-PDE activity of GDPD5. (iii) Alteration at an unknown site mediated by CDK1. Inhibition of CDK1 protein kinase reduces GDE-PDE activity of GDPD5 without altering phosphorylation at T587, and CDK1/5 inhibitor reduces activity of GDPD5- C25S/C571S-T587A. PMID:23589856

C-H bond functionalization via hydride transfer: formation of α-arylated piperidines and 1,2,3,4-tetrahydroisoquinolines via stereoselective intramolecular amination of benzylic C-H bonds.

PubMed

Vadola, Paul A; Carrera, Ignacio; Sames, Dalibor

2012-08-17

We here report a study of the intramolecular amination of sp(3) C-H bonds via the hydride transfer cyclization of N-tosylimines (HT-amination). In this transformation, 5-aryl aldehydes are subjected to N-toluenesulfonamide in the presence of BF(3)·OEt(2) to effect imine formation and HT-cyclization, leading to 2-arylpiperidines and 3-aryl-1,2,3,4-tetrahydroisoquinolines in a one-pot procedure. We examined the reactivity of a range of aldehyde substrates as a function of their conformational flexibility. Substrates of higher conformational rigidity were more reactive, giving higher yields of the desired products. However, a single substituent on the alkyl chain linking the N-tosylimine and the benzylic sp(3) C-H bonds was sufficient for HT-cyclization to occur. In addition, an examination of various arenes revealed that the electronic character of the hydridic C-H bonds dramatically affects the efficiency of the reaction. We also found that this transformation is highly stereoselective; 2-substituted aldehydes yield cis-2,5-disubstituted piperidines, while 3-substituted aldehydes afford trans-2,4-disubstituted piperidines. The stereoselectivity is a consequence of thermodynamic control. The pseudoallylic strain between the arene and tosyl group on the piperidine ring is proposed to rationalize the greater stability of the isomer with the aryl ring in the axial position. This preferential placement of the arene is proposed to affect the observed stereoselectivity.

Metal-free, visible-light-mediated direct C-H arylation of heteroarenes with aryl diazonium salts.

PubMed

Hari, Durga Prasad; Schroll, Peter; König, Burkhard

2012-02-15

Visible light along with 1 mol % eosin Y catalyzes the direct C-H bond arylation of heteroarenes with aryl diazonium salts by a photoredox process. We have investigated the scope of the reaction for several aryl diazonium salts and heteroarenes. The general and easy procedure provides a transition-metal-free alternative for the formation of aryl-heteroaryl bonds.

Structure and physicochemical characterization of a naproxen–picolinamide cocrystal

PubMed Central

Kerr, Hannah E.; Softley, Lorna K.; Suresh, Kuthuru; Hodgkinson, Paul; Evans, Ivana Radosavljevic

2017-01-01

Naproxen (NPX) is a nonsteroidal anti-inflammatory drug with pain- and fever-relieving properties, currently marketed in the sodium salt form to overcome solubility problems; however, alternative solutions for improving its solubility across all pH values are desirable. NPX is suitable for cocrystal formation, with hydrogen-bonding possibilities via the COOH group. The crystal structure is presented of a 1:1 cocrystal of NPX with picolinamide as a coformer [systematic name: (S)-2-(6-meth­oxy­naphthalen-2-yl)propanoic acid–pyridine-2-carbox­amide (1/1), C14H14O3·C6H6N2O]. The pharmaceutically relevant physical properties were investigated and the intrinsic dissolution rate was found to be essentially the same as that of commercial naproxen. An NMR crystallography approach was used to investigate the H-atom positions in the two crystallographically unique COOH–CONH hydrogen-bonded dimers. 1H solid-state NMR distinguished the two carboxyl protons, despite the very similar crystallographic environments. The nature of the hydrogen bonding was confirmed by solid-state NMR and density functional theory calculations. PMID:28257010

Structure and physicochemical characterization of a naproxen-picolinamide cocrystal.

PubMed

Kerr, Hannah E; Softley, Lorna K; Suresh, Kuthuru; Hodgkinson, Paul; Evans, Ivana Radosavljevic

2017-03-01

Naproxen (NPX) is a nonsteroidal anti-inflammatory drug with pain- and fever-relieving properties, currently marketed in the sodium salt form to overcome solubility problems; however, alternative solutions for improving its solubility across all pH values are desirable. NPX is suitable for cocrystal formation, with hydrogen-bonding possibilities via the COOH group. The crystal structure is presented of a 1:1 cocrystal of NPX with picolinamide as a coformer [systematic name: (S)-2-(6-methoxynaphthalen-2-yl)propanoic acid-pyridine-2-carboxamide (1/1), C 14 H 14 O 3 ·C 6 H 6 N 2 O]. The pharmaceutically relevant physical properties were investigated and the intrinsic dissolution rate was found to be essentially the same as that of commercial naproxen. An NMR crystallography approach was used to investigate the H-atom positions in the two crystallographically unique COOH-CONH hydrogen-bonded dimers. 1 H solid-state NMR distinguished the two carboxyl protons, despite the very similar crystallographic environments. The nature of the hydrogen bonding was confirmed by solid-state NMR and density functional theory calculations.

Rational approaches for engineering novel functionalities in carbon-carbon bond forming enzymes

PubMed Central

Baker, Perrin; Seah, Stephen Y. K.

2012-01-01

Enzymes that catalyze carbon-carbon bond formation can be exploited as biocatalyst for synthetic organic chemistry. However, natural enzymes frequently do not possess the required properties or specificities to catalyze industrially useful transformations. This mini-review describes recent work using knowledge-guided site-specific mutagenesis of key active site residues to alter substrate specificity, stereospecificity and reaction specificity of these enzymes. In addition, examples of de novo designed enzymes that catalyze C-C bond reactions not found in nature will be discussed. PMID:24688644

Simultaneous formation of 3-deoxy-d-threo-hexo-2-ulose and 3-deoxy-d-erythro-hexo-2-ulose during the degradation of d-glucose derived Amadori rearrangement products: Mechanistic considerations.

PubMed

Kaufmann, Martin; Krüger, Sophie; Mügge, Clemens; Kroh, Lothar W

2018-03-22

Analyzing classical model reaction systems of Amadori rearrangement products (ARP) it became apparent that the formation of 3-deoxy-d-threo-hexo-2-ulose (3-deoxygalactosone, 3-DGal) during the degradation of ARPs is highly dependent on pH and the amino acid residue of the respective ARP. Based on a detailed analysis of the NMR chemical shifts of the sugar moieties of different ARPs, it could be derived that the formation of 3-DGal is sensitive to the stability of a co-operative hydrogen bond network which involves HO-C3, the deprotonated carboxyl functionality and the protonated amino nitrogen of the amino acid substituent. Participating in this bond network, HO-C3 is partially protonated which facilitates the elimination of water at C3. Based on that, a new mechanism of 3-deoxyglycosone formation is proposed. Copyright © 2018 Elsevier Ltd. All rights reserved.

Cobalt catalyzed carbonylation of unactivated C(sp3)–H bonds† †Electronic supplementary information (ESI) available. CCDC 1507203 (2t) & 1507204 (2a). For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c6sc05026c Click here for additional data file. Click here for additional data file.

PubMed Central

Barsu, Nagaraju; Bolli, Shyam Kumar

2017-01-01

A general efficient regioselective cobalt catalyzed carbonylation of unactivated C(sp3)–H bonds of aliphatic amides was demonstrated using atmospheric (1–2 atm) carbon monoxide as a C1 source. This straightforward approach provides access to α-spiral succinimide regioselectively in a good yield. Cobalt catalyzed sp3 C–H bond carbonylation is reported for the first time including the functionalization of (β)-C–H bonds of α-1°, 2°, 3° carbons and even internal (β)-C–H bonds. Our initial mechanistic investigation reveals that the C–H activation step is irreversible and will possibly be the rate determining step. PMID:28451350

Theoretical study of the Diels-Alder reaction between o-benzoquinone and norbornadiene

NASA Astrophysics Data System (ADS)

Quijano-Quiñones, Ramiro F.; Quesadas-Rojas, M.; Cuevas, Gabriel; Mena-Rejón, Gonzalo J.

2013-06-01

The reaction between norbornadiene and o-benzoquinone is an important step in polyalicyclic rigid structures synthesis. It has been considered that this reaction is an example of Diels-Alder (DA) and hetero-Diels-Alder (HDA) cycloadditions with o-benzoquinone acting as diene (forming C-C bonds) and heterodiene (forming O-C bonds). We have performed a Density Functional Theory study of this reaction, employing B3LYP, mPW1PW91, and B1B95 functionals and 6-31G(d,p) and 6-31+G(d,p) Gaussian type basis sets. The results indicate that Diels-Alder is a feasible mechanism for both reactions, but should not be the main route to the formation of products with C-C bonds.

Multinuclear Solid-State Magnetic Resonance as a Sensitive Probe of Structural Changes upon the Occurrence of Halogen Bonding in Co-crystals.

PubMed

Widdifield, Cory M; Cavallo, Gabriella; Facey, Glenn A; Pilati, Tullio; Lin, Jingxiang; Metrangolo, Pierangelo; Resnati, Giuseppe; Bryce, David L

2013-09-02

Although the understanding of intermolecular interactions, such as hydrogen bonding, is relatively well-developed, many additional weak interactions work both in tandem and competitively to stabilize a given crystal structure. Due to a wide array of potential applications, a substantial effort has been invested in understanding the halogen bond. Here, we explore the utility of multinuclear ((13)C, (14/15)N, (19)F, and (127)I) solid-state magnetic resonance experiments in characterizing the electronic and structural changes which take place upon the formation of five halogen-bonded co-crystalline product materials. Single-crystal X-ray diffraction (XRD) structures of three novel co-crystals which exhibit a 1:1 stoichiometry between decamethonium diiodide (i.e., [(CH3)3N(+)(CH2)10N(+)(CH3)3][2 I(-)]) and different para-dihalogen-substituted benzene moieties (i.e., p-C6X2Y4, X=Br, I; Y=H, F) are presented. (13)C and (15)N NMR experiments carried out on these and related systems validate sample purity, but also serve as indirect probes of the formation of a halogen bond in the co-crystal complexes in the solid state. Long-range changes in the electronic environment, which manifest through changes in the electric field gradient (EFG) tensor, are quantitatively measured using (14)N NMR spectroscopy, with a systematic decrease in the (14)N quadrupolar coupling constant (CQ) observed upon halogen bond formation. Attempts at (127)I solid-state NMR spectroscopy experiments are presented and variable-temperature (19)F NMR experiments are used to distinguish between dynamic and static disorder in selected product materials, which could not be conclusively established using solely XRD. Quantum chemical calculations using the gauge-including projector augmented-wave (GIPAW) or relativistic zeroth-order regular approximation (ZORA) density functional theory (DFT) approaches complement the experimental NMR measurements and provide theoretical corroboration for the changes in NMR parameters observed upon the formation of a halogen bond. Copyright © 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim.

Programmable Assembly of Peptide Amphiphile via Noncovalent-to-Covalent Bond Conversion

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

Sato, Kohei; Ji, Wei; Palmer, Liam C.

Controlling the number of monomers in a supramolecular polymer has been a great challenge in programmable self-assembly of organic molecules. One approach has been to make use of frustrated growth of the supramolecular assembly by tuning the balance of attractive and repulsive intermolecular forces. We report here on the use of covalent bond formation among monomers, compensating for intermolecular electrostatic repulsion, as a mechanism to control the length of a supramolecular nanofiber formed by self-assembly of peptide amphiphiles. Circular dichroism spectroscopy in combination with dynamic light scattering, size-exclusion chromatography, and transmittance electron microscope analyses revealed that hydrogen bonds between peptidesmore » were reinforced by covalent bond formation, enabling the fiber elongation. To examine these materials for their potential biomedical applications, cytotoxicity of nanofibers against C2C12 premyoblast cells was tested. We demonstrated that cell viability increased with an increase in fiber length, presumably because of the suppressed disruption of cell membranes by the fiber end-caps.« less

Programmable Assembly of Peptide Amphiphile via Noncovalent-to-Covalent Bond Conversion

DOE PAGES

Sato, Kohei; Ji, Wei; Palmer, Liam C.; ...

2017-06-22

Controlling the number of monomers in a supramolecular polymer has been a great challenge in programmable self-assembly of organic molecules. One approach has been to make use of frustrated growth of the supramolecular assembly by tuning the balance of attractive and repulsive intermolecular forces. We report here on the use of covalent bond formation among monomers, compensating for intermolecular electrostatic repulsion, as a mechanism to control the length of a supramolecular nanofiber formed by self-assembly of peptide amphiphiles. Circular dichroism spectroscopy in combination with dynamic light scattering, size-exclusion chromatography, and transmittance electron microscope analyses revealed that hydrogen bonds between peptidesmore » were reinforced by covalent bond formation, enabling the fiber elongation. To examine these materials for their potential biomedical applications, cytotoxicity of nanofibers against C2C12 premyoblast cells was tested. We demonstrated that cell viability increased with an increase in fiber length, presumably because of the suppressed disruption of cell membranes by the fiber end-caps.« less

Tandem reactions initiated by copper-catalyzed cross-coupling: a new strategy towards heterocycle synthesis.

PubMed

Liu, Yunyun; Wan, Jie-Ping

2011-10-21

Copper-catalyzed cross-coupling reactions which lead to the formation of C-N, C-O, C-S and C-C bonds have been recognized as one of the most useful strategies in synthetic organic chemistry. During past decades, important breakthroughs in the study of Cu-catalyzed coupling processes demonstrated that Cu-catalyzed reactions are broadly applicable to a variety of research fields related to organic synthesis. Representatively, employing these coupling transformations as key steps, a large number of tandem reactions have been developed for the construction of various heterocyclic compounds. These tactics share the advantages of high atom economics of tandem reactions as well as the broad tolerance of Cu-catalyst systems. Therefore, Cu-catalyzed C-X (X = N, O, S, C) coupling transformation-initiated tandem reactions were quickly recognized as a strategy with great potential for synthesizing heterocyclic compounds and gained worldwide attention. In this review, recent research progress in heterocycle syntheses using tandem reactions initiated by copper-catalyzed coupling transformations, including C-N, C-O, C-S as well as C-C coupling processes are summarized.

Protonation switching to the least-basic heteroatom of carbamate through cationic hydrogen bonding promotes the formation of isocyanate cations.

PubMed

Kurouchi, Hiroaki; Sumita, Akinari; Otani, Yuko; Ohwada, Tomohiko

2014-07-07

We found that phenethylcarbamates that bear ortho-salicylate as an ether group (carbamoyl salicylates) dramatically accelerate OC bond dissociation in strong acid to facilitate generation of isocyanate cation (N-protonated isocyanates), which undergo subsequent intramolecular aromatic electrophilic cyclization to give dihydroisoquinolones. To generate isocyanate cations from carbamates in acidic media as electrophiles for aromatic substitution, protonation at the ether oxygen, the least basic heteroatom, is essential to promote CO bond cleavage. However, the carbonyl oxygen of carbamates, the most basic site, is protonated exclusively in strong acids. We found that the protonation site can be shifted to an alternative basic atom by linking methyl salicylate to the ether oxygen of carbamate. The methyl ester oxygen ortho to the phenolic (ether) oxygen of salicylate is as basic as the carbamate carbonyl oxygen, and we found that monoprotonation at the methyl ester oxygen in strong acid resulted in the formation of an intramolecular cationic hydrogen bond (>CO(+) H⋅⋅⋅O<) with the phenolic ether oxygen. This facilitates OC bond dissociation of phenethylcarbamates, thereby promoting isocyanate cation formation. In contrast, superacid-mediated diprotonation at the methyl ester oxygen of the salicylate and the carbonyl oxygen of the carbamate afforded a rather stable dication, which did not readily undergo CO bond dissociation. This is an unprecedented and unknown case in which the monocation has greater reactivity than the dication. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Corrosion Behavior and Strength of Dissimilar Bonding Material between Ti and Mg Alloys Fabricated by Spark Plasma Sintering

PubMed Central

Pripanapong, Patchara; Kariya, Shota; Luangvaranunt, Tachai; Umeda, Junko; Tsutsumi, Seiichiro; Takahashi, Makoto; Kondoh, Katsuyoshi

2016-01-01

Ti and solution treated Mg alloys such as AZ31B (ST), AZ61 (ST), AZ80 (ST) and AZ91 (ST) were successfully bonded at 475 °C by spark plasma sintering, which is a promising new method in welding field. The formation of Ti3Al intermetallic compound was found to be an important factor in controlling the bonding strength and galvanic corrosion resistance of dissimilar materials. The maximum bonding strength and bonding efficiency at 193 MPa and 96% were obtained from Ti/AZ91 (ST), in which a thick and uniform nano-level Ti3Al layer was observed. This sample also shows the highest galvanic corrosion resistance with a measured galvanic width and depth of 281 and 19 µm, respectively. The corrosion resistance of the matrix on Mg alloy side was controlled by its Al content. AZ91 (ST) exhibited the highest corrosion resistance considered from its corrode surface after corrosion test in Kroll’s etchant. The effect of Al content in Mg alloy on bonding strength and corrosion behavior of Ti/Mg alloy (ST) dissimilar materials is discussed in this work. PMID:28773788

Novel Au-TiC Catalysts for CO Oxidation and Desulfurization Processes

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

Rodriguez, J.A.; Liu, P.; Takahashi, Y.

2011-05-30

Recent articles dealing with the physical and chemical properties of novel Au-TiC catalysts are reviewed. High-resolution photoemission, scanning tunneling microscopy and first-principles periodic density-functional calculations were used to study the deposition of gold on a TiC(0 0 1) surface. Gold grows forming two-dimensional (very low coverage) and three-dimensional (medium and large coverage) islands on the carbide substrate. A positive shift in the binding energy of the C 1s core level is observed after the deposition of Au on TiC(0 0 1). The results of the density-functional calculations corroborate the formation of Au-C bonds. In general, the bond between Au andmore » the TiC(0 0 1) surface exhibits very little ionic character, but there is a substantial polarization of electrons around Au that facilitates bonding of the adatoms with electron-acceptor molecules (CO, O{sub 2}, C{sub 2}H{sub 4}, SO{sub 2}, thiophene, etc.). Experimental measurements indicate that Au/TiC(0 0 1) is a very good catalysts for the oxidation of CO, the destruction of SO{sub 2} and the hydrodesulfurization of thiophene. At temperatures below 200 K, Au/TiC(0 0 1) is able to perform the 2CO + O{sub 2} {yields} 2CO{sub 2} reaction and the full decomposition of SO{sub 2}. Furthermore, in spite of the very poor hydrodesulfurization performance of TiC(0 0 1) or Au(1 1 1), a Au/TiC(0 0 1) surface displays a hydrodesulfurization activity higher than that of conventional Ni/MoS{sub x} catalysts. Metal carbides are excellent supports for enhancing the chemical reactivity of gold. The Au/TiC system is more chemically active than systems generated by depositing Au nanoparticles on oxide surfaces.« less

Novel Au-TiC Catalysts for CO Oxidation and Desulfurization Processes

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

J Rodriguez; P Liu; Y Takahashi

2011-12-31

Recent articles dealing with the physical and chemical properties of novel Au-TiC catalysts are reviewed. High-resolution photoemission, scanning tunneling microscopy and first-principles periodic density-functional calculations were used to study the deposition of gold on a TiC(0 0 1) surface. Gold grows forming two-dimensional (very low coverage) and three-dimensional (medium and large coverage) islands on the carbide substrate. A positive shift in the binding energy of the C 1s core level is observed after the deposition of Au on TiC(0 0 1). The results of the density-functional calculations corroborate the formation of Au-C bonds. In general, the bond between Au andmore » the TiC(0 0 1) surface exhibits very little ionic character, but there is a substantial polarization of electrons around Au that facilitates bonding of the adatoms with electron-acceptor molecules (CO, O{sub 2}, C{sub 2}H{sub 4}, SO{sub 2}, thiophene, etc.). Experimental measurements indicate that Au/TiC(0 0 1) is a very good catalysts for the oxidation of CO, the destruction of SO{sub 2} and the hydrodesulfurization of thiophene. At temperatures below 200 K, Au/TiC(0 0 1) is able to perform the 2CO + O{sub 2} {yields} 2CO{sub 2} reaction and the full decomposition of SO{sub 2}. Furthermore, in spite of the very poor hydrodesulfurization performance of TiC(0 0 1) or Au(1 1 1), a Au/TiC(0 0 1) surface displays a hydrodesulfurization activity higher than that of conventional Ni/MoS{sub x} catalysts. Metal carbides are excellent supports for enhancing the chemical reactivity of gold. The Au/TiC system is more chemically active than systems generated by depositing Au nanoparticles on oxide surfaces.« less

Methyl 4-amino-3-methyl­benzoate

PubMed Central

Li, Xiang; Yuan, Lian-Shan; Wang, Dan; Liu, Shan; Yao, Cheng

2008-01-01

In the mol­ecule of the title compound, C9H11NO2, the methyl C and amino N atoms bonded to the benzene ring lie in the ring plane. Intra­molecular C—H⋯O hydrogen bonding results in the formation of a five-membered planar ring, which is oriented at a dihedral angle of 2.73 (3)° with respect to the benzene ring, so they are nearly coplanar. In the crystal structure, inter­molecular N—H⋯O hydrogen bonds link the mol­ecules into chains elongated along the c axis and stacked along the b axis. PMID:21202370

Hydrolysis of Ketene Catalyzed by Formic Acid: Modification of Reaction Mechanism, Energetics, and Kinetics with Organic Acid Catalysis

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

Louie, Matthew K.; Francisco, Joseph S.; Verdicchio, Marco

2015-05-14

The hydrolysis of ketene (H2C=C=O) to form acetic acid involving two water molecules and also separately in the presence of one to two water molecules and formic acid (FA) was investigated. Our results show that, while the currently accepted indirect mechanism, involving addition of water across the carbonyl C=O bond of ketene to form an ene-diol followed by tautomerization of the ene-diol to form acetic acid, is the preferred pathway when water alone is present, with formic acid as catalyst, addition of water across the ketene C=C double bond to directly produce acetic acid becomes the kinetically favored pathway formore » temperatures below 400 K. We find not only that the overall barrier for ketene hydrolysis involving one water molecule and formic acid (H2C2O + H2O + FA) is significantly lower than that involving two water molecules (H2C2O + 2H(2)O) but also that FA is able to reduce the barrier height for the direct path, involving addition of water across the C=C double bond, so that it is essentially identical with (6.4 kcal/mol) that for the indirect ene-diol formation path involving addition of water across the C=O bond. For the case of ketene hydrolysis involving two water molecules and formic acid (H2C2O + 2H(2)O + FA), the barrier for the direct addition of water across the C=C double bond is reduced even further and is 2.5 kcal/mol lower relative to the ene-diol path involving addition of water across the C=O bond. In fact, the hydrolysis barrier for the H2C2O + 2H(2)O + FA reaction through the direct path is sufficiently low (2.5 kcal/mol) for it to be an energetically accessible pathway for acetic acid formation under atmospheric conditions. Given the structural similarity between acetic and formic acid, our results also have potential implications for aqueous-phase chemistry. Thus, in an aqueous environment, even in the absence of formic acid, though the initial mechanism for ketene hydrolysis is expected to involve addition of water across the carbonyl bond as is currently accepted, the production and accumulation of acetic acid will likely alter the preferred pathway to one involving addition of water across the ketene C=C double bond as the reaction proceeds.« less

Formation of unexpected silicon- and disiloxane-bridged multiferrocenyl derivatives bearing Si-O-CH[double bond, length as m-dash]CH2 and Si-(CH2)2C(CH3)3 substituents via cleavage of tetrahydrofuran and trapping of its ring fragments.

PubMed

Bruña, Sonia; González-Vadillo, Ana Mª; Ferrández, Marta; Perles, Josefina; Montero-Campillo, M Merced; Mó, Otilia; Cuadrado, Isabel

2017-09-12

The formation of a family of silicon- and siloxane-bridged multiferrocenyl derivatives carrying different functional groups attached to silicon, including Fc 2 (CH 3 ) 3 C(CH 2 ) 2 SiCH[double bond, length as m-dash]CH 2 (5), Fc 2 (CH 2 [double bond, length as m-dash]CH-O)SiCH[double bond, length as m-dash]CH 2 (6), Fc 2 (OH)SiCH[double bond, length as m-dash]CH 2 (7), Fc 2 (CH 2 [double bond, length as m-dash]CH-O)Si-O-Si(O-CH[double bond, length as m-dash]CH 2 )Fc 2 (8) and Fc 2 (CH 2 [double bond, length as m-dash]CH-O)Si-O-SiFc 3 (9) is described. Silyl vinyl ether molecules 6, 8 and 9 and the heteroleptic vinylsilane 5 resulted from the competing metathesis reaction of lithioferrocene (FcLi), CH 2 [double bond, length as m-dash]CH-OLi or (CH 3 ) 3 C(CH 2 ) 2 Li with the corresponding multifunctional chlorosilane, Cl 3 SiCH[double bond, length as m-dash]CH 2 or Cl 3 Si-O-SiCl 3 . The last two organolithium species have been likely formed in situ by fragmentation of the tetrahydrofuran solvent. Diferrocenylvinyloxyvinylsilane 6 is noteworthy since it represents a rare example of a redox-active silyl mononomer in which two different C[double bond, length as m-dash]C polymerisable groups are directly connected to silicon. The molecular structures of the silicon-containing multiferrocenyl species 5, 6, 8 and 9 have been investigated by single-crystal X-ray diffraction studies, demonstrating the capture and storage processes of two ring fragments resulting from the cleavage of cyclic THF in redox-active and stable crystalline organometallic compounds. From electrochemical studies we found that by changing the anion of the supporting electrolyte from [PF 6 ] - to [B(C 6 F 5 ) 4 ] - , the redox behaviour of tetrametallic disiloxane 8 can be switched from a poorly resolved multistep redox process to four consecutive well-separated one-electron oxidations, corresponding to the sequential oxidation of the four ferrocenyl moieties.

A dielectric barrier discharge terminally inactivates RNase A by oxidizing sulfur-containing amino acids and breaking structural disulfide bonds

NASA Astrophysics Data System (ADS)

Lackmann, J.-W.; Baldus, S.; Steinborn, E.; Edengeiser, E.; Kogelheide, F.; Langklotz, S.; Schneider, S.; Leichert, L. I. O.; Benedikt, J.; Awakowicz, P.; Bandow, J. E.

2015-12-01

RNases are among the most stable proteins in nature. They even refold spontaneously after heat inactivation, regaining full activity. Due to their stability and universal presence, they often pose a problem when experimenting with RNA. We investigated the capabilities of nonthermal atmospheric-pressure plasmas to inactivate RNase A and studied the inactivation mechanism on a molecular level. While prolonged heating above 90 °C is required for heat inactivating RNase A, direct plasma treatment with a dielectric barrier discharge (DBD) source caused permanent inactivation within minutes. Circular dichroism spectroscopy showed that DBD-treated RNase A unfolds rapidly. Raman spectroscopy indicated methionine modifications and formation of sulfonic acid. A mass spectrometry-based analysis of the protein modifications that occur during plasma treatment over time revealed that methionine sulfoxide formation coincides with protein inactivation. Chemical reduction of methionine sulfoxides partially restored RNase A activity confirming that sulfoxidation is causal and sufficient for RNase A inactivation. Continued plasma exposure led to over-oxidation of structural disulfide bonds. Using antibodies, disulfide bond over-oxidation was shown to be a general protein inactivation mechanism of the DBD. The antibody’s heavy and light chains linked by disulfide bonds dissociated after plasma exposure. Based on their ability to inactivate proteins by oxidation of sulfur-containing amino acids and over-oxidation of disulfide bonds, DBD devices present a viable option for inactivating undesired or hazardous proteins on heat or solvent-sensitive surfaces.

A model complex of a possible intermediate in the mechanism of action of peptide deformylase: first example of an (N2S)zinc(II)-formate complex.

PubMed

Chang, S C; Sommer, R D; Rheingold, A L; Goldberg, D P

2001-11-21

The synthesis and crystallographic characterization of a new (N2S)zinc-alkyl complex and (N2S)zinc-formate complex is described; the bonding mode of the formate complex has implications for the mechanism of action of the enzyme peptide deformylase.

Thermal Condensation of Glycine and Alanine on Metal Ferrite Surface: Primitive Peptide Bond Formation Scenario.

PubMed

Iqubal, Md Asif; Sharma, Rachana; Jheeta, Sohan; Kamaluddin

2017-03-27

The amino acid condensation reaction on a heterogeneous mineral surface has been regarded as one of the important pathways for peptide bond formation. Keeping this in view, we have studied the oligomerization of the simple amino acids, glycine and alanine, on nickel ferrite (NiFe₂O₄), cobalt ferrite (CoFe₂O₄), copper ferrite (CuFe₂O₄), zinc ferrite (ZnFe₂O₄), and manganese ferrite (MnFe₂O₄) nanoparticles surfaces, in the temperature range from 50-120 °C for 1-35 days, without applying any wetting/drying cycles. Among the metal ferrites tested for their catalytic activity, NiFe₂O₄ produced the highest yield of products by oligomerizing glycine to the trimer level and alanine to the dimer level, whereas MnFe₂O₄ was the least efficient catalyst, producing the lowest yield of products, as well as shorter oligomers of amino acids under the same set of experimental conditions. It produced primarily diketopiperazine (Ala) with a trace amount of alanine dimer from alanine condensation, while glycine was oligomerized to the dimer level. The trend in product formation is in accordance with the surface area of the minerals used. A temperature as low as 50 °C can even favor peptide bond formation in the present study, which is important in the sense that the condensation process is highly feasible without any sort of localized heat that may originate from volcanoes or hydrothermal vents. However, at a high temperature of 120 °C, anhydrides of glycine and alanine formation are favored, while the optimum temperature for the highest yield of product formation was found to be 90 °C.

Thermal Condensation of Glycine and Alanine on Metal Ferrite Surface: Primitive Peptide Bond Formation Scenario

PubMed Central

Iqubal, Md. Asif; Sharma, Rachana; Jheeta, Sohan; Kamaluddin

2017-01-01

The amino acid condensation reaction on a heterogeneous mineral surface has been regarded as one of the important pathways for peptide bond formation. Keeping this in view, we have studied the oligomerization of the simple amino acids, glycine and alanine, on nickel ferrite (NiFe2O4), cobalt ferrite (CoFe2O4), copper ferrite (CuFe2O4), zinc ferrite (ZnFe2O4), and manganese ferrite (MnFe2O4) nanoparticles surfaces, in the temperature range from 50–120 °C for 1–35 days, without applying any wetting/drying cycles. Among the metal ferrites tested for their catalytic activity, NiFe2O4 produced the highest yield of products by oligomerizing glycine to the trimer level and alanine to the dimer level, whereas MnFe2O4 was the least efficient catalyst, producing the lowest yield of products, as well as shorter oligomers of amino acids under the same set of experimental conditions. It produced primarily diketopiperazine (Ala) with a trace amount of alanine dimer from alanine condensation, while glycine was oligomerized to the dimer level. The trend in product formation is in accordance with the surface area of the minerals used. A temperature as low as 50 °C can even favor peptide bond formation in the present study, which is important in the sense that the condensation process is highly feasible without any sort of localized heat that may originate from volcanoes or hydrothermal vents. However, at a high temperature of 120 °C, anhydrides of glycine and alanine formation are favored, while the optimum temperature for the highest yield of product formation was found to be 90 °C. PMID:28346388

FTIR cryospectroscopic and ab initio studies of desflurane-dimethyl ether H-bonded complexes.

PubMed

Melikova, S M; Rutkowski, K S; Rospenk, M

2017-09-05

The IR spectra of mixtures of desflurane and dimethyl ether are studied with the help of FTIR cryospectroscopy in liquefied Kr at T~118-158K. Comparative analysis of the experimental data and results of ab initio calculations show that either of the two C-H groups of desflurane is involved in heterodimer formation of comparable strengths. The blue frequency shift is found for stretching vibrations of those C-H donors which directly participate in H-bond formation. Additionally the complexes are stabilized by weaker contacts between hydrogen atoms of dimethyl ether and fluorine atoms of desflurane. Copyright © 2017 Elsevier B.V. All rights reserved.

Isonitrile-functionalized ruthenium nanoparticles: intraparticle charge delocalization through Ru=C=N interfacial bonds

NASA Astrophysics Data System (ADS)

Zhang, Fengqi; Huang, Lin; Zou, Jiasui; Yang, Jun; Kang, Xiongwu; Chen, Shaowei

2017-09-01

Ruthenium nanoparticles (2.06 ± 0.46 nm in diameter) stabilized by 1-hexyl-4-isocyanobenzene (CNBH), denoted as RuCNBH, were prepared by the self-assembly of isonitrile molecules onto the surface of "bare" Ru colloids by virtue of the formation of Ru=C=N- interfacial bonds. FTIR measurements showed that the stretching vibration of the terminal -N≡C bonds at 2119 cm-1 for the monomeric ligands disappeared and concurrently three new bands at 2115, 2043, and 1944 cm-1 emerged with RuCNBH nanoparticles, which was ascribed to the transformation of -N≡C to Ru=C=N- by back donation of Ru-d electrons to the π* orbital of the organic ligands. Metathesis reaction of RuCNBH with vinyl derivatives further corroborated the nature of the Ru=C interfacial bonds. When 1-isocyanopyrene (CNPy) was bounded onto the Ru nanoparticles surface through Ru=C=N interfacial bond (denoted as RuCNPy), the emission maximum was found to red-shift by 27 nm, as compared to that of the CNPy monomers, along with a reduced fluorescence lifetime, due to intraparticle charge delocalization that arose from the conjugated Ru=C=N- interfacial bonds. The results of this study further underline the significance of metal-organic interfacial bonds in the control of intraparticle charge-transfer dynamics and the optical and electronic properties of metal nanoparticles. [Figure not available: see fulltext.

Crystal structure of benzyl 3-(3-methyl-phen-yl)di-thio-carbazate.

PubMed

Aziz, NurFadhilah Abdul; Yusof, Enis Nadia Md; Ravoof, Thahira Begum S A; Tiekink, Edward R T

2015-04-01

In the title compound, C15H16N2S2, the central CN2S2 residue is almost planar (r.m.s. deviation = 0.0354 Å) and forms dihedral angles of 56.02 (4) and 75.52 (4)° with the phenyl and tolyl rings, respectively; the dihedral angle between the aromatic rings is 81.72 (5)°. The conformation about the N-N bond is gauche [C-N-N-C = -117.48 (15)°]. Overall, the mol-ecule has the shape of the letter L. In the crystal packing, supra-molecular chains along the a axis are formed by N-H⋯S(thione) hydrogen bonds whereby the thione S atom accepts two such bonds. The hydrogen bonding leads to alternating edge-shared eight-membered {⋯HNCS}2 and 10-membered {⋯HNNH⋯S}2 synthons. The chains are connected into layers by phen-yl-tolyl C-H⋯π inter-actions; the layers stack along the c axis with no specific inter-actions between them.

Novel type of ornithine-glutathione double conjugate excreted as a major metabolite into the bile of rats administered clebopride.

PubMed

Ishizuka, T; Komiya, I; Hiratsuka, A; Watabe, T

1990-06-01

Rats orally given radioactive Clebopride [[14C]CP; N-(1'-benzyl-4'-piperidyl)-2-[14C]methoxy-4-amino-5-chlorobenzamide++ +], an antiulcer agent, excreted a novel type of ornithine (Orn)-GSH double conjugate in the bile as a major metabolite [( 14C]BMCP), corresponding to 18% of the dose. The present study provides the first evidence for Orn conjugation of a xenobiotic in mammals and demonstrates that the structure of the radioactive conjugate differs fundamentally from those known in birds and reptiles. The structure of the biliary metabolite, [14C]BMCP, purified to homogeneity by silica gel thin layer and reverse phase high pressure liquid chromatography, was elucidated as S-[2-ornithylamino-4-[14C]methoxy-5-(1'-methyl-4'-piperidylamin o) carboxyphenyl]glutathione, based mainly on the following facts: 1) BMCP showed a protonated molecular ion (M + H)+ peak at m/z 683 in the secondary ion mass spectrum and 2) [14C]BMCP afforded Orn, glutamic acid, glycine, S-(2-amino-4-[14C]methoxy-5-carboxyphenyl)cysteine [( 14C]AMCC), and 1-methyl-4-aminopiperidine (MAP) quantitatively, in an equal molar ratio, by complete hydrolysis with peptidase. Thus, BMCP was a metabolite with three enzymatically hydrolyzable amide bonds in addition to the one existing originally in the parent structure of the drug, which produces MAP by peptic digestion. Of the three additional amide bonds of BMCP, one was a novel type of bond formed by condensation of the alpha-carboxylic acid group of Orn with the primary aromatic amino group of the drug and the other two were in the S-glutathionyl residue, substituted for the chlorine atom vicinal to the Orn-conjugating primary amino group in the aromatic ring and affording glutamic acid, glycine, and the S-cysteine conjugate AMCC by hydrolysis of BMCP with the peptidase. Substitution of a methyl group for the benzyl group at the piperidine ring nitrogen atom, leading to the formation of MAP by peptic digestion, also occurred during metabolism of CP to BMCP.

Catalytic routes and oxidation mechanisms in photoreforming of polyols

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

Sanwald, Kai E.; Berto, Tobias F.; Eisenreich, Wolfgang

2016-12-01

Photocatalytic reforming of biomass-derived oxygenates leads to H 2 generation and evolution of CO 2 via parallel formation of organic intermediates through anodic oxidations on a Rh/TiO 2 photocatalyst. The reaction pathways and kinetics in the photoreforming of C 3–C 6 polyols were explored. Polyols are converted via direct and indirect hole transfer pathways resulting in (i) oxidative rupture of C–C bonds, (ii) oxidation to a-oxygen functionalized aldoses and ketoses (carbonyl group formation) and (iii) light-driven dehydration. Direct hole transfer to chemisorbed oxygenates on terminal Ti(IV)-OH groups, generating alkoxy-radicals that undergo ß-C–C-cleavage, is proposed for the oxidative C–C rupture. Carbonylmore » group formation and dehydration are attributed to indirect hole transfer at surface lattice oxygen sites [Ti_ _ _O_ _ _Ti] followed by the generation of carbon-centered radicals. Polyol chain length impacts the contribution of the oxidation mechanisms favoring the C–C bond cleavage (internal preferred over terminal) as the dominant pathway with higher polyol carbon number.« less

Acid/base-regulated reversible electron transfer disproportionation of N–N linked bicarbazole and biacridine derivatives† †Electronic supplementary information (ESI) available: Experimental information, synthesis and characterization data, NMR spectra, solid state NMR data, X-ray data, ESR spectra, UV-Vis-NIR spectra, fluorescence spectra, kinetic experiments, theoretical calculations, Tables S1–S8, Scheme S1, Fig. S1–12, References. CCDC 1025063, 1038914, 1049677 and 1040722. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c5sc00946d

PubMed Central

Pandit, Palash; Yamamoto, Koji; Nakamura, Toshikazu; Nishimura, Katsuyuki; Kurashige, Yuki; Yanai, Takeshi; Nakamura, Go; Masaoka, Shigeyuki; Furukawa, Ko; Yakiyama, Yumi; Kawano, Masaki

2015-01-01

Regulation of electron transfer on organic substances by external stimuli is a fundamental issue in science and technology, which affects organic materials, chemical synthesis, and biological metabolism. Nevertheless, acid/base-responsive organic materials that exhibit reversible electron transfer have not been well studied and developed, owing to the difficulty in inventing a mechanism to associate acid/base stimuli and electron transfer. We discovered a new phenomenon in which N–N linked bicarbazole (BC) and tetramethylbiacridine (TBA) derivatives undergo electron transfer disproportionation by acid stimulus, forming their stable radical cations and reduced species. The reaction occurs through a biradical intermediate generated by the acid-triggered N–N bond cleavage reaction of BC or TBA, which acts as a two electron acceptor to undergo electron transfer reactions with two equivalents of BC or TBA. In addition, in the case of TBA the disproportionation reaction is highly reversible through neutralization with NEt3, which recovers TBA through back electron transfer and N–N bond formation reactions. This highly reversible electron transfer reaction is possible due to the association between the acid stimulus and electron transfer via the acid-regulated N–N bond cleavage/formation reactions which provide an efficient switching mechanism, the ability of the organic molecules to act as multi-electron donors and acceptors, the extraordinary stability of the radical species, the highly selective reactivity, and the balance of the redox potentials. This discovery provides new design concepts for acid/base-regulated organic electron transfer systems, chemical reagents, or organic materials. PMID:29218181

Mercury(II) Complex Formation With Glutathione in Alkaline Aqueous Solution

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

Mah, V.; Jalilehvand, F.

2009-05-19

The structure and speciation of the complexes formed between mercury(II) ions and glutathione (GSH = L-glutamyl-L-cysteinyl-glycine) have been studied for a series of alkaline aqueous solutions (C{sub Hg{sup 2+}} {approx} 18 mmol dm{sup -3} and C{sub GSH} = 40-200 mmol dm{sup -3} at pH {approx} 10.5) by means of extended X-ray absorption fine structure (EXAFS) and {sup 199}Hg NMR spectroscopy at ambient temperature. The dominant complexes are [Hg(GS){sub 2}]{sup 4-} and [Hg(GS){sub 3}]{sup 7-}, with mean Hg-S bond distances of 2.32(1) and 2.42(2) {angstrom} observed in digonal and trigonal Hg-S coordination, respectively. The proportions of the Hg{sup 2+}-glutathione complexes weremore » evaluated by fitting linear combinations of model EXAFS oscillations representing each species to the experimental EXAFS spectra. The [Hg(GS){sub 4}]{sup 10-} complex, with four sulfur atoms coordinated at a mean Hg-S bond distance of 2.52(2) {angstrom}, is present in minor amounts (<30%) in solutions containing a large excess of glutathione (C{sub GSH} {ge} 160 mmol dm{sup -3}). Comparable alkaline mercury(II) cysteine (H{sub 2}Cys) solutions were also investigated and a reduced tendency to form higher complexes was observed, because the deprotonated amino group of Cys{sup 2-} allows the stable [Hg(S,N-Cys){sub 2}]{sup 2-} chelate to form. The effect of temperature on the distribution of the Hg{sup 2+}-glutathione complexes was studied by comparing the EXAFS spectra at ambient temperature and at 25 K of a series of glycerol/water (33/67, v/v) frozen glasses with and C{sub Hg{sup 2+}} {approx} 7 mmol dm{sup -3} and C{sub GSH} = 16-81 mmol dm{sup -3}. Complexes with high Hg-S coordination numbers, [Hg(GS){sub 3}]{sup 7-} and [Hg(GS){sub 4}]{sup 10-}, became strongly favored when just a moderate excess of glutathione (C{sub GSH} {ge} 28 mmol dm{sup -3}) was used in the glassy samples, as expected for a stepwise exothermic bond formation. Addition of glycerol had no effect on the Hg(II)-glutathione speciation, as shown by the similarity of the EXAFS spectra obtained at room temperature for two parallel series of Hg(II)-glutathione solutions with C{sub Hg{sup 2+}} {approx} 7 mmol dm{sup -3}, with and without 33% glycerol. Also, the {sup 199}Hg NMR chemical shifts of a series of {approx} 18 mmol dm{sup -3} mercury(II) glutathione solutions with 33% glycerol were not significantly different from those of the corresponding series in aqueous solution.« less

78 FR 37277 - CDFI Bond Guarantee Program; Correction

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-20

... the CDFI Fund in the following format: no more than 40 single-sided pages; double spaced; 12 font size... mail to the attention of Lisa Jones, Program Manager, CDFI Bond Guarantee Program, CDFI Fund, U.S... to the attention of Lisa Jones, Program Manager, CDFI Bond Guarantee Program, CDFI Fund, 1801-6215...

Role of intramolecular hydrogen bonding in the excited-state intramolecular double proton transfer (ESIDPT) of calix[4]arene: A TDDFT study

NASA Astrophysics Data System (ADS)

Wang, Se; Wang, Zhuang; Hao, Ce

2016-01-01

The time-dependent density functional theory (TDDFT) method was performed to investigate the excited-state intramolecular double proton transfer (ESIDPT) reaction of calix[4] arene (C4A) and the role of the intramolecular hydrogen bonds in the ESIDPT process. The geometries of C4A in the ground state and excited states (S1, S2 and T1) were optimized. Four intramolecular hydrogen bonds formed in the C4A are strengthened or weakened in the S2 and T1 states compared to those in the ground state. Interestingly, upon excitation to the S1 state of C4A, two protons H1 and H2 transfer along the two intramolecular hydrogen bonds O1-H1···O2 and O2-H2···O3, while the other two protons do not transfer. The ESIDPT reaction breaks the primary symmetry of C4A in the ground state. The potential energy curves of proton transfer demonstrate that the ESIDPT process follows the stepwise mechanism but not the concerted mechanism. Findings indicate that intramolecular hydrogen bonding is critical to the ESIDPT reactions in intramolecular hydrogen-bonded systems.

Diffusion Bonding of Silicon Carbide for a Micro-Electro-Mechanical Systems Lean Direct Injector

NASA Technical Reports Server (NTRS)

Halbig, Michael C.; Singh, Mrityunjay; Shpargel, Tarah P.; Kiser, James D.

2006-01-01

Robust approaches for joining silicon carbide (SiC) to silicon carbide sub-elements have been developed for a micro-electro-mechanical systems lean direct injector (MEMS LDI) application. The objective is to join SiC sub-elements to form a leak-free injector that has complex internal passages for the flow and mixing of fuel and air. Previous bonding technology relied upon silicate glass interlayers that were not uniform or leak free. In a newly developed joining approach, titanium foils and physically vapor deposited titanium coatings were used to form diffusion bonds between SiC materials during hot pressing. Microscopy results show the formation of well adhered diffusion bonds. Initial tests show that the bond strength is much higher than required for the component system. Benefits of the joining technology are fabrication of leak free joints with high temperature and mechanical capability.

Direct observation of ligand transfer and bond formation in cytochrome c oxidase by using mid-infrared chirped-pulse upconversion

PubMed Central

Treuffet, Johanne; Kubarych, Kevin J.; Lambry, Jean-Christophe; Pilet, Eric; Masson, Jean-Baptiste; Martin, Jean-Louis; Vos, Marten H.; Joffre, Manuel; Alexandrou, Antigoni

2007-01-01

We have implemented the recently demonstrated technique of chirped-pulse upconversion of midinfrared femtosecond pulses into the visible in a visible pump–midinfrared probe experiment for high-resolution, high-sensitivity measurements over a broad spectral range. We have succeeded in time-resolving the CO ligand transfer process from the heme Fe to the neighboring CuB atom in the bimetallic active site of mammalian cytochrome c oxidase, which was known to proceed in <1 ps, using the full CO vibrational signature of Fe–CO bond breaking and CuB–CO bond formation. Our differential transmission results show a delayed onset of the appearance of the CuB-bound species (200 fs), followed by a 450-fs exponential rise. Trajectories calculated by using molecular-dynamics simulations with a Morse potential for the CuB–C interaction display a similar behavior. Both experimental and calculated data strongly suggest a ballistic contribution to the transfer process. PMID:17895387

Initial decomposition of the condensed-phase β-HMX under shock waves: molecular dynamics simulations.

PubMed

Ge, Ni-Na; Wei, Yong-Kai; Ji, Guang-Fu; Chen, Xiang-Rong; Zhao, Feng; Wei, Dong-Qing

2012-11-26

We have performed quantum-based multiscale simulations to study the initial chemical processes of condensed-phase octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) under shock wave loading. A self-consistent charge density-functional tight-binding (SCC-DFTB) method was employed. The results show that the initial decomposition of shocked HMX is triggered by the N-NO(2) bond breaking under the low velocity impact (8 km/s). As the shock velocity increases (11 km/s), the homolytic cleavage of the N-NO(2) bond is suppressed under high pressure, the C-H bond dissociation becomes the primary pathway for HMX decomposition in its early stages. It is accompanied by a five-membered ring formation and hydrogen transfer from the CH(2) group to the -NO(2) group. Our simulations suggest that the initial chemical processes of shocked HMX are dependent on the impact velocity, which gain new insights into the initial decomposition mechanism of HMX upon shock loading at the atomistic level, and have important implications for understanding and development of energetic materials.

Evidence against Stable Protein S-Nitrosylation as a Widespread Mechanism of Post-translational Regulation.

PubMed

Wolhuter, Kathryn; Whitwell, Harry J; Switzer, Christopher H; Burgoyne, Joseph R; Timms, John F; Eaton, Philip

2018-02-01

S-nitrosation, commonly referred to as S-nitrosylation, is widely regarded as a ubiquitous, stable post-translational modification that directly regulates many proteins. Such a widespread role would appear to be incompatible with the inherent lability of the S-nitroso bond, especially its propensity to rapidly react with thiols to generate disulfide bonds. As anticipated, we observed robust and widespread protein S-nitrosation after exposing cells to nitrosocysteine or lipopolysaccharide. Proteins detected using the ascorbate-dependent biotin switch method are typically interpreted to be directly regulated by S-nitrosation. However, these S-nitrosated proteins are shown to predominantly comprise transient intermediates leading to disulfide bond formation. These disulfides are likely to be the dominant end effectors resulting from elevations in nitrosating cellular nitric oxide species. We propose that S-nitrosation primarily serves as a transient intermediate leading to disulfide formation. Overall, we conclude that the current widely held perception that stable S-nitrosation directly regulates the function of many proteins is significantly incorrect. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Sulfur passivation techniques for III-V wafer bonding

NASA Astrophysics Data System (ADS)

Jackson, Michael James

The use of direct wafer bonding in a multijunction III-V solar cell structure requires the formation of a low resistance bonded interface with minimal thermal treatment. A wafer bonded interface behaves as two independent surfaces in close proximity, hence a major source of resistance is Fermi level pinning common in III-V surfaces. This study demonstrates the use of sulfur passivation in III-V wafer bonding to reduce the energy barrier at the interface. Two different sulfur passivation processes are addressed. A dry sulfur passivation method that utilizes elemental sulfur vapor activated by ultraviolet light in vacuum is compared with aqueous sulfide and native oxide etch treatments. Through the addition of a sulfur desorption step in vacuum, the UV-S treatment achieves bondable surfaces free of particles contamination or surface roughening. X-ray photoelectron spectroscopy measurements of the sulfur treated GaAs surfaces find lower levels of oxide and the appearance of sulfide species. After 4 hrs of air exposure, the UV-S treated GaAs actually showed an increase in the amount of sulfide bonded to the semiconductor, resulting in less oxidation compared to the aqueous sulfide treatment. Large area bonding is achieved for sulfur treated GaAs / GaAs and InP / InP with bulk fracture strength achieved after annealing at 400 °C and 300 °C respectively, without large compressive forces. The electrical conductivity across a sulfur treated 400 °C bonded n-GaAs/n-GaAs interface significantly increased with a short anneal (1-2 minutes) at elevated temperatures (50--600 °C). Interfaces treated with the NH4OH oxide etch, on the other hand, exhibited only mild improvement in accordance with previously published studies in this area. TEM and STEM images revealed similar interfacial microstructure changes with annealing for both sulfur treated and NH4OH interfaces, whereby some areas have direct semiconductor-semiconductor contact without any interfacial layer. Fitting the observed temperature dependence of zero bias conductance using a model for tunneling through a grain boundary reveals that the addition of sulfur at the interface lowered the interfacial energy barrier by 0.2 eV. The interface resistance for these sulfur-treated structures is less than 0.03 O·cm 2 at room temperature. These results emphasize that sulfur passivation techniques reduce interface states that otherwise limit the implementation of wafer bonding for high efficiency solar cells and other devices.

Carbon-hydrogen bond activation, C-N bond coupling, and cycloaddition reactivity of a three-coordinate nickel complex featuring a terminal imido ligand.

PubMed

Mindiola, Daniel J; Waterman, Rory; Iluc, Vlad M; Cundari, Thomas R; Hillhouse, Gregory L

2014-12-15

The three-coordinate imidos (dtbpe)Ni═NR (dtbpe = (t)Bu2PCH2CH2P(t)Bu2, R = 2,6-(i)Pr2C6H3, 2,4,6-Me3C6H2 (Mes), and 1-adamantyl (Ad)), which contain a legitimate Ni-N double bond as well as basic imido nitrogen based on theoretical analysis, readily deprotonate HC≡CPh to form the amide acetylide species (dtbpe)Ni{NH(Ar)}(C≡CPh). In the case of R = 2,6-(i)Pr2C6H3, reductive carbonylation results in formation of the (dtbpe)Ni(CO)2 along with the N-C coupled product keteneimine PhCH═C═N(2,6- (i)Pr2C6H3). Given the ability of the Ni═N bond to have biradical character as suggested by theoretical analysis, H atom abstraction can also occur in (dtbpe)Ni═N{2,6-(i)Pr2C6H3} when this species is treated with HSn((n)Bu)3. Likewise, the microscopic reverse reaction--conversion of the Ni(I) anilide (dtbpe)Ni{NH(2,6-(i)Pr2C6H3)} to the imido (dtbpe)Ni═N{2,6-(i)Pr2C6H3}--is promoted when using the radical Mes*O(•) (Mes* = 2,4,6-(t)Bu3C6H2). Reactivity studies involving the imido complexes, in particular (dtbpe)Ni═N{2,6-(i)Pr2C6H3}, are also reported with small, unsaturated molecules such as diphenylketene, benzylisocyanate, benzaldehyde, and carbon dioxide, including the formation of C-N and N-N bonds by coupling reactions. In addition to NMR spectroscopic data and combustion analysis, we also report structural studies for all the cycloaddition reactions involving the imido (dtbpe)Ni═N{2,6-(i)Pr2C6H3}.

The Intramolecular Hydrogen Bond N-H···S in 2,2'-Diaminodiphenyl Disulfide: Experimental and Computational Thermochemistry.

PubMed

Ramos, Fernando; Flores, Henoc; Hernández-Pérez, Julio M; Sandoval-Lira, Jacinto; Camarillo, E Adriana

2018-01-11

The intramolecular hydrogen bond of the N-H···S type has been investigated sparingly by thermochemical and computational methods. In order to study this interaction, the standard molar enthalpies of formation in gaseous phase of diphenyl disulfide, 2,2'-diaminodiphenyl disulfide and 4,4'-diaminodiphenyl disulfide at T = 298.15 K were determined by experimental thermochemical methods and computational calculations. The experimental enthalpies of formation in gas-phase were obtained from enthalpies of formation in crystalline phase and enthalpies of sublimation. Enthalpies of formation in crystalline phase were obtained using rotatory bomb combustion calorimetry. By thermogravimetry, enthalpies of vaporization were obtained, and by combining them with enthalpies of fusion, the enthalpies of sublimation were calculated. The Gaussian-4 procedure and the atomization method were applied to obtain enthalpies of formation in gas-phase of the compounds under study. Theoretical and experimental values are in good agreement. Through natural bond orbital (NBO) analysis and a topological analysis of the electronic density, the intramolecular hydrogen bridge (N-H···S) in the 2,2'-diaminodiphenyl disulfide was confirmed. Finally, an enthalpic difference of 11.8 kJ·mol -1 between the 2,2'-diaminodiphenyl disulfide and 4,4'-diaminodiphenyl disulfide was found, which is attributed to the intramolecular N-H···S interaction.

Possible evidence of amide bond formation between sinapinic acid and lysine-containing bacterial proteins by matrix-assisted laser desorption/ionization (MALDI) at 355 nm

USDA-ARS?s Scientific Manuscript database

We previously reported the apparent formation of matrix adducts of 3,5-dimethoxy-4-hydroxy-cinnamic acid (sinapinic acid or SA) via covalent attachment to disulfide bond-containing proteins (HdeA, HdeB and YbgS) from bacterial cell lysates ionized by matrix-assisted laser desorption/ionization (MALD...

Modular assembly of proteins on nanoparticles.

PubMed

Ma, Wenwei; Saccardo, Angela; Roccatano, Danilo; Aboagye-Mensah, Dorothy; Alkaseem, Mohammad; Jewkes, Matthew; Di Nezza, Francesca; Baron, Mark; Soloviev, Mikhail; Ferrari, Enrico

2018-04-16

Generally, the high diversity of protein properties necessitates the development of unique nanoparticle bio-conjugation methods, optimized for each different protein. Here we describe a universal bio-conjugation approach which makes use of a new recombinant fusion protein combining two distinct domains. The N-terminal part is Glutathione S-Transferase (GST) from Schistosoma japonicum, for which we identify and characterize the remarkable ability to bind gold nanoparticles (GNPs) by forming gold-sulfur bonds (Au-S). The C-terminal part of this multi-domain construct is the SpyCatcher from Streptococcus pyogenes, which provides the ability to capture recombinant proteins encoding a SpyTag. Here we show that SpyCatcher can be immobilized covalently on GNPs through GST without the loss of its full functionality. We then show that GST-SpyCatcher activated particles are able to covalently bind a SpyTag modified protein by simple mixing, through the spontaneous formation of an unusual isopeptide bond.

Communication: Surface-to-bulk diffusion of isolated versus interacting C atoms in Ni(111) and Cu(111) substrates: A first principle investigation.

PubMed

Harpale, Abhilash; Panesi, Marco; Chew, Huck Beng

2015-02-14

Using first principle calculations, we study the surface-to-bulk diffusion of C atoms in Ni(111) and Cu(111) substrates, and compare the barrier energies associated with the diffusion of an isolated C atom versus multiple interacting C atoms. We find that the preferential Ni-C bonding over C-C bonding induces a repulsive interaction between C atoms located at diagonal octahedral voids in Ni substrates. This C-C interaction accelerates C atom diffusion in Ni with a reduced barrier energy of ∼1 eV, compared to ∼1.4-1.6 eV for the diffusion of isolated C atoms. The diffusion barrier energy of isolated C atoms in Cu is lower than in Ni. However, bulk diffusion of interacting C atoms in Cu is not possible due to the preferential C-C bonding over C-Cu bonding, which results in C-C dimer pair formation near the surface. The dramatically different C-C interaction effects within the different substrates explain the contrasting growth mechanisms of graphene on Ni(111) and Cu(111) during chemical vapor deposition.

Nucleation-dependant chemical bonding paradigm: the effect of rare earth ions on the nucleation of urea in aqueous solution.

PubMed

Chen, Xiaoyan; Sun, Congting; Wu, Sixin; Xue, Dongfeng

2017-03-29

Rare earth ions can be used to construct a variety of novel structures and are favorable to chemical bonding regulation and design. In this study, the chemical bonding paradigm between rare earth ions (Ln 3+ ) and urea molecules in an aqueous solution can be tracked by the evolution of C[double bond, length as m-dash]O, NH 2 , and CN vibration bands during the urea nucleation stage. Rare earth ions such as La 3+ , Gd 3+ , and Lu 3+ can manipulate the nucleation time of urea via regulating the nucleation-dependant N-C[double bond, length as m-dash]OH-N hydrogen-bonding between urea molecules. Two types of chemical bondings between Ln 3+ and urea molecules have been confirmed, which are Ln 3+ O[double bond, length as m-dash]C-N and Ln 3+ NH 2 -C. Compared with Ln 3+ NH 2 -C, Ln 3+ prefers to coordinate with the O[double bond, length as m-dash]C bond in urea. With a higher concentration of rare earth ions in the solution, some N-C[double bond, length as m-dash]OH-N hydrogen bonds are broken as a consequence of the incorporation of Ln 3+ into the lattice, resulting in the decreased symmetry of local urea molecules in the crystalline nuclei and the consequent Ln 3+ concentration-dependent nucleation time of urea. Moreover, using the ionic electronegativity scale of Ln 3+ , the different effects of La 3+ , Gd 3+ , and Lu 3+ on urea nucleation can be further distinguished. The present study provides basic data for unrevealing the chemical bonding regulation role of rare earth ions in the formation of hydrogen bonded materials, which may give insight into the design and fabrication of novel materials utilizing rare earth ions to adjust the chemical bonding process.

Carbon–hydrogen bond activation, C–N bond coupling, and cycloaddition reactivity of a three-coordinate nickel complex featuring a terminal imido ligand

DOE PAGES

Mindiola, Daniel J.; Waterman, Rory; Iluc, Vlad M.; ...

2014-12-01

Here, the three-coordinate imidos (dtbpe)Ni=NR (dtbpe = tBu 2PCH 2CH 2PtBu 2, R = 2,6- iPr 2C 6H 3, 2,4,6-Me 3C 6H 2 (Mes), and 1-adamantyl (Ad)), which contain a legitimate Ni–N double bond as well as basic imido nitrogen based on theoretical analysis, readily deprotonate HC≡CPh to form the amide acetylide species (dtbpe)Ni{NH(Ar)}(C≡CPh). In the case of R = 2,6- iPr 2C 6H 3, reductive carbonylation results in formation of the (dtbpe)Ni(CO) 2 along with the N–C coupled product keteneimine PhCH=C=N(2,6- iPr 2C 6H 3). Given the ability of the Ni=N bond to have biradical character as suggested bymore » theoretical analysis, H atom abstraction can also occur in (dtbpe)Ni=N{2,6- iPr 2C 6H 3} when this species is treated with HSn( nBu) 3. Likewise, the microscopic reverse reaction—conversion of the Ni(I) anilide (dtbpe)Ni{NH(2,6- iPr 2C 6H 3)} to the imido (dtbpe)Ni=N{2,6- iPr 2C 6H 3}—is promoted when using the radical Mes*O • (Mes* = 2,4,6- tBu 3C 6H 2). Reactivity studies involving the imido complexes, in particular (dtbpe)Ni=N{2,6- iPr 2C 6H 3}, are also reported with small, unsaturated molecules such as diphenylketene, benzylisocyanate, benzaldehyde, and carbon dioxide, including the formation of C–N and N–N bonds by coupling reactions. In addition to NMR spectroscopic data and combustion analysis, we also report structural studies for all the cycloaddition reactions involving the imido (dtbpe)Ni=N{2,6- iPr 2C 6H 3}.« less

Carbon–Hydrogen Bond Activation, C–N Bond Coupling, and Cycloaddition Reactivity of a Three-Coordinate Nickel Complex Featuring a Terminal Imido Ligand

PubMed Central

2015-01-01

The three-coordinate imidos (dtbpe)Ni=NR (dtbpe = tBu2PCH2CH2PtBu2, R = 2,6-iPr2C6H3, 2,4,6-Me3C6H2 (Mes), and 1-adamantyl (Ad)), which contain a legitimate Ni–N double bond as well as basic imido nitrogen based on theoretical analysis, readily deprotonate HC≡CPh to form the amide acetylide species (dtbpe)Ni{NH(Ar)}(C≡CPh). In the case of R = 2,6-iPr2C6H3, reductive carbonylation results in formation of the (dtbpe)Ni(CO)2 along with the N–C coupled product keteneimine PhCH=C=N(2,6- iPr2C6H3). Given the ability of the Ni=N bond to have biradical character as suggested by theoretical analysis, H atom abstraction can also occur in (dtbpe)Ni=N{2,6-iPr2C6H3} when this species is treated with HSn(nBu)3. Likewise, the microscopic reverse reaction—conversion of the Ni(I) anilide (dtbpe)Ni{NH(2,6-iPr2C6H3)} to the imido (dtbpe)Ni=N{2,6-iPr2C6H3}—is promoted when using the radical Mes*O• (Mes* = 2,4,6-tBu3C6H2). Reactivity studies involving the imido complexes, in particular (dtbpe)Ni=N{2,6-iPr2C6H3}, are also reported with small, unsaturated molecules such as diphenylketene, benzylisocyanate, benzaldehyde, and carbon dioxide, including the formation of C–N and N–N bonds by coupling reactions. In addition to NMR spectroscopic data and combustion analysis, we also report structural studies for all the cycloaddition reactions involving the imido (dtbpe)Ni=N{2,6-iPr2C6H3}. PMID:25437507

Carbon–hydrogen bond activation, C–N bond coupling, and cycloaddition reactivity of a three-coordinate nickel complex featuring a terminal imido ligand

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

Mindiola, Daniel J.; Waterman, Rory; Iluc, Vlad M.

Here, the three-coordinate imidos (dtbpe)Ni=NR (dtbpe = tBu 2PCH 2CH 2PtBu 2, R = 2,6- iPr 2C 6H 3, 2,4,6-Me 3C 6H 2 (Mes), and 1-adamantyl (Ad)), which contain a legitimate Ni–N double bond as well as basic imido nitrogen based on theoretical analysis, readily deprotonate HC≡CPh to form the amide acetylide species (dtbpe)Ni{NH(Ar)}(C≡CPh). In the case of R = 2,6- iPr 2C 6H 3, reductive carbonylation results in formation of the (dtbpe)Ni(CO) 2 along with the N–C coupled product keteneimine PhCH=C=N(2,6- iPr 2C 6H 3). Given the ability of the Ni=N bond to have biradical character as suggested bymore » theoretical analysis, H atom abstraction can also occur in (dtbpe)Ni=N{2,6- iPr 2C 6H 3} when this species is treated with HSn( nBu) 3. Likewise, the microscopic reverse reaction—conversion of the Ni(I) anilide (dtbpe)Ni{NH(2,6- iPr 2C 6H 3)} to the imido (dtbpe)Ni=N{2,6- iPr 2C 6H 3}—is promoted when using the radical Mes*O • (Mes* = 2,4,6- tBu 3C 6H 2). Reactivity studies involving the imido complexes, in particular (dtbpe)Ni=N{2,6- iPr 2C 6H 3}, are also reported with small, unsaturated molecules such as diphenylketene, benzylisocyanate, benzaldehyde, and carbon dioxide, including the formation of C–N and N–N bonds by coupling reactions. In addition to NMR spectroscopic data and combustion analysis, we also report structural studies for all the cycloaddition reactions involving the imido (dtbpe)Ni=N{2,6- iPr 2C 6H 3}.« less

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

Johnson, Eric L.; Davis, Quincy C.; Morse, Michael D.

The abrupt onset of predissociation in the congested electronic spectra of jet-cooled VC, VN, and VS has been observed using resonant two-photon ionization spectroscopy. It is argued that because of the high density of electronic states in these molecules, the predissociation threshold occurs at the thermochemical threshold for the production of separated atoms in their ground electronic states. As a result, the measured threshold represents the bond dissociation energy. Using this method, bond dissociation energies of D{sub 0}(V C) = 4.1086(25) eV, D{sub 0}(V N) = 4.9968(20) eV, and D{sub 0}(V S) = 4.5353(25) eV are obtained. From these values,more » enthalpies of formation are derived as Δ{sub f,0K}H°(V C(g)) = 827.0 ± 8 kJ mol{sup −1}, Δ{sub f,0K}H°(V N(g)) = 500.9 ± 8 kJ mol{sup −1}, and Δ{sub f,0K}H°(V S(g)) = 349.3 ± 8 kJ mol{sup −1}. Using a thermochemical cycle and the well-known ionization energies of V, VC, and VN, our results also provide D{sub 0}(V{sup +}–C) = 3.7242(25) eV and D{sub 0}(V{sup +}–N) = 4.6871(20) eV. These values are compared to previous measurements and to computational results. The precision of these bond dissociation energies makes them good candidates for testing computational chemistry methods, particularly those that employ density functional theory.« less

Bodipy–C60 triple hydrogen bonding assemblies as heavy atom-free triplet photosensitizers: preparation and study of the singlet/triplet energy transfer† †Electronic supplementary information (ESI) available: Syntheses, structure characterization data, and UV/vis absorption and emission spectra. See DOI: 10.1039/c4sc03865g

PubMed Central

Guo, Song; Xu, Liang; Xu, Kejing; Küçüköz, Betül; Karatay, Ahmet; Yaglioglu, Halime Gul; Hayvali, Mustafa; Elmali, Ayhan

2015-01-01

Supramolecular triplet photosensitizers based on hydrogen bonding-mediated molecular assemblies were prepared. Three thymine-containing visible light-harvesting Bodipy derivatives (B-1, B-2 and B-3, which show absorption at 505 nm, 630 nm and 593 nm, respectively) were used as H-bonding modules, and 1,6-diaminopyridine-appended C60 was used as the complementary hydrogen bonding module (C-1), in which the C60 part acts as a spin converter for triplet formation. Visible light-harvesting antennae with methylated thymine were prepared as references (B-1-Me, B-2-Me and B-3-Me), which are unable to form strong H-bonds with C-1. Triple H-bonds are formed between each Bodipy antenna (B-1, B-2 and B-3) and the C60 module (C-1). The photophysical properties of the H-bonding assemblies and the reference non-hydrogen bond-forming mixtures were studied using steady state UV/vis absorption spectroscopy, fluorescence emission spectroscopy, electrochemical characterization, and nanosecond transient absorption spectroscopy. Singlet energy transfer from the Bodipy antenna to the C60 module was confirmed by fluorescence quenching studies. The intersystem crossing of the latter produced the triplet excited state. The nanosecond transient absorption spectroscopy showed that the triplet state is either localized on the C60 module (for assembly B-1·C-1), or on the styryl-Bodipy antenna (for assemblies B-2·C-1 and B-3·C-1). Intra-assembly forward–backward (ping-pong) singlet/triplet energy transfer was proposed. In contrast to the H-bonding assemblies, slow triplet energy transfer was observed for the non-hydrogen bonding mixtures. As a proof of concept, these supramolecular assemblies were used as triplet photosensitizers for triplet–triplet annihilation upconversion. PMID:29218142

Investigation of the interfacial reaction between metal and fluorine-contained polyimides

NASA Astrophysics Data System (ADS)

Yang, Ching-Yu; Chen, J. S.; Hsu, S. L. C.

2005-07-01

In this work, thin metal films (Cr and Ta) were deposited on fluorine-contained polyimides, 6FDA-BisAAF, and 6FDA-PPD. The chemical states of the metal/polyimide samples were characterized by using x-ray photoelectron spectroscopy (XPS). XPS analysis reveals that metal-C, C-O, and metal-O bondings are present in metallized 6FDA-BisAAF and 6FDA-PPD. C-F bonds are observed in bare 6FDA-BisAAF and 6FDA-PPD however, they are not seen in the metallized samples. Disappearance of the C-F bonding is attributed to the disruption of CF3 side groups from the main chains of 6FDA-BisAAF and 6FDA-PPD when the chains are exposed to the plasma during the metal deposition. Nevertheless, the disruption of CF3 side groups also creates sites for the formation of metal-C or C-O bondings, which provide a positive adhesion strength at the metal/polyimide interface, as revealed by the tape test.

On the nature of carbon-hydrogen bond activation at rhodium and related reactions.

PubMed

Jones, William D

2005-06-27

Over the past 20 years, substantial progress has been made in the understanding of the activation of C-H and other strong bonds by reactive metal complexes in low oxidation states. This paper will present an overview of the use of pentamethylcyclopentadienyl and trispyrazolylborate rhodium complexes for the activation of arene and alkane C-H bonds. Insights into bond strengths, kinetic and thermodynamic selectivities, and the nature of the intermediates involved will be reviewed. The role of eta-2 arene complexes will be shown to be critical to the C-H activation reactions. Some information about the fleeting alkane sigma-complexes will also be presented. In addition, use of these complexes with thiophenes has shown the ability to cleave C-S bonds. Mechanistic information has been obtained indicating coordination through sulfur prior to cleavage. Relevant examples of nickel-based C-S cleavage will also be given.

The antitumour drug 7-ethyl-10-hydroxycamptothecin monohydrate and its solid-state hydrolysis mechanism on heating.

PubMed

Ali, Md Ashraf; Noguchi, Shuji; Watanabe, Miteki; Iwao, Yasunori; Itai, Shigeru

2016-10-01

7-Ethyl-10-hydroxycamptothecin [systematic name: (4S)-4,11-diethyl-4,9-dihydroxy-1H-pyrano[3',4':6,7]indolizino[1,2-b]quinoline-3,14(4H,12H)-dione, SN-38] is an antitumour drug which exerts activity through the inhibition of topoisomerase I. The crystal structure of SN-38 as the monohydrate, C 22 H 20 N 2 O 5 ·H 2 O, reveals that it is a monoclinic crystal, with one SN-38 molecule and one water molecule in the asymmetric unit. When the crystal is heated to 473 K, approximately 30% of SN-38 is hydrolyzed at its lactone ring, resulting in the formation of the inactive carboxylate form. The molecular arrangement around the water molecule and the lactone ring of SN-38 in the crystal structure suggests that SN-38 is hydrolyzed by the water molecule at (x, y, z) nucleophilically attacking the carbonyl C atom of the lactone ring at (x - 1, y, z - 1). Hydrogen bonding around the water molecules and the lactone ring appears to promote this hydrolysis reaction: two carbonyl O atoms, which are hydrogen bonded as hydrogen-bond acceptors to the water molecule at (x, y, z), might enhance the nucleophilicity of this water molecule, while the water molecule at (-x, y + 1/2, -z), which is hydrogen bonded as a hydrogen-bond donor to the carbonyl O atom at (x - 1, y, z - 1), might enhance the electrophilicity of the carbonyl C atom.

Hydrogen bonds determine the signal arrangement in 13C NMR spectra of nicotinate

NASA Astrophysics Data System (ADS)

Gamov, G. A.; Kuranova, N. N.; Pogonin, A. E.; Aleksandriiskii, V. V.; Sharnin, V. A.

2018-02-01

Present work reports on studies of sodium nicotinate solutions in water and aqueous ethanol by means of 1H, 13C, 15N NMR spectroscopy. The H(2) nucleus was observed to be the least shielded among pyridine ring protons whilst C(6) signal placed in the lowest field in relation to the other pyridine carbons. The hydrogen bonds formation between nicotinate and water molecules was shown to be probable reason of signal arrangement in 13C NMR spectra of nicotinate. The heteronitrogen of nicotinate is less prone to the hydrogen bonding with water molecules than that of nicotinamide. The data on the change in the Gibbs energy of the nicotinate transfer and the results of the 13C NMR experiment are compared.

Supramolecular Cross-Links in Poly(alkyl methacrylate) Copolymers and Their Impact on the Mechanical and Reversible Adhesive Properties.

PubMed

Heinzmann, Christian; Salz, Ulrich; Moszner, Norbert; Fiore, Gina L; Weder, Christoph

2015-06-24

Hydrogen-bonded, side-chain-functionalized supramolecular poly(alkyl methacrylate)s were investigated as light- and temperature-responsive reversible adhesives that are useful for bonding and debonding on demand applications. Here, 2-hydroxyethyl methacrylate (HEMA) was functionalized with 2-ureido-4[1H]pyrimidinone (UPy) via a hexamethylenediisocyanate (HMDI) linker, to create a monomer (UPy-HMDI-HEMA) that serves to form supramolecular cross-links by way of forming quadruple hydrogen bonded dimers. UPy-HMDI-HEMA was copolymerized with either hexyl methacrylate or butyl methacrylate to create copolymers comprising 2.5, 5, or 10 mol % of the cross-linker. The mechanical properties of all (co)polymers were investigated with stress-strain experiments and dynamic mechanical analysis. Furthermore, the adhesive properties were studied at temperatures between 20 and 60 °C by testing single lap joints formed with stainless steel substrates. It was found that increasing the concentration of the UPy-HMDI-HEMA cross-linker leads to improved mechanical and adhesive properties at elevated temperatures. Concurrently, the reversibility of the bond formation remained unaffected, where rebonded samples displayed the same adhesive strength as regularly bonded samples. Debonding on demand abilities were also tested exemplarily for one copolymer, which for light-induced debonding experiments was blended with a UV-absorber that served as light-heat converter. Single lap joints were subjected to a constant force and heated or irradiated with UV light until debonding occurred. The necessary debonding temperature was comparable for direct heating and UV irradiation and varied between 28 and 82 °C, depending on the applied force. The latter also influenced the debonding time, which under the chosen conditions ranged from 30 s to 12 min.

A novel engineered interchain disulfide bond in the constant region enhances the thermostability of adalimumab Fab.

PubMed

Nakamura, Hitomi; Oda-Ueda, Naoko; Ueda, Tadashi; Ohkuri, Takatoshi

2018-01-01

We constructed a system for expressing the Fab of the therapeutic human monoclonal antibody adalimumab at a yield of 20 mg/L in the methylotrophic yeast Pichia pastoris. To examine the contribution of interchain disulfide bonds to conformational stability, we prepared adalimumab Fab from which the interchain disulfide bond at the C-terminal region at both the CH 1 and CL domains was deleted by substitution of Cys with Ala (Fab ΔSS ). DSC measurements showed that the Tm values of Fab ΔSS were approximately 5 °C lower than those of wild-type Fab, suggesting that the interchain disulfide bond contributes to conformational thermostability. Using computer simulations, we designed a novel interchain disulfide bond outside the C-terminal region to increase the stability of Fab ΔSS . The resulting Fab (mutSS Fab ΔSS ) had the mutations H:V177C and L:Q160C in Fab ΔSS , confirming the formation of the disulfide bond between CH 1 and CL. The thermostability of mutSS Fab ΔSS was approximately 5 °C higher than that of Fab ΔSS . Therefore, the introduction of the designed interchain disulfide bond enhanced the thermostability of Fab ΔSS and mitigated the destabilization caused by partial reduction of the interchain disulfide bond at the C-terminal region, which occurs in site-specific modification such as PEGylation. Copyright © 2017 Elsevier Inc. All rights reserved.

Nanoscale Charge Balancing Mechanism in Calcium-Silicate-Hydrate Gels: Novel Complex Disordered Materials from First-principles

NASA Astrophysics Data System (ADS)

Ozcelik, Ongun; White, Claire

Alkali-activated materials which have augmented chemical compositions as compared to ordinary Portland cement are sustainable technologies that have the potential to lower CO2 emissions associated with the construction industry. In particular, calcium-silicate-hydrate (C-S-H) gel is altered at the atomic scale due to changes in its chemical composition. Here, based on first-principles calculations, we predict a charge balancing mechanism at the molecular level in C-S-H gels when alkali atoms are introduced into their structure. This charge balancing process is responsible for the formation of novel structures which possess superior mechanical properties compared to their charge unbalanced counterparts. Different structural representations are obtained depending on the level of substitution and the degree of charge balancing incorporated in the structures. The impact of these charge balancing effects on the structures is assessed by analyzing their formation energies, local bonding environments, diffusion barriers and mechanical properties. These results provide information on the phase stability of alkali/aluminum containing C-S-H gels, shedding light on the fundamental mechanisms that play a crucial role in these complex disordered materials. We acknowledge funding from the Princeton Center for Complex Materials, a MRSEC supported by NSF.

Collapsed tetragonal phase as a strongly covalent and fully nonmagnetic state: Persistent magnetism with interlayer As-As bond formation in Rh-doped Ca0 .8Sr0 .2Fe2As2

NASA Astrophysics Data System (ADS)

Zhao, K.; Glasbrenner, J. K.; Gretarsson, H.; Schmitz, D.; Bednarcik, J.; Etter, M.; Sun, J. P.; Manna, R. S.; Al-Zein, A.; Lafuerza, S.; Scherer, W.; Cheng, J. G.; Gegenwart, P.

2018-02-01

A well-known feature of the CaFe2As2 -based superconductors is the pressure-induced collapsed tetragonal phase that is commonly ascribed to the formation of an interlayer As-As bond. Using detailed x-ray scattering and spectroscopy, we find that Rh-doped Ca0.8Sr0.2Fe2As2 does not undergo a first-order phase transition and that local Fe moments persist despite the formation of interlayer As-As bonds. Our density functional theory calculations reveal that the Fe-As bond geometry is critical for stabilizing magnetism and the pressure-induced drop in the c lattice parameter observed in pure CaFe2As2 is mostly due to a constriction within the FeAs planes. The collapsed tetragonal phase emerges when covalent bonding of strongly hybridized Fe 3 d and As 4 p states completely wins out over their exchange splitting. Thus the collapsed tetragonal phase is properly understood as a strong covalent phase that is fully nonmagnetic with the As-As bond forming as a by-product.

31 CFR 315.32 - Series A, B, C, D, F, G, J, and K bonds.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 31 Money and Finance:Treasury 2 2012-07-01 2012-07-01 false Series A, B, C, D, F, G, J, and K.... SAVINGS BONDS, SERIES A, B, C, D, E, F, G, H, J, AND K, AND U.S. SAVINGS NOTES Interest § 315.32 Series A, B, C, D, F, G, J, and K bonds. All bonds of these series have matured and no longer earn interest. ...

31 CFR 315.32 - Series A, B, C, D, F, G, J, and K bonds.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 31 Money and Finance:Treasury 2 2013-07-01 2013-07-01 false Series A, B, C, D, F, G, J, and K.... SAVINGS BONDS, SERIES A, B, C, D, E, F, G, H, J, AND K, AND U.S. SAVINGS NOTES Interest § 315.32 Series A, B, C, D, F, G, J, and K bonds. All bonds of these series have matured and no longer earn interest. ...

31 CFR 315.32 - Series A, B, C, D, F, G, J, and K bonds.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 31 Money and Finance: Treasury 2 2010-07-01 2010-07-01 false Series A, B, C, D, F, G, J, and K.... SAVINGS BONDS, SERIES A, B, C, D, E, F, G, H, J, AND K, AND U.S. SAVINGS NOTES Interest § 315.32 Series A, B, C, D, F, G, J, and K bonds. All bonds of these series have matured and no longer earn interest. ...

Discovery of SiCSi in IRC +10216: A missing link between gas and dust carriers of Si–C bonds

PubMed Central

Cernicharo, J.; McCarthy, M. C.; Gottlieb, C. A.; Agúndez, M.; Velilla Prieto, L.; Baraban, J. H.; Changala, P. B.; Guélin, M.; Kahane, C.; Martin-Drumel, M. A.; Patel, N. A.; Reilly, N. J.; Stanton, J. F.; Quintana-Lacaci, G.; Thorwirth, S.; Young, K. H.

2015-01-01

We report the discovery in space of a disilicon species, SiCSi, from observations between 80 and 350 GHz with the IRAM10 30m radio telescope. Owing to the close coordination between laboratory experiments and astrophysics, 112 lines have now been detected in the carbon-rich star CW Leo. The derived frequencies yield improved rotational and centrifugal distortion constants up to sixth order. From the line profiles and interferometric maps with the Submillimeter Array11, the bulk of the SiCSi emission arises from a region of 6″ in radius. The derived abundance is comparable to that of SiC2. As expected from chemical equilibrium calculations, SiCSi and SiC2 are the most abundant species harboring a Si–C bond in the dust formation zone and certainly both play a key role in the formation of SiC dust grains. PMID:26722621

A ReaxFF-based molecular dynamics study of the mechanisms of interactions between reactive oxygen plasma species and the Candida albicans cell wall

NASA Astrophysics Data System (ADS)

Zhao, T.; Shi, L.; Zhang, Y. T.; Zou, L.; Zhang, L.

2017-10-01

Atmospheric pressure non-equilibrium plasmas have attracted significant attention and have been widely used to inactivate pathogens, yet the mechanisms underlying the interactions between plasma-generated species and bio-organisms have not been elucidated clearly. In this paper, reactive molecular dynamics simulations are employed to investigate the mechanisms of interactions between reactive oxygen plasma species (O, OH, and O2) and β-1,6-glucan (a model for the C. albicans cell wall) from a microscopic point of view. Our simulations show that O and OH species can break structurally important C-C and C-O bonds, while O2 molecules exhibit only weak, non-bonded interactions with β-1,6-glucan. Hydrogen abstraction from hydroxyl or CH groups occurs first in all bond cleavage mechanisms. This is followed by a cascade of bond cleavage and double bond formation events. These lead to the destruction of the fungal cell wall. O and OH have similar effects related to their bond cleavage mechanisms. Our simulation results provide fundamental insights into the mechanisms underlying the interactions between reactive oxygen plasma species and the fungal cell wall of C. albicans at the atomic level.

Density functional theory study of the reaction mechanism for competitive carbon-hydrogen and carbon-halogen bond activations catalyzed by transition metal complexes.

PubMed

Yang, Xinzheng; Hall, Michael B

2009-03-12

Carbon-hydrogen and carbon-halogen bond activations between halobenzenes and metal centers were studied by density functional theory with the nonempirical meta-GGA Tao-Perdew-Staroverov-Scuseria functional and an all-electron correlation-consistent polarized valence double-zeta basis set. Our calculations demonstrate that the hydrogen on the metal center and halogen in halobenzene could exchange directly through a kite-shaped transition state. Transition states with this structure were previously predicted to have high energy barriers (J. Am. Chem. Soc. 2005, 127, 279), and this prediction misled others in proposing a mechanism for their recent experimental study (J. Am. Chem. Soc. 2006, 128, 3303). Furthermore, other halo-carbon activation pathways were found in the detailed mechanism for the competitive reactions between cationic titanium hydride complex [Cp*((t)Bu(3)P=N)TiH](+) and chlorobenzene under different pressure of H(2). These pathways include the ortho-C-H and Ti-H bond activations for the formation and release of H(2) and the indirect C-Cl bond activation via beta-halogen elimination for the movement of the C(6)H(4) ring and the formation of a C-N bond in the observed final product. A new stable isomer of the observed product with a similar total energy and an unexpected bridging between the Cp* ring and the metal center by a phenyl ring is also predicted.

Homolytic substitution at phosphorus for C–P bond formation in organic synthesis

PubMed Central

2013-01-01

Summary Organophosphorus compounds are important in organic chemistry. This review article covers emerging, powerful synthetic approaches to organophosphorus compounds by homolytic substitution at phosphorus with a carbon-centered radical. Phosphination reagents include diphosphines, chalcogenophosphines and stannylphosphines, which bear a weak P–heteroatom bond for homolysis. This article deals with two transformations, radical phosphination by addition across unsaturated C–C bonds and substitution of organic halides. PMID:23843922

Multiscale Molecular Dynamics Simulations of Model Hydrophobically Modified Ethylene Oxide Urethane Micelles.

PubMed

Yuan, Fang; Larson, Ronald G

2015-09-24

The flower-like micelles of various aggregation numbers of a model hydrophobically modified ethylene oxide urethane (HEUR) molecule, C16E45C16, and their corresponding starlike micelles, containing the surfactants C16E22 and C16E23, were studied by atomistic and coarse-grained molecular dynamic (MD) simulations. We used free energies from umbrella sampling to calculate the size distribution of micelle sizes and the average time for escape of a hydrophobic group from the micelle. Using the coarse-grained MARTINI force field, the most probable size of the model HEUR molecule was thereby determined to be about 80 hydrophobes per micelle and the average hydrophobe escape time to be about 0.1 s, both of which are consistent with previous experimental studies. Atomistic simulations reveal that hydrogen bond formation and the mean lifetime of hydration waters of the poly(ethylene oxide) (or PEO) groups are location-dependent in the HEUR micelle, with PEO groups immediately adjacent to the C16 groups forming the fewest hydrogen bonds with water and having hydration waters with longer lifetimes than those of the PEO groups located further away from the C16 groups.

27 CFR 41.114a - Qualification for extended deferral.

Code of Federal Regulations, 2010 CFR

2010-04-01

... bond or file a strengthening bond to increase the total amount of the bonds then in force to a..., as amended, 907, as amended; 26 U.S.C. 7101, 7652(a); 26 U.S.C. 7805) [T.D. ATF-5, 38 FR 19688, July 23, 1973. Redesignated at 40 FR 16835, Apr. 15, 1975, and amended by T.D. ATF-48, 44 FR 55855, Sept...

27 CFR 41.114a - Qualification for extended deferral.

Code of Federal Regulations, 2011 CFR

2011-04-01

... bond or file a strengthening bond to increase the total amount of the bonds then in force to a..., as amended, 907, as amended; 26 U.S.C. 7101, 7652(a); 26 U.S.C. 7805) [T.D. ATF-5, 38 FR 19688, July 23, 1973. Redesignated at 40 FR 16835, Apr. 15, 1975, and amended by T.D. ATF-48, 44 FR 55855, Sept...

C-H Bond Functionalization via Hydride Transfer: Formation of α-Arylated Piperidines and 1,2,3,4-Tetrahydroisoquinolines via Stereoselective Intramolecular Amination of Benzylic C-H Bonds

PubMed Central

Vadola, Paul A.; Carrera, Ignacio; Sames, Dalibor

2012-01-01

We here report a study of the intramolecular amination of sp3 C-H bonds via the hydride transfer cyclization of N-tosylimines (HT-amination). In this transformation, 5-aryl-aldehydes are subjected to N-toluenesulfonamide in the presence of BF3•OEt2 to effect imine formation and HT-cyclization, leading to 2-aryl-piperidines and 3-aryl-1,2,3,4-tetrahydroisoquinolines in a one-pot procedure. We examined the reactivity of a range of aldehyde substrates as a function of their conformational flexibility. Substrates of higher conformational rigidity were more reactive, giving higher yields of the desired products. However, a single substituent on the alkyl chain linking the N-tosylimine and the benzylic sp3 C-H bonds was sufficient for HT-cyclization to occur. In addition, an examination of various arenes revealed that the electronic character of the hydridic C-H bonds dramatically affects the efficiency of the reaction. We also found that this transformation is highly stereoselective; 2-substituted aldehydes yield cis-2,5-disubstituted piperidines, while 3-substituted aldehydes afford trans-2,4-disubstituted piperidines. The stereoselectivity is a consequence of thermodynamic control. The pseudo-allylic strain between the arene and tosyl group on the piperidine ring is proposed to rationalize the greater stability of the isomer with the aryl ring in the axial position. This preferential placement of the arene is proposed to affect the observed stereoselectivity. PMID:22672002

Regioselective Formation of α-Vinylpyrroles from the Ruthenium-Catalyzed Coupling Reaction of Pyrroles and Terminal Alkynes Involving C–H Bond Activation

PubMed Central

Gao, Ruili; Yi, Chae S.

2010-01-01

The cationic ruthenium catalyst, Ru3(CO)12/NH4PF6, was found to be highly effective for the intermolecular coupling reaction of pyrroles and terminal alkynes to give gem-selective α-vinylpyrroles. The carbon isotope effect on the α-pyrrole carbon and the Hammett correlation from a series of para-substituted N-arylpyrroles (ρ = −0.90) indicate a rate-limiting C–C bond formation step of the coupling reaction. PMID:20384382

The Heats of Formation of GaCl3 and its Fragments

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Arnold, James (Technical Monitor)

1998-01-01

The heats of formation of GaC13 and its fragments are computed. The geometries and frequencies are obtained at the B3LYP level. The CCSD(T) approach is used to solve the correlation problem. The effect of Ga 3d correlation is studied, and found to affect the bond energies by up to 1 kcal/mol. Both basis set extrapolation and bond functions are considered as ways to approach the basis set limit. Spin-orbit and scalar relativistic effects are also considered.

Hydrogen-Atom Transfer Oxidation with H2O2 Catalyzed by [FeII(1,2-bis(2,2'-bipyridyl-6-yl)ethane(H2O)2]2+: Likely Involvement of a (μ-Hydroxo)(μ-1,2-peroxo)diiron(III) Intermediate.

PubMed

Khenkin, Alexander M; Vedichi, Madhu; Shimon, Linda J W; Cranswick, Matthew A; Klein, Johannes E M N; Que, Lawrence; Neumann, Ronny

2017-11-01

The iron(II) triflate complex ( 1 ) of 1,2-bis(2,2'-bipyridyl-6-yl)ethane, with two bipyridine moieties connected by an ethane bridge, was prepared. Addition of aqueous 30% H 2 O 2 to an acetonitrile solution of 1 yielded 2 , a green compound with λ max =710 nm. Moessbauer measurements on 2 showed a doublet with an isomer shift (δ) of 0.35 mm/s and a quadrupole splitting (Δ E Q ) of 0.86 mm/s, indicative of an antiferromagnetically coupled diferric complex. Resonance Raman spectra showed peaks at 883, 556 and 451 cm -1 that downshifted to 832, 540 and 441 cm -1 when 1 was treated with H 2 18 O 2 . All the spectroscopic data support the initial formation of a (μ-hydroxo)(μ-1,2-peroxo)diiron(III) complex that oxidizes carbon-hydrogen bonds. At 0°C 2 reacted with cyclohexene to yield allylic oxidation products but not epoxide. Weak benzylic C-H bonds of alkylarenes were also oxidized. A plot of the logarithms of the second order rate constants versus the bond dissociation energies of the cleaved C-H bond showed an excellent linear correlation. Along with the observation that oxidation of the probe substrate 2,2-dimethyl-1-phenylpropan-1-ol yielded the corresponding ketone but no benzaldehyde, and the kinetic isotope effect, k H /k D , of 2.8 found for the oxidation of xanthene, the results support the hypothesis for a metal-based H-atom abstraction mechanism. Complex 2 is a rare example of a (μ-hydroxo)(μ-1,2-peroxo)diiron(III) complex that can elicit the oxidation of carbon-hydrogen bonds.

The low threshold voltage n-type silicon transistors based on a polymer/silica nanocomposite gate dielectric: The effect of annealing temperatures on their operation

NASA Astrophysics Data System (ADS)

Hashemi, Adeleh; Bahari, Ali; Ghasemi, Shahram

2017-09-01

In this work, povidone/silica nanocomposite dielectric layers were deposited on the n-type Si (100) substrates for application in n-type silicon field-effect transistors (FET). Thermogravimetric analysis (TGA) indicated that strong chemical interactions between polymer and silica nanoparticles were created. In order to examine the effect of annealing temperatures on chemical interactions and nanostructure properties, annealing process was done at 423-513 K. Atomic force microscopy (AFM) images show the very smooth surfaces with very low surface roughness (0.038-0.088 nm). The Si2p and C1s core level photoemission spectra were deconvoluted to the chemical environments of Si and C atoms respectively. The obtained results of deconvoluted X-ray photoelectron spectroscopy (XPS) spectra revealed a high percentage of silanol hydrogen bonds in the sample which was not annealed. These bonds were inversed to stronger covalence bonds (siloxan bonds) at annealing temperature of 423 K. By further addition of temperature, siloxan bonds were shifted to lower binding energy of about 1 eV and their intensity were abated at annealing temperature of 513 K. The electrical characteristics were extracted from current-Voltage (I-V) and capacitance-voltage (C-V) measurements in metal-insulator-semiconductor (MIS) structure. The all n-type Si transistors showed very low threshold voltages (-0.24 to 1 V). The formation of the strongest cross-linking at nanostructure of dielectric film annealed at 423 K caused resulted in an un-trapped path for the transport of charge carriers yielding the lowest threshold voltage (0.08 V) and the highest electron mobility (45.01 cm2/V s) for its FET. By increasing the annealing temperature (473 and 513 K) on the nanocomposite dielectric films, the values of the average surface roughness, the capacitance and the FET threshold voltage increased and the value of FET electron field-effect mobility decreased.

Spontaneous grafting of diazonium salts: chemical mechanism on metallic surfaces.

PubMed

Mesnage, Alice; Lefèvre, Xavier; Jégou, Pascale; Deniau, Guy; Palacin, Serge

2012-08-14

The spontaneous reaction of diazonium salts on various substrates has been widely employed since it consists of a simple immersion of the substrate in the diazonium salt solution. As electrochemical processes involving the same diazonium salts, the spontaneous grafting is assumed to give covalently poly(phenylene)-like bonded films. Resistance to solvents and to ultrasonication is commonly accepted as indirect proof of the existence of a covalent bond. However, the most relevant attempts to demonstrate a metal-C interface bond have been obtained by an XPS investigation of spontaneously grafted films on copper. Similarly, our experiments give evidence of such a bond in spontaneously grafted films on nickel substrates in acetonitrile. In the case of gold substrates, the formation of a spontaneous film was unexpected but reported in the literature in parallel to our observations. Even if no interfacial bond was observed, formation of the films was explained by grafting of aryl cations or radicals on the surface arising from dediazoniation, the film growing later by azo coupling, radical addition, or cationic addition on the grafted phenyl layer. Nevertheless, none of these mechanisms fits our experimental results showing the presence of an Au-N bond. In this work, we present a fine spectroscopic analysis of the coatings obtained on gold and nickel substrates that allow us to propose a chemical structure of such films, in particular, their interface with the substrates. After testing the most probable mechanisms, we have concluded in favor of the involvement of two complementary mechanisms which are the direct reaction of diazonium salts with the gold surface that accounts for the observed Au-N interfacial bonds as well as the formation of aryl cations able to graft on the substrate through Au-C linkages.

Energy for the interface system of (Nb, Mo)C/γ-Fe

NASA Astrophysics Data System (ADS)

Zhou, Yanyuan; Wang, Zhenqiang; Zhao, Jiaying; Leng, Zhe; Niu, Zhongyi; Guo, Chunhuan; Zhang, Zhengyan; Yang, Zhigang; Yao, Chunfa; Jiang, Fengchun

2017-08-01

The interfacial energies of MC/γ-Fe and formation energies of MC carbides have been investigated using first-principles calculations based on density functional theory (DFT). Results show that the replacement of Nb by Mo in the NbC lattice is unfavorable with respect to the formation energy. However, it reduces the lattice parameter of MC and decreases the σ_{{chemical}} (interfacial chemical energy) of MC/γ-Fe, thus favoring the formation of complex (Nb, Mo)C carbide. The substitution of Nb by Mo at the interface of MC/γ-Fe system promotes the hybridizations of Mo-1NNFe and C-1NNFe (or 2NNFe) (the first or second nearest neighboring Fe atoms), which leads to a decrease in σ_{{chemical}}. The influence of bond energy is estimated using the discrete lattice plane/nearest neighbor broken bond (DLP/NNBB) model. It is found that the reduced σ_{{chemical}} is attributed to the much smaller value of e_{{{{Fe-C}}}} - e_{{{{Mo-C}}}} (the difference between Fe-C and Mo-C interactions) compared to e_{{{{Fe-C}}}} - e_{{{{Nb-C}}}} (the difference between Fe-C and Nb-C interactions). The results obtained from the analysis of the precipitates in Nb- and Nb-Mo-bearing steels are in a good agreement with the calculations.

High performance supercapacitors based on highly conductive nitrogen-doped graphene sheets.

PubMed

Qiu, Yongcai; Zhang, Xinfeng; Yang, Shihe

2011-07-21

Thermal nitridation of reduced graphene oxide sheets yields highly conductive (∼1000-3000 S m(-1)) N-doped graphene sheets, as a result of the restoration of the graphene network by the formation of C-N bonded groups and N-doping. Even without carbon additives, supercapacitors made of the N-doped graphene electrodes can deliver remarkable energy and power when operated at higher voltages, in the range of 0-4 V. This journal is © the Owner Societies 2011

Amide Bond Formation Assisted by Vicinal Alkylthio Migration in Enaminones: Metal- and CO-Free Synthesis of α,β-Unsaturated Amides.

PubMed

Liu, Zhuqing; Huang, Fei; Wu, Ping; Wang, Quannan; Yu, Zhengkun

2018-05-18

Amide bond formation is one of the most important transformations in organic synthesis, drug development, and materials science. Efficient construction of amides has been among the most challenging tasks for organic chemists. Herein, we report a concise methodology for amide bond (-CONH-) formation assisted by vicinal group migration in alkylthio-functionalized enaminones (α-oxo ketene N, S-acetals) under mild conditions. Simple treatment of such enaminones with PhI(OAc) 2 at ambient temperature in air afforded diverse multiply functionalized α,β-unsaturated amides including β-cyclopropylated acrylamides, in which a wide array of functional groups such as aryl, (hetero)aryl, alkenyl, and alkyl can be conveniently introduced to a ketene moiety. The reaction mechanism was investigated by exploring the origins of the amide oxygen and carbon atoms as well as isolation and structural characterization of the reaction intermediates. The amide bond formation reactions could also be efficiently performed under solventless mechanical milling conditions.

Theory of chemical bonds in metalloenzymes XXI. Possible mechanisms of water oxidation in oxygen evolving complex of photosystem II

NASA Astrophysics Data System (ADS)

Yamaguchi, Kizashi; Shoji, Mitsuo; Isobe, Hiroshi; Yamanaka, Shusuke; Kawakami, Takashi; Yamada, Satoru; Katouda, Michio; Nakajima, Takahito

2018-03-01

Possible mechanisms for water cleavage in oxygen evolving complex (OEC) of photosystem II (PSII) have been investigated based on broken-symmetry (BS) hybrid DFT (HDFT)/def2 TZVP calculations in combination with available XRD, XFEL, EXAFS, XES and EPR results. The BS HDFT and the experimental results have provided basic concepts for understanding of chemical bonds of the CaMn4O5 cluster in the catalytic site of OEC of PSII for elucidation of the mechanism of photosynthetic water cleavage. Scope and applicability of the hybrid DFT (HDFT) methods have been examined in relation to relative stabilities of possible nine intermediates such as Mn-hydroxide, Mn-oxo, Mn-peroxo, Mn-superoxo, etc., in order to understand the O-O (O-OH) bond formation in the S3 and/or S4 states of OEC of PSII. The relative stabilities among these intermediates are variable, depending on the weight of the Hartree-Fock exchange term of HDFT. The Mn-hydroxide, Mn-oxo and Mn-superoxo intermediates are found to be preferable in the weak, intermediate and strong electron correlation regimes, respectively. Recent different serial femtosecond X-ray (SFX) results in the S3 state are investigated based on the proposed basic concepts under the assumption of different water-insertion steps for water cleavage in the Kok cycle. The observation of water insertion in the S3 state is compatible with previous large-scale QM/MM results and previous theoretical proposal for the chemical equilibrium mechanism in the S3 state . On the other hand, the no detection of water insertion in the S3 state based on other SFX results is consistent with previous proposal of the O-OH (or O-O) bond formation in the S4 state . Radical coupling and non-adiabatic one-electron transfer (NA-OET) mechanisms for the OO-bond formation are examined using the energy diagrams by QM calculations and by QM(UB3LYP)/MM calculations . Possible reaction pathways for the O-O and O-OH bond formations are also investigated based on two water-inlet pathways for oxygen evolution in OEC of PSII. Future perspectives are discussed in relation to post HDFT calculations of the energy diagrams for elucidation of the mechanism of water oxidation in OEC of PSII.

Utility of Horioka’s and Marra’s models for adhesive failure

Treesearch

Charles R. Frihart

2005-01-01

Bond formation primarily involves adhesive rheology and interface chemistry. Bonded assembly strength, however, primarily involves the viscoelastic dissipation of stress over the entire assembly. Models can aid in the understanding of where and why failure occurs and how to improve the strength of the assembly. Horioka and Marra have both proposed models which define...

Experimental evidence for the participation of deep eutectic solvents in silver chloride crystal formation at low temperature

NASA Astrophysics Data System (ADS)

Bhatt, Jitkumar; Mondal, Dibyendu; Prasad, Kamalesh

2016-05-01

Deep eutectic solvents (DESs) obtained by the complexation of choline chloride (ChoCl) as hydrogen bond acceptor and hydrogen bond donors such as ethylene glycol (ChoCl-EG 1:2) and glycerol (ChoCl-Gly 1:2) were used as media for the formation of AgCl crystals. Although formation of AgCl crystals was observed in both the solvents but the rate of formation of crystals was faster in ChoCl-EG 1:2 at low temperature (4-5 °C). In the crystals, cholinium cations were found to be present with chloride ions bridged with Ag ions resulting generation of 1D network of AgCl2 anions.

Carbamoyl anion-initiated cascade reaction for stereoselective synthesis of substituted α-hydroxy-β-amino amides.

PubMed

Lin, Chao-Yang; Ma, Peng-Ju; Sun, Zhao; Lu, Chong-Dao; Xu, Yan-Jun

2016-01-18

A carbamoyl anion-initiated cascade reaction with acylsilanes and imines has been used to rapidly construct substituted α-hydroxy-β-amino amides. The Brook rearrangement-mediated cascade allows the formation of two C-C bonds and one O-Si bond in a single pot. Using this approach, a range of α-aryl α-hydroxy-β-amino amides has been synthesized in high yields with excellent diastereoselectivities.

Crystal structure of 4-fluoro-N-[2-(4-fluoro-benzo-yl)hydra-zine-1-carbono-thio-yl]benzamide.

PubMed

Firdausiah, Syadza; Salleh Huddin, Ameera Aqeela; Hasbullah, Siti Aishah; Yamin, Bohari M; Yusoff, Siti Fairus M

2014-09-01

In the title compound, C15H11F2N3O2S, the dihedral angle between the fluoro-benzene rings is 88.43 (10)° and that between the central semithiocarbazide grouping is 47.00 (11)°. The dihedral angle between the amide group and attached fluoro-benzene ring is 50.52 (11)°; the equivalent angle between the carbonyl-thio-amide group and its attached ring is 12.98 (10)°. The major twists in the mol-ecule occur about the C-N-N-C bonds [torsion angle = -138.7 (2)°] and the Car-Car-C-N (ar = aromatic) bonds [-132.0 (2)°]. An intra-molecular N-H⋯O hydrogen bond occurs, which generates an S(6) ring. In the crystal, the mol-ecules are linked by N-H⋯O and N-H⋯S hydrogen bonds, generating (001) sheets. Weak C-H⋯O and C-H⋯F inter-actions are also observed.

A novel carotenoid cleavage activity involved in the biosynthesis of Citrus fruit-specific apocarotenoid pigments

PubMed Central

Rodrigo, María J.; Alquézar, Berta; Al-Babili, Salim

2013-01-01

Citrus is the first tree crop in terms of fruit production. The colour of Citrus fruit is one of the main quality attributes, caused by the accumulation of carotenoids and their derivative C30 apocarotenoids, mainly β-citraurin (3-hydroxy-β-apo-8′-carotenal), which provide an attractive orange-reddish tint to the peel of oranges and mandarins. Though carotenoid biosynthesis and its regulation have been extensively studied in Citrus fruits, little is known about the formation of C30 apocarotenoids. The aim of this study was to the identify carotenoid cleavage enzyme(s) [CCD(s)] involved in the peel-specific C30 apocarotenoids. In silico data mining revealed a new family of five CCD4-type genes in Citrus. One gene of this family, CCD4b1, was expressed in reproductive and vegetative tissues of different Citrus species in a pattern correlating with the accumulation of C30 apocarotenoids. Moreover, developmental processes and treatments which alter Citrus fruit peel pigmentation led to changes of β-citraurin content and CCD4b1 transcript levels. These results point to the involvement of CCD4b1 in β-citraurin formation and indicate that the accumulation of this compound is determined by the availability of the presumed precursors zeaxanthin and β-cryptoxanthin. Functional analysis of CCD4b1 by in vitro assays unequivocally demonstrated the asymmetric cleavage activity at the 7′,8′ double bond in zeaxanthin and β-cryptoxanthin, confirming its role in C30 apocarotenoid biosynthesis. Thus, a novel plant carotenoid cleavage activity targeting the 7′,8′ double bond of cyclic C40 carotenoids has been identified. These results suggest that the presented enzyme is responsible for the biosynthesis of C30 apocarotenoids in Citrus which are key pigments in fruit coloration. PMID:24006419

Modeling the IR spectra of aqueous metal carboxylate complexes: correlation between bonding geometry and stretching mode wavenumber shifts.

PubMed

Sutton, Catherine C R; da Silva, Gabriel; Franks, George V

2015-04-27

A widely used principle is that shifts in the wavenumber of carboxylate stretching modes upon bonding with a metal center can be used to infer if the geometry of the bonding is monodentate or bidentate. We have tested this principle with ab initio modeling for aqueous metal carboxylate complexes and have shown that it does indeed hold. Modeling of the bonding of acetate and formate in aqueous solution to a range of cations was used to predict the infrared spectra of the metal-carboxylate complexes, and the wavenumbers of the symmetric and antisymmetric vibrational modes are reported. Furthermore, we have shown that these shifts in wavenumber occur primarily due to how bonding with the metal changes the carboxylate C-O bond lengths and O-C-O angle. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effect of bond coat and preheat on the microstructure, hardness, and porosity of flame sprayed tungsten carbide coatings

NASA Astrophysics Data System (ADS)

Winarto, Winarto; Sofyan, Nofrijon; Rooscote, Didi

2017-06-01

Thermally sprayed coatings are used to improve the surface properties of tool steel materials. Bond coatings are commonly used as intermediate layers deposited on steel substrates (i.e. H13 tool steel) before the top coat is applied in order to enhance a number of critical performance criteria including adhesion of a barrier coating, limiting atomic migration of the base metal, and corrosion resistance. This paper presents the experimental results regarding the effect of nickel bond coat and preheats temperatures (i.e. 200°C, 300°C and 400°C) on microstructure, hardness, and porosity of tungsten carbide coatings sprayed by flame thermal coating. Micro-hardness, porosity and microstructure of tungsten carbide coatings are evaluated by using micro-hardness testing, optical microscopy, scanning electron microscopy, and X-ray diffraction. The results show that nickel bond coatings reduce the susceptibility of micro crack formation at the bonding area interfaces. The percentage of porosity level on the tungsten carbide coatings with nickel bond coat decreases from 5.36 % to 2.78% with the increase of preheat temperature of the steel substrate of H13 from 200°C to 400°C. The optimum hardness of tungsten carbide coatings is 1717 HVN in average resulted from the preheat temperature of 300°C.

Photophysics of indole-2-carboxylic acid (I2C) and indole-5-carboxylic acid (I5C): Heavy atom effect

NASA Astrophysics Data System (ADS)

Kowalska-Baron, Agnieszka; Gałęcki, Krystian; Wysocki, Stanisław

2013-12-01

In this study the effect of carboxylic group substitution in the 2 and 5 position of indole ring on the photophysics of the parent indole chromophore has been studied. The photophysical parameters crucial in triplet state decay mechanism of aqueous indole-2-carboxylic acid (I2C) and indole-5-carboxylic acid (I5C) have been determined applying our previously proposed methodology based on the heavy atom effect and fluorescence and phosphorescence decay kinetics [Kowalska-Baron et al., 2012]. The determined time-resolved phosphorescence spectra of I2C and I5C are red-shifted as compared to that of the parent indole. This red-shift was especially evident in the case of I2C and may indicate the possibility of hydrogen bonded complex formation incorporating carbonyl Cdbnd O, the NH group of I2C and, possibly, surrounding water molecules. The possibility of the excited state charge transfer process and the subsequent electronic charge redistribution in such a hydrogen bonded complex may also be postulated. The resulting stabilization of the I2C triplet state is manifested by its relatively long phosphorescence lifetime in aqueous solution (912 μs). The relatively short phosphorescence lifetime of I5C (56 μs) may be the consequence of more effective ground-state quenching of I5C triplet state. This hypothesis may be strengthened by the significantly larger value of the determined rate constant of I5C triplet state quenching by its ground-state (4.4 × 108 M-1 s-1) as compared to that for indole (6.8 × 107 M-1 s-1) and I2C (2.3 × 107 M-1 s-1). The determined bimolecular rate constant for triplet state quenching by iodide kqT1 is equal to 1 × 104 M-1 s-1; 6 × 103 M-1 s-1 and 2.7 × 104 M-1 s-1 for indole, I2C and I5C, respectively. In order to obtain a better insight into iodide quenching of I2C and I5C triplet states in aqueous solution, the temperature dependence of the bimolecular rate constants for iodide quenching of the triplet states has been expressed in Arrhenius form. The linearity of the obtained Arrhenius plots clearly indicated the existence of one temperature-dependent non-radiative process for the de-excitation of I2C and I5C triplet state in the presence of iodide. This process may be attributed to the solute-quenching by iodide and, most probably, proceeds via reversibly formed exciplex. The activation energies obtained from linear Arrhenius plots (1.89 kcal/mol for I5C; 2.55 kcal/mol for I2C) are smaller as compared to that for diffusion controlled reactions in aqueous solution (about 4 kcal/mol), which may indicate the great importance of the electrostatic interactions between solute and iodide ions in lowering the energy barrier needed for the formation of the triplet-quencher complex. Based on the theoretical predictions (at the DFT(CAM-B3LYP)/6-31 + G(d,p) level of theory) and careful analysis of the obtained FTIR spectra it may be concluded that in the solid state I2C and I5C molecules form associates by intermolecular NH⋯Odbnd C and OH⋯Odbnd C hydrogen bonding interactions, whereas the existence of intramolecular NH⋯Odbnd C interactions in the solid state of I2C and I5C is highly unlikely.

Redox biology of Mycobacterium tuberculosis H37Rv: protein-protein interaction between GlgB and WhiB1 involves exchange of thiol-disulfide

PubMed Central

Garg, Saurabh; Alam, Md Suhail; Bajpai, Richa; Kishan, KV Radha; Agrawal, Pushpa

2009-01-01

Background Mycobacterium tuberculosis, an intracellular pathogen encounters redox stress throughout its life inside the host. In order to protect itself from the redox onslaughts of host immune system, M. tuberculosis appears to have developed accessory thioredoxin-like proteins which are represented by ORFs encoding WhiB-like proteins. We have earlier reported that WhiB1/Rv3219 is a thioredoxin like protein of M. tuberculosis and functions as a protein disulfide reductase. Generally thioredoxins have many substrate proteins. The current study aims to identify the substrate protein(s) of M. tuberculosis WhiB1. Results Using yeast two-hybrid screen, we identified alpha (1,4)-glucan branching enzyme (GlgB) of M. tuberculosis as a interaction partner of WhiB1. In vitro GST pull down assay confirmed the direct physical interaction between GlgB and WhiB1. Both mass spectrometry data of tryptic digests and in vitro labeling of cysteine residues with 4-acetamido-4' maleimidyl-stilbene-2, 2'-disulfonic acid showed that in GlgB, C95 and C658 are free but C193 and C617 form an intra-molecular disulfide bond. WhiB1 has a C37XXC40 motif thus a C40S mutation renders C37 to exist as a free thiol to form a hetero-disulfide bond with the cysteine residue of substrate protein. A disulfide mediated binary complex formation between GlgB and WhiB1C40S was shown by both in-solution protein-protein interaction and thioredoxin affinity chromatography. Finally, transfer of reducing equivalent from WhiB1 to GlgB disulfide was confirmed by 4-acetamido-4' maleimidyl-stilbene-2, 2'-disulfonic acid trapping by the reduced disulfide of GlgB. Two different thioredoxins, TrxB/Rv1471 and TrxC/Rv3914 of M. tuberculosis could not perform this reaction suggesting that the reduction of GlgB by WhiB1 is specific. Conclusion We conclude that M. tuberculosis GlgB has one intra-molecular disulfide bond which is formed between C193 and C617. WhiB1, a thioredoxin like protein interacts with GlgB and transfers its electrons to the disulfide thus reduces the intra-molecular disulfide bond of GlgB. For the first time, we report that GlgB is one of the in vivo substrate of M. tuberculosis WhiB1. PMID:19121228

Intermolecular interactions of trifluorohalomethanes with Lewis bases in the gas phase: an ab initio study.

PubMed

Wang, Yi-Siang; Yin, Chih-Chien; Chao, Sheng D

2014-10-07

We perform an ab initio computational study of molecular complexes with the general formula CF3X-B that involve one trifluorohalomethane CF3X (X = Cl or Br) and one of a series of Lewis bases B in the gas phase. The Lewis bases are so chosen that they provide a range of electron-donating abilities for comparison. Based on the characteristics of their electron pairs, we consider the Lewis bases with a single n-pair (NH3 and PH3), two n-pairs (H2O and H2S), two n-pairs with an unsaturated bond (H2CO and H2CS), and a single π-pair (C2H4) and two π-pairs (C2H2). The aim is to systematically investigate the influence of the electron pair characteristics and the central atom substitution effects on the geometries and energetics of the formed complexes. The counterpoise-corrected supermolecule MP2 and coupled-cluster single double with perturbative triple [CCSD(T)] levels of theory have been employed, together with a series of basis sets up to aug-cc-pVTZ. The angular and radial configurations, the binding energies, and the electrostatic potentials of the stable complexes have been compared and discussed as the Lewis base varies. For those complexes where halogen bonding plays a significant role, the calculated geometries and energetics are consistent with the σ-hole model. Upon formation of stable complexes, the C-X bond lengths shorten, while the C-X vibrational frequencies increase, thus rendering blueshifting halogen bonds. The central atom substitution usually enlarges the intermolecular bond distances while it reduces the net charge transfers, thus weakening the bond strengths. The analysis based on the σ-hole model is grossly reliable but requires suitable modifications incorporating the central atom substitution effects, in particular, when interaction components other than electrostatic contributions are involved.

Perfluorinated Ligands in Organometallic Chemistry

DTIC Science & Technology

1989-12-12

C49t00ooVER ,or C M’ AD"OV’~mDecember 12) 199IFinal 1/1/86 to 8/31/89C smuS. FUNOING NUMgIERS cJ Perfluorinated Ligands in Organometallic Chemistry 612...compounds, stabilized by tridentate perfluorinated ligands. Dinuclear rhodium complexes of OFCOT undergo a selective C-F bond activation reaction...hexafluorocyclooctatrieneyne ligand. Stereospecific cleavage of a fluorinated C-C bond,#-bond in perfluorocyclopropene by platinum and iridium complexes has been achieved

Formation of bound residues during microbial degradation of [{sup 14}C]anthracene in soil

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

Kaestner, M.; Streibich, S.; Beyrer, M.

1999-05-01

Carbon partitioning and residue formation during microbial degradation of polycyclic aromatic hydrocarbons (PAH) in soil and soil-compost mixtures were examined by using [{sup 14}C]anthracenes labeled at different positions. In native soil 43.8% of [9-{sup 14}C]anthracene was mineralized by the autochthonous microflora and 45.4% was transformed into bound residues within 176 days. Addition of compost increased the metabolism and decreased the residue formation (20.7% of the anthracene was transformed). Thus, the higher organic carbon content after compost was added did not increase the level of residue formation. [{sup 14}C]anthracene labeled at position 1,2,3,4,4a,5a was metabolized more rapidly and resulted in formationmore » of higher levels of residues (28.5%) by the soil-compost mixture than [{sup 14}C]anthracene radiolabeled at position C-9 (20.7%). Two phases of residue formation were observed in the experiments. In the first phase the original compound was sequestered in the soil, as indicated by its limited extractability. In the second phase metabolites were incorporated into humic substances after microbial degradation of the PAH (biogenic residue formation). PAH metabolites undergo oxidative coupling to phenolic compounds to form nonhydrolyzable humic substance-like macromolecules. The authors found indications that monomeric educts are coupled by C-C- or either bonds. Hydrolyzable ester bonds or sorption of the parent compounds plays a minor role in residue formation. Moreover, experiments performed with {sup 14}CO{sub 2} revealed that residues may arise from CO{sub 2} in the soil in amounts typical for anthracene biodegradation. The extent of residue formation depends on the metabolic capacity of the soil microflora and the characteristics of the soil. The position of the {sup 14}C label is another important factor which controls mineralization and residue formation from metabolized compounds.« less

Reactive molecular dynamics simulation of solid nitromethane impact on (010) surfaces induced and nonimpact thermal decomposition.

PubMed

Guo, Feng; Cheng, Xin-lu; Zhang, Hong

2012-04-12

Which is the first step in the decomposition process of nitromethane is a controversial issue, proton dissociation or C-N bond scission. We applied reactive force field (ReaxFF) molecular dynamics to probe the initial decomposition mechanisms of nitromethane. By comparing the impact on (010) surfaces and without impact (only heating) for nitromethane simulations, we found that proton dissociation is the first step of the pyrolysis of nitromethane, and the C-N bond decomposes in the same time scale as in impact simulations, but in the nonimpact simulation, C-N bond dissociation takes place at a later time. At the end of these simulations, a large number of clusters are formed. By analyzing the trajectories, we discussed the role of the hydrogen bond in the initial process of nitromethane decompositions, the intermediates observed in the early time of the simulations, and the formation of clusters that consisted of C-N-C-N chain/ring structures.

The Dissociation Energies of CH4 and C2H2 Revisited

NASA Technical Reports Server (NTRS)

Partridge, Harry; Bauschlicher, Charles W., Jr.; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

The bond dissociation energies of CH4 and C2H2 and their fragments are investigated using basis set extrapolations and high levels of correlation. The computed bond dissociation energies (D(sub e)) are accurate to within 0.2 kcal/mol. The agreement with the experimental (D(sub 0)) values is excellent if we assume that the zero-point energy of C2H is 9.18 kcal/mol. The effect of core (1s) correlation on the bond dissociation energies of C-H bonds is shown to vary from 0.2 to 0.7 kcal/mol and that for C-C bonds varies from 0.4 to 2.2 kcal/mol.

Origin and diagenetic transformations of C 25 and C 30 highly branched isoprenoid sulphur compounds: Further evidence for the formation of organically bound sulphur during early diagenesis

NASA Astrophysics Data System (ADS)

Kohnen, M. E. L.; Damsté, J. S. Slnninghe; Kock-van Dalen, A. C.; Haven, H. L. Ten; Rullkötter, J.; De Leeuw, J. W.

1990-11-01

A number of C 25 and C 30 highly branched isoprenoid (HBI) sulphur compounds (E.G., thiolanes, 1-oxo-thiolanes, thiophenes, and benzo[ b]thiophenes) with 2,6,10,14-tetramethyl-7-(3-methylpentyl)pentadecane and 2,6,10,14,18-pentamethyl-7-(3-methylpentyl)nonadecane carbon skeletons were identified in sediments, ranging from Holocene to Upper Cretaceous. These identifications are based on mass spectral characterisation, desulphurisation, and, in some cases, by comparison of mass spectral and relative retention time data with those of authentic standards. The presence of unsaturated C 25 and C 30 HBI thiolanes in a Recent sediment from the Black Sea (age 3-6 × 10 3 a) strongly supports their formation during early diagenesis. The co-occurrence of HBI polyenes (C 25 and C 30) and unsaturated HBI thiolanes (C 25 and C 30) possessing two double bonds less than the corresponding HBI polyenes, in this Recent sediment, testifies to the formation of unsaturated HBI thiolanes by a reaction of inorganic sulphur species with double bonds of the HBI polyenes. Furthermore, a diagenetic scheme for HBI sulphur compounds is proposed based on the identification of HBI sulphur compounds in sediment samples with different maturity levels.

Orientation and Order of the Amide Group of Sphingomyelin in Bilayers Determined by Solid-State NMR

PubMed Central

Matsumori, Nobuaki; Yamaguchi, Toshiyuki; Maeta, Yoshiko; Murata, Michio

2015-01-01

Sphingomyelin (SM) and cholesterol (Chol) are considered essential for the formation of lipid rafts; however, the types of molecular interactions involved in this process, such as intermolecular hydrogen bonding, are not well understood. Since, unlike other phospholipids, SM is characterized by the presence of an amide group, it is essential to determine the orientation of the amide and its order in the lipid bilayers to understand the nature of the hydrogen bonds in lipid rafts. For this study, 1′-13C-2-15N-labeled and 2′-13C-2-15N-labeled SMs were prepared, and the rotational-axis direction and order parameters of the SM amide in bilayers were determined based on 13C and 15N chemical-shift anisotropies and intramolecular 13C-15N dipole coupling constants. Results revealed that the amide orientation was minimally affected by Chol, whereas the order was enhanced significantly in its presence. Thus, Chol likely promotes the formation of an intermolecular hydrogen-bond network involving the SM amide without significantly changing its orientation, providing a higher order to the SM amide. To our knowledge, this study offers new insight into the significance of the SM amide orientation with regard to molecular recognition in lipid rafts, and therefore provides a deeper understanding of the mechanism of their formation. PMID:26083921

Ethers on Si(001): A Prime Example for the Common Ground between Surface Science and Molecular Organic Chemistry.

PubMed

Pecher, Lisa; Laref, Slimane; Raupach, Marc; Tonner, Ralf

2017-11-20

By using computational chemistry it has been shown that the adsorption of ether molecules on Si(001) under ultrahigh vacuum conditions can be understood with classical concepts of organic chemistry. Detailed analysis of the two-step reaction mechanism-1) formation of a dative bond between the ether oxygen atom and a Lewis acidic surface atom and 2) nucleophilic attack of a nearby Lewis basic surface atom-shows that it mirrors acid-catalyzed ether cleavage in solution. The O-Si dative bond is the strongest of its kind, and the reactivity in step 2 defies the Bell-Evans-Polanyi principle. Electron rearrangement during C-O bond cleavage has been visualized with a newly developed method for analyzing bonding, which shows that the mechanism of nucleophilic substitutions on semiconductor surfaces is identical to molecular S N 2 reactions. Our findings illustrate how surface science and molecular chemistry can mutually benefit from each other and unexpected insight can be gained. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Addition of aluminium, zinc and magnesium hydrides to rhodium(iii)† †Electronic supplementary information (ESI) available. CCDC 1047853–1047855 1056989. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c5sc01309g Click here for additional data file. Click here for additional data file.

PubMed Central

Ekkert, Olga; White, Andrew J. P.; Toms, Harold

2015-01-01

We report the addition of M–H bonds (M = Al, Zn, Mg) to a Rh(iii) intermediate generated from the reductive elimination of triethylsilane from [Cp*Rh(H)2(SiEt3)2]. A series of new heterobimetallic complexes possessing Rh–M bonds have been isolated and characterised by a number of spectroscopic (1H, 29Si, 13C, 103Rh NMR, infrared, and X-ray diffraction) and computational techniques (NBO and QTAIM analysis). Experimental and computational data are consistent with cleavage of the M–H bond upon addition to rhodium with formation of new Rh–M and Rh–H bonds. Upon photolysis the Al analogue of this series undergoes a further elimination reaction producing triethylsilane and a highly unusual Rh2Al2H4 containing cluster proposed to contain an Al(i) bridging ligand. PMID:28757949

Silylene-Nickel Promoted Cleavage of B-O Bonds: From Catechol Borane to the Hydroborylene Ligand.

PubMed

Hadlington, Terrance J; Szilvási, Tibor; Driess, Matthias

2017-06-19

The first 16 valence electron [bis(NHC)](silylene)Ni 0 complex 1, [( TMS L)ClSi:→Ni(NHC) 2 ], bearing the acyclic amido-chlorosilylene ( TMS L)ClSi: ( TMS L=N(SiMe 3 )Dipp; Dipp=2,6-Pr i 2 C 6 H 4 ) and two NHC ligands (N-heterocyclic carbene=:C[(Pr i )NC(Me)] 2 ) was synthesized in high yield and structurally characterized. Compound 1 is capable of facile dihydrogen activation under ambient conditions to give the corresponding HSi-NiH complex 2. Most notably, 1 reacts with catechol borane to afford the unprecedented hydroborylene-coordinated (chloro)(silyl)nickel(II) complex 3, {[cat( TMS L)Si](Cl)Ni←:BH(NHC) 2 }, via the cleavage of two B-O bonds and simultaneous formation of two Si-O bonds. The mechanism for the formation of 3 was rationalized by means of DFT calculations, which highlight the powerful synergistic effects of the Si:→Ni moiety in the breaking of incredibly strong B-O bonds. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Theoretical study of the S…Cl interaction between sulfides and atomic chlorine. Nature and strength of the two-center three-electron bond

NASA Astrophysics Data System (ADS)

Sutradhar, Dipankar; Zeegers-Huyskens, Thérèse; Chandra, Asit. K.

2017-05-01

The interaction between sulfides (H2S, CH3SH, CH3CH2SH, CH3SCH3 and CH3SCH2F) and atomic chlorine is investigated using DFT based LC-BLYP and CCSD(T) methods in conjugation with the aug-cc-pVTZ basis set. The intermolecular S…Cl distances in the complexes range between 2.5922 Å (H2S…Cl) and 2.5273 Å (CH3SCH3…Cl). The interaction energies ranging between -29.1 and -77.5 kJ mol-1 reveal the formation of relatively strong 2c-3e S…Cl bonds. The binding energies are linearly related to the proton affinity of the sulfides, to the charge transfer taking place from the sulfides to the Cl atom and inversely proportional to the difference between the ionization potential of the sulfides and the electron affinity of the Cl atom. The spin density analysis suggests that almost 48% of the spin is transferred from the Cl to the S atom in the strongest CH3SCH3…Cl complex. The AIM analysis shows that the S…Cl interaction possess a significant covalent character which decreases with decreasing binding strength of the complexes. All the data indicate that the S…Cl 2c-3e bonds are stronger than the O…Cl or N…Cl bonds and more covalent in nature. The variation of the CH distances and the blue shifts of the ν(CH) vibration resulting from the interaction with Cl are discussed.

Photophysics of indole-2-carboxylic acid (I2C) and indole-5-carboxylic acid (I5C): heavy atom effect.

PubMed

Kowalska-Baron, Agnieszka; Gałęcki, Krystian; Wysocki, Stanisław

2013-12-01

In this study the effect of carboxylic group substitution in the 2 and 5 position of indole ring on the photophysics of the parent indole chromophore has been studied. The photophysical parameters crucial in triplet state decay mechanism of aqueous indole-2-carboxylic acid (I2C) and indole-5-carboxylic acid (I5C) have been determined applying our previously proposed methodology based on the heavy atom effect and fluorescence and phosphorescence decay kinetics [Kowalska-Baron et al., 2012]. The determined time-resolved phosphorescence spectra of I2C and I5C are red-shifted as compared to that of the parent indole. This red-shift was especially evident in the case of I2C and may indicate the possibility of hydrogen bonded complex formation incorporating carbonyl CO, the NH group of I2C and, possibly, surrounding water molecules. The possibility of the excited state charge transfer process and the subsequent electronic charge redistribution in such a hydrogen bonded complex may also be postulated. The resulting stabilization of the I2C triplet state is manifested by its relatively long phosphorescence lifetime in aqueous solution (912 μs). The relatively short phosphorescence lifetime of I5C (56 μs) may be the consequence of more effective ground-state quenching of I5 C triplet state. This hypothesis may be strengthened by the significantly larger value of the determined rate constant of I5C triplet state quenching by its ground-state (4.4 × 10(8)M(-1)s(-1)) as compared to that for indole (6.8 × 10(7)M(-1)s(-1)) and I2C (2.3 × 10(7)M(-1)s(-1)). The determined bimolecular rate constant for triplet state quenching by iodide [Formula: see text] is equal to 1 × 10(4)M(-1)s(-1); 6 × 10(3)M(-1)s(-1) and 2.7 × 10(4)M(-1)s(-1) for indole, I2 C and I5 C, respectively. In order to obtain a better insight into iodide quenching of I2C and I5C triplet states in aqueous solution, the temperature dependence of the bimolecular rate constants for iodide quenching of the triplet states has been expressed in Arrhenius form. The linearity of the obtained Arrhenius plots clearly indicated the existence of one temperature-dependent non-radiative process for the de-excitation of I2C and I5C triplet state in the presence of iodide. This process may be attributed to the solute-quenching by iodide and, most probably, proceeds via reversibly formed exciplex. The activation energies obtained from linear Arrhenius plots (1.89 kcal/mol for I5 C; 2.55 kcal/mol for I2 C) are smaller as compared to that for diffusion controlled reactions in aqueous solution (about 4 kcal/mol), which may indicate the great importance of the electrostatic interactions between solute and iodide ions in lowering the energy barrier needed for the formation of the triplet-quencher complex. Based on the theoretical predictions (at the DFT(CAM-B3LYP)/6-31+G(d,p) level of theory) and careful analysis of the obtained FTIR spectra it may be concluded that in the solid state I2 C and I5 C molecules form associates by intermolecular NH · · · OC and OH · · · OC hydrogen bonding interactions, whereas the existence of intramolecular NH · · · OC interactions in the solid state of I2C and I5C is highly unlikely. Copyright © 2013 Elsevier B.V. All rights reserved.

Gold-based electrical interconnections for microelectronic devices

DOEpatents

Peterson, Kenneth A.; Garrett, Stephen E.; Reber, Cathleen A.; Watson, Robert D.

2002-01-01

A method of making an electrical interconnection from a microelectronic device to a package, comprising ball or wedge compression bonding a gold-based conductor directly to a silicon surface, such as a polysilicon bonding pad in a MEMS or IMEMS device, without using layers of aluminum or titanium disposed in-between the conductor and the silicon surface. After compression bonding, optional heating of the bond above 363 C. allows formation of a liquid gold-silicon eutectic phase containing approximately 3% (by weight) silicon, which significantly improves the bond strength by reforming and enhancing the initial compression bond. The same process can be used for improving the bond strength of Au--Ge bonds by forming a liquid Au-12Ge eutectic phase.

UbiX is a flavin prenyltransferase required for bacterial ubiquinone biosynthesis

PubMed Central

White, Mark D.; Payne, Karl A.P.; Fisher, Karl; Marshall, Stephen A.; Parker, David; Rattray, Nicholas J.W.; Trivedi, Drupad K.; Goodacre, Royston; Rigby, Stephen E.J.; Scrutton, Nigel S.; Hay, Sam; Leys, David

2016-01-01

Ubiquinone, or coenzyme Q, is a ubiquitous lipid-soluble redox cofactor that is an essential component of electron transfer chains1. Eleven genes have been implicated in bacterial ubiquinone biosynthesis, including ubiX and ubiD, which are responsible for decarboxylation of the 3-octaprenyl-4-hydroxybenzoate precursor2. Despite structural and biochemical characterization of UbiX as an FMN-binding protein, no decarboxylase activity has been detected3–4. We report here that UbiX produces a novel flavin-derived cofactor required for the decarboxylase activity of UbiD5. UbiX acts as a flavin prenyltransferase, linking a dimethylallyl moiety to the flavin N5 and C6 atoms. This adds a fourth non-aromatic ring to the flavin isoalloxazine group. In contrast to other prenyltransferases6–7, UbiX is metal-independent and requires dimethylallyl-monophosphate as substrate. Kinetic crystallography reveals that the prenyl transferase mechanism of UbiX resembles that of the terpene synthases8. The active site environment is dominated by π-systems, which assist phosphate-C1’ bond breakage following FMN reduction, leading to formation of the N5-C1’ bond. UbiX then acts as a chaperone for adduct reorientation, via transient carbocation species, leading ultimately to formation of the dimethylallyl C3’-C6 bond. The study establishes the mechanism for formation of a new flavin-derived cofactor, extending both flavin and terpenoid biochemical repertoire. PMID:26083743

Computational insights into crystal plane dependence of thermal activity of anion (C and N)-substituted titania.

PubMed

V, Sai Phani Kumar; Arya, Rahul; Deshpande, Parag A

2017-11-29

Geometry optimizations of anion (C and N) doped anatase TiO 2 were carried out by using DFT+U calculations. Various anion vacancy sites were examined to study the synergistic effects of anion doping accompanied with anion vacancy formation on lattice oxygen activation. Two non-identical crystal planes (0 0 1) and (1 0 0) were chosen for C and N substitutions. Energetically favoured N-vacancy pairs were identified on TiO 2 surfaces. Substitution of N along with anion vacancies at various sites was energetically more favoured than that of C-doping in bulk TiO 2 while the energies were comparable for surface substitutions. Bond length distributions due to the formation of differential bonds were determined. Net oxygen activation and accompanying reversible oxygen exchange capacities were compared for TiO 2-2x C x and TiO 2-3x N 2x . Substitution of C in the surface exposed (1 0 0) plane of TiO 2 resulted in 47.6% and 23.8% of bond elongation and compression, respectively, resulting in 23.8% of net oxygen activation which was higher when compared to N substitution in the (1 0 0) plane of TiO 2 resulting in a net oxygen activation of 17%.

Ligand-to-ligand charge-transfer transitions of platinum(II) complexes with arylacetylide ligands with different chain lengths: spectroscopic characterization, effect of molecular conformations, and density functional theory calculations.

PubMed

Tong, Glenna So Ming; Law, Yuen-Chi; Kui, Steven C F; Zhu, Nianyong; Leung, King Hong; Phillips, David Lee; Che, Chi-Ming

2010-06-11

The complexes [Pt(tBu(3)tpy){C[triple bond]C(C(6)H(4)C[triple bond]C)(n-1)R}](+) (n = 1: R = alkyl and aryl (Ar); n = 1-3: R = phenyl (Ph) or Ph-N(CH(3))(2)-4; n = 1 and 2, R = Ph-NH(2)-4; tBu(3)tpy = 4,4',4''-tri-tert-butyl-2,2':6',2''-terpyridine) and [Pt(Cl(3)tpy)(C[triple bond]CR)](+) (R = tert-butyl (tBu), Ph, 9,9'-dibutylfluorene, 9,9'-dibutyl-7-dimethyl-amine-fluorene; Cl(3)tpy = 4,4',4''-trichloro-2,2':6',2''-terpyridine) were prepared. The effects of substituent(s) on the terpyridine (tpy) and acetylide ligands and chain length of arylacetylide ligands on the absorption and emission spectra were examined. Resonance Raman (RR) spectra of [Pt(tBu(3)tpy)(C[triple bond]CR)](+) (R = n-butyl, Ph, and C(6)H(4)-OCH(3)-4) obtained in acetonitrile at 298 K reveal that the structural distortion of the C[triple bond]C bond in the electronic excited state obtained by 502.9 nm excitation is substantially larger than that obtained by 416 nm excitation. Density functional theory (DFT) and time-dependent DFT (TDDFT) calculations on [Pt(H(3)tpy)(C[triple bond]CR)](+) (R = n-propyl (nPr), 2-pyridyl (Py)), [Pt(H(3)tpy){C[triple bond]C(C(6)H(4)C[triple bond]C)(n-1)Ph}](+) (n = 1-3), and [Pt(H(3)tpy){C[triple bond]C(C(6)H(4)C[triple bond]C)(n-1)C(6)H(4)-N(CH(3))(2)-4}](+)/+H(+) (n = 1-3; H(3)tpy = nonsubstituted terpyridine) at two different conformations were performed, namely, with the phenyl rings of the arylacetylide ligands coplanar ("cop") with and perpendicular ("per") to the H(3)tpy ligand. Combining the experimental data and calculated results, the two lowest energy absorption peak maxima, lambda(1) and lambda(2), of [Pt(Y(3)tpy)(C[triple bond]CR)](+) (Y = tBu or Cl, R = aryl) are attributed to (1)[pi(C[triple bond]CR)-->pi*(Y(3)tpy)] in the "cop" conformation and mixed (1)[d(pi)(Pt)-->pi*(Y(3)tpy)]/(1)[pi(C[triple bond]CR)-->pi*(Y(3)tpy)] transitions in the "per" conformation. The lowest energy absorption peak lambda(1) for [Pt(tBu(3)tpy){C[triple bond]C(C(6)H(4)C[triple bond]C)(n-1)C(6)H(4)-H-4}](+) (n = 1-3) shows a redshift with increasing chain length. However, for [Pt(tBu(3)tpy){C[triple bond]C(C6H4C[triple bond]C)(n-1)C(6)H(4)-N(CH(3))(2)-4}](+) (n = 1-3), lambda(1) shows a blueshift with increasing chain length n, but shows a redshift after the addition of acid. The emissions of [Pt(Y(3)tpy)(C[triple bond]CR)](+) (Y = tBu or Cl) at 524-642 nm measured in dichloromethane at 298 K are assigned to the (3)[pi(C[triple bond]CAr)-->pi*(Y(3)tpy)] excited states and mixed (3)[d(pi)(Pt)-->pi*(Y(3)tpy)]/(3)[pi(C[triple bond]C)-->pi*(Y(3)tpy)] excited states for R = aryl and alkyl groups, respectively. [Pt(tBu(3)tpy){C[triple bond]C(C(6)H(4)C[triple bond]C)(n-1)C(6)H(4)-N(CH(3))(2)-4}](+) (n = 1 and 2) are nonemissive, and this is attributed to the small energy gap between the singlet ground state (S(0)) and the lowest triplet excited state (T(1)).

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.

Inverse-Micelle-Encapsulated Water-Enabled Bond Breaking of Dialkyl Diselenide/Disulfide: A Critical Step for Synthesizing High- Quality Gold Nanoparticles

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

Zaluzhna, Oksana; Li, Ying; Allison, Thomas C.

2012-10-09

Inverse-micelle-encapsulated water formed in the two-phase Brust-Schiffrin method (BSM) synthesis of Au nanoparticles (NPs) is identified as essential for dialkyl diselenide/disulfide to react with the Au(III) complex in which the Se-Se/S-S bond is broken, leading to formation of higher-quality Au NPs.

A Possible Sink for Methane on Mars

NASA Astrophysics Data System (ADS)

Nørnberg, P.; Jensen, S. J. K.; Skibsted, J.; Jakobsen, H. J.; ten Kate, I. L.; Gunnlaugsson, H. P.; Merrison, J. P.; Finster, K.; Bak, E.; Iversen, J. J.; Kondrup, J. C.

2014-07-01

Mechanical simulated wind activation of mineral surfaces act as a trap for Methane through formation of covalent Si-C bonds stable up to temperatures above 250 C. This mechanism is proposed as a Methane sink on Mars.

Metalloprotein entatic control of ligand-metal bonds quantified by ultrafast x-ray spectroscopy

DOE PAGES

Mara, Michael W.; Hadt, Ryan G.; Reinhard, Marco Eli; ...

2017-06-23

The multifunctional protein cytochrome c (cyt c) plays key roles in electron transport and apoptosis, switching function by modulating bonding between a heme iron and the sulfur in a methionine residue. This Fe–S(Met) bond is too weak to persist in the absence of protein constraints. We ruptured the bond in ferrous cyt c using an optical laser pulse and monitored the bond reformation within the protein active site using ultrafast x-ray pulses from an x-ray free-electron laser, determining that the Fe–S(Met) bond enthalpy is ~4 kcal/mol stronger than in the absence of protein constraints. As a result, the 4 kcal/molmore » is comparable with calculations of stabilization effects in other systems, demonstrating how biological systems use an entatic state for modest yet accessible energetics to modulate chemical function.« less

Metalloprotein entatic control of ligand-metal bonds quantified by ultrafast x-ray spectroscopy

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

Mara, Michael W.; Hadt, Ryan G.; Reinhard, Marco Eli

The multifunctional protein cytochrome c (cyt c) plays key roles in electron transport and apoptosis, switching function by modulating bonding between a heme iron and the sulfur in a methionine residue. This Fe–S(Met) bond is too weak to persist in the absence of protein constraints. We ruptured the bond in ferrous cyt c using an optical laser pulse and monitored the bond reformation within the protein active site using ultrafast x-ray pulses from an x-ray free-electron laser, determining that the Fe–S(Met) bond enthalpy is ~4 kcal/mol stronger than in the absence of protein constraints. As a result, the 4 kcal/molmore » is comparable with calculations of stabilization effects in other systems, demonstrating how biological systems use an entatic state for modest yet accessible energetics to modulate chemical function.« less

Quantum Chemical Molecular Dynamics Simulations of 1,3-Dichloropropene Combustion.

PubMed

Ahubelem, Nwakamma; Shah, Kalpit; Moghtaderi, Behdad; Page, Alister J

2015-09-03

Oxidative decomposition of 1,3-dichloropropene was investigated using quantum chemical molecular dynamics (QM/MD) at 1500 and 3000 K. Thermal oxidation of 1,3-dichloropropene was initiated by (1) abstraction of allylic H/Cl by O2 and (2) intra-annular C-Cl bond scission and elimination of allylic Cl. A kinetic analysis shows that (2) is the more dominant initiation pathway, in agreement with QM/MD results. These QM/MD simulations reveal new routes to the formation of major products (H2O, CO, HCl, CO2), which are propagated primarily by the chloroperoxy (ClO2), OH, and 1,3-dichloropropene derived radicals. In particular, intra-annular C-C/C-H bond dissociation reactions of intermediate aldehydes/ketones are shown to play a dominant role in the formation of CO and CO2. Our simulations demonstrate that both combustion temperature and radical concentration can influence the product yield, however not the combustion mechanism.

The long underestimated carbonyl function of carbohydrates – an organocatalyzed shot into carbohydrate chemistry.

PubMed

Mahrwald, R

2015-09-21

The aggressive and strong development of organocatalysis provides several protocols for the convenient utilization of the carbonyl function of unprotected carbohydrates in C-C-bond formation processes. These amine-catalyzed mechanisms enable multiple cascade-protocols for the synthesis of a wide range of carbohydrate-derived compound classes. Several, only slightly different protocols, have been developed for the application of 1,3-dicarbonyl compounds in the stereoselective chain-elongation of unprotected carbohydrates and the synthesis of highly functionalized C-glycosides of defined configuration. In addition, C-glycosides can also be accessed by amine-catalyzed reactions with methyl ketones. By a one-pot cascade reaction of isocyanides with unprotected aldoses and amino acids access to defined configured glycopeptide mimetics is achieved. Depending on the reaction conditions different origins to control the installation of configuration during the bond-formation process were observed.

Copper-catalyzed synthesis of phenanthridine derivatives under an oxygen atmosphere starting from biaryl-2-carbonitriles and Grignard reagents.

PubMed

Zhang, Line; Ang, Gim Yean; Chiba, Shunsuke

2010-08-20

A copper-catalyzed synthesis of phenanthridine derivatives was developed starting from biaryl-2-carbonitriles and Grignard reagents. The present transformation is carried out by a sequence of nucleophilic addition of Grignard reagents to biaryl-2-carbonitriles to form N-H imines and their Cu-catalyzed C-N bond formation on the aromatic C-H bond, where molecular oxygen is a prerequisite to achieve the catalytic process.

Contributions of a disulfide bond and a reduced cysteine side chain to the intrinsic activity of the high-density lipoprotein receptor SR-BI.

PubMed

Yu, Miao; Lau, Thomas Y; Carr, Steven A; Krieger, Monty

2012-12-18

The high-density lipoprotein (HDL) receptor scavenger receptor class B, type I (SR-BI), binds HDL and mediates selective cholesteryl ester uptake. SR-BI's structure and mechanism are poorly understood. We used mass spectrometry to assign the two disulfide bonds in SR-BI that connect cysteines within the conserved Cys(321)-Pro(322)-Cys(323) (CPC) motif and connect Cys(280) to Cys(334). We used site-specific mutagenesis to evaluate the contributions of the CPC motif and the side chain of extracellular Cys(384) to HDL binding and lipid uptake. The effects of CPC mutations on activity were context-dependent. Full wild-type (WT) activity required Pro(322) and Cys(323) only when Cys(321) was present. Reduced intrinsic activities were observed for CXC and CPX, but not XXC, XPX, or XXX mutants (X ≠ WT residue). Apparently, a free thiol side chain at position 321 that cannot form an intra-CPC disulfide bond with Cys(323) is deleterious, perhaps because of aberrant disulfide bond formation. Pro(322) may stabilize an otherwise strained CPC disulfide bond, thus supporting WT activity, but this disulfide bond is not absolutely required for normal activity. C(384)X (X = S, T, L, Y, G, or A) mutants exhibited altered activities that varied with the side chain's size: larger side chains phenocopied WT SR-BI treated with its thiosemicarbazone inhibitor BLT-1 (enhanced binding, weakened uptake); smaller side chains produced almost inverse effects (increased uptake:binding ratio). C(384)X mutants were BLT-1-resistant, supporting the proposal that Cys(384)'s thiol interacts with BLT-1. We discuss the implications of our findings on the functions of the extracellular loop cysteines in SR-BI and compare our results to those presented by other laboratories.

The structure of the ends of α-helices in globular proteins: effect of additional hydrogen bonds and implications for helix formation.

PubMed

Leader, David P; Milner-White, E James

2011-03-01

We prepared a set of about 2000 α-helices from a relational database of high-resolution three-dimensional structures of globular proteins, and identified additional main chain i ← i+3 hydrogen bonds at the ends of the helices (i.e., where the hydrogen bonding potential is not fulfilled by canonical i ← i+4 hydrogen bonds). About one-third of α-helices have such additional hydrogen bonds at the N-terminus, and more than half do so at the C-terminus. Although many of these additional hydrogen bonds at the C-terminus are associated with Schellman loops, the majority are not. We compared the dihedral angles at the termini of α-helices having or lacking the additional hydrogen bonds. Significant differences were found, especially at the C-terminus, where the dihedral angles at positions C2 and C1 in the absence of additional hydrogen bonds deviate substantially from those occurring within the α-helix. Using a novel approach we show how the structure of the C-terminus of the α-helix can emerge from that of constituent overlapping α-turns and β-turns, which individually show a variation in dihedral angles at different positions. We have also considered the direction of propagation of the α-helix using this approach. If one assumes that helices start as a single α-turn and grow by successive addition of further α-turns, the paths for growth in the N → C and C → N directions differ in a way that suggests that extension in the C → N direction is favored. Copyright © 2010 Wiley-Liss, Inc.

Nonadiabatic one-electron transfer mechanism for the O-O bond formation in the oxygen-evolving complex of photosystem II

NASA Astrophysics Data System (ADS)

Shoji, Mitsuo; Isobe, Hiroshi; Shigeta, Yasuteru; Nakajima, Takahito; Yamaguchi, Kizashi

2018-04-01

The reaction mechanism of the O2 formation in the S4 state of the oxygen-evolving complex of photosystem II was clarified at the quantum mechanics/molecular mechanics (QM/MM) level. After the Yz (Y161) oxidation and the following proton transfer in the S3 state, five reaction steps are required to produce the molecular dioxygen. The highest barrier step is the first proton transfer reaction (0 → 1). The following reactions involving electron transfers were precisely analyzed in terms of their energies, structures and spin densities. We found that the one-electron transfer from the Mn4Ca cluster to Y161 triggers the O-O sigma bond formation.

Interfacial Connection Mechanisms in Calcium-Silicate-Hydrates/Polymer Nanocomposites: A Molecular Dynamics Study.

PubMed

Zhou, Yang; Hou, Dongshuai; Manzano, Hegoi; Orozco, Carlos A; Geng, Guoqing; Monteiro, Paulo J M; Liu, Jiaping

2017-11-22

Properties of organic/inorganic composites can be highly dependent on the interfacial connections. In this work, molecular dynamics, using pair-potential-based force fields, was employed to investigate the structure, dynamics, and stability of interfacial connections between calcium-silicate-hydrates (C-S-H) and organic functional groups of three different polymer species. The calculation results suggest that the affinity between C-S-H and polymers is influenced by the polarity of the functional groups and the diffusivity and aggregation tendency of the polymers. In the interfaces, the calcium counterions from C-S-H act as the coordination atoms in bridging the double-bonded oxygen atoms in the carboxyl groups (-COOH), and the Ca-O connection plays a dominant role in binding poly(acrylic acid) (PAA) due to the high bond strength defined by time-correlated function. The defective calcium-silicate chains provide significant numbers of nonbridging oxygen sites to accept H-bonds from -COOH groups. As compared with PAA, the interfacial interactions are much weaker between C-S-H and poly(vinyl alcohol) (PVA) or poly(ethylene glycol) (PEG). Predominate percentage of the -OH groups in the PVA form H-bonds with inter- and intramolecule, which results in the polymer intertwining and reduces the probability of H-bond connections between PVA and C-S-H. On the other hand, the inert functional groups (C-O-C) in poly(ethylene glycol) (PEG) make this polymer exhibit unfolded configurations and move freely with little restrictions. The interaction mechanisms interpreted in this organic-inorganic interface can give fundamental insights into the polymer modification of C-S-H and further implications to improving cement-based materials from the genetic level.

Hydrogen bonded C-H···Y (Y = O, S, Hal) molecular complexes: A natural bond orbital analysis

NASA Astrophysics Data System (ADS)

Isaev, A. N.

2016-03-01

Hydrogen bonded C-H···Y complexes formed by H2O, H2S molecules, hydrogen halides, and halogen-ions with methane, halogen substituted methane as well as with the C2H2 and NCH molecules were studied at the MP2/aug-cc-pVDZ level. The structure of NBOs corresponding to lone pair of acceptor Y, n Y, and vacant anti-σ-bond C-H of proton donor was analyzed and estimates of second order perturbation energy E(2) characterizing donor-acceptor n Y → σ C-H * charge-transfer interaction were obtained. Computational results for complexes of methane and its halogen substituted derivatives show that for each set of analogous structures, the EnY→σ*C-H (2) energy tends to grow with an increase in the s-component percentage in the lone pair NBO of acceptor Y. Calculations for different C···Y distances show that the equilibrium geometries of complexes lie in the region where the E(2) energy is highest and it changes symbatically with the length of the covalent E-H bond when the R(C···Y) distance is varied. The performed analysis allows us to divide the hydrogen bonded complexes into two groups, depending on the pattern of overlapping for NBOs of the hydrogen bridge.

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

Jankowski, A.F.; Hayes, J.P.; Kanna, R.L.

The formation of high energy density, storage devices is achievable using composite material systems. Alternate layering of carbon aerogel wafers and Ni foils with rnicroporous separators is a prospective composite for capacitor applications. An inherent problem exists to form a physical bond between Ni and the porous carbon wafer. The bonding process must be limited to temperatures less than 1000{degrees}C, at which point the aerogel begins to degrade. The advantage of a low temperature eutectic in the Ni-Ti alloy system solves this problem. Ti, a carbide former, is readily adherent as a sputter deposited thin film onto the carbon wafer.more » A vacuum bonding process is then used to join the Ni foil and Ti coating through eutectic phase formation. The parameters required for successfld bonding are described along with a structural characterization of the Ni foil-carbon aerogel wafer interface.« less

Properties at the interface of graphene and Ti2C MXene

NASA Astrophysics Data System (ADS)

Paul, Pallavi; Chakraborty, Poulami; Das, Tilak; Nafday, Dhani; Saha-Dasgupta, Tanusri

2017-07-01

Employing ab initio calculations, we characterize the interfaces formed between graphene, a much discussed two-dimensional material, and MXene, another two-dimensional material of recent interest. Our study considering the specific case of Ti2C , a member of the MXene family, shows the formation of chemical bonds between Ti atoms and C atoms of graphene. This results in reconstruction of the electronic structure at the interface, making the interface metallic, though graphene is a zero-gap semiconductor and Ti2C is an antiferromagnetic insulator in their respective native form. The optical and phonon properties of the interfaces are found to be strongly dependent on the stacking arrangement, driven by the nature of chemical-bond formation. Consideration of O-passivated Ti2C is found to weaken the interaction between graphene and Ti2C substantially, making it a physisorption process rather than chemisorption in the unpassivated situation. Our first-principles study is expected to motivate future experimental investigation.

Hydrolysis of VX on Concrete: Rate of Degradation by Direct Surface Interrogation using an Ion Trap Secondary Ion Mass Spectrometer

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

Groenewold, Gary Steven; Appelhans, Anthony David; Gresham, Garold Linn

2002-09-01

The nerve agent VX (O-ethyl S-2-diisopropylaminoethyl methylphosphonothiolate) is lethal at very low levels of exposure, which can occur by dermal contact with contaminated surfaces. Hence, behavior of VX in contact with common urban or industrial surfaces is a subject of acute interest. In the present study, VX was found to undergo complete degradation when in contact with concrete surfaces. The degradation was directly interrogated at submonolayer concentrations by periodically performing secondary ion mass spectrometry (SIMS) analyses after exposure of the concrete to VX. The abundance of the [VX + H]+ ion in the SIMS spectra was observed to decrease inmore » an exponential fashion, consistent with first-order or pseudo-first-order behavior. This phenomenon enabled the rate constant to be determined at 0.005 min-1 at 25 C, which corresponds to a half-life of about 3 h on the concrete surface. The decrease in [VX + H]+ was accompanied by an increase in the abundance of the principal degradation product diisopropylaminoethanethiol (DESH), which arises by cleavage of the P-S bond. Degradation to form DESH is accompanied by the formation of ethyl methylphosphonic acid, which is observable only in the negative ion spectrum. A second degradation product was also implicated, which corresponded to a diisopropylvinylamine isomer (perhaps N,N-diisopropyl aziridinium) that arose via cleavage of the S-C bond. No evidence was observed for the formation of the toxic S-2-diisopropylaminoethyl methylphosphonothioic acid. The degradation rate constants were measured at four different temperatures (24-50 C), which resulted in a linear Arrhenius relationship and an activation energy of 52 kJ mol-1. This value agrees with previous values observed for VX hydrolysis in alkaline solutions, which suggests that the degradation of submonolayer VX is dominated by alkaline hydrolysis within the adventitious water film on the concrete surface.« less

Hydrolysis of VX on concrete: rate of degradation by direct surface interrogation using an ion trap secondary ion mass spectrometer.

PubMed

Groenewold, Gary S; Williams, John M; Appelhans, Anthony D; Gresham, Garold L; Olson, John E; Jeffery, Mark T; Rowland, Brad

2002-11-15

The nerve agent VX (O-ethyl S-2-diisopropylaminoethyl methylphosphonothiolate) is lethal at very low levels of exposure, which can occur by dermal contact with contaminated surfaces. Hence, behavior of VX in contact with common urban or industrial surfaces is a subject of acute interest. In the present study, VX was found to undergo complete degradation when in contact with concrete surfaces. The degradation was directly interrogated at submonolayer concentrations by periodically performing secondary ion mass spectrometry (SIMS) analyses after exposure of the concrete to VX. The abundance of the [VX + H]+ ion in the SIMS spectra was observed to decrease in an exponential fashion, consistent with first-order or pseudo-first-order behavior. This phenomenon enabled the rate constant to be determined at 0.005 min(-1) at 25 degrees C, which corresponds to a half-life of about 3 h on the concrete surface. The decrease in [VX + H]+ was accompanied by an increase in the abundance of the principal degradation product diisopropylaminoethanethiol (DESH), which arises by cleavage of the P-S bond. Degradation to form DESH is accompanied by the formation of ethyl methylphosphonic acid, which is observable only in the negative ion spectrum. A second degradation product was also implicated, which corresponded to a diisopropylvinylamine isomer (perhaps N,N-diisopropyl aziridinium) that arose via cleavage of the S-C bond. No evidence was observed for the formation of the toxic S-2-diisopropylaminoethyl methylphosphonothioic acid. The degradation rate constants were measured at four different temperatures (24-50 degrees C), which resulted in a linear Arrhenius relationship and an activation energy of 52 kJ mol(-1). This value agrees with previous values observed for VX hydrolysis in alkaline solutions, which suggests that the degradation of submonolayer VX is dominated by alkaline hydrolysis within the adventitious water film on the concrete surface.

(Meth­oxy­methyl­idene)di­methyl­aza­nium tetra­phenyl­borate aceto­nitrile monosolvate

PubMed Central

Tiritiris, Ioannis; Saur, Stefan; Kantlehner, Willi

2014-01-01

In the cation of the title salt, C4H10NO+·C24H20B−·C2H3N, the C—N bond lengths are 1.2864 (16), 1.4651 (17) and 1.4686 (16) Å, indicating double- and single-bond character, respectively. The C—O bond length of 1.2978 (15) Å shows double-bond character, pointing towards charge delocalization within the NCO plane of the iminium ion. C—H⋯π inter­actions are present between the methine H atom and two of the phenyl rings of the tetra­phenyl­borate ion. The latter forms an aromatic pocket in which the cation is embedded. The iminium ion is further connected through a C—H⋯N hydrogen bond to the aceto­nitrile mol­ecule. This leads to the formation of a two-dimensional supramolecular pattern along the bc plane. PMID:24765028

SHuffle, a novel Escherichia coli protein expression strain capable of correctly folding disulfide bonded proteins in its cytoplasm

PubMed Central

2012-01-01

Background Production of correctly disulfide bonded proteins to high yields remains a challenge. Recombinant protein expression in Escherichia coli is the popular choice, especially within the research community. While there is an ever growing demand for new expression strains, few strains are dedicated to post-translational modifications, such as disulfide bond formation. Thus, new protein expression strains must be engineered and the parameters involved in producing disulfide bonded proteins must be understood. Results We have engineered a new E. coli protein expression strain named SHuffle, dedicated to producing correctly disulfide bonded active proteins to high yields within its cytoplasm. This strain is based on the trxB gor suppressor strain SMG96 where its cytoplasmic reductive pathways have been diminished, allowing for the formation of disulfide bonds in the cytoplasm. We have further engineered a major improvement by integrating into its chromosome a signal sequenceless disulfide bond isomerase, DsbC. We probed the redox state of DsbC in the oxidizing cytoplasm and evaluated its role in assisting the formation of correctly folded multi-disulfide bonded proteins. We optimized protein expression conditions, varying temperature, induction conditions, strain background and the co-expression of various helper proteins. We found that temperature has the biggest impact on improving yields and that the E. coli B strain background of this strain was superior to the K12 version. We also discovered that auto-expression of substrate target proteins using this strain resulted in higher yields of active pure protein. Finally, we found that co-expression of mutant thioredoxins and PDI homologs improved yields of various substrate proteins. Conclusions This work is the first extensive characterization of the trxB gor suppressor strain. The results presented should help researchers design the appropriate protein expression conditions using SHuffle strains. PMID:22569138

A slow-forming isopeptide bond in the structure of the major pilin SpaD from Corynebacterium diphtheriae has implications for pilus assembly

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

Kang, Hae Joo; Paterson, Neil G.; Kim, Chae Un

2014-05-01

Two crystal structures of the major pilin SpaD from C. diphtheriae have been determined at 1.87 and 2.5 Å resolution. The N-terminal domain is found to contain an isopeptide bond that forms slowly over time in the recombinant protein. Given its structural context, this provides insight into the relationship between internal isopeptide-bond formation and pilus assembly. The Gram-positive organism Corynebacterium diphtheriae, the cause of diphtheria in humans, expresses pili on its surface which it uses for adhesion and colonization of its host. These pili are covalent protein polymers composed of three types of pilin subunit that are assembled by specificmore » sortase enzymes. A structural analysis of the major pilin SpaD, which forms the polymeric backbone of one of the three types of pilus expressed by C. diphtheriae, is reported. Mass-spectral and crystallographic analysis shows that SpaD contains three internal Lys–Asn isopeptide bonds. One of these, shown by mass spectrometry to be located in the N-terminal D1 domain of the protein, only forms slowly, implying an energy barrier to bond formation. Two crystal structures, of the full-length three-domain protein at 2.5 Å resolution and of a two-domain (D2-D3) construct at 1.87 Å resolution, show that each of the three Ig-like domains contains a single Lys–Asn isopeptide-bond cross-link, assumed to give mechanical stability as in other such pili. Additional stabilizing features include a disulfide bond in the D3 domain and a calcium-binding loop in D2. The N-terminal D1 domain is more flexible than the others and, by analogy with other major pilins of this type, the slow formation of its isopeptide bond can be attributed to its location adjacent to the lysine used in sortase-mediated polymerization during pilus assembly.« less

pKa values of hyodeoxycholic and cholic acids in the binary mixed micelles sodium-hyodeoxycholate-Tween 40 and sodium-cholate-Tween 40: Thermodynamic stability of the micelle and the cooperative hydrogen bond formation with the steroid skeleton.

PubMed

Poša, Mihalj; Pilipović, Ana; Bećarević, Mirjana; Farkaš, Zita

2017-01-01

Due to a relatively small size of bile acid salts, their mixed micelles with nonionic surfactants are analysed. Of the special interests are real binary mixed micelles that are thermodynamically more stable than ideal mixed micelles. Thermodynamic stability is expressed with an excess Gibbs energy (G E ) or over an interaction parameter (β ij ). In this paper sodium salts of cholic (C) and hyodeoxycholic acid (HD) in their mixed micelles with Tween 40 (T40) are analysed by potentiometric titration and their pKa values are determined. Examined bile acids in mixed micelles with T40 have higher pKa values than free bile acids. The increase of ΔpKa acid constant of micellary bound C and HD is in a correlation with absolute values of an interaction parameter. According to an interaction parameter and an excess Gibbs energy, mixed micelle HD-T40 are thermodynamically more stable than mixed micelles C-T40. ΔpKa values are higher for mixed micelles with Tween 40 whose second building unit is HD, related to the building unit C. In both micellar systems, ΔpKa increases with the rise of a molar fraction of Tween 40 in binary mixtures of surfactants with sodium salts of bile acids. This suggests that, ΔpKa can be a measure of a thermodynamic stabilization of analysed binary mixed micelles as well as an interaction parameter. ΔpKa values are confirmed by determination of a distribution coefficient of HD and C in systems: water phase with Tween 40 in a micellar concentration and 1-octanol, with a change of a pH value of a water phase. Conformational analyses suggests that synergistic interactions between building units of analysed binary micelles originates from formation of hydrogen bonds between steroid OH groups and polyoxyethylene groups of the T40. Relative similarity and spatial orientation of C 3 and C 6 OH group allows cooperative formation of hydrogen bonds between T40 and HD - excess entropy in formation of mixed micelle. If a water solution of analysed binary mixtures of surfactants contains urea in concentration of 4M significant decreases of an interaction parameter value happens which confirms the importance of hydrogen bonds in synergistic interactions (urea compete in hydrogen bonds). Copyright © 2016 Elsevier Inc. All rights reserved.

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

Nahum, T.; Dodiuk, H.; Dotan, A.

Superhydrophobic surfaces with contact angle (CA) >150 and sliding angle (SA) <10 have been aroused curiosity over the years due to their various applications. Superhydrophobicity can be obtained tailoring the chemistry and the roughness of the surface, mimicking the Lotus flower. Most superhydrophobic surfaces based on secondary bonding lose their roughness in harsh conditions and are unsuitable for practical applications. Photoreactive SiO{sub 2} nanoparticles (NPs) based on benzophenone (BP) can be a very effective tool for formation of reactive species that function as a molecular bridge by covalent bonding between the NP and any polymer matrix with C-C and C-Hmore » bonds. The present work focused on thermoset radiation curing urethane acrylate. Upon UV irradiation reactive excited nπ* triplet benzophenone species are formed and react through hydrogen abstraction to form ketyl radicals which interact with a radicals from the UV irradiated polymer matrix to yield covalent bonding. Roughness was achieved by dipping the substrate in SiO{sub 2}@BPs NPs dispersion followed by irradiation. Fluoroalkylsilane was used to obtain hydrophobic top layer. AFM nano manipulation was used to verify the immobilization of NPs. Evaluation of durability was made using air flow at 300 km/hr. Preliminary results indicate the formation of super hydrophobic surfaces (CA>150 and SA<10) with improved stability.« less

Copper-Catalyzed Domino Three-Component Approach for the Assembly of 2-Aminated Benzimidazoles and Quinazolines.

PubMed

Tran, Lam Quang; Li, Jihui; Neuville, Luc

2015-06-19

A copper-promoted three-component synthesis of 2-aminobenzimidazoles (1) or of 2-aminoquinazolines (2) involving cyanamides, arylboronic acids, and amines has been developed. The operationally simple oxidative process, performed in the presence of K2CO3, a catalytic amount of CuCl2·2H2O, 2,2'-bipyridine, and an O2 atmosphere (1 atm), allows the rapid assembly of either benzimidazoles or quinazolines starting from aryl- or benzyl-substituted cyanamides, respectively. In this process, the copper promotes the formation of three bonds, two C-N bonds, and an additional bond resulting from C-H functionalization event.

Supramolecular interactions in carboxylate and sulfonate salts of 2,6-diamino-4-chloropyrimidinium.

PubMed

Mohana, Marimuthu; Thomas Muthiah, Packianathan; Butcher, Ray J

2017-07-01

Two new salts, namely 2,6-diamino-4-chloropyrimidinium 2-carboxy-3-nitrobenzoate, C 4 H 6 ClN 4 + ·C 8 H 4 NO 6 - , (I), and 2,6-diamino-4-chloropyrimidinium p-toluenesulfonate monohydrate, C 4 H 6 ClN 4 + ·C 7 H 7 O 3 S - ·H 2 O, (II), have been synthesized and characterized by single-crystal X-ray diffraction. In both crystal structures, the N atom in the 1-position of the pyrimidine ring is protonated. In salt (I), the protonated N atom and the amino group of the pyrimidinium cation interact with the carboxylate group of the anion through N-H...O hydrogen bonds to form a heterosynthon with an R 2 2 (8) ring motif. In hydrated salt (II), the presence of the water molecule prevents the formation of the familiar R 2 2 (8) ring motif. Instead, an expanded ring [i.e. R 3 2 (8)] is formed involving the sulfonate group, the pyrimidinium cation and the water molecule. Both salts form a supramolecular homosynthon [R 2 2 (8) ring motif] through N-H...N hydrogen bonds. The molecular structures are further stabilized by π-π stacking, and C=O...π, C-H...O and C-H...Cl interactions.

Effect of polynucleotides on the dimerization of glycine. [abiological protein synthesis in primitive earth conditions

NASA Technical Reports Server (NTRS)

Mizutani, H.; Ponnamperuma, C.

1981-01-01

Results from experiments to determine the effect of polynucleotides on abiological formation of peptide bonds are reported. The reaction between glycine molecules in an aqueous phase in the presence of a condensing agent was chosen as a model, with polyphosphates being selected as the condensing agent for biologically relevant peptide formation. Four types of polynucleotides were used: polygluanic acid (G), polyuridic acid (U), polyadenylic acid (A), and polycytidylic acid (C); the effects of small anions, acetate, chloride, and phosphate, were also studied. Procedures are given, including concentrations, pH, and incubation time, and the type of amino acid analyzer. The diglycine yields were, in order of most to least: G, C, A, U, and are diagrammed as a function of time; rate of formation followed the same order of magnitude as the final yields. Anion presence displayed no discernible effect. The results are taken to indicate that polynucleotides do have an effect on the formation of peptide bonds, an effect significant in the understanding of chemical evolution.

High performance C/S composite cathodes with conventional carbonate-based electrolytes in Li-S battery.

PubMed

Zheng, Shiyou; Han, Pan; Han, Zhuo; Zhang, Huijuan; Tang, Zhihong; Yang, Junhe

2014-04-29

High stable C/S composites are fabricated by a novel high-temperature sulfur infusion into micro-mesoporous carbon method following with solvent cleaning treatment. The C/S composite cathodes show high Coulombic efficiency, long cycling stability and good rate capability in the electrolyte of 1.0 M LiPF6 + EC/DEC (1:1 v/v), for instance, the reversible capacity of the treated C/S-50 (50% S) cathode retains around 860 mAh/g even after 500 cycles and the Coulombic efficiency is close to 100%, which demonstrates the best electrochemical performance of carbon-sulfur composite cathodes using the carbonate-based electrolyte reported to date. It is believed that the chemical bond of C-S is responsible for the superior electrochemical properties in Li-S battery, that is, the strong interaction between S and carbon matrix significantly improves the conductivity of S, effectively buffers the structural strain/stress caused by the large volume change during lithiation/delithiation, completely eliminates the formation of high-order polysulfide intermediates, and substantially avoids the shuttle reaction and the side reaction between polysulfide anions and carbonate solvent, and thus enables the C/S cathode to use conventional carbonate-based electrolytes and achieve outstanding electrochemical properties in Li-S battery. The results may substantially contribute to the progress of the Li-S battery technology.

Photosynthesis. Electronic structure of the oxygen-evolving complex in photosystem II prior to O-O bond formation.

PubMed

Cox, Nicholas; Retegan, Marius; Neese, Frank; Pantazis, Dimitrios A; Boussac, Alain; Lubitz, Wolfgang

2014-08-15

The photosynthetic protein complex photosystem II oxidizes water to molecular oxygen at an embedded tetramanganese-calcium cluster. Resolving the geometric and electronic structure of this cluster in its highest metastable catalytic state (designated S3) is a prerequisite for understanding the mechanism of O-O bond formation. Here, multifrequency, multidimensional magnetic resonance spectroscopy reveals that all four manganese ions of the catalyst are structurally and electronically similar immediately before the final oxygen evolution step; they all exhibit a 4+ formal oxidation state and octahedral local geometry. Only one structural model derived from quantum chemical modeling is consistent with all magnetic resonance data; its formation requires the binding of an additional water molecule. O-O bond formation would then proceed by the coupling of two proximal manganese-bound oxygens in the transition state of the cofactor. Copyright © 2014, American Association for the Advancement of Science.

Binuclear Pt-Tl bonded complex with square pyramidal coordination around Pt: a combined multinuclear NMR, EXAFS, UV-Vis, and DFT/TDDFT study in dimethylsulfoxide solution.

PubMed

Purgel, Mihály; Maliarik, Mikhail; Glaser, Julius; Platas-Iglesias, Carlos; Persson, Ingmar; Tóth, Imre

2011-07-04

The structure and bonding of a new Pt-Tl bonded complex formed in dimethylsulfoxide (dmso), (CN)(4)Pt-Tl(dmso)(5)(+), have been studied by multinuclear NMR and UV-vis spectroscopies, and EXAFS measurements in combination with density functional theory (DFT) and time dependent density functional theory (TDDFT) calculations. This complex is formed following the equilibrium reaction Pt(CN)(4)(2-) + Tl(dmso)(6)(3+) ⇆ (CN)(4)Pt-Tl(dmso)(5)(+) + dmso. The stability constant of the Pt-Tl bonded species, as determined using (13)C NMR spectroscopy, amounts to log K = 2.9 ± 0.2. The (NC)(4)Pt-Tl(dmso)(5)(+) species constitutes the first example of a Pt-Tl bonded cyanide complex in which the sixth coordination position around Pt (in trans with respect to the Tl atom) is not occupied. The spectral parameters confirm the formation of the metal-metal bond, but differ substantially from those measured earlier in aqueous solution for complexes (CN)(5)Pt-Tl(CN)(n)(H(2)O)(x)(n-) (n = 0-3). The (205) Tl NMR chemical shift, δ = 75 ppm, is at extraordinary high field, while spin-spin coupling constant, (1)J(Pt-Tl) = 93 kHz, is the largest measured to date for a Pt-Tl bond in the absence of supporting bridging ligands. The absorption spectrum is dominated by two strong absorption bands in the UV region that are assigned to MMCT (Pt → Tl) and LMCT (dmso → Tl) bands, respectively, on the basis of MO and TDDFT calculations. The solution of the complex has a bright yellow color as a result of a shoulder present on the low energy side of the band at 355 nm. The geometry of the (CN)(4)Pt-Tl core can be elucidated from NMR data, but the particular stoichiometry and structure involving the dmso ligands are established by using Tl and Pt L(III)-edge EXAFS measurements. The Pt-Tl bond distance is 2.67(1) Å, the Tl-O bond distance is 2.282(6) Å, and the Pt-C-N entity is linear with Pt-C and Pt···N distances amounting to 1.969(6) and 3.096(6) Å, respectively. Geometry optimizations on the (CN)(4)Pt-Tl(dmso)(5)(+) system by using DFT calculations (B3LYP model) provide bond distances in excellent agreement with the EXAFS data. The four cyanide ligands are located in a square around the Pt atom, while the Tl atom is coordinated in a distorted octahedral fashion with the metal being located 0.40 Å above the equatorial plane described by four oxygen atoms of dmso ligands. The four equatorial Tl-O bonds and the four cyano ligands around the Pt atom are arranged in an alternate geometry. The coordination environment around Pt may be considered as being square pyramidal, where the apical position is occupied by the Tl atom. The optimized geometry of (CN)(4)Pt-Tl(dmso)(5)(+) is asymmetrical (C(1) point group). This low symmetry might be responsible for the unusually large NMR linewidths observed due to intramolecular chemical exchange processes. The nature of the Pt-Tl bond has been studied by MO analysis. The metal-metal bond formation in (CN)(4)Pt-Tl(dmso)(5)(+) can be simply interpreted as the result of a Pt(5d(z(2)))(2) → Tl(6s)(0) donation. This bonding scheme may rationalize the smaller thermodynamic stability of this adduct compared to the related complexes with (CN)(5)Pt-Tl entity, where the linear C-Pt-Tl unit constitutes a very stable bonding system. © 2011 American Chemical Society

Interconnect mechanisms in microelectronic packaging

NASA Astrophysics Data System (ADS)

Roma, Maria Penafrancia C.

Global economic, environmental and market developments caused major impact in the microelectronics industry. Astronomical rise of gold metal prices over the last decade shifted the use of copper and silver alloys as bonding wires. Environmental legislation on the restriction of the use of Pb launched worldwide search for lead-free solders and platings. Finally, electrical and digital uses demanded smaller, faster and cheaper devices. Ultra-fine pitch bonding, decreasing bond wire sizes and hard to bond substrates have put the once-robust stitch bond in the center of reliability issues due to stitch bond lift or open wires .Unlike the ball bond, stitch bonding does not lead to intermetallic compound formation but adhesion is dependent on mechanical deformation, interdiffusion, solid solution formation, void formation and mechanical interlocking depending on the wire material, bond configuration, substrate type , thickness and surface condition. Using Au standoff stitch bonds on NiPdAu plated substrates eliminated stitch bond lift even when the Au and Pd layers are reduced. Using the Matano-Boltzmann analysis on a STEM (Scanning Transmission Analysis) concentration profile the interdiffusion coefficient is measured to be 10-16 cm 2/s. Wire pull strength data showed that the wire pull strength is 0.062N and increases upon stress testing. Meanwhile, coating the Cu wire with Pd, not only increases oxidation resistance but also improved adhesion due to the formation of a unique interfacial adhesion layers. Adhesion strength as measured by pull showed the Cu wire bonded to Ag plated Cu substrate (0.132N) to be stronger than the Au wire bonded on the same substrate (0.124N). Ag stitch bonded to Au is predicted to be strong but surface modification made the adhesion stronger. However, on the Ag ball bonded to Al showed multiple IMC formation with unique morphology exposed by ion milling and backscattered scanning electron microscopy. Adding alloying elements in the Ag wire alloy showed differences in adhesion strength and IMC formation. Bond strength by wire pull testing showed the 95Ag alloy with higher values while shear bond testing showed the 88Ag higher bond strength. Use of Cu pillars in flip chips and eutectic bonding in wafer level chip scale packages are direct consequences of diminishing interconnect dimension as a result of the drive for miniaturization. The combination of Cu-Sn interdiffusion, Kirkendall mechanism and heterogeneous vacancy precipitation are the main causes of IMC and void formation in Cu pillar - Sn solder - Cu lead frame sandwich structure. However, adding a Ni barrier agent showed less porous IMC layer as well as void formation as a result of the modified Cu and Sn movement well as the void formation. Direct die to die bonding using Al-Ge eutectic bonds is necessary when 3D integration is needed to reduce the footprint of a package. Hermeticity and adhesion strength are a function of the Al/Ge thickness ratio, bonding pressure, temperature and time. Scanning Electron Microscope (SEM) and Focused Ion Beam (FIB) allowed imaging of interfacial microstructures, porosity, grain morphology while Scanning Transmission Electron microscope (STEM) provided diffusion profile and confirmed interdiffusion. Ion polishing technique provided information on porosity and when imaged using backscattered mode, grain structure confirmed mechanical deformation of the bonds. Measurements of the interfacial bond strength are made by wire pull tests and ball shear tests based on existing industry standard tests. However, for the Al-Ge eutectic bonds, no standard strength is available so a test is developed using the stud pull test method using the Dage 4000 Plus to yield consistent results. Adhesion strengths of 30-40 MPa are found for eutectic bonded packages however, as low as 20MPa was measured in low temperature bonded areas.

Carbon Displacement-Induced Single Carbon Atomic Chain Formation and its Effects on Sliding of SiC Fibers in SiC/graphene/SiC Composite

DOE PAGES

Wallace, Joseph B.; Chen, Di; Shao, Lin

2015-11-03

Understanding radiation effects on the mechanical properties of SiC composites is important to their application in advanced reactor designs. By means of molecular dynamics simulations, we found that due to strong interface bonding between the graphene layers and SiC, the sliding friction of SiC fibers is largely determined by the frictional behavior between graphene layers. Upon sliding, carbon displacements between graphene layers can act as seed atoms to induce the formation of single carbon atomic chains (SCACs) by pulling carbon atoms from the neighboring graphene planes. The formation, growth, and breaking of SCACs determine the frictional response to irradiation.

[Effect of different heat treatment on the bonding strength of porcelain and Co-Cr alloy].

PubMed

Liao, Juan-kun; Ye, Jian-tao; Zhu, Feng; Zhang, Cui-cui; Wen, Xiao-shan; Zhang, Yi-ping; Li, Bo-hua

2011-12-01

To investigate and compare the effect of different heat treatment on the metal- ceramic bonding strength and the interfacial microstructure of the Co-Cr alloy. Thirty specimens were made according to ISO 9693,and then divided into 3 groups (n=10) through the measurements .Group A(degassed 60s):degassed and then maintained 60s in 980 degrees centigrade Group B(degassed 60s and preoxidation 60s): degassed and maintained 60s in 980 degrees centigrade, then were maintained continuously for 60s in 980 degrees centigrade after re-gassed,Group C(degassed 120s): degassed and maintained 120s in 980 degrees centigrade. The bonding strengths of the three groups were evaluated through three point bending test. Six specimens divided into 3 group were made in the same method to observe the metal-ceramic interface through scanning electronic microscope(SEM) and energy dispersive spectrum(EDS).The bonding strength data were analyzed using ANOVA and Bonferroni's test by SPSS13.0 software package. The mean value of bonding strength was (39.03±2.70)MPa for group A, (34.43±2.36)MPa for group B, (31.65±1.49)MPa for group C, respectively. There were significant difference between every two groups (P<0.05). SEM demonstrated that the width of interfacial transition layer was 12.3-16.4μm in group A, 15.2-21.8μm in group B and 26.3-32.2μm in group C. Higher metal-ceramic bonding strength for Co-Cr alloy will be formed under the situation of degassed,and maintained 60s in 980 degrees centigrade ; while extending degassed time, prolonging the heat maintained time and preoxidation after degassing will reduce metal-ceramic bonding strength.

Out-of-water constitutional self-organization of chitosan-cinnamaldehyde dynagels.

PubMed

Marin, Luminita; Moraru, Simona; Popescu, Maria-Cristina; Nicolescu, Alina; Zgardan, Cristina; Simionescu, Bogdan C; Barboiu, Mihail

2014-04-14

An investigation of the constitutional adaptive gelation process of chitosan/cinnamaldehyde (C/Cy) dynagels is reported. These gels generate timely variant macroscopic organization across extended scales. In the first stage, imine-bond formation takes place "in-water" and generates low-ordered hydrogels. The progressive formation of imine bonds further induces "out-of-water" increased reactivity within interdigitated hydrophobic self-assembled layers of Cy, with a protecting environmental effect against hydrolysis and that leads to the stabilization of the imine bonds. The hydrophobic swelling due to Cy layers at the interfaces reaches a critical step when lamellar self-organized hybrids are generated (24 hours). This induces an important restructuration of the hydrogels on the micrometric scale, thus resulting in the formation of highly ordered microporous xerogel morphologies of high potential interest for chemical separations, drug delivery, and sensors. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A synthetic, catalytic and theoretical investigation of an unsymmetrical SCN pincer palladacycle

PubMed Central

Roffe, Gavin W.; Boonseng, Sarote; Baltus, Christine B.; Coles, Simon J.; Day, Iain J.; Jones, Rhiannon N.; Press, Neil J.; Ruiz, Mario; Tizzard, Graham J.; Cox, Hazel

2016-01-01

The SCN ligand 2-{3-[(methylsulfanyl)methyl]phenyl}pyridine, 1, has been synthesized starting from an initial Suzuki–Miyaura (SM) coupling between 3-((hydroxymethyl)phenyl)boronic acid and 2-bromopyridine. The C–H activation of 1 with in situ formed Pd(MeCN)4(BF4)2 has been studied and leads to a mixture of palladacycles, which were characterized by X-ray crystallography. The monomeric palladacycle LPdCl 6, where L-H = 1, has been synthesized, and tested in SM couplings of aryl bromides, where it showed moderate activity. Density functional theory and the atoms in molecules (AIM) method have been used to investigate the formation and bonding of 6, revealing a difference in the nature of the Pd–S and Pd–N bonds. It was found that S-coordination to the metal in the rate determining C–H bond activation step leads to better stabilization of the Pd(II) centre (by 13–28 kJ mol−1) than with N-coordination. This is attributed to the electron donating ability of the donor atoms determined by Bader charges. The AIM analysis also revealed that the Pd–N bonds are stronger than the Pd–S bonds influencing the stability of key intermediates in the palladacycle formation reaction pathway. PMID:27152207

31 CFR 315.30 - Series E bonds and savings notes.

Code of Federal Regulations, 2010 CFR

2010-07-01

...) FISCAL SERVICE, DEPARTMENT OF THE TREASURY BUREAU OF THE PUBLIC DEBT REGULATIONS GOVERNING U.S. SAVINGS BONDS, SERIES A, B, C, D, E, F, G, H, J, AND K, AND U.S. SAVINGS NOTES Interest § 315.30 Series E bonds... 31 Money and Finance: Treasury 2 2010-07-01 2010-07-01 false Series E bonds and savings notes. 315...

An allosteric disulfide bond is involved in enhanced activation of factor XI by protein disulfide isomerase.

PubMed

Zucker, M; Seligsohn, U; Yeheskel, A; Mor-Cohen, R

2016-11-01

Essentials Reduction of three disulfide bonds in factor (F) XI enhances chromogenic substrate cleavage. We measured FXI activity upon reduction and identified a bond involved in the enhanced activity. Reduction of FXI augments FIX cleavage, probably by faster conversion of FXI to FXIa. The Cys362-Cys482 disulfide bond is responsible for FXI enhanced activation upon its reduction. Background Reduction of factor (F) XI by protein disulfide isomerase (PDI) has been shown to enhance the ability of FXI to cleave its chromogenic substrate. Three disulfide bonds in FXI (Cys118-Cys147, Cys362-Cys482, and Cys321-Cys321) are involved in this augmented activation. Objectives To characterize the mechanisms by which PDI enhances FXI activity. Methods FXI activity was measured following PDI reduction. Thiols that were exposed in FXI after PDI reduction were labeled with 3-(N-maleimidopropionyl)-biocytin (MPB) and detected with avidin. The rate of conversion of FXI to activated FXI (FXIa) following thrombin activation was assessed with western blotting. FXI molecules harboring mutations that disrupt the three disulfide bonds (C147S, C321S, and C482S) were expressed in cells. The antigenicity of secreted FXI was measured with ELISA, and its activity was assessed by the use of a chromogenic substrate. The effect of disulfide bond reduction was analyzed by the use of molecular dynamics. Results Reduction of FXI by PDI enhanced cleavage of both its chromogenic substrate, S2366, and its physiologic substrate, FIX, and resulted in opening of the Cys362-Cys482 bond. The rate of conversion of FXI to FXIa was increased following its reduction by PDI. C482S-FXI showed enhanced activity as compared with both wild-type FXI and C321S-FXI. MD showed that disruption of the Cys362-Cys482 bond leads to a broader thrombin-binding site in FXI. Conclusions Reduction of FXI by PDI enhances its ability to cleave FIX, probably by causing faster conversion of FXI to FXIa. The Cys362-Cys482 disulfide bond is involved in enhancing FXI activation following its reduction, possibly by increasing thrombin accessibility to FXI. © 2016 International Society on Thrombosis and Haemostasis.

Hydrogen bonding interactions in PN...HX complexes: DFT and ab initio studies of structure, properties and topology.

PubMed

Varadwaj, Pradeep Risikrishna

2010-05-01

Spin-restricted DFT (X3LYP and B3LYP) and ab initio (MP2(fc) and CCSD(fc)) calculations in conjunction with the Aug-CC-pVDZ and Aug-CC-pVTZ basis sets were performed on a series of hydrogen bonded complexes PN...HX (X = F, Cl, Br) to examine the variations of their equilibrium gas phase structures, energetic stabilities, electronic properties, and vibrational characteristics in their electronic ground states. In all cases the complexes were predicted to be stable with respect to the constituent monomers. The interaction energy (Delta E) calculated using a super-molecular model is found to be in this order: PN...HF > PN...HCl > PN...HBr in the series examined. Analysis of various physically meaningful contributions arising from the Kitaura-Morokuma (KM) and reduced variational space self-consistent-field (RVS-SCF) energy decomposition procedures shows that the electrostatic energy has significant contribution to the over-all interaction energy. Dipole moment enhancement (Delta mu) was observed in these complexes expected of predominant dipole-dipole electrostatic interaction and was found to follow the trend PN...HF > PN...HCl > PN...HBr at the CCSD level. However, the DFT (X3LYP and B3LYP) and MP2 levels less accurately determined these values (in this order HF < HCl < HBr). Examination of the harmonic vibrational modes reveals that the PN and HX bands exhibit characteristic blue- and red shifts with concomitant bond contraction and elongation, respectively, on hydrogen bond formation. The topological or critical point (CP) analysis using the static quantum theory of atoms in molecules (QTAIM) of Bader was considered to classify and to gain further insight into the nature of interaction existing in the monomers PN and HX, and between them on H-bond formation. It is found from the analysis of the electron density rho ( c ), the Laplacian of electron charge density nabla(2)rho(c), and the total energy density (H ( c )) at the critical points between the interatomic regions that the interaction N...H is indeed electrostatic in origin (rho(c) > 0, nabla(2)rho(c) > 0 and H(c) > 0 at the BCP) whilst the bonds in PN (rho(c) > 0, nabla(2)rho(c) > 0 and H(c) < 0) and HX ((rho(c) > 0, nabla(2)rho(c) < 0 and H(c) < 0)) are predominantly covalent. A natural bond orbital (NBO) analysis of the second order perturbation energy lowering, E((2)), caused by charge transfer mechanism shows that the interaction N...H is n(N) --> BD*(HX) delocalization.

Role of ring-constrained γ-amino acid residues in α/γ-peptide folding: single-conformation UV and IR spectroscopy.

PubMed

Kusaka, Ryoji; Zhang, Di; Walsh, Patrick S; Gord, Joseph R; Fisher, Brian F; Gellman, Samuel H; Zwier, Timothy S

2013-10-24

The capped α/γ-peptide foldamers Ac-γACHC-Ala-NH-benzyl (γα) and Ac-Ala-γACHC-NH-benzyl (αγ) were studied in the gas phase under jet-cooled conditions using single-conformation spectroscopy. These molecules serve as models for local segments of larger heterogeneous 1:1 α/γ-peptides that have recently been synthesized and shown to form a 12-helix composed of repeating C12 H-bonded rings both in crystalline form and in solution [Guo, L.; et al. J. Am. Chem. Soc. 2009, 131, 16018]. The γα and αγ peptide subunits are structurally constrained at the Cβ-Cγ bond of the γ-residue with a cis-cyclohexyl ring and by an ethyl group at the Cα position. These triamides are the minimum length necessary for the formation of the C12 H-bond. Resonant two-photon ionization (R2PI) provides ultraviolet spectra that have contributions from all conformational isomers, while IR-UV hole-burning (IR-UV HB) and resonant ion-dip infrared (RIDIR) spectroscopies are used to record single-conformation UV and IR spectra, respectively. Four and six conformers are identified in the R2PI spectra of the γα and αγ peptides, respectively. RIDIR spectra in the NH stretch, amide I (C═O stretch), and amide II (NH bend) regions are compared with the predictions of density functional theory (DFT) calculations at the M05-2X/6-31+G* level, leading to definite assignments for the H-bonding architectures of the conformers. While the C12 H-bond is present in both γα and αγ, C9 rings are more prevalent, with seven of ten conformers incorporating a C9 H-bond involving in the γ-residue. Nevertheless, comparison of the assigned structures of gas-phase γα and αγ with the crystal structures for γα and larger α/γ-peptides reveals that the constrained γ-peptide backbone formed by the C9 ring is structurally similar to that formed by the larger C12 ring present in the 12-helix. These results confirm that the ACHC/ethyl constrained γ-residue is structurally preorganized to play a significant role in promoting C12 H-bond formation in larger α/γ-peptides.

Activation of methyl acetate on Pd(111)

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

Xu, Lijun; Xu, Ye

2010-01-01

The absorption and activation of methyl acetate (CH{sub 3}COOCH{sub 3}), one of the simplest carboxylic esters, on Pd(111) have been studied using self-consistent periodic density functional theory calculations. Methyl acetate adsorbs weakly through the carbonyl oxygen. Its activation occurs via dehydrogenation, instead of direct C-O bond dissociation, on clean Pd(111): It is much more difficult to dissociate the C--O bonds ({epsilon}{sub a} ? 2.0 eV for the carbonyl and acetate-methyl bonds; {epsilon}{sub a} = 1.0 eV for the acetyl-methoxy bond) than to dissociate the C-H bonds to produce enolate (CH{sub 2}COOCH{sub 3}; {epsilon}{sub a} = 0.74 eV) or methylene acetatemore » (CH{sub 3}COOCH{sub 2}; {epsilon}{sub a} = 0.82 eV). The barriers for C-H and C-O bond dissociation are directly calculated for enolate and methylene acetate, and estimated for further dehydrogenated derivatives (CH{sub 3}COOCH, CH{sub 2}COOCH{sub 2}, and CHCOOCH{sub 3}) based on the Bronsted-Evans-Polanyi linear energy relations formed by the calculated steps. The enolate pathway leads to successive dehydrogenation to CCOOCH{sub 3}, whereas methylene acetate readily dissociates to yield acetyl. The selectivity for dissociating the acyl-alkoxy C-O bond, which is desired for alcohol formation, is therefore fundamentally limited by the facility of dehydrogenation under vacuum/low-pressure conditions on Pd(111).« less

Bonding in gold-rare earth [Au2M] (M = Eu, Yb, Lu) ions. A strong covalent gold-lanthanide bond

NASA Astrophysics Data System (ADS)

Páez-Hernández, Dayán; Muñoz-Castro, Alvaro; Arratia-Perez, Ramiro

2017-09-01

The electronic structure and bonding nature of a series of intermetallic gold-lanthanide [Au2Ln] molecules, where Ln = Eu, Yb, Lu is predicted via the DFT and CASSCF/CASPT2 calculations. The 2c-2e bond model shows a good description of the intermetallic bonding which have a large covalent component with important contribution from bonding interaction between the 6s-Au and the 6s-Ln shell of orbitals.

Insights into the role of the unusual disulfide bond in copper-zinc superoxide dismutase.

PubMed

Sea, Kevin; Sohn, Se Hui; Durazo, Armando; Sheng, Yuewei; Shaw, Bryan F; Cao, Xiaohang; Taylor, Alexander B; Whitson, Lisa J; Holloway, Stephen P; Hart, P John; Cabelli, Diane E; Gralla, Edith Butler; Valentine, Joan Selverstone

2015-01-23

The functional and structural significance of the intrasubunit disulfide bond in copper-zinc superoxide dismutase (SOD1) was studied by characterizing mutant forms of human SOD1 (hSOD) and yeast SOD1 lacking the disulfide bond. We determined x-ray crystal structures of metal-bound and metal-deficient hC57S SOD1. C57S hSOD1 isolated from yeast contained four zinc ions per protein dimer and was structurally very similar to wild type. The addition of copper to this four-zinc protein gave properly reconstituted 2Cu,2Zn C57S hSOD, and its spectroscopic properties indicated that the coordination geometry of the copper was remarkably similar to that of holo wild type hSOD1. In contrast, the addition of copper and zinc ions to apo C57S human SOD1 failed to give proper reconstitution. Using pulse radiolysis, we determined SOD activities of yeast and human SOD1s lacking disulfide bonds and found that they were enzymatically active at ∼10% of the wild type rate. These results are contrary to earlier reports that the intrasubunit disulfide bonds in SOD1 are essential for SOD activity. Kinetic studies revealed further that the yeast mutant SOD1 had less ionic attraction for superoxide, possibly explaining the lower rates. Saccharomyces cerevisiae cells lacking the sod1 gene do not grow aerobically in the absence of lysine, but expression of C57S SOD1 increased growth to 30-50% of the growth of cells expressing wild type SOD1, supporting that C57S SOD1 retained a significant amount of activity. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Insights into the Role of the Unusual Disulfide Bond in Copper-Zinc Superoxide Dismutase*

PubMed Central

Sea, Kevin; Sohn, Se Hui; Durazo, Armando; Sheng, Yuewei; Shaw, Bryan F.; Cao, Xiaohang; Taylor, Alexander B.; Whitson, Lisa J.; Holloway, Stephen P.; Hart, P. John; Cabelli, Diane E.; Gralla, Edith Butler; Valentine, Joan Selverstone

2015-01-01

The functional and structural significance of the intrasubunit disulfide bond in copper-zinc superoxide dismutase (SOD1) was studied by characterizing mutant forms of human SOD1 (hSOD) and yeast SOD1 lacking the disulfide bond. We determined x-ray crystal structures of metal-bound and metal-deficient hC57S SOD1. C57S hSOD1 isolated from yeast contained four zinc ions per protein dimer and was structurally very similar to wild type. The addition of copper to this four-zinc protein gave properly reconstituted 2Cu,2Zn C57S hSOD, and its spectroscopic properties indicated that the coordination geometry of the copper was remarkably similar to that of holo wild type hSOD1. In contrast, the addition of copper and zinc ions to apo C57S human SOD1 failed to give proper reconstitution. Using pulse radiolysis, we determined SOD activities of yeast and human SOD1s lacking disulfide bonds and found that they were enzymatically active at ∼10% of the wild type rate. These results are contrary to earlier reports that the intrasubunit disulfide bonds in SOD1 are essential for SOD activity. Kinetic studies revealed further that the yeast mutant SOD1 had less ionic attraction for superoxide, possibly explaining the lower rates. Saccharomyces cerevisiae cells lacking the sod1 gene do not grow aerobically in the absence of lysine, but expression of C57S SOD1 increased growth to 30–50% of the growth of cells expressing wild type SOD1, supporting that C57S SOD1 retained a significant amount of activity. PMID:25433341

Reduction of [Cp*Sb]4 with Subvalent Main-Group Metal Reductants: Syntheses and Structures of [(L1 Mg)4 (Sb4 )] and [(L2 Ga)2 (Sb4 )] Containing Edge-Missing Sb4 Units.

PubMed

Ganesamoorthy, Chelladurai; Krüger, Julia; Wölper, Christoph; Nizovtsev, Anton S; Schulz, Stephan

2017-02-16

[Cp*Sb] 4 (Cp*=C 5 Me 5 ) reacts with [L 1 Mg] 2 and L 2 Ga with formation of [(L 1 Mg) 4 (μ 4 ,η 1:2:2:2 -Sb 4 )] (L 1 =iPr 2 NC[N(2,6-iPr 2 C 6 H 3 )] 2 , 1) and [(L 2 Ga) 2 (μ,η 2:2 -Sb 4 )] (L 2 =HC[C(Me)N(2,6-iPr 2 C 6 H 3 )] 2 , 2). The cleavage of the Sb-Sb and Sb-C bonds in [Cp*Sb] 4 are the crucial steps in both reactions. The formation of 1 occurred by elimination of the Cp* anion and formation of Cp*MgL 1 , while 2 was formed by reductive elimination of Cp* 2 and oxidative addition of L 2 Ga to the Sb 4 unit. 1 and 2 were characterized by heteronuclear NMR spectroscopy and single-crystal X-ray diffraction, and their bonding situation was studied by quantum chemical calculations. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

19 CFR Appendix C to Part 113 - Bond for Deferral of Duty on Large Yachts Imported for Sale at United States Boat Shows

Code of Federal Regulations, 2014 CFR

2014-04-01

... for Sale at United States Boat Shows C Appendix C to Part 113 Customs Duties U.S. CUSTOMS AND BORDER... Appendix C to Part 113—Bond for Deferral of Duty on Large Yachts Imported for Sale at United States Boat Shows Bond for Deferral of Duty on Large Yachts Imported for Sale at United States Boat Shows ____, as...

19 CFR Appendix C to Part 113 - Bond for Deferral of Duty on Large Yachts Imported for Sale at United States Boat Shows

Code of Federal Regulations, 2013 CFR

2013-04-01

... for Sale at United States Boat Shows C Appendix C to Part 113 Customs Duties U.S. CUSTOMS AND BORDER... Appendix C to Part 113—Bond for Deferral of Duty on Large Yachts Imported for Sale at United States Boat Shows Bond for Deferral of Duty on Large Yachts Imported for Sale at United States Boat Shows ____, as...

19 CFR Appendix C to Part 113 - Bond for Deferral of Duty on Large Yachts Imported for Sale at United States Boat Shows

Code of Federal Regulations, 2012 CFR

2012-04-01

... for Sale at United States Boat Shows C Appendix C to Part 113 Customs Duties U.S. CUSTOMS AND BORDER... Appendix C to Part 113—Bond for Deferral of Duty on Large Yachts Imported for Sale at United States Boat Shows Bond for Deferral of Duty on Large Yachts Imported for Sale at United States Boat Shows ____, as...

Mechanisms of Insertion of dCTP and dTTP Opposite the DNA Lesion O6-Methyl-2'-deoxyguanosine by Human DNA Polymerase η.

PubMed

Patra, Amitraj; Zhang, Qianqian; Guengerich, F Peter; Egli, Martin

2016-11-11

O 6 -Methyl-2'-deoxyguanosine (O 6 -MeG) is a ubiquitous DNA lesion, formed not only by xenobiotic carcinogens but also by the endogenous methylating agent S-adenosylmethionine. It can introduce mutations during DNA replication, with different DNA polymerases displaying different ratios of correct or incorrect incorporation opposite this nucleoside. Of the "translesion" Y-family human DNA polymerases (hpols), hpol η is most efficient in incorporating equal numbers of correct and incorrect C and T bases. However, the mechanistic basis for this specific yet indiscriminate activity is not known. To explore this question, we report biochemical and structural analysis of the catalytic core of hpol η. Activity assays showed the truncated form displayed similar misincorporation properties as the full-length enzyme, incorporating C and T equally and extending from both. X-ray crystal structures of both dC and dT paired with O 6 -MeG were solved in both insertion and extension modes. The structures revealed a Watson-Crick-like pairing between O 6 -MeG and 2"-deoxythymidine-5"-[(α, β)-imido]triphosphate (approximating dT) at both the insertion and extension stages with formation of two H-bonds. Conversely, both the structures with O 6 - MeG opposite dCTP and dC display sheared configuration of base pairs but to different degrees, with formation of two bifurcated H-bonds and two single H-bonds in the structures trapped in the insertion and extension states, respectively. The structural data are consistent with the observed tendency of hpol η to insert both dC and dT opposite the O 6 -MeG lesion with similar efficiencies. Comparison of the hpol η active site configurations with either O 6 -MeG:dC or O 6 -MeG:dT bound compared with the corresponding situations in structures of complexes of Sulfolobus solfataricus Dpo4, a bypass pol that favors C relative to T by a factor of ∼4, helps rationalize the more error-prone synthesis opposite the lesion by hpol η. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Mechanisms of Insertion of dCTP and dTTP Opposite the DNA Lesion O6-Methyl-2′-deoxyguanosine by Human DNA Polymerase η*

PubMed Central

Patra, Amitraj; Zhang, Qianqian; Guengerich, F. Peter; Egli, Martin

2016-01-01

O6-Methyl-2′-deoxyguanosine (O6-MeG) is a ubiquitous DNA lesion, formed not only by xenobiotic carcinogens but also by the endogenous methylating agent S-adenosylmethionine. It can introduce mutations during DNA replication, with different DNA polymerases displaying different ratios of correct or incorrect incorporation opposite this nucleoside. Of the “translesion” Y-family human DNA polymerases (hpols), hpol η is most efficient in incorporating equal numbers of correct and incorrect C and T bases. However, the mechanistic basis for this specific yet indiscriminate activity is not known. To explore this question, we report biochemical and structural analysis of the catalytic core of hpol η. Activity assays showed the truncated form displayed similar misincorporation properties as the full-length enzyme, incorporating C and T equally and extending from both. X-ray crystal structures of both dC and dT paired with O6-MeG were solved in both insertion and extension modes. The structures revealed a Watson-Crick-like pairing between O6-MeG and 2"-deoxythymidine-5"-[(α, β)-imido]triphosphate (approximating dT) at both the insertion and extension stages with formation of two H-bonds. Conversely, both the structures with O6- MeG opposite dCTP and dC display sheared configuration of base pairs but to different degrees, with formation of two bifurcated H-bonds and two single H-bonds in the structures trapped in the insertion and extension states, respectively. The structural data are consistent with the observed tendency of hpol η to insert both dC and dT opposite the O6-MeG lesion with similar efficiencies. Comparison of the hpol η active site configurations with either O6-MeG:dC or O6-MeG:dT bound compared with the corresponding situations in structures of complexes of Sulfolobus solfataricus Dpo4, a bypass pol that favors C relative to T by a factor of ∼4, helps rationalize the more error-prone synthesis opposite the lesion by hpol η. PMID:27694439

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.

Chemisorption of 1,1-dichloroethene on the Si(1 1 1)-7 × 7 surface

NASA Astrophysics Data System (ADS)

Andersen, T. H.; Zahl, M. G.; Svenum, I.-H.; Børve, K. J.; Borg, A.; Sæthre, L. J.

2007-12-01

Chemisorption of 1,1-dichloroethene (Cl 2C dbnd CH 2) to a Si(1 1 1)-7 × 7 surface was studied by means of X-ray photoelectron spectroscopy using synchrotron radiation, recording chlorine 2p and carbon 1s spectra. For carbon 1s, spectral assignment of the chemisorbed species is based on quantum chemical calculations of chemical shifts in model compounds. The results confirm the identity of covalently bonded 1-chlorovinyl (-CCl dbnd CH 2) and vinylidene ( lbond2 C dbnd CH 2) adspecies. Upon chemisorption at room temperature it was found that about one-third of the molecules break one C-Cl bond while about two-thirds of the adsorbates break two C-Cl bonds. We do not, however, find evidence for isomerization of lbond2 C dbnd CH 2 to di-bonded vinylene (-CH dbnd CH-).

Cooperative Light-Activated Iodine and Photoredox Catalysis for the Amination of Csp3 -H Bonds.

PubMed

Becker, Peter; Duhamel, Thomas; Stein, Christopher J; Reiher, Markus; Muñiz, Kilian

2017-06-26

An unprecedented method that makes use of the cooperative interplay between molecular iodine and photoredox catalysis has been developed for dual light-activated intramolecular benzylic C-H amination. Iodine serves as the catalyst for the formation of a new C-N bond by activating a remote Csp3 -H bond (1,5-HAT process) under visible-light irradiation while the organic photoredox catalyst TPT effects the reoxidation of the molecular iodine catalyst. To explain the compatibility of the two involved photochemical steps, the key N-I bond activation was elucidated by computational methods. The new cooperative catalysis has important implications for the combination of non-metallic main-group catalysis with photocatalysis. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

DISCOVERY OF SiCSi IN IRC+10216: A MISSING LINK BETWEEN GAS AND DUST CARRIERS OF Si–C BONDS

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

Cernicharo, J.; Agúndez, M.; Prieto, L. Velilla

2015-06-10

We report the discovery in space of a disilicon species, SiCSi, from observations between 80 and 350 GHz with the IRAM 30 m radio telescope. Owing to the close coordination between laboratory experiments and astrophysics, 112 lines have now been detected in the carbon-rich star CW Leo. The derived frequencies yield improved rotational and centrifugal distortion constants up to sixth order. From the line profiles and interferometric maps with the Submillimeter Array, the bulk of the SiCSi emission arises from a region of 6″ in radius. The derived abundance is comparable to that of SiC{sub 2}. As expected from chemicalmore » equilibrium calculations, SiCSi and SiC{sub 2} are the most abundant species harboring a Si−C bond in the dust formation zone and certainly both play a key role in the formation of SiC dust grains.« less

C-terminal peptide extension via gas-phase ion/ion reactions

PubMed Central

Peng, Zhou; McLuckey, Scott A.

2015-01-01

The formation of peptide bonds is of great importance from both a biological standpoint and in routine organic synthesis. Recent work from our group demonstrated the synthesis of peptides in the gas-phase via ion/ion reactions with sulfo-NHS reagents, which resulted in conjugation of individual amino acids or small peptides to the N-terminus of an existing ‘anchor’ peptide. Here, we demonstrate a complementary approach resulting in the C-terminal extension of peptides. Individual amino acids or short peptides can be prepared as reagents by incorporating gas phase-labile protecting groups to the reactive C-terminus and then converting the N-terminal amino groups to the active ketenimine reagent. Gas-phase ion/ion reactions between the anionic reagents and doubly protonated “anchor” peptide cations results in extension of the “anchor” peptide with new amide bond formation at the C-terminus. We have demonstrated that ion/ion reactions can be used as a fast, controlled, and efficient means for C-terminal peptide extension in the gas phase. PMID:26640400

Allosteric Breakage of the Hydrogen Bond within the Dual-Histidine Motif in the Active Site of Human Pin1 PPIase.

PubMed

Wang, Jing; Tochio, Naoya; Kawasaki, Ryosuke; Tamari, Yu; Xu, Ning; Uewaki, Jun-Ichi; Utsunomiya-Tate, Naoko; Tate, Shin-Ichi

2015-08-25

Intimate cooperativity among active site residues in enzymes is a key factor for regulating elaborate reactions that would otherwise not occur readily. Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (Pin1) is the phosphorylation-dependent cis-trans peptidyl-prolyl isomerase (PPIase) that specifically targets phosphorylated Ser/Thr-Pro motifs. Residues C113, H59, H157, and T152 form a hydrogen bond network in the active site, as in the noted connection. Theoretical studies have shown that protonation to thiolate C113 leads to rearrangement of this hydrogen bond network, with switching of the tautomeric states of adjacent histidines (H59 and H157) [Barman, A., and Hamelberg, D. (2014) Biochemistry 53, 3839-3850]. This is called the "dual-histidine motif". Here, C113A and C113S Pin1 mutants were found to alter the protonation states of H59 according to the respective residue type replaced at C113, and the mutations resulted in disruption of the hydrogen bond within the dual-histidine motif. In the C113A mutant, H59 was observed to be in exchange between ε- and δ-tautomers, which widened the entrance of the active site cavity, as seen by an increase in the distance between residues A113 and S154. The C113S mutant caused H59 to exchange between the ε-tautomer and imidazolium while not changing the active site structure. Moreover, the imidazole ring orientations of H59 and H157 were changed in the C113S mutant. These results demonstrated that a mutation at C113 modulates the hydrogen bond network dynamics. Thus, C113 acts as a pivot to drive the concerted function among the residues in the hydrogen bond network, as theoretically predicted.

Regioselective cis-trans isomerization of arachidonic double bonds by thiyl radicals: the influence of phospholipid supramolecular organization.

PubMed

Ferreri, Carla; Samadi, Abdelouahid; Sassatelli, Fabio; Landi, Laura; Chatgilialoglu, Chryssostomos

2004-02-04

Trans unsaturated fatty acids in humans may be originated by two different contributions. The exogenous track is due to dietary supplementation of trans fats and the endogenous path deals with free-radical-catalyzed cis-trans isomerization of fatty acids. Arachidonic acid residue (5c,8c,11c,14c-20:4), which has only two out of the four double bonds deriving from the diet, was used to differentiate the two paths and to assess the importance of a radical reaction. A detailed study on the formation of trans phospholipids catalyzed by the HOCH2CH2S* radical was carried out on L-alpha-phosphatidylcholine from egg lecithin and 1-stearoyl-2-arachidonoyl-L-alpha-phosphatidylcholine (SAPC) in homogeneous solution or in large unilamellar vesicles (LUVET). Thiyl radicals were generated from the corresponding thiol by either gamma-irradiation or UV photolysis, and the reaction course was followed by GC, Ag/TLC, and 13C NMR analyses. The isomerization was found to be independent of cis double bond location (random process) in i-PrOH solution. In the case of vesicles, the supramolecular organization of lipids produced a dramatic change of the isomerization outcome: (i) in egg lecithin, the reactivity of arachidonate moieties is higher than that of oleate and linoleate residues, (ii) in the linoleate residues of egg lecithin, the 9t,12c-18:2 isomer prevailed on the 9c,12t-18:2 isomer (3:1 ratio), and (iii) a regioselective isomerization of SAPC arachidonate residues occurred in the 5 and 8 positions. This effect of "positional preference" indicates that thiyl radicals entering the hydrophobic region of the membrane bilayer start to isomerize polyunsaturated fatty acid residues having the double bonds nearest to the membrane surfaces. We propose that arachidonic acid and its trans isomers can function as biomarkers in membranes for distinguishing the two trans fatty acid-forming pathways.

The gas-phase reaction between silylene and 2-butyne: kinetics, isotope studies, pressure dependence studies and quantum chemical calculations.

PubMed

Becerra, Rosa; Cannady, J Pat; Dormer, Guy; Walsh, Robin

2009-07-14

Time-resolved kinetic studies of the reactions of silylene, SiH(2), and dideutero-silylene, SiD(2), generated by laser flash photolysis of phenylsilane and phenylsilane-d(3), respectively, have been carried out to obtain rate coefficients for their bimolecular reactions with 2-butyne, CH(3)C[triple bond, length as m-dash]CCH(3). The reactions were studied in the gas phase over the pressure range 1-100 Torr in SF(6) bath gas at five temperatures in the range 294-612 K. The second-order rate coefficients, obtained by extrapolation to the high pressure limits at each temperature, fitted the Arrhenius equations where the error limits are single standard deviations: log(k(H)(Infinity)/cm(3) molecule(-1) s(-1) = (-9.67 +/- 0.04) + (1.71 +/- 0.33) kJ mol(1)/RTIn10log(k(D)(Infinity)/cm(3) molecule(-1) s(-1) = (-9.65 +/- 0.01) + (1.92 +/- 0.13) kJ mol(-1)/RTIn10. Additionally, pressure-dependent rate coefficients for the reaction of SiH(2) with 2-butyne in the presence of He (1-100 Torr) were obtained at 301, 429 and 613 K. Quantum chemical (ab initio) calculations of the SiC(4)H(8) reaction system at the G3 level support the formation of 2,3-dimethylsilirene [cyclo-SiH(2)C(CH(3))[double bond, length as m-dash]C(CH(3))-] as the sole end product. However, reversible formation of 2,3-dimethylvinylsilylene [CH(3)CH[double bond, length as m-dash]C(CH(3))SiH] is also an important process. The calculations also indicate the probable involvement of several other intermediates, and possible products. RRKM calculations are in reasonable agreement with the pressure dependences at an enthalpy value for 2,3-dimethylsilirene fairly close to that suggested by the ab initio calculations. The experimental isotope effects deviate significantly from those predicted by RRKM theory. The differences can be explained by an isotopic scrambling mechanism, involving H-D exchange between the hydrogens of the methyl groups and the D-atoms in the ring in 2,3-dimethylsilirene-1,1-d(2). A detailed mechanism involving several intermediate species, which is consistent with the G3 energy surface, is proposed to account for this.

Chromophore dynamics in the PYP photocycle from femtosecond stimulated Raman spectroscopy.

PubMed

Creelman, Mark; Kumauchi, Masato; Hoff, Wouter D; Mathies, Richard A

2014-01-23

Femtosecond stimulated Raman spectroscopy (FSRS) is used to examine the structural dynamics of the para-hydroxycinnamic acid (HCA) chromophore during the first 300 ps of the photoactive yellow protein (PYP) photocycle, as the system transitions from its vertically excited state to the early ground state cis intermediate, I0. A downshift in both the C7═C8 and C1═O stretches upon photoexcitation reveals that the chromophore has shifted to an increasingly quinonic form in the excited state, indicating a charge shift from the phenolate moiety toward the C9═O carbonyl, which continues to increase for 170 fs. In addition, there is a downshift in the C9═O carbonyl out-of-plane vibration on an 800 fs time scale as PYP transitions from its excited state to I0, indicating that weakening of the hydrogen bond with Cys69 and out-of-plane rotation of the C9═O carbonyl are key steps leading to photoproduct formation. HOOP intensity increases on a 3 ps time scale during the formation of I0, signifying distortion about the C7═C8 bond. Once on the I0 surface, the C7═C8 and C1═O stretches blue shift, indicating recovery of charge to the phenolate, while persistent intensity in the HOOP and carbonyl out-of-plane modes reveal HCA to be a cissoid structure with significant distortion about the C7═C8 bond and of C9═O out of the molecular plane.

Preparation of catalytically active, covalent α-polylysine-enzyme conjugates via UV/vis-quantifiable bis-aryl hydrazone bond formation.

PubMed

Grotzky, Andrea; Manaka, Yuichi; Kojima, Taisuke; Walde, Peter

2011-01-10

Covalent UV/vis-quantifiable bis-aryl hydrazone bond formation was investigated for the preparation of conjugates between α-poly-d-lysine (PDL) and either α-chymotrypsin (α-CT) or horseradish peroxidase (HRP). PDL and the enzymes were first modified via free amino groups with the linking reagents succinimidyl 6-hydrazinonicotinate acetone hydrazone (S-HyNic, at pH 7.6) and succinimidyl 4-formylbenzoate (S-4FB, at pH 7.2), respectively. The modified PDL and enzymes were then conjugated at pH 4.7, whereby polymer chains carrying several enzymes were obtained. Kinetics of the bis-aryl hydrazone bond formation was investigated spectrophotometrically at 354 nm. Retention of the enzymatic activity after conjugate formation was confirmed by using the substrates N-succinimidyl-l-Ala-l-Ala-l-Pro-l-Phe-p-nitroanilide (for α-CT) and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS, for HRP). Thus, not only a mild and efficient preparation and convenient quantification of a conjugate between the polycationic α-polylysine and enzymes could be shown, but also the complete preservation of the enzymatic activity.

Disulphide bonds in casein micelle from milk.

PubMed

Bouguyon, Edwige; Beauvallet, Christian; Huet, Jean-Claude; Chanat, Eric

2006-05-05

Mammary epithelial cells synthesised and secreted caseins, the major milk proteins in most mammals, as large aggregates called micelles into the alveolar lumen they surround. We investigated the implication of the highly conserved cysteine(s) of kappa-casein in disulphide bond formation in casein micelles from several species. Dimers were found in all milks studied, confirming previous observation in ruminants. More importantly, the study of interchain disulphide bridges in mouse and rat casein micelles revealed that any casein possessing a cysteine is engaged in disulphide bond interchange; these species express four or five cysteine-containing caseins, respectively. We found that the main rodent caseins form both homo- and heterodimers. Additionally, disulphide bond formation among milk proteins was specific since the interaction of the caseins with cysteine-containing whey proteins was not observed in native casein micelles.

Molecular structures of five adducts assembled from p-dimethylaminobenzaldehyde and organic acids

NASA Astrophysics Data System (ADS)

Jin, Shouwen; Wang, Lanqing; Liu, Hui; Liu, Li; Zhang, Huan; Wang, Daqi; Li, Minghui; Guo, Jianzhong; Guo, Ming

2016-07-01

Five adducts 1-5 derived from p-dimethylaminobenzaldehyde have been prepared and characterized by X-ray diffraction analysis, IR, mp, and elemental analysis. Of the five adducts two are organic salts (1, and 2) and the other three (3-5) are cocrystals. In salts 1, and 2, the L molecules are protonated. The supramolecular architectures of the adducts 1-5 involve extensive intermolecular N-H⋯O, O-H⋯O, O-H⋯S, and C-H⋯O hydrogen bonds as well as other non-covalent interactions. The role of weak and strong non-covalent interactions in the crystal packing is ascertained. The complexes displayed 2D/3D framework structure for the synergistic effect of the various non-covalent interactions. The results presented herein tell that the strength and directionality of the N-H⋯O, O-H⋯O, and O-H⋯S hydrogen bonds between organic acids and p-dimethylaminobenzaldehyde are sufficient to bring about the formation of binary cocrystals or organic salts.

Understanding peptide competitive inhibition of botulinum neurotoxin A binding to SV2 protein via molecular dynamics simulations.

PubMed

Chang, Shan; He, Hong-Qiu; Shen, Lin; Wan, Hua

2015-10-01

Botulinum neurotoxins (BoNTs) are known as the most toxic natural substances. Synaptic vesicle protein 2 (SV2) has been proposed to be a protein receptor for BoNT/A. Recently, two short peptides (BoNT/A-A2 and SV2C-A3) were designed to inhibit complex formation between the BoNT/A receptor-binding domain (BoNT/A-RBD) and the synaptic vesicle protein 2C luminal domain (SV2C-LD). In this article, the two peptide complex systems are studied by molecular dynamics (MD) simulations. The structural stability analysis indicates that BoNT/A-A2 system is more stable than SV2C-A3 system. The conformational analysis implies that the β-sheet in BoNT/A-A2 system maintains its secondary structure but the two β-strands in SV2C-A3 system have remarkable conformational changes. Based on the calculation of hydrogen bonds, hydrophobic interactions and cation-π interactions, it is found that the internal hydrogen bonds play crucial roles in the structural stability of the peptides. Because of the stable secondary structure, the β-sheet in BoNT/A-A2 system establishes effective interactions at the interface and inhibits BoNT/A-RBD binding to SV2C-LD. In contrast, without other β-strands forming internal hydrogen bonds, the two isolated β-strands in SV2C-A3 system become the random coil. This conformational change breaks important hydrogen bonds and weakens cation-π interaction in the interface, so the complex formation is only partially inhibited by the two β-strands. These results are consistent with experimental studies and may be helpful in understanding the inhibition mechanisms of peptide inhibitors. © 2015 Wiley Periodicals, Inc.

Reactive molecular simulation on the calcium silicate hydrates/polyethylene glycol composites

NASA Astrophysics Data System (ADS)

Zhou, Yang; Hou, Dongshuai; Jiang, Jinyang; She, Wei; Yu, Jiao

2017-11-01

Calcium silicate hydrates (C-S-H) may potentially exhibit extraordinary performance when modified by polymers, in which way the properties of cement-based materials can be improved from the genetic level. In this molecular dynamics simulation of the interaction between C-S-H and polyethylene glycol, apart from the H bond network connection in the interface, another chemical adsorption was observed. Calcium of C-S-H broke the Csbnd O bond of PEG and formed a new Casbnd C connection, which created a stronger link between the organic and inorganic phases.

Catalytic alkylation of remote C-H bonds enabled by proton-coupled electron transfer

NASA Astrophysics Data System (ADS)

Choi, Gilbert J.; Zhu, Qilei; Miller, David C.; Gu, Carol J.; Knowles, Robert R.

2016-11-01

Despite advances in hydrogen atom transfer (HAT) catalysis, there are currently no molecular HAT catalysts that are capable of homolysing the strong nitrogen-hydrogen (N-H) bonds of N-alkyl amides. The motivation to develop amide homolysis protocols stems from the utility of the resultant amidyl radicals, which are involved in various synthetically useful transformations, including olefin amination and directed carbon-hydrogen (C-H) bond functionalization. In the latter process—a subset of the classical Hofmann-Löffler-Freytag reaction—amidyl radicals remove hydrogen atoms from unactivated aliphatic C-H bonds. Although powerful, these transformations typically require oxidative N-prefunctionalization of the amide starting materials to achieve efficient amidyl generation. Moreover, because these N-activating groups are often incorporated into the final products, these methods are generally not amenable to the direct construction of carbon-carbon (C-C) bonds. Here we report an approach that overcomes these limitations by homolysing the N-H bonds of N-alkyl amides via proton-coupled electron transfer. In this protocol, an excited-state iridium photocatalyst and a weak phosphate base cooperatively serve to remove both a proton and an electron from an amide substrate in a concerted elementary step. The resultant amidyl radical intermediates are shown to promote subsequent C-H abstraction and radical alkylation steps. This C-H alkylation represents a catalytic variant of the Hofmann-Löffler-Freytag reaction, using simple, unfunctionalized amides to direct the formation of new C-C bonds. Given the prevalence of amides in pharmaceuticals and natural products, we anticipate that this method will simplify the synthesis and structural elaboration of amine-containing targets. Moreover, this study demonstrates that concerted proton-coupled electron transfer can enable homolytic activation of common organic functional groups that are energetically inaccessible using traditional HAT-based approaches.

Catalytic alkylation of remote C-H bonds enabled by proton-coupled electron transfer.

PubMed

Choi, Gilbert J; Zhu, Qilei; Miller, David C; Gu, Carol J; Knowles, Robert R

2016-11-10

Despite advances in hydrogen atom transfer (HAT) catalysis, there are currently no molecular HAT catalysts that are capable of homolysing the strong nitrogen-hydrogen (N-H) bonds of N-alkyl amides. The motivation to develop amide homolysis protocols stems from the utility of the resultant amidyl radicals, which are involved in various synthetically useful transformations, including olefin amination and directed carbon-hydrogen (C-H) bond functionalization. In the latter process-a subset of the classical Hofmann-Löffler-Freytag reaction-amidyl radicals remove hydrogen atoms from unactivated aliphatic C-H bonds. Although powerful, these transformations typically require oxidative N-prefunctionalization of the amide starting materials to achieve efficient amidyl generation. Moreover, because these N-activating groups are often incorporated into the final products, these methods are generally not amenable to the direct construction of carbon-carbon (C-C) bonds. Here we report an approach that overcomes these limitations by homolysing the N-H bonds of N-alkyl amides via proton-coupled electron transfer. In this protocol, an excited-state iridium photocatalyst and a weak phosphate base cooperatively serve to remove both a proton and an electron from an amide substrate in a concerted elementary step. The resultant amidyl radical intermediates are shown to promote subsequent C-H abstraction and radical alkylation steps. This C-H alkylation represents a catalytic variant of the Hofmann-Löffler-Freytag reaction, using simple, unfunctionalized amides to direct the formation of new C-C bonds. Given the prevalence of amides in pharmaceuticals and natural products, we anticipate that this method will simplify the synthesis and structural elaboration of amine-containing targets. Moreover, this study demonstrates that concerted proton-coupled electron transfer can enable homolytic activation of common organic functional groups that are energetically inaccessible using traditional HAT-based approaches.

Efficient photocatalytic selective nitro-reduction and C-H bond oxidation over ultrathin sheet mediated CdS flowers.

PubMed

Pahari, Sandip Kumar; Pal, Provas; Srivastava, Divesh N; Ghosh, Subhash Ch; Panda, Asit Baran

2015-06-28

We report here a visible light driven selective nitro-reduction and oxidation of saturated sp(3) C-H bonds using ultrathin (0.8 nm) sheet mediated uniform CdS flowers as catalyst under a household 40 W CFL lamp and molecular oxygen as oxidant. The CdS flowers were synthesized using a simple surfactant assisted hydrothermal method.

13C and 19F solid-state NMR and X-ray crystallographic study of halogen-bonded frameworks featuring nitrogen-containing heterocycles.

PubMed

Szell, Patrick M J; Gabriel, Shaina A; Gill, Russell D D; Wan, Shirley Y H; Gabidullin, Bulat; Bryce, David L

2017-03-01

Halogen bonding is a noncovalent interaction between the electrophilic region of a halogen (σ-hole) and an electron donor. We report a crystallographic and structural analysis of halogen-bonded compounds by applying a combined X-ray diffraction (XRD) and solid-state nuclear magnetic resonance (SSNMR) approach. Single-crystal XRD was first used to characterize the halogen-bonded cocrystals formed between two fluorinated halogen-bond donors (1,4-diiodotetrafluorobenzene and 1,3,5-trifluoro-2,4,6-triiodobenzene) and several nitrogen-containing heterocycles (acridine, 1,10-phenanthroline, 2,3,5,6-tetramethylpyrazine, and hexamethylenetetramine). New structures are reported for the following three cocrystals, all in the P2 1 /c space group: acridine-1,3,5-trifluoro-2,4,6-triiodobenzene (1/1), C 6 F 3 I 3 ·C 13 H 9 N, 1,10-phenanthroline-1,3,5-trifluoro-2,4,6-triiodobenzene (1/1), C 6 F 3 I 3 ·C 12 H 8 N 2 , and 2,3,5,6-tetramethylpyrazine-1,3,5-trifluoro-2,4,6-triiodobenzene (1/1), C 6 F 3 I 3 ·C 8 H 12 N 2 . 13 C and 19 F solid-state magic-angle spinning (MAS) NMR is shown to be a convenient method to characterize the structural features of the halogen-bond donor and acceptor, with chemical shifts attributable to cocrystal formation observed in the spectra of both nuclides. Cross polarization (CP) from 19 F to 13 C results in improved spectral sensitivity in characterizing the perfluorinated halogen-bond donor when compared to conventional 1 H CP. Gauge-including projector-augmented wave density functional theory (GIPAW DFT) calculations of magnetic shielding constants, along with optimization of the XRD structures, provide a final set of structures in best agreement with the experimental 13 C and 19 F chemical shifts. Data for carbons bonded to iodine remain outliers due to well-known relativistic effects.

The triel bond: a potential force for tuning anion-π interactions

NASA Astrophysics Data System (ADS)

Esrafili, Mehdi D.; Mousavian, Parisasadat

2018-02-01

Using ab-initio calculations, the mutual influence between anion-π and B···N or B···C triel bond interactions is investigated in some model complexes. The properties of these complexes are studied by molecular electrostatic potential, noncovalent interaction index, quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analyses. According to the results, the formation of B···N or B···C triel bond interactions in the multi-component systems makes a significant shortening of anion-π distance. Such remarkable variation in the anion-π distances has not been reported previously. The strengthening of the anion-π bonding in the multi-component systems depend significantly on the nature of the anion, and it becomes larger in the order Br- > Cl- > F-. The parameters derived from the QTAIM and NBO methodologies are used to study the mechanism of the cooperativity between the anion-π and triel bond interactions in the multi-component complexes.

Copper-containing monooxygenases: enzymatic and biomimetic studies of the O-atom transfer catalysis.

PubMed

Blain, Ingrid; Slama, Patrick; Giorgi, Michel; Tron, Thierry; Réglier, Marius

2002-04-01

This review reports our recent studies or the mechanism of O-atom transfer to a benzylic C-H bond promoted by Dopamine beta-Hydroxylase (DBH) and its biomimetic models. We demonstrate that it is possible to carry out parallel and comparative studies on this enzyme (DBH) and its biomimetic models with the same substrate: 2-aminoindane (3). It was chosen because its two stereogenic centers, both in benzylic positions, make it very powerful for studying the stereochemistry of an O-atom transfer reaction. DBH-catalyzed hydroxylation of 3 produced exclusively 14% of trans-(1S,2S)-2-amino-1-indanol (4) (93% ee). Studies with stereospecifically deuterium-labeled 2-aminoindanes (1R,2S)-3b and (1S,2S)-3a showed that the formation of 4 was the rcsult of an overall process with retention of configuration where an O-atom is stereospecifically inserted in the trans pro-S position of the substrate. With copper(I) and (II) complexes of IndPY2 ligands we studied the reaction with dioxygen and observed an O-atom transfer to a benzylic C-H bond which was performed in the same manner as that of DBH. With the deuterium-labeled cis-2-d-IndPY2 ligand, we demonstrated that the reaction occurs by a stereospecific process with retention of configuration. In both cases (enzymatic vs. biomimetic) the O-atom transfers occur in a two-step process involving radical intermediates.

Theoretical Study on the Catalytic Reduction Mechanism of NO by CO on Tetrahedral Rh4 Subnanocluster.

PubMed

Yang, Hua-Qing; Fu, Hong-Quan; Su, Ben-Fang; Xiang, Bo; Xu, Qian-Qian; Hu, Chang-Wei

2015-11-25

The catalytic mechanism of 2NO + 2CO → N2 + 2CO2 on Rh4 cluster has been systematically investigated on the ground and first excited states at the B3LYP/6-311+G(2d),SDD level. For the overall reaction of 2NO + 2CO → N2 + 2CO2, the main reaction pathways take place on the facet site rather than the edge site of the Rh4 cluster. The turnover frequency (TOF) determining transition states are characteristic of the second N-O bond cleavage with rate constant k4 = 1.403 × 10(11) exp (-181 203/RT) and the N-N bond formation for the intermediate N2O formation with rate constant k2 = 3.762 × 10(12) exp (-207 817/RT). The TOF-determining intermediates of (3)N(b)Rh4NO and (3)N(b)Rh4O(b)(NO) are associated with the nitrogen-atom molecular complex, which is in agreement with the experimental observation of surface nitrogen. On the facet site of Rh4 cluster, the formation of CO2 stems solely from the recombination of CO and O atom, while N2 originates partly from the recombination of two N atoms and partly from the decomposition of N2O. For the N-O bond cleavage or the synchronous N-O bond cleavage and C-O bond formation, the neutral Rh4 cluster exhibits better catalytic performance than the cationic Rh4(+) cluster. Alternatively, for N-N bond formation, the cationic Rh4(+) cluster possesses better catalytic performance than the neutral Rh4 cluster.

Picolinic and isonicotinic acids: a Fourier transform microwave spectroscopy study.

PubMed

Peña, Isabel; Varela, Marcelino; Franco, Vanina G; López, Juan C; Cabezas, Carlos; Alonso, José L

2014-12-04

The rotational spectra of laser ablated picolinic and isonicotinic acids have been studied using broadband chirped pulse (CP-FTMW) and narrowband molecular beam (MB-FTMW) Fourier transform microwave spectroscopies. Two conformers of picolinic acid, s-cis-I and s-cis-II, and one conformer of isonicotinic acid have been identified through the analysis of their rotational spectra. The values of the inertial defect and the quadrupole coupling constants obtained for the most stable s-cis-I conformer of picolinic acid, evidence the formation of an O-H···N hydrogen bond between the acid group and the endocyclic N atom. The stabilization provided by this hydrogen bond compensates the destabilization energy due to the adoption of a -COOH trans configuration in this conformer. Its rs structure has been derived from the rotational spectra of several (13)C, (15)N, and (18)O species observed in their natural abundances. Mesomeric effects have been revealed by comparing the experimental values of the (14)N nuclear quadrupole coupling constants in the isomeric series of picolinic, isonicotinic, and nicotinic acids.

A theoretical study of the hydrogen bonding between the vic-, cis- and trans-C 2H 2F 2 isomers and hydrogen fluoride

NASA Astrophysics Data System (ADS)

Rusu, Victor H.; da Silva, João Bosco P.; Ramos, Mozart N.

2009-04-01

MP2/6-31++G(d,p) and B3LYP/6-31++G(d,p) theoretical calculations have been employed to investigate the hydrogen bonding formation involving the vic-, cis- and trans-C 2H 2F 2 isomers and hydrogen fluoride. Our calculations have revealed for each isomer the preferential existence of two possible hydrogen-bonded complexes: a non-cyclic complex and a cyclic complex. For all the three isomers the binding energies for the non-cyclic and cyclic hydrogen complexes are essentially equal using both the MP2 and B3LYP calculations, being that the cyclic structure is slightly more stable. For instance, the binding energies including BSSE and ZPE corrections for the non-cyclic and cyclic structures of cis-C 2H 2F···HF are 8.7 and 9.0 kJ mol -1, respectively, using B3LYP calculations. The cyclic complex formation reduces the polarity, in contrast to what occurs with the non-cyclic complex. This result is more accentuated in vic-C 2H 2F 2···HF. In this latter, Δ μ(cyclic) is -3.07 D, whereas Δ μ(non-cyclic) is +1.92 D using B3LYP calculations. Their corresponding MP2 values are +0.44 D and -1.89 D, respectively. As expected, the complexation produces an H sbnd F stretching frequency downward shift, whereas its IR intensity is enhanced. On the other hand, the vibrational modes of the vic-, cis- and trans-C 2H 2F 2 isomers are little affected by complexation. The new vibrational modes due to hydrogen bonding formation show several interesting features, in particular the HF bending modes which are pure rotations in the free molecule.

Organic Compounds Produced by Photolysis of Realistic Interstellar and Cometary Ice Analogs Containing Methanol

NASA Technical Reports Server (NTRS)

Bernstein, Max P.; Sandford, Scott A.; Allamandola, Louis J.; Chang, Sherwood; Scharberg, Maureen A.

1995-01-01

The InfraRed (IR) spectra of UltraViolet (UV) and thermally processed, methanol-containing interstellar / cometary ice analogs at temperatures from 12 to 300 K are presented. Infrared spectroscopy, H-1 and C-13 Nuclear Magnetic Resonance (NMR) spectroscopy, and gas chromatography-mass spectrometry indicate that CO (carbon monoxide), CO2 (carbon dioxide), CH4 (methane), HCO (the formyl radical), H2CO (formaldehyde), CH3CH2OH (ethanol), HC([double bond]O)NH2 (formamide), CH3C([double bond]O)NH2 (acetamide), and R[single bond]C[triple bond]N (nitriles) are formed. In addition, the organic materials remaining after photolyzed ice analogs have been warmed to room temperature contain (in rough order of decreasing abundance), (1) hexamethylenetetramine (HMT, C6H12N4), (2) ethers, alcohols, and compounds related to PolyOxyMethylene (POM, ([single bond]CH2O[single bond](sub n)), and (3) ketones (R[single bond]C([double bond]O)[single bond]R') and amides (H2NC([double bond]O)[single bond]R). Most of the carbon in these residues is thought to come from the methanol in the original ice. Deuterium and C-13 isotopic labeling demonstrates that methanol is definitely the source of carbon in HMT. High concentrations of HMT in interstellar and cometary ices could have important astrophysical consequences. The ultraviolet photolysis of HMT frozen in H2O ice readily produces the 'XCN' band observed in the spectra of protostellar objects and laboratory ices, as well as other nitriles. Thus, HMT may be a precursor of XCN and a source of CN in comets and the interstellar medium. Also, HMT is known to hydrolyze under acidic conditions to yield ammonia, formaldehyde, and amino acids. Thus, HMT may be a significant source of prebiogenic compounds on asteroidal parent bodies. A potential mechanism for the radiative formation of HMT in cosmic ices is outlined.

Exploration and exploitation of homologous series of bis(acrylamido)alkanes containing pyridyl and phenyl groups: β-sheet versus two-dimensional layers in solid-state photochemical [2 + 2] reactions.

PubMed

Garai, Mousumi; Biradha, Kumar

2015-09-01

The homologous series of phenyl and pyridyl substituted bis(acrylamido)alkanes have been synthesized with the aim of systematic analysis of their crystal structures and their solid-state [2 + 2] reactivities. The changes in the crystal structures with respect to a small change in the molecular structure, that is by varying alkyl spacers between acrylamides and/or by varying the end groups (phenyl, 2-pyridyl, 3-pyridyl, 4-pyridyl) on the C-terminal of the amide, were analyzed in terms of hydrogen-bonding interference (N-H⋯Npy versus N-H⋯O=C) and network geometries. In this series, a greater tendency towards the formation of N-H⋯O hydrogen bonds (β-sheets and two-dimensional networks) over N-H⋯N hydrogen bonds was observed. Among all the structures seven structures were found to have the required alignments of double bonds for the [2 + 2] reaction such that the formations of single dimer, double dimer and polymer are facilitated. However, only four structures were found to exhibit such a solid-state [2 + 2] reaction to form a single dimer and polymers. The two-dimensional hydrogen-bonding layer via N-H⋯O hydrogen bonds was found to promote solid-state [2 + 2] photo-polymerization in a single-crystal-to-single-crystal manner. Such two-dimensional layers were encountered only when the spacer between acryl amide moieties is butyl. Only four out of the 16 derivatives were found to form hydrates, two each from 2-pyridyl and 4-pyridyl derivatives. The water molecules in these structures govern the hydrogen-bonding networks by the formation of an octameric water cluster and one-dimensional zigzag water chains. The trends in the melting points and densities were also analyzed.

Substrate-Triggered Formation and Remarkable Stability of the C-H-Cleaving Chloroferryl Intermediate in the Aliphatic Halogenase, SyrB2†

PubMed Central

Matthews, Megan L.; Krest, Courtney M.; Barr, Eric W.; Vaillancourt, Frédéric H.; Walsh, Christopher T.; Green, Michael T.; Krebs, Carsten; Bollinger, J. Martin

2009-01-01

Aliphatic halogenases activate O2, cleave α-ketoglutarate (αKG) to CO2 and succinate, and form haloferryl [X-Fe(IV)=O; X = Cl, Br] complexes that cleave aliphatic C-H bonds to install halogens during the biosynthesis of natural products by non-ribosomal peptide synthetases (NRPSs). For the related αKG-dependent dioxygenases, it has been shown that reaction of the Fe(II) cofactor with O2 to form the C-H-cleaving ferryl complex is “triggered” by binding of the target substrate. In this study, we have tested for and defined structural determinants of substrate triggering (ST) in the halogenase, SyrB2, from the syringomycin E biosynthetic NRPS of Pseudomonas syringae B301D. As for other halogen ases, the substrate of SyrB2 is complex, consisting of l-Thr tethered via thioester linkage to a covalently bound phosphopantetheine (PPant) cofactor of a carrier protein, SyrB1. Without an appended amino acid, SyrB1 does not trigger formation of the chloroferryl intermediate state in SyrB2, even in the presence of free l-Thr or its analogues, but SyrB1 charged either by l-Thr or by any of several non-native amino acids does trigger the reaction by as much as 8,000-fold (for l-Thr-S-SyrB1). Triggering efficacy is sensitive to the structures of both the amino acid and the carrier protein, being diminished by 5–20-fold when the native l-Thr is replaced by another amino acid and by ∼ 40-fold when SyrB1 is replaced by a heterologous carrier protein, CytC2. The directing effect of the carrier protein and consequent tolerance for profound modifications to the target amino acid allow the chloroferryl state to be formed in the presence of substrates that perturb the ratio of its two putative coordination isomers, lack the target C-H bond (l-Ala-S-SyrB1), or contain a C-H bond of enhanced strength (l-cyclopropylglycyl-S-SyrB1). For the latter two cases, the SyrB2 chloroferryl state so formed exhibits unprecedented stability (t1/2 = 30 – 110 min at 0 °C), can be trapped in high concentration and purity by manual freezing without a cryo-solvent, and represents an ideal target for structural characterization. As initial steps toward this goal, extended x-ray absorption fine structure (EXAFS) spectroscopy has been used to determine the Fe-O and Fe-Cl distances and density functional theory (DFT) calculations have been used to confirm that the measured distances are consistent with the anticipated structure of the intermediate. PMID:19245217

Potent and selective inhibitors of 11β-hydroxysteroid dehydrogenase type 1 labeled with carbon-13 and carbon-14.

PubMed

Latli, Bachir; Hrapchak, Matt; Savoie, Jolaine; Zhan, Yongda; Busacca, Carl A; Senanayake, Chris H

2017-07-01

(S)-6-(2-Hydroxy-2-methylpropyl)-3-((S)-1-(4-(1-methyl-2-oxo-1,2-dihydropyridin-4-yl)phenyl)ethyl)-6-phenyl-1,3-oxazinan-2-one (1) and (4aR,9aS)-1-(1H-benzo[d]midazole-5-carbonyl)-2,3,4,4a,9,9a-hexahydro-1-H-indeno[2,1-b]pyridine-6-carbonitrile hydrochloride (2) are potent and selective inhibitor of 11β-hydroxysteroid dehydrogenase type 1 enzyme. These 2 drug candidates developed for the treatment of type-2 diabetes were prepared labeled with carbon-13 and carbon-14 to enable drug metabolism, pharmacokinetics, bioanalytical, and other studies. In the carbon-13 synthesis, benzoic- 13 C 6 acid was converted in 7 steps and in 16% overall yield to [ 13 C 6 ]-(1). Aniline- 13 C 6 was converted in 7 steps to 1H-benzimidazole-1-2,3,4,5,6- 13 C 6 -5-carboxylic acid and then coupled to a tricyclic chiral indenopiperidine to afford [ 13 C 6 ]-(2) in 19% overall yield. The carbon-14 labeled (1) was prepared efficiently in 2 radioactive steps in 41% overall yield from an advanced intermediate using carbon-14 labeled methyl magnesium iodide and Suzuki-Miyaura cross coupling via in situ boronate formation. As for the synthesis of [ 14 C]-(2), 1H-benzimidazole-5-carboxylic- 14 C acid was first prepared in 4 steps using potassium cyanide- 14 C, then coupled to the chiral indenopiperidine using amide bond formation conditions in 26% overall yield. Copyright © 2017 John Wiley & Sons, Ltd.

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.

Counteranion Driven Homochiral Assembly of a Cationic C3-Symmetric Gelator through Ion-Pair Assisted Hydrogen Bond.

PubMed

Maity, Arunava; Gangopadhyay, Monalisa; Basu, Arghya; Aute, Sunil; Babu, Sukumaran Santhosh; Das, Amitava

2016-09-07

The helical handedness in achiral self-assemblies is mostly complex due to spontaneous symmetry breaking or kinetically controlled random assembly formation. Here an attempt has been made to address this issue through chiral anion exchange. A new class of cationic achiral C3-symmetric gelator devoid of any conventional gelation assisting functional units is found to form both right- and left-handed helical structures. A chiral counteranion exchange-assisted approach is successfully introduced to control the chirality sign and thereby to obtain preferred homochiral assemblies. Formation of anion-assisted chiral assembly was confirmed by circular dichroism (CD) spectroscopy, microscopic images, and crystal structure. The X-ray crystal structure reveals the construction of helical assemblies with opposite handedness for (+)- and (-)-chiral anion reformed gelators. The appropriate counteranion driven ion-pair-assisted hydrogen-bonding interactions are found responsible for the helical bias control in this C3-symmetric gelator.

Crystal structure of N′′-benzyl-N′′-[3-(benzyl­dimethyl­aza­nium­yl)prop­yl]-N,N,N′,N′-tetra­methyl­guanidinium bis­(tetra­phenyl­borate)

PubMed Central

Tiritiris, Ioannis; Kantlehner, Willi

2015-01-01

In the crystal structure of the title salt, C24H38N4 2+·2C24H20B−, the C—N bond lengths in the central CN3 unit of the guanidinium ion are 1.3364 (13), 1.3407 (13) and 1.3539 (13) Å, indicating partial double-bond character. The central C atom is bonded to the three N atoms in a nearly ideal trigonal–planar geometry and the positive charge is delocalized in the CN3 plane. The bonds between the N atoms and the terminal methyl groups of the guanidinium moiety and the four C—N bonds to the central N atom of the (benzyl­dimethyl­aza­nium­yl)propyl group have single-bond character. In the crystal, C—H⋯π inter­actions between the guanidin­ium H atoms and the phenyl C atoms of the tetra­phenyl­borate ions are present, leading to the formation of a two-dimensional supra­molecular pattern parallel to the ac plane. PMID:26870511

On the mechanism of the palladium catalyzed intramolecular Pauson-Khand-type reaction.

PubMed

Lan, Yu; Deng, Lujiang; Liu, Jing; Wang, Can; Wiest, Olaf; Yang, Zhen; Wu, Yun-Dong

2009-07-17

Density functional theory calculations and experimental studies have been carried out on the intramolecular Pauson-Khand-Type reaction mediated by a PdCl(2)-thiourea catalyst, which proceeds under mild reaction conditions and provides a useful alternative to traditional Pauson-Khand reactions. The classical mechanism of the Pauson-Khand reaction involving the alkyne/alkene C-C bond formation as the key step has been found to be energetically unfavorable and is not in line with the experimental observations. A novel reaction mechanism has been proposed for the reaction. The first step involves the cis-halometalation of the alkyne, followed by sequential alkene and carbonyl insertion. The rate-determining fourth step is an intramolecular C-Cl oxidative addition, leading to a Pd(IV) intermediate. A C-C bond formation by reductive elimination completes the reaction. The mechanism is in agreement with the key experimental observations including (1) the need of a chloride for catalytic activity and the absence of catalysis with Pd(OAc)(2) alone; (2) the rate acceleration by the addition of LiCl; both with PdCl(2) and Pd(OAc)(2) catalysts; and (3) the preferred formation of the trans diastereomer in substituted cases. The cis halometalation and the formation and stability of the Pd(IV) intermediate is studied in detail and provides general insights into these novel steps.

Studies on the regioselectivity and kinetics of the action of trypsin on proinsulin and its derivatives using mass spectrometry.

PubMed

Gardner, Qurra-tul-Ann Afza; Younas, Hooria; Akhtar, Muhammad

2013-01-01

Human M-proinsulin was cleaved by trypsin at the R(31)R(32)-E(33) and K(64)R(65)-G(66) bonds (B/C and C/A junctions), showing the same cleavage specificity as exhibited by prohormone convertases 1 and 2 respectively. Buffalo/bovine M-proinsulin was also cleaved by trypsin at the K(59)R(60)-G(61) bond but at the B/C junction cleavage occurred at the R(31)R(32)-E(33) as well as the R(31)-R(32)E(33) bond. Thus, the human isoform in the native state, with a 31 residue connecting C-peptide, seems to have a unique structure around the B/C and C/A junctions and cleavage at these sites is predominantly governed by the structure of the proinsulin itself. In the case of both the proinsulin species the cleavage at the B/C junction was preferred (65%) over that at the C/A junction (35%) supporting the earlier suggestion of the presence of some form of secondary structure at the C/A junction. Proinsulin and its derivatives, as natural substrates for trypsin, were used and mass spectrometric analysis showed that the k(cat.)/K(m) values for the cleavage were most favourable for the scission of the bonds at the two junctions (1.02±0.08×10(5)s(-1)M(-1)) and the cleavage of the K(29)-T(30) bond of M-insulin-RR (1.3±0.07×10(5)s(-1)M(-1)). However, the K(29)-T(30) bond in M-insulin, insulin as well as M-proinsulin was shielded from attack by trypsin (k(cat.)/K(m) values around 1000s(-1)M(-1)). Hence, as the biosynthetic path follows the sequence; proinsulin→insulin-RR→insulin, the K(29)-T(30) bond becomes shielded, exposed then shielded again respectively. Copyright © 2012 Elsevier B.V. All rights reserved.

Low temperature InP /Si wafer bonding using boride treated surface

NASA Astrophysics Data System (ADS)

Huang, Hui; Ren, Xiaomin; Wang, Wenjuan; Song, Hailan; Wang, Qi; Cai, Shiwei; Huang, Yongqing

2007-04-01

An approach for InP /Si wafer bonding based on boride-solution treatment was presented. The bonding energy is higher than the InP fracture energy by annealing at 280°C. An In0.53Ga0.47As/InP multiple-quantum-well (MQW) structure grown on InP was transferred onto Si substrate via the bonding process. X-ray diffraction and photoluminescence reveal that crystal quality of the bonded MQW was preserved. A thin B2O3-POx-SiO2 oxide layer of about 28nm thick at the bonding interface was detected. X-ray photoelectron spectroscopy and Raman analyses indicate that the formation of oxygen bridging bonds by boride treatment is responsible for the strong fusion obtained at such low temperature.

31 CFR 315.27 - Application for relief-nonreceipt of bond.

Code of Federal Regulations, 2010 CFR

2010-07-01

... (Continued) FISCAL SERVICE, DEPARTMENT OF THE TREASURY BUREAU OF THE PUBLIC DEBT REGULATIONS GOVERNING U.S. SAVINGS BONDS, SERIES A, B, C, D, E, F, G, H, J, AND K, AND U.S. SAVINGS NOTES Relief for Loss, Theft... bearing the same issue date as the bond that was not received. ...

31 CFR 315.27 - Application for relief-nonreceipt of bond.

Code of Federal Regulations, 2014 CFR

2014-07-01

... (Continued) FISCAL SERVICE, DEPARTMENT OF THE TREASURY BUREAU OF THE FISCAL SERVICE REGULATIONS GOVERNING U.S. SAVINGS BONDS, SERIES A, B, C, D, E, F, G, H, J, AND K, AND U.S. SAVINGS NOTES Relief for Loss, Theft... bearing the same issue date as the bond that was not received. ...

31 CFR 315.27 - Application for relief-nonreceipt of bond.

Code of Federal Regulations, 2012 CFR

2012-07-01

... (Continued) FISCAL SERVICE, DEPARTMENT OF THE TREASURY BUREAU OF THE PUBLIC DEBT REGULATIONS GOVERNING U.S. SAVINGS BONDS, SERIES A, B, C, D, E, F, G, H, J, AND K, AND U.S. SAVINGS NOTES Relief for Loss, Theft... bearing the same issue date as the bond that was not received. ...

31 CFR 315.27 - Application for relief-nonreceipt of bond.

Code of Federal Regulations, 2011 CFR

2011-07-01

... (Continued) FISCAL SERVICE, DEPARTMENT OF THE TREASURY BUREAU OF THE PUBLIC DEBT REGULATIONS GOVERNING U.S. SAVINGS BONDS, SERIES A, B, C, D, E, F, G, H, J, AND K, AND U.S. SAVINGS NOTES Relief for Loss, Theft... bearing the same issue date as the bond that was not received. ...

31 CFR 315.27 - Application for relief-nonreceipt of bond.

Code of Federal Regulations, 2013 CFR

2013-07-01

... (Continued) FISCAL SERVICE, DEPARTMENT OF THE TREASURY BUREAU OF THE PUBLIC DEBT REGULATIONS GOVERNING U.S. SAVINGS BONDS, SERIES A, B, C, D, E, F, G, H, J, AND K, AND U.S. SAVINGS NOTES Relief for Loss, Theft... bearing the same issue date as the bond that was not received. ...

31 CFR 315.2 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-07-01

..., DEPARTMENT OF THE TREASURY BUREAU OF THE PUBLIC DEBT REGULATIONS GOVERNING U.S. SAVINGS BONDS, SERIES A, B, C, D, E, F, G, H, J, AND K, AND U.S. SAVINGS NOTES General Information § 315.2 Definitions. As used in... the context indicates otherwise. General references to bonds and direct references to Series E bonds...

Structural insights into the interactions of phorbol ester and bryostatin complexed with protein kinase C: a comparative molecular dynamics simulation study.

PubMed

Thangsunan, Patcharapong; Tateing, Suriya; Hannongbua, Supa; Suree, Nuttee

2016-07-01

Protein kinase C (PKC) isozymes are important regulatory enzymes that have been implicated in many diseases, including cancer, Alzheimer's disease, and in the eradication of HIV/AIDS. Given their potential clinical ramifications, PKC modulators, e.g. phorbol esters and bryostatin, are also of great interest in the drug development. However, structural details on the binding between PKC and its modulators, especially bryostatin - the highly potent and non-tumor promoting activator for PKCs, are still lacking. Here, we report the first comparative molecular dynamics study aimed at gaining structural insight into the mechanisms by which the PKC delta cys2 activator domain is used in its binding to phorbol ester and bryostatin-1. As anticipated in the phorbol ester binding, hydrogen bonds are formed through the backbone atoms of Thr242, Leu251, and Gly253 of PKC. However, the opposition of H-bond formation between Thr242 and Gly253 may cause the phorbol ester complex to become less stable when compared with the bryostatin binding. For the PKC delta-bryostatin complex, hydrogen bonds are formed between the Gly253 backbone carbonyl and the C30 carbomethoxy substituent of the ligand. Additionally, the indole Nε1 of the highly homologous Trp252 also forms an H-bond to the C20 ester group on bryostatin. Backbone fluctuations also suggest that this latter H-bond formation may abrogate the transient interaction between Trp252 and His269, thus dampening the fluctuations observed on the nearby Zn(2+)-coordinating residues. This new dynamic fluctuation dampening model can potentially benefit future design of new PKC modulators.

Apatite-forming PEEK with TiO2 surface layer coating.

PubMed

Kizuki, Takashi; Matsushita, Tomiharu; Kokubo, Tadashi

2015-01-01

Polyetheretherketone (PEEK) is widely used in orthopedic implants, such as spinal fusion devices, because of its moderate elastic modulus, as well as relatively high mechanical strength. However, it does not bond to living bone, and hence it needs autograft to be fixed to the bone. In this study, we attempted to add bone-bonding properties to PEEK by coating with TiO2 synthesized by the sol-gel process. When a TiO2 sol solution consisting of titanium isopropoxide, water, ethanol, and nitric acid was deposited on a PEEK substrate without any pretreatment, the formed TiO2 gel layer was easily peeled off after subsequent treatments. However, when the same solution was deposited on PEEK that was preliminarily subjected to UV or O2 plasma treatment, the deposited TiO2 gel layer strongly adhered to the substrate even after subsequent treatments. The strong adhesion was attributed to the interaction among the C-O, C=O, and O-C=O groups on the PEEK owing to the UV or O2 plasma treatment and the Ti-O bond of the TiO2 gel. Apatite did not form on the as-formed TiO2 gel layer in a simulated body fluid (SBF) even within 3 days; however, apatite formed after soaking in 0.1 M HCl solution at 80 °C for 24 h. This apatite formation was attributed to positive surface charge of the TiO2 gel layer induced by the acid treatment. The PEEK with the TiO2 gel layer coating formed by the proposed process is expected to bond to living bone, because a positively charged titanium oxide which facilitates the formation of apatite in SBF within a short period is known to bond to living bone.

Selectin catch-bonds mechanotransduce integrin activation and neutrophil arrest on inflamed endothelium under shear flow.

PubMed

Morikis, Vasilios A; Chase, Shannon; Wun, Ted; Chaikof, Elliot L; Magnani, John L; Simon, Scott I

2017-11-09

E-selectin extends from the plasma membrane of inflamed endothelium and serves to capture leukocytes from flowing blood via long-lived catch-bonds that support slow leukocyte rolling under shear stress. Its ligands are glycosylated with the tetrasaccharide sialyl Lewis x (sLe x ), which contributes to bond affinity and specificity. E-selectin-mediated rolling transmits signals into neutrophils that trigger activation of high-affinity β 2 -integrins necessary for transition to shear-resistant adhesion and transendothelial migration. Rivipansel is a glycomimetic drug that inhibits E-selectin-mediated vaso-occlusion induced by integrin-dependent sickle-red blood cell-leukocyte adhesion. How Rivipansel antagonizes ligand recognition by E-selectin and blocks outside-in signaling of integrin-mediated neutrophil arrest while maintaining rolling immune-surveillance is unknown. Here, we demonstrate that sLe x expressed on human L-selectin is preferentially bound by E-selectin and, on ligation, initiates secretion of MRP8/14 that binds TLR4 to elicit the extension of β 2 -integrin to an intermediate affinity state. Neutrophil rolling over E-selectin at precise shear stress transmits tension and catch-bond formation with L-selectin via sLe x , resulting in focal clusters that deliver a distinct signal to upshift β 2 -integrins to a high-affinity state. Rivipansel effectively blocked formation of selectin catch-bonds, revealing a novel mechanotransduction circuit that rapidly converts extended β 2 -integrins to high-affinity shear-resistant bond clusters with intracellular adhesion molecule 1 on inflamed endothelium.

High-Level ab Initio Predictions for the Ionization Energies, Bond Dissociation Energies, and Heats of Formation of Titanium Oxides and Their Cations (TiOn/TiOn+, n = 1 and 2).

PubMed

Pan, Yi; Luo, Zhihong; Chang, Yih-Chung; Lau, Kai-Chung; Ng, C Y

2017-01-26

The ionization energies (IEs) of TiO and TiO 2 and the 0 K bond dissociation energies (D 0 ) and the heats of formation at 0 K (ΔH° f0 ) and 298 K (ΔH° f298 ) for TiO/TiO + and TiO 2 /TiO 2 + are predicted by the wave-function-based CCSDTQ/CBS approach. The CCSDTQ/CBS calculations involve the approximation to the complete basis set (CBS) limit at the coupled cluster level up to full quadruple excitations along with the zero-point vibrational energy (ZPVE), high-order correlation (HOC), core-valence (CV) electronic, spin-orbit (SO) coupling, and scalar relativistic (SR) effect corrections. The present calculations yield IE(TiO) = 6.815 eV and are in good agreement with the experimental IE value of 6.819 80 ± 0.000 10 eV determined in a two-color laser-pulsed field ionization-photoelectron (PFI-PE) study. The CCSDT and MRCI+Q methods give the best predictions to the harmonic frequencies: ω e (ω e + ) = 1013 (1069) and 1027 (1059) cm -1 and the bond lengths r e (r e + ) = 1.625 (1.587) and 1.621 (1.588) Å, for TiO (TiO + ) compared with the experimental values. Two nearly degenerate, stable structures are found for TiO 2 cation: TiO 2 + (C 2v ) structure has two equivalent TiO bonds, while the TiO 2 + (C s ) structure features a long and a short TiO bond. The IEs for the TiO 2 + (C 2v )←TiO 2 and TiO 2 + (C s )←TiO 2 ionization transitions are calculated to be 9.515 and 9.525 eV, respectively, giving the theoretical adiabatic IE value in good agreement with the experiment IE(TiO 2 ) = 9.573 55 ± 0.000 15 eV obtained in the previous vacuum ultraviolet (VUV)-PFI-PE study of TiO 2 . The potential energy surface of TiO 2 + along the normal vibrational coordinates of asymmetric stretching mode (ω 3 + ) is nearly flat and exhibits a double-well potential with the well of TiO 2 + (C s ) situated around the central well of TiO 2 + (C 2v ). This makes the theoretical calculation of ω 3 + infeasible. For the symmetric stretching (ω 1 + ), the current theoretical predictions overestimate the experimental value of 829.1 ± 2.0 cm -1 by more than 100 cm -1 . This work together with the previous experimental and theoretical investigations supports the conclusion that the CCSDTQ/CBS approach is capable of providing reliable IE and D 0 predictions for TiO/TiO + and TiO 2 /TiO 2 + with error limits less than or equal to 60 meV. The CCSDTQ/CBS calculations give the predictions of D 0 (Ti + -O) - D 0 (Ti-O) = 0.004 eV and D 0 (O-TiO) - D 0 (O-TiO + ) = 2.699 eV, which are also consistent with the respective experimental determination of 0.008 32 ± 0.000 10 and 2.753 75 ± 0.000 18 eV.

Atomic-scale models of early-stage alkali depletion and SiO2-rich gel formation in bioactive glasses.

PubMed

Tilocca, Antonio

2015-01-28

Molecular dynamics simulations of Na(+)/H(+)-exchanged 45S5 Bioglass® models reveal that a large fraction of the hydroxyl groups introduced into the proton-exchanged, hydrated glass structure do not initially form covalent bonds with Si and P network formers but remain free and stabilised by the modifier metal cations, whereas substantial Si-OH and P-OH bonding is observed only at higher Na(+)/H(+) exchange levels. The strong affinity between free OH groups and modifier cations in the highly fragmented 45S5 glass structure appears to represent the main driving force for this effect. This suggests an alternative direct route for the formation of a repolymerised silica-rich gel in the early stages of the bioactive mechanism, not considered before, which does not require sequential repeated breakings of Si-O-Si bonds and silanol condensations.

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.

Reactions of small organic molecules on silver(110)

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

Ayre, C.R.

1992-01-01

The interaction of two pairs of molecules (1) acetone (CH[sub 3])[sub 2]C=O and isobutylene (CH[sub 3])[sub 2] C=CH[sub 2] and (2) 1,2-propanediol CH[sub 3] CH (OH)CH[sub 2]OH and 1,3-propanediol HOCH[sub 2]CH[sub 2]CH[sub 2]OH with clean and oxygen-activated Ag(110) has been explored to investigate the effects of molecular structure on reactivity. Experimental techniques employed include temperature programmed reaction spectroscopy, isotopic labelling, surface displacement reactions, and electron energy loss spectroscopy. Acetone and isobutylene were studied to explore the relative importance of C=O and C=C bonds in governing the reactivity of structurally similar compounds. Nucleophilic attack by oxygen at the electron-deficient carbonyl carbonmore » in acetone results in reversible formation of the metallacycle (CH[sub 3])[sub 2]COO[sub (a)] at 110 K. Upon heating C-H bond activation by O[sub (a)] occurs near 215 K to yield acetone enolate CH[sub 2]=C(CH[sub 3])O[sub (a)] and evolve H[sub 2]O[sub (g)]. Atomic oxygen activates methyl C-H bonds in isobutylene via an acid-base mechanism. Although the major products are CO[sub 2(g)] and H[sub 2]O[sub (g)], a small amount of (CH[sub 3])[sub 2]C=CH[sub 2(g)] evolves near 310 K. Evidence for the formation of [pi]-2-methylallyl CH[sub 3]C(CH[sub 2])[sub 2(a)] and trimethylenementhane C(CH[sub 2])[sub 3(a)] is presented. The reaction of 1,2-propanediol CH[sub 3] CH(OH)CH[sub 2] OH with oxygen-activated Ag(110) has been compared with that of 1,3-propanediol HOCH[sub 2]CH[sub 2]CH[sub 2]OH to evaluate the effects of varying the position of O-H bonds in both diols to produce the corresponding dialkoxides.« less

Photoinduced Intramolecular Bifurcate Hydrogen Bond: Unusual Mutual Influence of the Components.

PubMed

Sigalov, Mark V; Shainyan, Bagrat A; Sterkhova, Irina V

2017-09-01

A series of 7-hydroxy-2-methylidene-2,3-dihydro-1H-inden-1-ones with 2-pyrrolyl (3), 4-dimethylaminophenyl (4), 4-nitrophenyl (5), and carboxyl group (6) as substituents at the exocyclic double bond was synthesized in the form of the E-isomers (4-6) or predominantly as the Z-isomer (3) which in solution is converted to the E-isomer. The synthesized compounds and their model analogues were studied by NMR spectroscopy, X-ray analysis, and MP2 theoretical calculations. The E-isomers having intramolecular O-H···O═C hydrogen bond are converted by UV irradiation to the Z-isomers having bifurcated O-H···O···H-X hydrogen bond. Unexpected shortening (and, thus, strengthening) of the O-H···O═C component of the bifurcated hydrogen bond upon the formation of the C═O···H-X hydrogen bond was found experimentally, proved theoretically (MP2), and explained by a roundabout interaction of the H-donor (HX) and H-acceptor (C═O) via the system of conjugated bonds.

Calculation of the structure of carbon clusters based on fullerene-like C24 and C48 molecules

NASA Astrophysics Data System (ADS)

Krylova, K. A.; Baimova, Yu. A.; Dmitriev, S. V.; Mulyukov, R. R.

2016-02-01

Equilibrium structures obtained by linking with valence bonds the carbon carcasses of two fullerene-like molecules have been studied by molecular dynamics simulation. In free fullerene, carbon atoms form sp 2 hybridized bonds, but at places of links between fullerenes, sp 3 hybridized bonds are formed, which determines the changes in the properties of such structures. In the literature, the topology of diamond-like phases is described, but equilibrium clusters based on fullerene-like molecules are underexplored. The right angles between the C-C bonds are energetically unfavorable, and the reduction in the energy of clusters in the process of relaxation is connected with the optimization of valence angles, which leads to a reduction in the symmetry of clusters and, in a number of cases, even to disruption of some valence bonds. It is shown that different fashions of linking two fullerenes result in the formation of clusters with different structures and energies. Different initial conditions can lead to different configurations of clusters with the same topology. Among the analyzed clusters, a structure with the minimum potential energy per atom was found. The results of this work contribute to the study of the real structure of carbon clusters.

[Study on the choice of functional monomer before preparation of myclobutanil molecularly imprinted polymer].

PubMed

Gao, Wen-Hui; Liu, Bo; Li, Xing-Feng; Han, Jun-Hua; Jia, Ying-Min

2014-03-01

To prepare myclobutanil molecularly imprinted polymer, a method was established for the choice of the appropriate functional monomer and its dosage. UV spectra was applied to study the combination form, the effect intensity, the optimal concentration ratio and the numbers of binding sites between myclobutanil and methyl acrylic acid (MAA) or acrylamide (AM) functional monomer. The results showed that hydrogen-bonding interaction could be formed between myclobutanil and methyl acrylic acid (MAA) or acrylamide (AM) functional monomer. The pi electron of the triazole ring conjugated double bond in my clobutanil could transit to pi* conjugate antibonding orbital when it absorbed energy. The formation of hydrogen bond could make pi-->pi* absorption band transit. Maximum absorption wavelength produced red shift with the increase in the functional monomer concentration in the system. The research revealed that the optimal concentration ratios between myclobutanil and the two monomers were c(M):c(MAA) = 1:4, c(M):c(AM) = 1:2. Myclobutanil and the both the functional monomers had the bonding ability, and strong bonding force. The prepared molecularly imprinted polymer using AM as a functional monomer had better stability and specificity of recognition for myclobutanil.

Concurrent Formation of Carbon–Carbon Bonds and Functionalized Graphene by Oxidative Carbon-Hydrogen Coupling Reaction

PubMed Central

Morioku, Kumika; Morimoto, Naoki; Takeuchi, Yasuo; Nishina, Yuta

2016-01-01

Oxidative C–H coupling reactions were conducted using graphene oxide (GO) as an oxidant. GO showed high selectivity compared with commonly used oxidants such as (diacetoxyiodo) benzene and 2,3-dichloro-5,6-dicyano-p-benzoquinone. A mechanistic study revealed that radical species contributed to the reaction. After the oxidative coupling reaction, GO was reduced to form a material that shows electron conductivity and high specific capacitance. Therefore, this system could concurrently achieve two important reactions: C–C bond formation via C–H transformation and production of functionalized graphene. PMID:27181191

On the Bonding Strength of Fe-Based Self-Fluxing Alloy Coating Deposited by Different Methods on the Steel Substrate

NASA Astrophysics Data System (ADS)

Feldshtein, E.; Kardapolava, M.; Dyachenko, O.

2018-05-01

In the present paper, the bonding strength of Fe-based self-fluxing alloy coating deposited by plasma spraying, gluing and laser remelting and alloying on the steel substrate have been investigated. When flame melting, a globular structure is formed. Against the background of the solid solution carbide-boride phases are clearly distinguishable, between which the Fe-Fe2B and Fe-FeB eutectic colonies are situated. Laser remelting leads to the formation of metastable structures, reinforced with dendrites, consisting of alloyed Fe-α and Fe-γ. At the low laser beam speeds the coating is melted completely with the formation of a cast structure with the dendrites. When the laser beam speed is increased, the dendritic structure gets fragmented. Structures of coatings alloyed with B4C and remelted by the laser beam vary with the increase of the spot speed. The bonding strength of coating without subsequent remelting decreases by 4-5 times in comparison with remelted. The bonding strength of the reinforced glue coating has adhesive and adhesive-cohesive character. When the load increases in the coating, microcracks develop, which gradually spread to the center of the bonding surface. For plasma coatings after laser remelting without additional alloying, the maximum bonding strength is observed with the minimum laser beam speed. With increasing the laser beam speed it decreases almost 1.5 times. In glue coatings reinforced with B4C particulates by laser remelting, the bonding strength is lower by 1.2-1.4 times in comparison with plasma coating.

Formation of a 1,4-diamino-2,3-disila-1,3-butadiene derivative.

PubMed

Mondal, Kartik Chandra; Roesky, Herbert W; Dittrich, Birger; Holzmann, Nicole; Hermann, Markus; Frenking, Gernot; Meents, Alke

2013-10-30

A 1,4-diamino-2,3-disila-1,3-butadiene derivative of composition (Me2-cAAC)2(Si2Cl2) (Me2-cAAC = :C(CMe2)2(CH2)N-2,6-iPr2C6H3) was synthesized by reduction of the Me2-cAAC:SiCl4 adduct with KC8. This compound is stable at 0 °C for 3 months in an inert atmosphere. Theoretical studies reveal that the silicon atoms exhibit pyramidal coordination, where the Cl-Si-Si-Cl dihedral angle is twisted by 43.3° (calcd 45.9°). The two silicon-carbon bonds are intermediates between single and double Si-C bonds due to twisting of the C-Si-Si-C dihedral angle (163.6°).

2-Amino-5-chloro-pyrimidin-1-ium hydrogen maleate.

PubMed

Fun, Hoong-Kun; Hemamalini, Madhukar; Rajakannan, Venkatachalam

2012-01-01

In the title salt, C(4)H(5)ClN(3) (+)·C(4)H(3)O(4) (-), the 2-amino-5-chloro-pyrimidinium cation is protonated at one of its pyrimidine N atoms. In the roughly planar (r.m.s. deviation = 0.026 Å) hydrogen malate anion, an intra-molecular O-H⋯O hydrogen bond generates an S(7) ring. In the crystal, the protonated N atom and the 2-amino group of the cation are hydrogen bonded to the carboxyl-ate O atoms of the anion via a pair of N-H⋯O hydrogen bonds, forming an R(2) (2)(8) ring motif. The ion pairs are connected via further N-H⋯O hydrogen bonds and a short C-H⋯O inter-action, forming layers lying parallel to the bc plane.

TiO(2) doping by hydroxyurea at the nucleation stage: towards a new photocatalyst in the visible spectral range.

PubMed

Azouani, R; Tieng, S; Chhor, K; Bocquet, J-F; Eloy, P; Gaigneaux, E M; Klementiev, K; Kanaev, A V

2010-10-07

We report an original method of preparation of OCN-doped TiO(2) for photocatalysis in the visible spectral range. The preparation is achieved by a sol-gel route using titanium tetraisopropoxide precursor. Special attention was paid to fluid micromixing, which enables homogeneous reaction conditions in the reactor bulk and monodispersity of the produced clusters/nanoparticles. The dopant hydroxyurea (HyU, CH(4)N(2)O(2)) is injected into the reactive fluid at the nucleation stage, which lasts tens of milliseconds. The doping results in a strong yellow coloration of the nanocolloids due to the absorption band in the spectral range 380-550 nm and accelerates the aggregation kinetics of both nuclei at the induction stage and sub-nuclei units (clusters) at the nucleation stage. FTIR, Raman and UV-visible absorption analyses show the formation of a stable HyU-TiO(2) complex. EXAFS spectra indicate no appreciable changes of the first-shell Ti atom environment. The doping agent takes available surface sites of TiO(2) clusters/nanoparticles attaining ∼10% molar loading. The reaction kinetics then accelerates due to a longer collisional lifetime between nanoparticles induced by the formation of a weak [double bond, length as m-dash]OTi bond. The OCN-group bonding to titanium atoms produces a weakening of the C[double bond, length as m-dash]O double bond and a strengthening of the C-N and N-O bonds.

Quantum Chemical Insight into the Interactions and Thermodynamics Present in Choline Chloride Based Deep Eutectic Solvents.

PubMed

Wagle, Durgesh V; Deakyne, Carol A; Baker, Gary A

2016-07-14

We report quantum chemical calculations performed on three popular deep eutectic solvents (DESs) in order to elucidate the molecular interactions, charge transfer interactions, and thermodynamics associated with these systems. The DESs studied comprise 1:2 choline chloride/urea (reline), 1:2 choline chloride/ethylene glycol (ethaline), and 1:1 choline chloride/malonic acid (maloline). The excellent correlation between calculated and experimental vibrational spectra allowed for identification of dominant interactions in the DES systems. The DESs were found to be stabilized by both conventional hydrogen bonds and C-H···O/C-H···π interactions between the components. The hydrogen-bonding network established in the DES is clearly distinct from that which exists within the neat hydrogen-bond donor dimer. Charge decomposition analysis indicates significant charge transfer from choline and chloride to the hydrogen-bond donor with a higher contribution from the cation, and a density of states analysis confirms the direction of the charge transfer. Consequently, the sum of the bond orders of the choline-Cl(-) interactions in the DESs correlates directly with the melting temperatures of the DESs, a correlation that offers insight into the effect of the tuning of the choline-Cl(-) interactions by the hydrogen-bond donors on the physical properties of the DESs. Finally, the differences in the vibrational entropy changes upon DES formation are consistent with the trend in the overall entropy changes upon DES formation.

Shock response of 1,3,5-trinitroperhydro-1,3,5-triazine (RDX): The C-N bond scission studied by molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Yuan, Jiao-Nan; Wei, Yong-Kai; Zhang, Xiu-Qing; Chen, Xiang-Rong; Ji, Guang-Fu; Kotni, Meena Kumari; Wei, Dong-Qing

2017-10-01

The shock response has a great influence on the design, synthesis, and application of energetic materials in both industrial and military areas. Therefore, the initial decomposition mechanism of bond scission at the atomistic level of condensed-phase α-RDX under shock loading has been studied based on quantum molecular dynamics simulations in combination with a multi-scale shock technique. First, based on the frontier molecular orbital theory, our calculated result shows that the N-NO2 bond is the weakest bond in the α-RDX molecule in the ground state, which may be the initial bond for pyrolysis. Second, the changes of bonds under shock loading are investigated by the changes of structures, kinetic bond lengths, and Laplacian bond orders during the simulation. Also, the variation of thermodynamic properties with time in shocked α-RDX at 10 km/s along the lattice vector a for a timescale of up to 3.5 ps is presented. By analyzing the detailed structural changes of RDX under shock loading, we find that the shocked RDX crystal undergoes a process of compression and rotation, which leads to the C-N bond initial rupture. The time variation of dynamic bond lengths in a shocked RDX crystal is calculated, and the result indicates that the C-N bond is easier to rupture than other bonds. The Laplacian bond orders are used to predict the molecular reactivity and stability. The values of the calculated bond orders show that the C-N bonds are more sensitive than other bonds under shock loading. In a word, the C-N bond scission has been validated as the initial decomposition in a RDX crystal shocked at 10 km/s. Finally, the bond-length criterion has been used to identify individual molecules in the simulation. The distance thresholds up to which two particles are considered direct neighbors and assigned to the same cluster have been tested. The species and density numbers of the initial decomposition products are collected according to the trajectory.

Organic chemistry. Functionalization of C(sp3)-H bonds using a transient directing group.

PubMed

Zhang, Fang-Lin; Hong, Kai; Li, Tuan-Jie; Park, Hojoon; Yu, Jin-Quan

2016-01-15

Proximity-driven metalation has been extensively exploited to achieve reactivity and selectivity in carbon-hydrogen (C-H) bond activation. Despite the substantial improvement in developing more efficient and practical directing groups, their stoichiometric installation and removal limit efficiency and, often, applicability as well. Here we report the development of an amino acid reagent that reversibly reacts with aldehydes and ketones in situ via imine formation to serve as a transient directing group for activation of inert C-H bonds. Arylation of a wide range of aldehydes and ketones at the β or γ positions proceeds in the presence of a palladium catalyst and a catalytic amount of amino acid. The feasibility of achieving enantioselective C-H activation reactions using a chiral amino acid as the transient directing group is also demonstrated. Copyright © 2016, American Association for the Advancement of Science.

Hugoniot curve calculation of nitromethane decomposition mixtures: A reactive force field molecular dynamics approach

NASA Astrophysics Data System (ADS)

Guo, Feng; Zhang, Hong; Hu, Hai-Quan; Cheng, Xin-Lu; Zhang, Li-Yan

2015-11-01

We investigate the Hugoniot curve, shock-particle velocity relations, and Chapman-Jouguet conditions of the hot dense system through molecular dynamics (MD) simulations. The detailed pathways from crystal nitromethane to reacted state by shock compression are simulated. The phase transition of N2 and CO mixture is found at about 10 GPa, and the main reason is that the dissociation of the C-O bond and the formation of C-C bond start at 10.0-11.0 GPa. The unreacted state simulations of nitromethane are consistent with shock Hugoniot data. The complete pathway from unreacted to reacted state is discussed. Through chemical species analysis, we find that the C-N bond breaking is the main event of the shock-induced nitromethane decomposition. Project supported by the National Natural Science Foundation of China (Grant No. 11374217) and the Shandong Provincial Natural Science Foundation, China (Grant No. ZR2014BQ008).

Infrared spectra of the ammonium ion in ammonium metavanadate NH 4VO 3

NASA Astrophysics Data System (ADS)

de Waal, D.; Heyns, A. M.; Range, K.-J.; Eglmeier, C.

The ND stretching modes of isotopically dilute NH 3D + ions in NH 4VO 3 are in agreement with the predicted splitting into C s, C s and C1(2) components under C s site symmetry for the NH +4 ion. The three bands observed represent the three NH bonding distances in the crystal, and the position, shape and low temperature behaviour of each band confirms the existence of two types of hydrogen bonding in NH 4VO 3. The low temperature infrared modes of NH +4 and ND +4 in NH 4VO 3 and ND 4VO 3, respectively, can be assigned under space group Pbcm. Temperature dependence of these modes also reflects the presence of both normal and bifurcated hydrogen bonds in NH 4VO 3.

Effect of Pd surface structure on the activation of methyl acetate

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

Xu, Lijun; Xu, Ye

2011-01-01

The activation of methyl acetate (CH3COOCH3; MA) has been studied using periodic density functional theory calculations to probe the effect of Pd surface structure on the selectivity in MA activation. The adsorption of MA, dehydrogenated derivatives, enolate (CH2COOCH3; ENL) and methylene acetate (CH3COOCH2; MeA), and several dissociation products (including acetate, acetyl, ketene, methoxy, formaldehyde, CO, C, O, and H); and C-H and C-O (mainly in the RCO-OR position) bond dissociation in MA, ENL, and MeA, are calculated on Pd(111) terrace, step, and kink; and on Pd(100) terrace and step. The adsorption of most species is not strongly affected between (111)-more » to (100)-type surfaces, but is clearly enhanced by step/kink compared to the corresponding terrace. Going from terrace to step edge and from (111)- to (100)-type surfaces both stabilize the transition states of C-O bond dissociation steps. Going from terrace to step edge also stabilizes the transition states of C-H bond dissociation steps, but going from (111)- to (100)-type surfaces does not clearly do so. We propose that compared to the Pd(111) terrace, the Pd(100) terrace is more selective for C-O bond dissociation that is desirable for alcohol formation, whereas the Pd step edges are more selective for C-H bond dissociation.« less

Do dihydroxymagnesium carboxylates form Grignard-type reagents? A theoretical investigation on decarboxylative fragmentation.

PubMed

Ruf, Alexander; Kanawati, Basem; Schmitt-Kopplin, Philippe

2018-03-27

Dihydroxymagnesium carboxylates [(OH) 2 MgO 2 CR] were probed for decarboxylation on a theoretical level, by utilizing both Møller-Plesset perturbation theory (MP2) and density functional theory (B3LYP-DFT) computations. This study is connected to the question of whether this recently introduced, astrobiologically relevant chemical class may form Grignard-type reagent molecules. To extract trends for a broad molecular mass range, different linear alkyl chain lengths between C 4 and C 11 were computed. The forward energy barrier for decarboxylation reactions increases linearly as a function of the ligand's chain length. Decarboxylation-type fragmentations of these organomagnesium compounds seem to be improbable in non-catalytic, low energetic environments. A high forward energy barrier (E MP2  > 55 kcal mol -1 ) towards a described transition state restricts the release of CO 2 . Nevertheless, we propose the release of CO 2 on a theoretical level, as been revealed via an intramolecular nucleophilic attack mechanism. Once the challenging transition state for decarboxylation is overcome, a stable Mg-C bond is formed. These mechanistic insights were gained by help of natural bond orbital analysis. The Cα atom (first carbon atom in the ligand chain attached to the carboxyl group) is thought to prefer binding towards the electrophilic magnesium coordination center, rather than towards the electrophilic CO 2 -carbon atom. Additionally, the putatively formed Grignard-type OH-bearing product molecules possess a more polarized Mg-C bond in comparison to RMgCl species. Therefore, carbanion formation from OH-bearing Grignard-type molecules is made feasible for triggering C-C bond formation reactions. Graphical abstract This study asks whether recently introduced, astrobiologically dihydroxymagnesium carboxylates form Grignard-type reagent molecules via decarboxylative fragmentation.

Iridium complexes containing mesoionic C donors: selective C(sp3)-H versus C(sp2)-H bond activation, reactivity towards acids and bases, and catalytic oxidation of silanes and water.

PubMed

Petronilho, Ana; Woods, James A; Mueller-Bunz, Helge; Bernhard, Stefan; Albrecht, Martin

2014-11-24

Metalation of a C2-methylated pyridylimidazolium salt with [IrCp*Cl2]2 affords either an ylidic complex, resulting from C(sp(3))-H bond activation of the C2-bound CH3 group if the metalation is performed in the presence of a base, such as AgO2 or Na2CO3, or a mesoionic complex via cyclometalation and thermally induced heterocyclic C(sp(2))-H bond activation, if the reaction is performed in the absence of a base. Similar cyclometalation and complex formation via C(sp(2))-H bond activation is observed when the heterocyclic ligand precursor consists of the analogous pyridyltriazolium salt, that is, when the metal bonding at the C2 position is blocked by a nitrogen rather than a methyl substituent. Despite the strongly mesoionic character of both the imidazolylidene and the triazolylidene, the former reacts rapidly with D(+) and undergoes isotope exchange at the heterocyclic C5 position, whereas the triazolylidene ligand is stable and only undergoes H/D exchange under basic conditions, where the imidazolylidene is essentially unreactive. The high stability of the Ir-C bond in aqueous solution over a broad pH range was exploited in catalytic water oxidation and silane oxidation. The catalytic hydrosilylation of ketones proceeds with turnover frequencies as high as 6,000 h(-1) with both the imidazolylidene and the triazolylidene system, whereas water oxidation is enhanced by the stronger donor properties of the imidazol-4-ylidene ligands and is more than three times faster than with the triazolylidene analogue. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cryosolution infrared study of hydrogen bonded halothane acetylene complex

NASA Astrophysics Data System (ADS)

Melikova, S. M.; Rutkowski, K. S.; Rospenk, M.

2018-05-01

The interactions between halothane (2-bromo-2-chloro-1,1,1-trifluoroethane) and acetylene (C2H2) are studied by FTIR spectroscopy. Results obtained in liquid cryosolutions in Kr suggest weak complex formation stabilized by H - bond. The complexation enthalpy (∼11 kJ/mol) is evaluated in a series of temperature measurements (T ∼ 120-160 K) of integrated intensity of selected bands performed in liquefied Kr. The quantum chemical MP2/6-311++G(2d,2p) calculations predict four different structures of the complex. The most stable and populated (94% at T∼120 K) structure corresponds to the H - bond between H atom of halothane and pi-electron of triple bond between C atoms of acetylene. Wave numbers of vibrational bands of the most stable structure are calculated in anharmonic approximation implemented in Gaussian program.

Direct C-H alkylation and indole formation of anilines with diazo compounds under rhodium catalysis.

PubMed

Mishra, Neeraj Kumar; Choi, Miji; Jo, Hyeim; Oh, Yongguk; Sharma, Satyasheel; Han, Sang Hoon; Jeong, Taejoo; Han, Sangil; Lee, Seok-Yong; Kim, In Su

2015-12-18

The rhodium(III)-catalyzed direct functionalization of aniline C-H bonds with α-diazo compounds is described. These transformations provide a facile construction of ortho-alkylated anilines with diazo malonates or highly substituted indoles with diazo acetoacetates.

Bite angle effects of diphosphines in C-C and C-X bond forming cross coupling reactions.

PubMed

Birkholz, Mandy-Nicole; Freixa, Zoraida; van Leeuwen, Piet W N M

2009-04-01

Catalytic reactions of C-C and C-X bond formation are discussed in this critical review with particular emphasis on cross coupling reactions catalyzed by palladium and wide bite angle bidentate diphosphine ligands. Especially those studies have been collected that allow comparison of the ligand bite angles for the selected ligands: dppp, BINAP, dppf, DPEphos and Xantphos. Similarities with hydrocyanation and CO/ethene/MeOH reactions have been highlighted, while rhodium hydroformylation has been mentioned as a contrasting example, in which predictability is high and steric and electronic effects follow smooth trends. In palladium catalysis wide bite angles and bulkiness of the ligands facilitate generally the reductive elimination thus giving more efficient cross coupling catalysis (174 references).

TEM Observation of the Ti Interlayer Between SiC Substrates During Diffusion Bonding

NASA Technical Reports Server (NTRS)

Tsuda, Hiroshi; Mori, Shigeo; Halbig, Michael C.; Singh, Mori

2012-01-01

Diffusion bonding was carried out to join SiC to SiC substrates using titanium interlayers. In this study, 10 m and 20 m thick physical vapor deposited (PVD) Ti surface coatings, and 10 and 20 m thick Ti foils were used. Diffusion bonding was performed at 1250 C for PVD Ti coatings and 1200 C for Ti foil. This study investigates the microstructures of the phases formed during diffusion bonding through TEM and selected-area diffraction analysis of a sample prepared with an FIB, which allows samples to be taken from the reacted area. In all samples, Ti3SiC2, Ti5Si3Cx and TiSi2 phases were identified. In addition, TiC and unknown phases also appeared in the samples in which Ti foils were used as interlayers. Furthermore, Ti3SiC2 phases show high concentration and Ti5Si3Cx formed less when samples were processed at a higher temperature and thinner interlayer samples were used. It appears that the formation of microcracks is caused by the presence of intermediate phase Ti5Si3Cx, which has anisotropic thermal expansion, and by the presence of an unidentified Ti-Si-C ternary phase with relatively low Si content.

Recombinant Cyanobacteria for the Asymmetric Reduction of C=C Bonds Fueled by the Biocatalytic Oxidation of Water.

PubMed

Köninger, Katharina; Gómez Baraibar, Álvaro; Mügge, Carolin; Paul, Caroline E; Hollmann, Frank; Nowaczyk, Marc M; Kourist, Robert

2016-04-25

A recombinant enoate reductase was expressed in cyanobacteria and used for the light-catalyzed, enantioselective reduction of C=C bonds. The coupling of oxidoreductases to natural photosynthesis allows asymmetric syntheses fueled by the oxidation of water. Bypassing the addition of sacrificial cosubstrates as electron donors significantly improves the atom efficiency and avoids the formation of undesired side products. Crucial factors for product formation are the availability of NADPH and the amount of active enzyme in the cells. The efficiency of the reaction is comparable to typical whole-cell biotransformations in E. coli. Under optimized conditions, a solution of 100 mg prochiral 2-methylmaleimide was reduced to optically pure 2-methylsuccinimide (99 % ee, 80 % yield of isolated product). High product yields and excellent optical purities demonstrate the synthetic usefulness of light-catalyzed whole-cell biotransformations using recombinant cyanobacteria. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Central Doping of a Foreign Atom into the Silver Cluster for Catalytic Conversion of CO2 toward C-C Bond Formation.

PubMed

Liu, Yuanyuan; Chai, Xiaoqi; Cai, Xiao; Chen, Mingyang; Jin, Rongchao; Ding, Weiping; Zhu, Yan

2018-06-19

Clusters with an exact number of atoms are of particular research interest in catalysis. Their catalytic behaviors can be potentially altered with the addition or removal of a single atom. Herein we explore the effects of the single-foreign-atom (Au, Pd and Pt) doping into the core of an Ag cluster with 25-atoms on the catalytic properties, where the foreign atom is protected by 24 Ag atoms (i.e., Au@Ag24, Pd@Ag24, and Pt@Ag24). The central doping of a single atom into the Ag25 cluster is found to have a substantial influence on the catalytic performance in the carboxylation reaction of CO2 with terminal alkyne through C-C bond formation to produce propiolic acid. Our studies reveal that the catalytic properties of the cluster catalysts can be dramatically changed with the subtle alteration by a single atom away from the active sites. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Recognition of a novel type X═N-Hal···Hal (X = C, S, P; Hal = F, Cl, Br, I) halogen bonding.

PubMed

Gushchin, Pavel V; Kuznetsov, Maxim L; Haukka, Matti; Kukushkin, Vadim Yu

2013-04-04

The chlorination of the eight-membered platinum(II) chelates [PtCl2{NH═C(NR2)N(Ph)C(═NH)N(Ph)C(NR2)═NH}] (R = Me (1); R2 = (CH2)5 (2)) with uncomplexed imino group with Cl2 gives complexes bearing the ═N-Cl moiety [PtCl4{NH═C(NR2)N(Ph)C(═NCl)N(Ph)C(NR2)═NH}] (R = Me (3); R2 = (CH2)5 (4)). X-ray study for 3 revealed a novel type intermolecular halogen bonding ═N-Cl···Cl(-), formed between the Cl atom of the chlorinated imine and the chloride bound to the platinum(IV) center. The processing relevant structural data retrieved from the Cambridge Structural Database (CSDB) shows that this type of halogen bonding is realized in 18 more molecular species having X═N-Hal moieties (X = C, P, S, V, W; Hal = Cl, Br, I), but this weak ═N-Hal···Hal(-) bonding was totally neglected in the previous works. The presence of the halogen bonding in 3 was confirmed by theoretical calculations at the density functional theory (DFT, M06-2X) level, and its nature was analyzed.

Monoclinic structures of niobium trisulfide

NASA Astrophysics Data System (ADS)

Bloodgood, Matthew A.; Wei, Pingrong; Aytan, Ece; Bozhilov, Krassimir N.; Balandin, Alexander A.; Salguero, Tina T.

2018-02-01

Two new polymorphs of niobium trisulfide are established by single crystal x-ray diffraction. NbS3-iv crystallizes in the monoclinic space group P21/c with lattice parameters a = 6.7515(5) Å, b = 4.9736(4) Å, c = 18.1315(13) Å, and β = 90.116(2)°. Its structure is based on chains of [NbS6] trigonal prisms containing Nb-Nb pairs with a bond length of 3.0448(8) Å; this pairing causes the chains to corrugate slightly along their axis, a feature also present in triclinic NbS3-i that leads to semiconductor properties. The stacking arrangement of chains is different in these polymorphs, however, with NbS3-i having an ABCDE repeating sequence of chain bilayers and NbS3-iv having an AB repeating sequence. HRTEM studies show the presence of topotactically-oriented intergrown zones and numerous dislocations, which result in mosaic structuring. A second new polymorph, NbS3-v, crystallizes in the monoclinic space group P21/m with lattice parameters a = 4.950(5) Å, b = 3.358(4) Å, c = 9.079(10) Å, β = 97.35(2)°. In contrast to NbS3-iv, NbS3-v maintains fixed a Nb-Nb bond distance of 3.358(4) Å along the chains, and it has an ABCDE repeating sequence of chain bilayers similar to NbS3-i. High resolution scanning transmission electron microscopy (HR-STEM) imaging of an exfoliated NbS3-v nanoribbon shows the continuous [NbS6] chains oriented along the b-axis. These results provide the first firmly established structural data for monoclinic NbS3. In addition, SEM images show the formation of NbS3 rings and cylinders, and a combination of powder x-ray diffraction and Raman spectroscopy provides a way to distinguish between NbS3 polymorphs.

Joining of alumina via copper/niobium/copper interlayers

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

Marks, Robert A.; Chapman, Daniel R.; Danielson, David T.

2000-03-15

Alumina has been joined at 1150 degrees C and 1400 degrees C using multilayer copper/niobium/copper interlayers. Four-point bend strengths are sensitive to processing temperature, bonding pressure, and furnace environment (ambient oxygen partial pressure). Under optimum conditions, joints with reproducibly high room temperature strengths (approximately equal 240 plus/minus 20 MPa) can be produced; most failures occur within the ceramic. Joints made with sapphire show that during bonding an initially continuous copper film undergoes a morphological instability, resulting in the formation of isolated copper-rich droplets/particles at the sapphire/interlayer interface, and extensive regions of direct bonding between sapphire and niobium. For optimized aluminamore » bonds, bend tests at 800 degrees C-1100 degrees C indicate significant strength is retained; even at the highest test temperature, ceramic failure is observed. Post-bonding anneals at 1000 degrees C in vacuum or in gettered argon were used to assess joint stability and to probe the effect of ambient oxygen partial pressure on joint characteristics. Annealing in vacuum for up to 200 h causes no significant decrease in room temperature bend strength or change in fracture path. With increasing anneal time in a lower oxygen partial pressure environment, the fracture strength decreases only slightly, but the fracture path shifts from the ceramic to the interface.« less

The crystal structure of the C45S mutant of annelid Arenicola marina peroxiredoxin 6 supports its assignment to the mechanistically typical 2-Cys subfamily without any formation of toroid-shaped decamers

PubMed Central

Smeets, Aude; Loumaye, Eléonore; Clippe, André; Rees, Jean-François; Knoops, Bernard; Declercq, Jean-Paul

2008-01-01

The peroxiredoxins (PRDXs) define a superfamily of thiol-dependent peroxidases able to reduce hydrogen peroxide, alkyl hydroperoxides, and peroxynitrite. Besides their cytoprotective antioxidant function, PRDXs have been implicated in redox signaling and chaperone activity, the latter depending on the formation of decameric high-molecular-weight structures. PRDXs have been mechanistically divided into three major subfamilies, namely typical 2-Cys, atypical 2-Cys, and 1-Cys PRDXs, based on the number and position of cysteines involved in the catalysis. We report the structure of the C45S mutant of annelid worm Arenicola marina PRDX6 in three different crystal forms determined at 1.6, 2.0, and 2.4 Å resolution. Although A. marina PRDX6 was cloned during the search of annelid homologs of mammalian 1-Cys PRDX6s, the crystal structures support its assignment to the mechanistically typical 2-Cys PRDX subfamily. The protein is composed of two distinct domains: a C-terminal domain and an N-terminal domain exhibiting a thioredoxin fold. The subunits are associated in dimers compatible with the formation of intersubunit disulfide bonds between the peroxidatic and the resolving cysteine residues in the wild-type enzyme. The packing of two crystal forms is very similar, with pairs of dimers associated as tetramers. The toroid-shaped decamers formed by dimer association and observed in most typical 2-Cys PRDXs is not present. Thus, A. marina PRDX6 presents structural features of typical 2-Cys PRDXs without any formation of toroid-shaped decamers, suggesting that it should function more like a cytoprotective antioxidant enzyme or a modulator of peroxide-dependent cell signaling rather than a molecular chaperone. PMID:18359859

Bioinformatic and Biochemical Characterizations of C–S Bond Formation and Cleavage Enzymes in the Fungus Neurospora crassa Ergothioneine Biosynthetic Pathway

PubMed Central

2015-01-01

Ergothioneine is a histidine thiol derivative. Its mycobacterial biosynthetic pathway has five steps (EgtA-E catalysis) with two novel reactions: a mononuclear nonheme iron enzyme (EgtB) catalyzed oxidative C–S bond formation and a PLP-mediated C–S lyase (EgtE) reaction. Our bioinformatic and biochemical analyses indicate that the fungus Neurospora crassa has a more concise ergothioneine biosynthetic pathway because its nonheme iron enzyme, Egt1, makes use of cysteine instead of γ-Glu-Cys as the substrate. Such a change of substrate preference eliminates the competition between ergothioneine and glutathione biosyntheses. In addition, we have identified the N. crassa C–S lyase (NCU11365) and reconstituted its activity in vitro, which makes the future ergothioneine production through metabolic engineering feasible. PMID:25275953

Non-additivity of functional group contributions in protein-ligand binding: a comprehensive study by crystallography and isothermal titration calorimetry.

PubMed

Baum, Bernhard; Muley, Laveena; Smolinski, Michael; Heine, Andreas; Hangauer, David; Klebe, Gerhard

2010-04-09

Additivity of functional group contributions to protein-ligand binding is a very popular concept in medicinal chemistry as the basis of rational design and optimized lead structures. Most of the currently applied scoring functions for docking build on such additivity models. Even though the limitation of this concept is well known, case studies examining in detail why additivity fails at the molecular level are still very scarce. The present study shows, by use of crystal structure analysis and isothermal titration calorimetry for a congeneric series of thrombin inhibitors, that extensive cooperative effects between hydrophobic contacts and hydrogen bond formation are intimately coupled via dynamic properties of the formed complexes. The formation of optimal lipophilic contacts with the surface of the thrombin S3 pocket and the full desolvation of this pocket can conflict with the formation of an optimal hydrogen bond between ligand and protein. The mutual contributions of the competing interactions depend on the size of the ligand hydrophobic substituent and influence the residual mobility of ligand portions at the binding site. Analysis of the individual crystal structures and factorizing the free energy into enthalpy and entropy demonstrates that binding affinity of the ligands results from a mixture of enthalpic contributions from hydrogen bonding and hydrophobic contacts, and entropic considerations involving an increasing loss of residual mobility of the bound ligands. This complex picture of mutually competing and partially compensating enthalpic and entropic effects determines the non-additivity of free energy contributions to ligand binding at the molecular level. (c) 2010 Elsevier Ltd. All rights reserved.

Recyclable cross-linked anion exchange membrane for alkaline fuel cell application

NASA Astrophysics Data System (ADS)

Hou, Jianqiu; Liu, Yazhi; Ge, Qianqian; Yang, Zhengjin; Wu, Liang; Xu, Tongwen

2018-01-01

Cross-linking can effectively solve the conductivity-swelling dilemma in anion exchange membranes (AEMs) but will generate solid wastes. To address this, we developed an AEM cross-linked via disulfide bonds, bearing quaternary ammonium groups, which can be easily recycled. The membrane (RC-QPPO) with IEC of 1.78 mmol g-1, when cross-linked, showed enhanced mechanical properties and good hydroxide conductivity (24.6 mS cm-1 at 30 °C). Even at higher IEC value (2.13 mmol g-1), it still has low water uptake, low swelling ratio and delivers a peak power density of 150 mW cm-2 at 65 °C. Exploiting the formation of disulfide bonds from -SH groups, the membrane can be readily cross-linked in alkaline condition and recycled by reversibly breaking disulfide bonds with dithiothreitol (DTT). The recycled membrane solution can be directly utilized to cast a brand-new AEM. By washing away the residual DTT with water and exposure to air, it can be cross-linked again and this process is repeatable. During the recycling and cross-linking processes, the membrane showed a slight IEC decrease of 5% due to functional group degradation. The strategy presented here is promising in enhancing AEM properties and reducing the impact of artificial polymers on the environment.

Sulfonamidation of Aryl and Heteroaryl Halides through Photosensitized Nickel Catalysis.

PubMed

Kim, Taehoon; McCarver, Stefan J; Lee, Chulbom; MacMillan, David W C

2018-03-19

Herein we report a highly efficient method for nickel-catalyzed C-N bond formation between sulfonamides and aryl electrophiles. This technology provides generic access to a broad range of N-aryl and N-heteroaryl sulfonamide motifs, which are widely represented in drug discovery. Initial mechanistic studies suggest an energy-transfer mechanism wherein C-N bond reductive elimination occurs from a triplet excited Ni II complex. Late-stage sulfonamidation in the synthesis of a pharmacologically relevant structure is also demonstrated. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Benzylic Fluorination of Aza-Heterocycles Induced by Single-Electron Transfer to Selectfluor.

PubMed

Danahy, Kelley E; Cooper, Julian C; Van Humbeck, Jeffrey F

2018-04-23

A selective and mild method for the benzylic fluorination of aromatic azaheterocycles with Selectfluor is described. These reactions take place by a previously unreported mechanism, in which electron transfer from the heterocyclic substrate to the electrophilic fluorinating agent Selectfluor eventually yields a benzylic radical, thus leading to the desired C-F bond formation. This mechanism enables high intra- and intermolecular selectivity for aza-heterocycles over other benzylic components with similar C-H bond-dissociation energies. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Straightforward Entry toward Highly Substituted 2,3-Dihydrobenz[ b]oxepines by Ring Expansion of Benzopyryliums with Donor-Acceptor Diazo Compounds.

PubMed

Courant, Thibaut; Pasco, Morgane; Lecourt, Thomas

2018-05-04

Ylide-type reactivity of diazo compounds is exploited in a new way to prepare benzo[ b]oxepines thanks to the formation of three chemical bonds and two contiguous and highly substituted stereocenters in a single pot. This cationic reaction cascade first involves addition of a donor-acceptor-substituted diazo compound to a benzopyrylium. Selective 1,2 migration of the endocyclic C-C bond then results in a ring-expansion and generates a second oxocarbenium that is trapped by a nucleophile added sequentially.

Determination of retinal chromophore structure in bacteriorhodopsin with resonance Raman spectroscopy.

PubMed

Smith, S O; Lugtenburg, J; Mathies, R A

1985-01-01

The analysis of the vibrational spectrum of the retinal chromophore in bacteriorhodopsin with isotopic derivatives provides a powerful "structural dictionary" for the translation of vibrational frequencies and intensities into structural information. Of importance for the proton-pumping mechanism is the unambiguous determination of the configuration about the C13=C14 and C=N bonds, and the protonation state of the Schiff base nitrogen. Vibrational studies have shown that in light-adapted BR568 the Schiff base nitrogen is protonated and both the C13=C14 and C=N bonds are in a trans geometry. The formation of K625 involves the photochemical isomerization about only the C13=C14 bond which displaces the Schiff base proton into a different protein environment. Subsequent Schiff base deprotonation produces the M412 intermediate. Thermal reisomerization of the C13=C14 bond and reprotonation of the Schiff base occur in the M412------O640 transition, resetting the proton-pumping mechanism. The vibrational spectra can also be used to examine the conformation about the C--C single bonds. The frequency of the C14--C15 stretching vibration in BR568, K625, L550 and O640 argues that the C14--C15 conformation in these intermediates is s-trans. Conformational distortions of the chromophore have been identified in K625 and O640 through the observation of intense hydrogen out-of-plane wagging vibrations in the Raman spectra (see Fig. 2). These two intermediates are the direct products of chromophore isomerization. Thus it appears that following isomerization in a tight protein binding pocket, the chromophore cannot easily relax to a planar geometry. The analogous observation of intense hydrogen out-of-plane modes in the primary photoproduct in vision (Eyring et al., 1982) suggests that this may be a general phenomenon in protein-bound isomerizations. Future resonance Raman studies should provide even more details on how bacterio-opsin and retinal act in concert to produce an efficient light-energy convertor. Important unresolved questions involve the mechanism by which the protein catalyzes deprotonation of the L550 intermediate and the mechanism of the thermal conversion of M412 back to BR568. Also, it has been shown that under conditions of high ionic strength and/or low light intensity two protons are pumped per photocycle (Kuschmitz & Hess, 1981). How might this be accomplished?(ABSTRACT TRUNCATED AT 400 WORDS)

Synthesis and structures of six closely related N-[3-(2-chlorobenzoyl)-5-ethylthiophen-2-yl]arylamides, together with an isolated reaction intermediate: order versus disorder, molecular conformations and hydrogen bonding in zero, one and two dimensions.

PubMed

Sagar, Belakavadi K; Yathirajan, Hemmige S; Rathore, Ravindranath S; Glidewell, Christopher

2018-02-01

Six closely related N-[3-(2-chlorobenzoyl)-5-ethylthiophen-2-yl]arylamides have been synthesized and structurally characterized, together with a representative reaction intermediate. In each of N-[3-(2-chlorobenzoyl)-5-ethylthiophen-2-yl]benzamide, C 20 H 16 ClNO 2 S, (I), N-[3-(2-chlorobenzoyl)-5-ethylthiophen-2-yl]-4-phenylbenzamide, C 26 H 20 ClNO 2 S, (II), and 2-bromo-N-[3-(2-chlorobenzoyl)-5-ethylthiophen-2-yl]benzamide, C 20 H 15 BrClNO 2 S, (III), the molecules are disordered over two sets of atomic sites, with occupancies of 0.894 (8) and 0.106 (8) in (I), 0.832 (5) and 0.168 (5) in (II), and 0.7006 (12) and 0.2994 (12) in (III). In each of N-[3-(2-chlorobenzoyl)-5-ethylthiophen-2-yl]-2-iodobenzamide, C 20 H 15 ClINO 2 S, (IV), and N-[3-(2-chlorobenzoyl)-5-ethylthiophen-2-yl]-2-methoxybenzamide, C 21 H 18 ClNO 3 S, (V), the molecules are fully ordered, but in N-[3-(2-chlorobenzoyl)-5-ethylthiophen-2-yl]-2,6-difluorobenzamide, C 20 H 14 ClF 2 NO 2 S, (VI), which crystallizes with Z' = 2 in the space group C2/c, one of the two independent molecules is fully ordered, while the other is disordered over two sets of atomic sites having occupancies of 0.916 (3) and 0.084 (3). All of the molecules in compounds (I)-(VI) exhibit an intramolecular N-H...O hydrogen bond. The molecules of (I) and (VI) are linked by C-H...O hydrogen bonds to form finite zero-dimensional dimers, which are cyclic in (I) and acyclic in (VI), those of (III) are linked by C-H...π(arene) hydrogen bonds to form simple chains, and those of (IV) and (V) are linked into different types of chains of rings, built in each case from a combination of C-H...O and C-H...π(arene) hydrogen bonds. Two C-H...O hydrogen bonds link the molecules of (II) into sheets containing three types of ring. In benzotriazol-1-yl 3,4-dimethoxybenzoate, C 15 H 13 N 3 O 4 , (VII), the benzoate component is planar and makes a dihedral angle of 84.51 (6)° with the benzotriazole unit. Comparisons are made with related compounds.