Kinetics of carbonyl reductase from human brain.

OpenAIRE

Bohren, K M; von Wartburg, J P; Wermuth, B

1987-01-01

Initial-rate analysis of the carbonyl reductase-catalysed reduction of menadione by NADPH gave families of straight lines in double-reciprocal plots consistent with a sequential mechanism being obeyed. The fluorescence of NADPH was increased up to 7-fold with a concomitant shift of the emission maximum towards lower wavelength in the presence of carbonyl reductase, and both NADPH and NADP+ caused quenching of the enzyme fluorescence, indicating formation of a binary enzyme-coenzyme complex. D...

Spectroscopic and theoretical studies on the aromaticity of pyrrol-2-yl-carbonyl conformers

Science.gov (United States)

Dubis, Alina T.; Wojtulewski, Sławomir; Filipkowski, Karol

2013-06-01

The aromaticity of s-cis and s-trans pyrrol-2-yl carbonyl conformers was studied by FT-IR, 1H NMR spectroscopy and DFT calculations at the B3LYP/6-311++G(d,p) level of theory. The Harmonic Oscillator Model of Aromaticity (HOMA) and Nucleus Independent Chemical Shift (NICS) indices were calculated to estimate π-electron delocalization in the pyrrole ring. The usefulness of infrared spectroscopy in the evaluation of the aromaticity of the homogeneous set of pyrroles is discussed. The influence of 2-substitution on different aspects of aromaticity and stability of the pyrrol-2-yl carbonyl conformers is also discussed. It is concluded that the substitution effect of the title pyrrole derivatives can be explained on the basis of theoretical and experimental measurements of π-electron delocalization, including IR data.

De novo protein structure generation from incomplete chemical shift assignments

Energy Technology Data Exchange (ETDEWEB)

Shen Yang [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Vernon, Robert; Baker, David [University of Washington, Department of Biochemistry and Howard Hughes Medical Institute (United States); Bax, Ad [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)], E-mail: bax@nih.gov

2009-02-15

NMR chemical shifts provide important local structural information for proteins. Consistent structure generation from NMR chemical shift data has recently become feasible for proteins with sizes of up to 130 residues, and such structures are of a quality comparable to those obtained with the standard NMR protocol. This study investigates the influence of the completeness of chemical shift assignments on structures generated from chemical shifts. The Chemical-Shift-Rosetta (CS-Rosetta) protocol was used for de novo protein structure generation with various degrees of completeness of the chemical shift assignment, simulated by omission of entries in the experimental chemical shift data previously used for the initial demonstration of the CS-Rosetta approach. In addition, a new CS-Rosetta protocol is described that improves robustness of the method for proteins with missing or erroneous NMR chemical shift input data. This strategy, which uses traditional Rosetta for pre-filtering of the fragment selection process, is demonstrated for two paramagnetic proteins and also for two proteins with solid-state NMR chemical shift assignments.

Influence of the Dielectric Medium on the Carbonyl Infrared Absorption Peak of Acetylferrocene

Directory of Open Access Journals (Sweden)

F. López-Linares

2005-02-01

Full Text Available The solvent effect on the position of the carbonyl vibrational stretching ofacetylferrocene in aprotic media was studied in this work. The solvent-induced shifts in thisorganometallic compound were interpreted in terms of the alternative reaction field model(SCRF-MO proposed by Kolling. In contrast to the established trends for carbonyl groupsin organic systems, the results suggest that the continuum models for the reaction field arenot adequate and that the influence of dipolarity-polarizability described by aninhomogeneous coupling function θ (ε L(n 2 that assumes optical dielectric saturation isresponsible for the carbonyl band shift and, there is empirical evidence that the effect offield-induced intermolecular interaction on band shift, interpreted in terms of the van derWaals forces from the solvent, have a important contribution to this phenomena.

MR chemical shift imaging of human atheroma

International Nuclear Information System (INIS)

Mohiaddin, R.H.; Underwood, R.; Firmin, D.; Abdulla, A.K.; Rees, S.; Longmore, D.

1988-01-01

The lipid content of atheromatous plaques has been measured with chemical shift MR imaging by taking advantage of the different resonance frequencies of protons in lipid and water. Fifteen postmortem aortic specimens of the human descending aorta and the aortae of seven patients with documented peripheral vascular disease were studied at 0.5 T. Spin-echo images were used to localize the lesions before acquisition of the chemical shift images. The specimens were examined histologically, and the lipid distribution in the plaque showed good correlation with the chemical shift data. Validation in vivo and clinical applications remain to be established

Reciprocal carbonyl-carbonyl interactions in small molecules and proteins.

Science.gov (United States)

Rahim, Abdur; Saha, Pinaki; Jha, Kunal Kumar; Sukumar, Nagamani; Sarma, Bani Kanta

2017-07-19

Carbonyl-carbonyl n→π* interactions where a lone pair (n) of the oxygen atom of a carbonyl group is delocalized over the π* orbital of a nearby carbonyl group have attracted a lot of attention in recent years due to their ability to affect the 3D structure of small molecules, polyesters, peptides, and proteins. In this paper, we report the discovery of a "reciprocal" carbonyl-carbonyl interaction with substantial back and forth n→π* and π→π* electron delocalization between neighboring carbonyl groups. We have carried out experimental studies, analyses of crystallographic databases and theoretical calculations to show the presence of this interaction in both small molecules and proteins. In proteins, these interactions are primarily found in polyproline II (PPII) helices. As PPII are the most abundant secondary structures in unfolded proteins, we propose that these local interactions may have implications in protein folding.Carbonyl-carbonyl π* non covalent interactions affect the structure and stability of small molecules and proteins. Here, the authors carry out experimental studies, analyses of crystallographic databases and theoretical calculations to describe an additional type of carbonyl-carbonyl interaction.

DNA damage by carbonyl stress in human skin cells

International Nuclear Information System (INIS)

Roberts, Michael J.; Wondrak, Georg T.; Laurean, Daniel Cervantes; Jacobson, Myron K.; Jacobson, Elaine L.

2003-01-01

Reactive carbonyl species (RCS) are potent mediators of cellular carbonyl stress originating from endogenous chemical processes such as lipid peroxidation and glycation. Skin deterioration as observed in photoaging and diabetes has been linked to accumulative protein damage from glycation, but the effects of carbonyl stress on skin cell genomic integrity are ill defined. In this study, the genotoxic effects of acute carbonyl stress on HaCaT keratinocytes and CF3 fibroblasts were assessed. Administration of the α-dicarbonyl compounds glyoxal and methylglyoxal as physiologically relevant RCS inhibited skin cell proliferation, led to intra-cellular protein glycation as evidenced by the accumulation of N ε -(carboxymethyl)-L-lysine (CML) in histones, and caused extensive DNA strand cleavage as assessed by the comet assay. These effects were prevented by treatment with the carbonyl scavenger D-penicillamine. Both glyoxal and methylglyoxal damaged DNA in intact cells. Glyoxal caused DNA strand breaks while methylglyoxal produced extensive DNA-protein cross-linking as evidenced by pronounced nuclear condensation and total suppression of comet formation. Glycation by glyoxal and methylglyoxal resulted in histone cross-linking in vitro and induced oxygen-dependent cleavage of plasmid DNA, which was partly suppressed by the hydroxyl scavenger mannitol. We suggest that a chemical mechanism of cellular DNA damage by carbonyl stress occurs in which histone glycoxidation is followed by reactive oxygen induced DNA stand breaks. The genotoxic potential of RCS in cultured skin cells and its suppression by a carbonyl scavenger as described in this study have implications for skin damage and carcinogenesis and its prevention by agents selective for carbonyl stress

DNA damage by carbonyl stress in human skin cells

Energy Technology Data Exchange (ETDEWEB)

Roberts, Michael J.; Wondrak, Georg T.; Laurean, Daniel Cervantes; Jacobson, Myron K.; Jacobson, Elaine L

2003-01-28

Reactive carbonyl species (RCS) are potent mediators of cellular carbonyl stress originating from endogenous chemical processes such as lipid peroxidation and glycation. Skin deterioration as observed in photoaging and diabetes has been linked to accumulative protein damage from glycation, but the effects of carbonyl stress on skin cell genomic integrity are ill defined. In this study, the genotoxic effects of acute carbonyl stress on HaCaT keratinocytes and CF3 fibroblasts were assessed. Administration of the {alpha}-dicarbonyl compounds glyoxal and methylglyoxal as physiologically relevant RCS inhibited skin cell proliferation, led to intra-cellular protein glycation as evidenced by the accumulation of N{sup {epsilon}}-(carboxymethyl)-L-lysine (CML) in histones, and caused extensive DNA strand cleavage as assessed by the comet assay. These effects were prevented by treatment with the carbonyl scavenger D-penicillamine. Both glyoxal and methylglyoxal damaged DNA in intact cells. Glyoxal caused DNA strand breaks while methylglyoxal produced extensive DNA-protein cross-linking as evidenced by pronounced nuclear condensation and total suppression of comet formation. Glycation by glyoxal and methylglyoxal resulted in histone cross-linking in vitro and induced oxygen-dependent cleavage of plasmid DNA, which was partly suppressed by the hydroxyl scavenger mannitol. We suggest that a chemical mechanism of cellular DNA damage by carbonyl stress occurs in which histone glycoxidation is followed by reactive oxygen induced DNA stand breaks. The genotoxic potential of RCS in cultured skin cells and its suppression by a carbonyl scavenger as described in this study have implications for skin damage and carcinogenesis and its prevention by agents selective for carbonyl stress.

Probabilistic validation of protein NMR chemical shift assignments

International Nuclear Information System (INIS)

Dashti, Hesam; Tonelli, Marco; Lee, Woonghee; Westler, William M.; Cornilescu, Gabriel; Ulrich, Eldon L.; Markley, John L.

2016-01-01

Data validation plays an important role in ensuring the reliability and reproducibility of studies. NMR investigations of the functional properties, dynamics, chemical kinetics, and structures of proteins depend critically on the correctness of chemical shift assignments. We present a novel probabilistic method named ARECA for validating chemical shift assignments that relies on the nuclear Overhauser effect data. ARECA has been evaluated through its application to 26 case studies and has been shown to be complementary to, and usually more reliable than, approaches based on chemical shift databases. ARECA is available online at http://areca.nmrfam.wisc.edu/ http://areca.nmrfam.wisc.edu/

Probabilistic validation of protein NMR chemical shift assignments

Energy Technology Data Exchange (ETDEWEB)

Dashti, Hesam [University of Wisconsin-Madison, Graduate Program in Biophysics, Biochemistry Department (United States); Tonelli, Marco; Lee, Woonghee; Westler, William M.; Cornilescu, Gabriel [University of Wisconsin-Madison, Biochemistry Department, National Magnetic Resonance Facility at Madison (United States); Ulrich, Eldon L. [University of Wisconsin-Madison, BioMagResBank, Biochemistry Department (United States); Markley, John L., E-mail: markley@nmrfam.wisc.edu, E-mail: jmarkley@wisc.edu [University of Wisconsin-Madison, Biochemistry Department, National Magnetic Resonance Facility at Madison (United States)

2016-01-15

Data validation plays an important role in ensuring the reliability and reproducibility of studies. NMR investigations of the functional properties, dynamics, chemical kinetics, and structures of proteins depend critically on the correctness of chemical shift assignments. We present a novel probabilistic method named ARECA for validating chemical shift assignments that relies on the nuclear Overhauser effect data. ARECA has been evaluated through its application to 26 case studies and has been shown to be complementary to, and usually more reliable than, approaches based on chemical shift databases. ARECA is available online at http://areca.nmrfam.wisc.edu/ http://areca.nmrfam.wisc.edu/.

13C NMR investigation of the structure of cationic carbonyls in transition metal zeolites

International Nuclear Information System (INIS)

Ben Taarit, Y.

1979-01-01

13 C NMR spectroscopy was used to investigate the nature of carbon monoxide adsorbed on transition metal ions hosted in a synthetic faujastite type zeolite. The adsorbed CO species was characterised by a highly shielded carbon nucleus. Using the Pople approximation for the paramagnetic shielding term, the observed chemical shift was rationalised assuming the formation of a cationic carbonyl species with an appreciable electronic transfer from the carbon lone pair to the transition metal ion and negligible π back-bonding if at all. (Auth.)

Counterion influence on chemical shifts in strychnine salts

Energy Technology Data Exchange (ETDEWEB)

Metaxas, Athena E.; Cort, John R.

2013-05-01

The highly toxic plant alkaloid strychnine is often isolated in the form of the anion salt of its protonated tertiary amine. Here we characterize the relative influence of different counterions on 1H and 13C chemical shifts in several strychnine salts in D2O, methanol-d4 (CD3OD) and chloroform-d (CDCl3) solvents. In organic solvents, but not in water, substantial variation in chemical shifts of protons near the tertiary amine was observed among different salts. These secondary shifts reveal differences in the way each anion influences electronic structure within the protonated amine. The distributions of secondary shifts allow salts to be easily distinguished from each other as well as from the free base form. The observed effects are much greater in organic solvents than in water. Slight concentration-dependence in chemical shifts of some protons near the amine was observed for two salts in CDCl3, but this effect is small compared to the influence of the counterion. Distinct chemical shifts in different salt forms of the same compound may be useful as chemical forensic signatures for source attribution and sample matching of alkaloids such as strychnine and possibly other organic acid and base salts.

A probabilistic approach for validating protein NMR chemical shift assignments

International Nuclear Information System (INIS)

Wang Bowei; Wang, Yunjun; Wishart, David S.

2010-01-01

It has been estimated that more than 20% of the proteins in the BMRB are improperly referenced and that about 1% of all chemical shift assignments are mis-assigned. These statistics also reflect the likelihood that any newly assigned protein will have shift assignment or shift referencing errors. The relatively high frequency of these errors continues to be a concern for the biomolecular NMR community. While several programs do exist to detect and/or correct chemical shift mis-referencing or chemical shift mis-assignments, most can only do one, or the other. The one program (SHIFTCOR) that is capable of handling both chemical shift mis-referencing and mis-assignments, requires the 3D structure coordinates of the target protein. Given that chemical shift mis-assignments and chemical shift re-referencing issues should ideally be addressed prior to 3D structure determination, there is a clear need to develop a structure-independent approach. Here, we present a new structure-independent protocol, which is based on using residue-specific and secondary structure-specific chemical shift distributions calculated over small (3-6 residue) fragments to identify mis-assigned resonances. The method is also able to identify and re-reference mis-referenced chemical shift assignments. Comparisons against existing re-referencing or mis-assignment detection programs show that the method is as good or superior to existing approaches. The protocol described here has been implemented into a freely available Java program called 'Probabilistic Approach for protein Nmr Assignment Validation (PANAV)' and as a web server (http://redpoll.pharmacy.ualberta.ca/PANAVhttp://redpoll.pharmacy.ualberta.ca/PANAV) which can be used to validate and/or correct as well as re-reference assigned protein chemical shifts.

Rapid and reliable protein structure determination via chemical shift threading.

Science.gov (United States)

Hafsa, Noor E; Berjanskii, Mark V; Arndt, David; Wishart, David S

2018-01-01

Protein structure determination using nuclear magnetic resonance (NMR) spectroscopy can be both time-consuming and labor intensive. Here we demonstrate how chemical shift threading can permit rapid, robust, and accurate protein structure determination using only chemical shift data. Threading is a relatively old bioinformatics technique that uses a combination of sequence information and predicted (or experimentally acquired) low-resolution structural data to generate high-resolution 3D protein structures. The key motivations behind using NMR chemical shifts for protein threading lie in the fact that they are easy to measure, they are available prior to 3D structure determination, and they contain vital structural information. The method we have developed uses not only sequence and chemical shift similarity but also chemical shift-derived secondary structure, shift-derived super-secondary structure, and shift-derived accessible surface area to generate a high quality protein structure regardless of the sequence similarity (or lack thereof) to a known structure already in the PDB. The method (called E-Thrifty) was found to be very fast (often chemical shift refinement, these results suggest that protein structure determination, using only NMR chemical shifts, is becoming increasingly practical and reliable. E-Thrifty is available as a web server at http://ethrifty.ca .

Ozone Effects on Protein Carbonyl Content in the Frontal ...

Science.gov (United States)

Oxidative stress (OS) plays an important role in susceptibility and disease in old age. Understanding age-related susceptibility is a critical part of community-based human health risk assessment of chemical exposures. There is growing concern over a common air pollutant, ozone (03), and adverse health effects including dysfunction of the pulmonary, cardiac, and nervous systems. The objective of this study was to test whether OS plays a role in the adverse effects caused by 03 exposure, and if so, if effects were age-dependent. We selected protein carbonyl as an indicator of OS because carbonyl content of cells is a useful indicator of oxidative protein damage and has been linked to chemical-induced adverse effects. Male Brown Norway rats (4, 12, and 24 months) were exposed to 03 (0,0.25 or 1 ppm) via inhalation for 6 h/day, 2 days per week for 13 weeks. Frontal cortex (FC) and cerebellum (CB) were dissected, quick frozen on dry ice, and stored at -80°C. Protein carbonyls were assayed using commercial kits. Hydrogen peroxide, a positive control, increased protein carbonyls in cortical tissue in vitro in a concentration-dependent manner. Significant effects of age on protein carbonyls in FC and a significant effect of age and 03 dose on protein carbonyls in CB were observed. In control rats, there was an age-dependent increase in protein carbonyls indicating increased OS in 12 and 24 month old rats compared to 4 month old rats. Although 03 increase

Carbonyl Compounds Generated from Electronic Cigarettes

Directory of Open Access Journals (Sweden)

Kanae Bekki

2014-10-01

Full Text Available Electronic cigarettes (e-cigarettes are advertised as being safer than tobacco cigarettes products as the chemical compounds inhaled from e-cigarettes are believed to be fewer and less toxic than those from tobacco cigarettes. Therefore, continuous careful monitoring and risk management of e-cigarettes should be implemented, with the aim of protecting and promoting public health worldwide. Moreover, basic scientific data are required for the regulation of e-cigarette. To date, there have been reports of many hazardous chemical compounds generated from e-cigarettes, particularly carbonyl compounds such as formaldehyde, acetaldehyde, acrolein, and glyoxal, which are often found in e-cigarette aerosols. These carbonyl compounds are incidentally generated by the oxidation of e-liquid (liquid in e-cigarette; glycerol and glycols when the liquid comes in contact with the heated nichrome wire. The compositions and concentrations of these compounds vary depending on the type of e-liquid and the battery voltage. In some cases, extremely high concentrations of these carbonyl compounds are generated, and may contribute to various health effects. Suppliers, risk management organizations, and users of e-cigarettes should be aware of this phenomenon.

Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information

International Nuclear Information System (INIS)

Fritzsching, K. J.; Yang, Y.; Schmidt-Rohr, K.; Hong Mei

2013-01-01

We introduce a Python-based program that utilizes the large database of 13 C and 15 N chemical shifts in the Biological Magnetic Resonance Bank to rapidly predict the amino acid type and secondary structure from correlated chemical shifts. The program, called PACSYlite Unified Query (PLUQ), is designed to help assign peaks obtained from 2D 13 C– 13 C, 15 N– 13 C, or 3D 15 N– 13 C– 13 C magic-angle-spinning correlation spectra. We show secondary-structure specific 2D 13 C– 13 C correlation maps of all twenty amino acids, constructed from a chemical shift database of 262,209 residues. The maps reveal interesting conformation-dependent chemical shift distributions and facilitate searching of correlation peaks during amino-acid type assignment. Based on these correlations, PLUQ outputs the most likely amino acid types and the associated secondary structures from inputs of experimental chemical shifts. We test the assignment accuracy using four high-quality protein structures. Based on only the Cα and Cβ chemical shifts, the highest-ranked PLUQ assignments were 40–60 % correct in both the amino-acid type and the secondary structure. For three input chemical shifts (CO–Cα–Cβ or N–Cα–Cβ), the first-ranked assignments were correct for 60 % of the residues, while within the top three predictions, the correct assignments were found for 80 % of the residues. PLUQ and the chemical shift maps are expected to be useful at the first stage of sequential assignment, for combination with automated sequential assignment programs, and for highly disordered proteins for which secondary structure analysis is the main goal of structure determination.

1H NMR spectra. Part 30(+): 1H chemical shifts in amides and the magnetic anisotropy, electric field and steric effects of the amide group.

Science.gov (United States)

Abraham, Raymond J; Griffiths, Lee; Perez, Manuel

2013-03-01

The (1)H spectra of 37 amides in CDCl(3) solvent were analysed and the chemical shifts obtained. The molecular geometries and conformational analysis of these amides were considered in detail. The NMR spectral assignments are of interest, e.g. the assignments of the formamide NH(2) protons reverse in going from CDCl(3) to more polar solvents. The substituent chemical shifts of the amide group in both aliphatic and aromatic amides were analysed using an approach based on neural network data for near (≤3 bonds removed) protons and the electric field, magnetic anisotropy, steric and for aromatic systems π effects of the amide group for more distant protons. The electric field is calculated from the partial atomic charges on the N.C═O atoms of the amide group. The magnetic anisotropy of the carbonyl group was reproduced with the asymmetric magnetic anisotropy acting at the midpoint of the carbonyl bond. The values of the anisotropies Δχ(parl) and Δχ(perp) were for the aliphatic amides 10.53 and -23.67 (×10(-6) Å(3)/molecule) and for the aromatic amides 2.12 and -10.43 (×10(-6) Å(3)/molecule). The nitrogen anisotropy was 7.62 (×10(-6) Å(3)/molecule). These values are compared with previous literature values. The (1)H chemical shifts were calculated from the semi-empirical approach and also by gauge-independent atomic orbital calculations with the density functional theory method and B3LYP/6-31G(++) (d,p) basis set. The semi-empirical approach gave good agreement with root mean square error of 0.081 ppm for the data set of 280 entries. The gauge-independent atomic orbital approach was generally acceptable, but significant errors (ca. 1 ppm) were found for the NH and CHO protons and also for some other protons. Copyright © 2013 John Wiley & Sons, Ltd.

Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information

Energy Technology Data Exchange (ETDEWEB)

Fritzsching, K. J.; Yang, Y.; Schmidt-Rohr, K.; Hong Mei, E-mail: mhong@iastate.edu [Iowa State University, Department of Chemistry (United States)

2013-06-15

We introduce a Python-based program that utilizes the large database of {sup 13}C and {sup 15}N chemical shifts in the Biological Magnetic Resonance Bank to rapidly predict the amino acid type and secondary structure from correlated chemical shifts. The program, called PACSYlite Unified Query (PLUQ), is designed to help assign peaks obtained from 2D {sup 13}C-{sup 13}C, {sup 15}N-{sup 13}C, or 3D {sup 15}N-{sup 13}C-{sup 13}C magic-angle-spinning correlation spectra. We show secondary-structure specific 2D {sup 13}C-{sup 13}C correlation maps of all twenty amino acids, constructed from a chemical shift database of 262,209 residues. The maps reveal interesting conformation-dependent chemical shift distributions and facilitate searching of correlation peaks during amino-acid type assignment. Based on these correlations, PLUQ outputs the most likely amino acid types and the associated secondary structures from inputs of experimental chemical shifts. We test the assignment accuracy using four high-quality protein structures. Based on only the C{alpha} and C{beta} chemical shifts, the highest-ranked PLUQ assignments were 40-60 % correct in both the amino-acid type and the secondary structure. For three input chemical shifts (CO-C{alpha}-C{beta} or N-C{alpha}-C{beta}), the first-ranked assignments were correct for 60 % of the residues, while within the top three predictions, the correct assignments were found for 80 % of the residues. PLUQ and the chemical shift maps are expected to be useful at the first stage of sequential assignment, for combination with automated sequential assignment programs, and for highly disordered proteins for which secondary structure analysis is the main goal of structure determination.

Empirical correlation between protein backbone {sup 15}N and {sup 13}C secondary chemical shifts and its application to nitrogen chemical shift re-referencing

Energy Technology Data Exchange (ETDEWEB)

Wang Liya [Cold Spring Harbor Laboratory (United States); Markley, John L. [University of Wisconsin, Biochemistry Department (United States)], E-mail: markley@nmrfam.wisc.edu

2009-06-15

The linear analysis of chemical shifts (LACS) has provided a robust method for identifying and correcting {sup 13}C chemical shift referencing problems in data from protein NMR spectroscopy. Unlike other approaches, LACS does not require prior knowledge of the three-dimensional structure or inference of the secondary structure of the protein. It also does not require extensive assignment of the NMR data. We report here a way of extending the LACS approach to {sup 15}N NMR data from proteins, so as to enable the detection and correction of inconsistencies in chemical shift referencing for this nucleus. The approach is based on our finding that the secondary {sup 15}N chemical shift of the backbone nitrogen atom of residue i is strongly correlated with the secondary chemical shift difference (experimental minus random coil) between the alpha and beta carbons of residue i - 1. Thus once alpha and beta {sup 13}C chemical shifts are available (their difference is referencing error-free), the {sup 15}N referencing can be validated, and an appropriate offset correction can be derived. This approach can be implemented prior to a structure determination and can be used to analyze potential referencing problems in database data not associated with three-dimensional structure. Application of the LACS algorithm to the current BMRB protein chemical shift database, revealed that nearly 35% of the BMRB entries have {delta}{sup 15}N values mis-referenced by over 0.7 ppm and over 25% of them have {delta}{sup 1}H{sup N} values mis-referenced by over 0.12 ppm. One implication of the findings reported here is that a backbone {sup 15}N chemical shift provides a better indicator of the conformation of the preceding residue than of the residue itself.

Unraveling the meaning of chemical shifts in protein NMR.

Science.gov (United States)

Berjanskii, Mark V; Wishart, David S

2017-11-01

Chemical shifts are among the most informative parameters in protein NMR. They provide wealth of information about protein secondary and tertiary structure, protein flexibility, and protein-ligand binding. In this report, we review the progress in interpreting and utilizing protein chemical shifts that has occurred over the past 25years, with a particular focus on the large body of work arising from our group and other Canadian NMR laboratories. More specifically, this review focuses on describing, assessing, and providing some historical context for various chemical shift-based methods to: (1) determine protein secondary and super-secondary structure; (2) derive protein torsion angles; (3) assess protein flexibility; (4) predict residue accessible surface area; (5) refine 3D protein structures; (6) determine 3D protein structures and (7) characterize intrinsically disordered proteins. This review also briefly covers some of the methods that we previously developed to predict chemical shifts from 3D protein structures and/or protein sequence data. It is hoped that this review will help to increase awareness of the considerable utility of NMR chemical shifts in structural biology and facilitate more widespread adoption of chemical-shift based methods by the NMR spectroscopists, structural biologists, protein biophysicists, and biochemists worldwide. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.

Toward structural dynamics: protein motions viewed by chemical shift modulations and direct detection of C'N multiple-quantum relaxation.

Science.gov (United States)

Mori, Mirko; Kateb, Fatiha; Bodenhausen, Geoffrey; Piccioli, Mario; Abergel, Daniel

2010-03-17

Multiple quantum relaxation in proteins reveals unexpected relationships between correlated or anti-correlated conformational backbone dynamics in alpha-helices or beta-sheets. The contributions of conformational exchange to the relaxation rates of C'N coherences (i.e., double- and zero-quantum coherences involving backbone carbonyl (13)C' and neighboring amide (15)N nuclei) depend on the kinetics of slow exchange processes, as well as on the populations of the conformations and chemical shift differences of (13)C' and (15)N nuclei. The relaxation rates of C'N coherences, which reflect concerted fluctuations due to slow chemical shift modulations (CSMs), were determined by direct (13)C detection in diamagnetic and paramagnetic proteins. In well-folded proteins such as lanthanide-substituted calbindin (CaLnCb), copper,zinc superoxide dismutase (Cu,Zn SOD), and matrix metalloproteinase (MMP12), slow conformational exchange occurs along the entire backbone. Our observations demonstrate that relaxation rates of C'N coherences arising from slow backbone dynamics have positive signs (characteristic of correlated fluctuations) in beta-sheets and negative signs (characteristic of anti-correlated fluctuations) in alpha-helices. This extends the prospects of structure-dynamics relationships to slow time scales that are relevant for protein function and enzymatic activity.

Evaluating amber force fields using computed NMR chemical shifts.

Science.gov (United States)

Koes, David R; Vries, John K

2017-10-01

NMR chemical shifts can be computed from molecular dynamics (MD) simulations using a template matching approach and a library of conformers containing chemical shifts generated from ab initio quantum calculations. This approach has potential utility for evaluating the force fields that underlie these simulations. Imperfections in force fields generate flawed atomic coordinates. Chemical shifts obtained from flawed coordinates have errors that can be traced back to these imperfections. We use this approach to evaluate a series of AMBER force fields that have been refined over the course of two decades (ff94, ff96, ff99SB, ff14SB, ff14ipq, and ff15ipq). For each force field a series of MD simulations are carried out for eight model proteins. The calculated chemical shifts for the 1 H, 15 N, and 13 C a atoms are compared with experimental values. Initial evaluations are based on root mean squared (RMS) errors at the protein level. These results are further refined based on secondary structure and the types of atoms involved in nonbonded interactions. The best chemical shift for identifying force field differences is the shift associated with peptide protons. Examination of the model proteins on a residue by residue basis reveals that force field performance is highly dependent on residue position. Examination of the time course of nonbonded interactions at these sites provides explanations for chemical shift differences at the atomic coordinate level. Results show that the newer ff14ipq and ff15ipq force fields developed with the implicitly polarized charge method perform better than the older force fields. © 2017 Wiley Periodicals, Inc.

Relative Configuration of Natural Products Using NMR Chemical Shifts

Science.gov (United States)

By comparing calculated with experimental NMR chemical shifts, we were able to determine the relative configurations of three monoterpene diastereomers produced by the walkingstick Anisomorpha buprestoides. The combined RMSDs of both 1H and 13C quantum chemically calculated shifts were able to predi...

SimShiftDB; local conformational restraints derived from chemical shift similarity searches on a large synthetic database

Energy Technology Data Exchange (ETDEWEB)

Ginzinger, Simon W. [Center of Applied Molecular Engineering, University of Salzburg, Department of Molecular Biology, Division of Bioinformatics (Austria)], E-mail: simon@came.sbg.ac.at; Coles, Murray [Max-Planck-Institute for Developmental Biology, Department of Protein Evolution (Germany)], E-mail: Murray.Coles@tuebingen.mpg.de

2009-03-15

We present SimShiftDB, a new program to extract conformational data from protein chemical shifts using structural alignments. The alignments are obtained in searches of a large database containing 13,000 structures and corresponding back-calculated chemical shifts. SimShiftDB makes use of chemical shift data to provide accurate results even in the case of low sequence similarity, and with even coverage of the conformational search space. We compare SimShiftDB to HHSearch, a state-of-the-art sequence-based search tool, and to TALOS, the current standard tool for the task. We show that for a significant fraction of the predicted similarities, SimShiftDB outperforms the other two methods. Particularly, the high coverage afforded by the larger database often allows predictions to be made for residues not involved in canonical secondary structure, where TALOS predictions are both less frequent and more error prone. Thus SimShiftDB can be seen as a complement to currently available methods.

SimShiftDB; local conformational restraints derived from chemical shift similarity searches on a large synthetic database

International Nuclear Information System (INIS)

Ginzinger, Simon W.; Coles, Murray

2009-01-01

We present SimShiftDB, a new program to extract conformational data from protein chemical shifts using structural alignments. The alignments are obtained in searches of a large database containing 13,000 structures and corresponding back-calculated chemical shifts. SimShiftDB makes use of chemical shift data to provide accurate results even in the case of low sequence similarity, and with even coverage of the conformational search space. We compare SimShiftDB to HHSearch, a state-of-the-art sequence-based search tool, and to TALOS, the current standard tool for the task. We show that for a significant fraction of the predicted similarities, SimShiftDB outperforms the other two methods. Particularly, the high coverage afforded by the larger database often allows predictions to be made for residues not involved in canonical secondary structure, where TALOS predictions are both less frequent and more error prone. Thus SimShiftDB can be seen as a complement to currently available methods

Role of quantitative chemical shift magnetic resonance imaging and chemical shift subtraction technique in discriminating adenomatous from non adenomatous adrenal solid lesions

Directory of Open Access Journals (Sweden)

Ahmed H. Afifi

2017-03-01

Conclusion: The signal intensity index and adrenal to spleen ratio are the most reliable quantitative chemical shift MRI methods in differentiation of adrenal adenomas from other non-adenomatous adrenal solid lesions. Chemical shift subtraction MRI is a recent technique that gives highly confident discrimination between two categories of pathology without using of any reference organ.

PPM-One: a static protein structure based chemical shift predictor

International Nuclear Information System (INIS)

Li, Dawei; Brüschweiler, Rafael

2015-01-01

We mined the most recent editions of the BioMagResDataBank and the protein data bank to parametrize a new empirical knowledge-based chemical shift predictor of protein backbone atoms using either a linear or an artificial neural network model. The resulting chemical shift predictor PPM-One accepts a single static 3D structure as input and emulates the effect of local protein dynamics via interatomic steric contacts. Furthermore, the chemical shift prediction was extended to most side-chain protons and it is found that the prediction accuracy is at a level allowing an independent assessment of stereospecific assignments. For a previously established set of test proteins some overall improvement was achieved over current top-performing chemical shift prediction programs

A robust algorithm for optimizing protein structures with NMR chemical shifts

Energy Technology Data Exchange (ETDEWEB)

Berjanskii, Mark; Arndt, David; Liang, Yongjie; Wishart, David S., E-mail: david.wishart@ualberta.ca [University of Alberta, Department of Computing Science (Canada)

2015-11-15

Over the past decade, a number of methods have been developed to determine the approximate structure of proteins using minimal NMR experimental information such as chemical shifts alone, sparse NOEs alone or a combination of comparative modeling data and chemical shifts. However, there have been relatively few methods that allow these approximate models to be substantively refined or improved using the available NMR chemical shift data. Here, we present a novel method, called Chemical Shift driven Genetic Algorithm for biased Molecular Dynamics (CS-GAMDy), for the robust optimization of protein structures using experimental NMR chemical shifts. The method incorporates knowledge-based scoring functions and structural information derived from NMR chemical shifts via a unique combination of multi-objective MD biasing, a genetic algorithm, and the widely used XPLOR molecular modelling language. Using this approach, we demonstrate that CS-GAMDy is able to refine and/or fold models that are as much as 10 Å (RMSD) away from the correct structure using only NMR chemical shift data. CS-GAMDy is also able to refine of a wide range of approximate or mildly erroneous protein structures to more closely match the known/correct structure and the known/correct chemical shifts. We believe CS-GAMDy will allow protein models generated by sparse restraint or chemical-shift-only methods to achieve sufficiently high quality to be considered fully refined and “PDB worthy”. The CS-GAMDy algorithm is explained in detail and its performance is compared over a range of refinement scenarios with several commonly used protein structure refinement protocols. The program has been designed to be easily installed and easily used and is available at http://www.gamdy.ca http://www.gamdy.ca.

The PROSECCO server for chemical shift predictions in ordered and disordered proteins.

Science.gov (United States)

Sanz-Hernández, Máximo; De Simone, Alfonso

2017-11-01

The chemical shifts measured in solution-state and solid-state nuclear magnetic resonance (NMR) are powerful probes of the structure and dynamics of protein molecules. The exploitation of chemical shifts requires methods to correlate these data with the protein structures and sequences. We present here an approach to calculate accurate chemical shifts in both ordered and disordered proteins using exclusively the information contained in their sequences. Our sequence-based approach, protein sequences and chemical shift correlations (PROSECCO), achieves the accuracy of the most advanced structure-based methods in the characterization of chemical shifts of folded proteins and improves the state of the art in the study of disordered proteins. Our analyses revealed fundamental insights on the structural information carried by NMR chemical shifts of structured and unstructured protein states.

Chemical Shift Imaging (CSI) by precise object displacement

OpenAIRE

Leclerc, Sebastien; Trausch, Gregory; Cordier, Benoit; Grandclaude, Denis; Retournard, Alain; Fraissard, Jacques; Canet, Daniel

2006-01-01

International audience; A mechanical device (NMR lift) has been built for displacing vertically an object (typically a NMR sample tube) inside the NMR probe with an accuracy of 1 Μm. A series of single pulse experiments are performed for incremented vertical positions of the sample. With a sufficiently spatially selective rf field, one obtains chemical shift information along the displacement direction (one dimensional Chemical Shift Imaging – CSI). Knowing the vertical radio-frequency (rf) f...

Catalytic production of metal carbonyls from metal oxides

Science.gov (United States)

Sapienza, Richard S.; Slegeir, William A.; Foran, Michael T.

1984-01-01

This invention relates to the formation of metal carbonyls from metal oxides and specially the formation of molybdenum carbonyl and iron carbonyl from their respective oxides. Copper is used here in admixed form or used in chemically combined form as copper molybdate. The copper/metal oxide combination or combined copper is utilized with a solvent, such as toluene and subjected to carbon monoxide pressure of 25 atmospheres or greater at about 150.degree.-260.degree. C. The reducing metal copper is employed in catalytic concentrations or combined concentrations as CuMoO.sub.4 and both hydrogen and water present serve as promoters. It has been found that the yields by this process have been salutary and that additionally the catalytic metal may be reused in the process to good effect.

Chemical shifts of oxygen-17 NMR in polyoxotungstates

International Nuclear Information System (INIS)

Kazanskij, L.P.; Fedotov, M.A.; Spitsyn, V.I.

1977-01-01

17 O NMR spectra of aqueous solutions containing paratungstate BH 2 W 12 O 42 10- and metatungstate H 2 W 12 O 40 6- anions have been measured. On the basis of the obtained data a scale of chemical shifts for oxygen atoms connected by various bonds with tungsten atoms is suggested. The obtained data are compared with the Raman spectra of crystalline salts and their aqueous solutions. Chemical shifts of 17 O NMR spectra have been also measured in other heteropolyanions

Correlation of chemical shifts predicted by molecular dynamics simulations for partially disordered proteins

Energy Technology Data Exchange (ETDEWEB)

Karp, Jerome M.; Erylimaz, Ertan; Cowburn, David, E-mail: cowburn@cowburnlab.org, E-mail: David.cowburn@einstein.yu.edu [Albert Einstein College of Medicine of Yeshiva University, Department of Biochemistry (United States)

2015-01-15

There has been a longstanding interest in being able to accurately predict NMR chemical shifts from structural data. Recent studies have focused on using molecular dynamics (MD) simulation data as input for improved prediction. Here we examine the accuracy of chemical shift prediction for intein systems, which have regions of intrinsic disorder. We find that using MD simulation data as input for chemical shift prediction does not consistently improve prediction accuracy over use of a static X-ray crystal structure. This appears to result from the complex conformational ensemble of the disordered protein segments. We show that using accelerated molecular dynamics (aMD) simulations improves chemical shift prediction, suggesting that methods which better sample the conformational ensemble like aMD are more appropriate tools for use in chemical shift prediction for proteins with disordered regions. Moreover, our study suggests that data accurately reflecting protein dynamics must be used as input for chemical shift prediction in order to correctly predict chemical shifts in systems with disorder.

Nucleic acid helix structure determination from NMR proton chemical shifts

Energy Technology Data Exchange (ETDEWEB)

Werf, Ramon M. van der; Tessari, Marco; Wijmenga, Sybren S., E-mail: S.Wijmenga@science.ru.nl [Radboud University Nijmegen, Department of Biophysical Chemistry, Institute of Molecules and Materials (Netherlands)

2013-06-15

We present a method for de novo derivation of the three-dimensional helix structure of nucleic acids using non-exchangeable proton chemical shifts as sole source of experimental restraints. The method is called chemical shift de novo structure derivation protocol employing singular value decomposition (CHEOPS) and uses iterative singular value decomposition to optimize the structure in helix parameter space. The correct performance of CHEOPS and its range of application are established via an extensive set of structure derivations using either simulated or experimental chemical shifts as input. The simulated input data are used to assess in a defined manner the effect of errors or limitations in the input data on the derived structures. We find that the RNA helix parameters can be determined with high accuracy. We finally demonstrate via three deposited RNA structures that experimental proton chemical shifts suffice to derive RNA helix structures with high precision and accuracy. CHEOPS provides, subject to further development, new directions for high-resolution NMR structure determination of nucleic acids.

Accessible surface area from NMR chemical shifts

Energy Technology Data Exchange (ETDEWEB)

Hafsa, Noor E.; Arndt, David; Wishart, David S., E-mail: david.wishart@ualberta.ca [University of Alberta, Department of Computing Science (Canada)

2015-07-15

Accessible surface area (ASA) is the surface area of an atom, amino acid or biomolecule that is exposed to solvent. The calculation of a molecule’s ASA requires three-dimensional coordinate data and the use of a “rolling ball” algorithm to both define and calculate the ASA. For polymers such as proteins, the ASA for individual amino acids is closely related to the hydrophobicity of the amino acid as well as its local secondary and tertiary structure. For proteins, ASA is a structural descriptor that can often be as informative as secondary structure. Consequently there has been considerable effort over the past two decades to try to predict ASA from protein sequence data and to use ASA information (derived from chemical modification studies) as a structure constraint. Recently it has become evident that protein chemical shifts are also sensitive to ASA. Given the potential utility of ASA estimates as structural constraints for NMR we decided to explore this relationship further. Using machine learning techniques (specifically a boosted tree regression model) we developed an algorithm called “ShiftASA” that combines chemical-shift and sequence derived features to accurately estimate per-residue fractional ASA values of water-soluble proteins. This method showed a correlation coefficient between predicted and experimental values of 0.79 when evaluated on a set of 65 independent test proteins, which was an 8.2 % improvement over the next best performing (sequence-only) method. On a separate test set of 92 proteins, ShiftASA reported a mean correlation coefficient of 0.82, which was 12.3 % better than the next best performing method. ShiftASA is available as a web server ( http://shiftasa.wishartlab.com http://shiftasa.wishartlab.com ) for submitting input queries for fractional ASA calculation.

Identifying secondary structures in proteins using NMR chemical shift 3D correlation maps

Science.gov (United States)

Kumari, Amrita; Dorai, Kavita

2013-06-01

NMR chemical shifts are accurate indicators of molecular environment and have been extensively used as aids in protein structure determination. This work focuses on creating empirical 3D correlation maps of backbone chemical shift nuclei for use as identifiers of secondary structure elements in proteins. A correlated database of backbone nuclei chemical shifts was constructed from experimental structural data gathered from entries in the Protein Data Bank (PDB) as well as isotropic chemical shift values from the RefDB database. Rigorous statistical analysis of the maps led to the conclusion that specific correlations between triplets of backbone chemical shifts are best able to differentiate between different secondary structures such as α-helices, β-strands and turns. The method is compared with similar techniques that use NMR chemical shift information as aids in biomolecular structure determination and performs well in tests done on experimental data determined for different types of proteins, including large multi-domain proteins and membrane proteins.

Prediction of Xaa-Pro peptide bond conformation from sequence and chemical shifts

Energy Technology Data Exchange (ETDEWEB)

Shen Yang; Bax, Ad, E-mail: bax@nih.go [National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Laboratory of Chemical Physics (United States)

2010-03-15

We present a program, named Promega, to predict the Xaa-Pro peptide bond conformation on the basis of backbone chemical shifts and the amino acid sequence. Using a chemical shift database of proteins of known structure together with the PDB-extracted amino acid preference of cis Xaa-Pro peptide bonds, a cis/trans probability score is calculated from the backbone and {sup 13}C{sup {beta}} chemical shifts of the proline and its neighboring residues. For an arbitrary number of input chemical shifts, which may include Pro-{sup 13}C{sup {gamma}}, Promega calculates the statistical probability that a Xaa-Pro peptide bond is cis. Besides its potential as a validation tool, Promega is particularly useful for studies of larger proteins where Pro-{sup 13}C{sup {gamma}} assignments can be challenging, and for on-going efforts to determine protein structures exclusively on the basis of backbone and {sup 13}C{sup {beta}} chemical shifts.

Protein Structure Determination Using Chemical Shifts

DEFF Research Database (Denmark)

Christensen, Anders Steen

is determined using only chemical shifts recorded and assigned through automated processes. The CARMSD to the experimental X-ray for this structure is 1.1. Å. Additionally, the method is combined with very sparse NOE-restraints and evolutionary distance restraints and tested on several protein structures >100...

Carbonyl atmospheric reaction products of aromatic hydrocarbons in ambient air

Science.gov (United States)

Obermeyer, Genevieve; Aschmann, Sara M.; Atkinson, Roger; Arey, Janet

To convert gaseous carbonyls to oximes during sampling, an XAD-4 resin denuder system pre-coated with O-(2,3,4,5,6-pentafluorobenzyl)hydroxylamine and followed by analysis with methane positive chemical ionization gas chromatography/mass spectrometry was used to measure carbonyls in ambient air samples in Riverside, CA. In conjunction with similar analyses of environmental chamber OH radical-initiated reactions of o- and p-xylene, 1,2,4-trimethylbenzene, ethylbenzene, 4-hydroxy-2-butanone and 1,4-butanediol, we identified benzaldehyde, o-, m- and p-tolualdehyde and acetophenone and the dicarbonyls glyoxal, methylglyoxal, biacetyl, ethylglyoxal, 1,4-butenedial, 3-hexene-2,5-dione, 3-oxo-butanal, 1,4-butanedial and malonaldehyde in the ambient air samples. As discussed, these carbonyls and dicarbonyls can be formed from the OH radical-initiated reactions of aromatic hydrocarbons and other volatile organic compounds emitted into the atmosphere, and we conclude that in situ atmospheric formation is a major source of these carbonyls in our Riverside, CA, ambient air samples.

Protein carbonylation in plants

DEFF Research Database (Denmark)

Møller, Ian Max; Havelund, Jesper; Rogowska-Wrzesinska, Adelina

2017-01-01

This chapter provides an overview of the current knowledge on protein carbonylation in plants and its role in plant physiology. It starts with a brief outline of the turnover and production sites of reactive oxygen species (ROS) in plants and the causes of protein carbonylation. This is followed...... by a description of the methods used to study protein carbonylation in plants, which is also very brief as the methods are similar to those used in studies on animals. The chapter also focuses on protein carbonylation in plants in general and in mitochondria and in seeds in particular, as case stories where...... specific carbonylated proteins have been identified. Protein carbonylation appears to accumulate at all stages of seed development and germination investigated to date. In some cases, such as seed aging, it is probably simply an accumulation of oxidative damage. However, in other cases protein...

Structure and Reactivity of Zeolite- and Carbon-Supported Catalysts for the Oxidative Carbonylation of Alcohols

OpenAIRE

Briggs, Daniel Neal

2010-01-01

AbstractStructure and Reactivity of Zeolite- and Carbon-Supported Catalysts for the Oxidative Carbonylation of AlcoholsbyDaniel Neal BriggsDoctor of Philosophy in Chemical EngineeringUniversity of California, BerkeleyProfessor Alexis T. Bell, Chair The oxidative carbonylation of alcohols to produce dialkyl carbonates is a process that takes place commercially in a slurry of cuprous chloride in the appropriate alcohol. While this process is chemically efficient, it incurs costs in terms of ene...

Further conventions for NMR shielding and chemical shifts (IUPAC Recommendations 2008)

Energy Technology Data Exchange (ETDEWEB)

Harris, R.K. [University of Durham, Durham (United Kingdom). Dept. of Chemistry; Becker, E.D. [National Institutes of Health, Bethesda, MD (United States); Menezes, S.M. Cabral de [PETROBRAS, Rio de Janeiro, RJ (Brazil). Centro de Pesquisas (CENPES); Granger, P. [University Louis Pasteur, Strasbourg (France). Inst. of Chemistry; Hoffman, R.E. [The Hebrew University of Jerusalem, Safra Campus, Jerusalem (Israel). Dept. of Organic Chemistry; Zilm, K.W., E-mail: r.k.harris@durham.ac.uk [Yale University, New Haven, CT (United States). Dept. of Chemistry

2008-07-01

IUPAC has published a number of recommendations regarding the reporting of nuclear magnetic resonance (NMR) data, especially chemical shifts. The most recent publication [Pure Appl. Chem. 73, 1795 (2001)] recommended that tetramethylsilane (TMS) serve as a universal reference for reporting the shifts of all nuclides, but it deferred recommendations for several aspects of this subject. This document first examines the extent to which the {sup 1}H shielding in TMS itself is subject to change by variation in temperature, concentration, and solvent. On the basis of recently published results, it has been established that the shielding of TMS in solution [along with that of sodium-3- (trimethylsilyl)propanesulfonate, DSS, often used as a reference for aqueous solutions] varies only slightly with temperature but is subject to solvent perturbations of a few tenths of a part per million (ppm). Recommendations are given for reporting chemical shifts under most routine experimental conditions and for quantifying effects of temperature and solvent variation, including the use of magnetic susceptibility corrections and of magic-angle spinning (MAS). This document provides the first IUPAC recommendations for referencing and reporting chemical shifts in solids, based on high-resolution MAS studies. Procedures are given for relating {sup 13}C NMR chemical shifts in solids to the scales used for high resolution studies in the liquid phase. The notation and terminology used for describing chemical shift and shielding tensors in solids are reviewed in some detail, and recommendations are given for best practice. (author)

Further conventions for NMR shielding and chemical shifts (IUPAC Recommendations 2008)

International Nuclear Information System (INIS)

Harris, R.K.; Menezes, S.M. Cabral de; Granger, P.; Hoffman, R.E.; Zilm, K.W.

2008-01-01

IUPAC has published a number of recommendations regarding the reporting of nuclear magnetic resonance (NMR) data, especially chemical shifts. The most recent publication [Pure Appl. Chem. 73, 1795 (2001)] recommended that tetramethylsilane (TMS) serve as a universal reference for reporting the shifts of all nuclides, but it deferred recommendations for several aspects of this subject. This document first examines the extent to which the 1 H shielding in TMS itself is subject to change by variation in temperature, concentration, and solvent. On the basis of recently published results, it has been established that the shielding of TMS in solution [along with that of sodium-3- (trimethylsilyl)propanesulfonate, DSS, often used as a reference for aqueous solutions] varies only slightly with temperature but is subject to solvent perturbations of a few tenths of a part per million (ppm). Recommendations are given for reporting chemical shifts under most routine experimental conditions and for quantifying effects of temperature and solvent variation, including the use of magnetic susceptibility corrections and of magic-angle spinning (MAS). This document provides the first IUPAC recommendations for referencing and reporting chemical shifts in solids, based on high-resolution MAS studies. Procedures are given for relating 13 C NMR chemical shifts in solids to the scales used for high resolution studies in the liquid phase. The notation and terminology used for describing chemical shift and shielding tensors in solids are reviewed in some detail, and recommendations are given for best practice. (author)

Validation of protein carbonyl measurement

DEFF Research Database (Denmark)

Augustyniak, Edyta; Adam, Aisha; Wojdyla, Katarzyna

2015-01-01

Protein carbonyls are widely analysed as a measure of protein oxidation. Several different methods exist for their determination. A previous study had described orders of magnitude variance that existed when protein carbonyls were analysed in a single laboratory by ELISA using different commercial...... protein carbonyl analysis across Europe. ELISA and Western blotting techniques detected an increase in protein carbonyl formation between 0 and 5min of UV irradiation irrespective of method used. After irradiation for 15min, less oxidation was detected by half of the laboratories than after 5min...... irradiation. Three of the four ELISA carbonyl results fell within 95% confidence intervals. Likely errors in calculating absolute carbonyl values may be attributed to differences in standardisation. Out of up to 88 proteins identified as containing carbonyl groups after tryptic cleavage of irradiated...

The direct measurement of the heteronuclear chemical shifts relative to tetramethylsilane

International Nuclear Information System (INIS)

Moritz, A.G.

1988-12-01

The measurement of heteronuclear chemical shifts using absolute frequencies of the heteronucleus and the 1 H resonance of tetramethylsilane has been examined. This method avoids the problems associated with external standards and gives results which can be obtained quickly and with high precision. The method has a number of advantages in the accurate measurement of chemical shifts, as for example 31 P in chemical warfare agents and related chemicals and allows multinuclear data to be obtained without dynamic range or potential interference problems. 15 refs., 4 tabs

Transition metal catalyzed carbonylation reactions carbonylative activation of C-X bonds

CERN Document Server

Beller, Matthias

2014-01-01

This book provides students and researchers in organic synthesis with a detailed discussion of carbonylation from the basics through to applications. It discusses the past, present and future of carbonylation reactions.

NMR chemical shifts in amino acids: Effects of environments, electric field, and amine group rotation

International Nuclear Information System (INIS)

Yoon, Young-Gui; Pfrommer, Bernd G.; Louie, Steven G.; Canning, Andrew

2002-01-01

The authors present calculations of NMR chemical shifts in crystalline phases of some representative amino acids such as glycine, alanine, and alanyl-alanine. To get an insight on how different environments affect the chemical shifts, they study the transition from the crystalline phase to completely isolated molecules of glycine. In the crystalline limit, the shifts are dominated by intermolecular hydrogen-bonds. In the molecular limit, however, dipole electric field effects dominate the behavior of the chemical shifts. They show that it is necessary to average the chemical shifts in glycine over geometries. Tensor components are analyzed to get the angle dependent proton chemical shifts, which is a more refined characterization method

Temperature dependence of 1H NMR chemical shifts and its influence on estimated metabolite concentrations.

Science.gov (United States)

Wermter, Felizitas C; Mitschke, Nico; Bock, Christian; Dreher, Wolfgang

2017-12-01

Temperature dependent chemical shifts of important brain metabolites measured by localised 1 H MRS were investigated to test how the use of incorrect prior knowledge on chemical shifts impairs the quantification of metabolite concentrations. Phantom measurements on solutions containing 11 metabolites were performed on a 7 T scanner between 1 and 43 °C. The temperature dependence of the chemical shift differences was fitted by a linear model. Spectra were simulated for different temperatures and analysed by the AQSES program (jMRUI 5.2) using model functions with chemical shift values for 37 °C. Large differences in the temperature dependence of the chemical shift differences were determined with a maximum slope of about ±7.5 × 10 -4  ppm/K. For 32-40 °C, only minor quantification errors resulted from using incorrect chemical shifts, with the exception of Cr and PCr. For 1-10 °C considerable quantification errors occurred if the temperature dependence of the chemical shifts was neglected. If 1 H MRS measurements are not performed at 37 °C, for which the published chemical shift values have been determined, the temperature dependence of chemical shifts should be considered to avoid systematic quantification errors, particularly for measurements on animal models at lower temperatures.

Theoretical Study of the NMR Chemical Shift of Xe in Supercritical Condition

DEFF Research Database (Denmark)

Lacerda Junior, Evanildo Gomes; Sauer, Stephan P. A.; Mikkelsen, Kurt Valentin

2018-01-01

In this work we investigate the level of theory necessary for reproducing the non-linear variation of the 129Xe nuclear magnetic resonance (NMR) chemical shift with the density of Xe in supercritical conditions. In detail we study how the 129Xe chemical shift depends under these conditions...... on electron correlation, relativistic and many-body effects. The latter are included using a sequential-QM/MM methodology, in which a classical MD simulation is performed first and the chemical shift is then obtained as an average of quantum calculations of 250 MD snapshots conformations carried out for Xen...... this approach we obtain very good agreement with the experimental data, showing that the chemical shift of 129Xe in supercritical conditions is very well described by cluster calculations at the HF level, with small contributions from relativistic and electron correlation effects....

Development of an automatic sampling device for the continuous measurement of atmospheric carbonyls compounds

International Nuclear Information System (INIS)

Perraud, V.

2007-12-01

Two sampling strategies were studied to develop an automatic instrument for the continuous measurement of atmospheric carbonyl compounds. Because of its specificity towards carbonyls compounds, sampling by using a transfer of gaseous phase in a liquid phase associated with a simultaneous chemical derivatization of the trapped compounds was first studied. However, this method do not allow a quantitative sampling of all studied carbonyl compounds, nor a continuous measurement in the field. To overcome the difficulties, a second strategy was investigated: the cryogenic adsorption onto solid adsorbent followed by thermodesorption and a direct analysis by GC/MS. Collection efficiency using different solid adsorbents was found greater than 95% for carbonyl compounds consisting of 1 to 7 carbons. This work is a successful first step towards the realization of the automatic sampling device for a continuous measurement of atmospheric carbonyls compounds. (author)

Plasma-treated carbonyl iron particles as a dispersed phase in magnetorheological fluids

OpenAIRE

Sedlačík, M.; Pavlínek, V.; Lehocký, M.; Mráček, A.; Grulich, O.; Švrčinová, P. (Petra); Filip, P. (Petr); Vesel, A.

2011-01-01

The aim of this paper is to document suitability of plasma-treated carbonyl iron particles as a dispersed phase in magnetorheological fluids. Surface-modified carbonyl iron particles were prepared via their exposure to 50% argon and 50% octafluorocyclobutane plasma. The X-ray photoelectron spectroscopy was used for analysis of chemical bonding states in the surface layer. Plasma-treated particles were adopted for a dispersed phase in magnetorheological (MR) fluids, and the MR behaviour was in...

29Si NMR Chemical Shift Calculation for Silicate Species by Gaussian Software

Science.gov (United States)

Azizi, S. N.; Rostami, A. A.; Godarzian, A.

2005-05-01

Hartree-Fock self-consistent-field (HF-SCF) theory and the Gauge-including atomic orbital (GIAO) methods are used in the calculation of 29Si NMR chemical shifts for ABOUT 90 units of 19 compounds of various silicate species of precursors for zeolites. Calculations have been performed at geometries optimized at the AM1 semi-empirical method. The GIAO-HF-SCF calculations were carried out with using three different basis sets: 6-31G*, 6-31+G** and 6-311+G(2d,p). To demonstrate the quality of the calculations the calculated chemical shifts, δ, were compared with the corresponding experimental values for the compounds in study. The results, especially with 6-31+g** are in excellent agreement with experimental values. The calculated chemical shifts, in practical point of view, appear to be accurate enough to aid in experimental peak assignments. The difference between the experimental and calculated 29Si chemical shift values not only depends on the Qn units but also it seems that basis set effects and the level of theory is more important. For the series of molecules studied here, the standard deviations and mean absolute errors for 29Si chemical shifts relative to TMS determined using Hartree--Fock 6-31+G** basis is nearly in all cases smaller than the errors for shifts determined using HF/6-311+G(2d,p).

Proton chemical shift tensors determined by 3D ultrafast MAS double-quantum NMR spectroscopy

International Nuclear Information System (INIS)

Zhang, Rongchun; Mroue, Kamal H.; Ramamoorthy, Ayyalusamy

2015-01-01

Proton NMR spectroscopy in the solid state has recently attracted much attention owing to the significant enhancement in spectral resolution afforded by the remarkable advances in ultrafast magic angle spinning (MAS) capabilities. In particular, proton chemical shift anisotropy (CSA) has become an important tool for obtaining specific insights into inter/intra-molecular hydrogen bonding. However, even at the highest currently feasible spinning frequencies (110–120 kHz), 1 H MAS NMR spectra of rigid solids still suffer from poor resolution and severe peak overlap caused by the strong 1 H– 1 H homonuclear dipolar couplings and narrow 1 H chemical shift (CS) ranges, which render it difficult to determine the CSA of specific proton sites in the standard CSA/single-quantum (SQ) chemical shift correlation experiment. Herein, we propose a three-dimensional (3D) 1 H double-quantum (DQ) chemical shift/CSA/SQ chemical shift correlation experiment to extract the CS tensors of proton sites whose signals are not well resolved along the single-quantum chemical shift dimension. As extracted from the 3D spectrum, the F1/F3 (DQ/SQ) projection provides valuable information about 1 H– 1 H proximities, which might also reveal the hydrogen-bonding connectivities. In addition, the F2/F3 (CSA/SQ) correlation spectrum, which is similar to the regular 2D CSA/SQ correlation experiment, yields chemical shift anisotropic line shapes at different isotropic chemical shifts. More importantly, since the F2/F1 (CSA/DQ) spectrum correlates the CSA with the DQ signal induced by two neighboring proton sites, the CSA spectrum sliced at a specific DQ chemical shift position contains the CSA information of two neighboring spins indicated by the DQ chemical shift. If these two spins have different CS tensors, both tensors can be extracted by numerical fitting. We believe that this robust and elegant single-channel proton-based 3D experiment provides useful atomistic-level structural and dynamical

Resolution of NMR chemical shift images into real and imaginary components

International Nuclear Information System (INIS)

Yamamoto, E.; Kohno, H.

1986-01-01

Fast chemical shift imaging of two-line materials is described using a modified spin-echo sequence. The method resolves the two chemical shift images into real and imaginary components representing the reconstructed image. The measuring time is reduced to half of that for the conventional method proposed by Dixon et al, and quantitative evaluation of the images becomes possible. Reference material with a single resonant line is used to eliminate the phase error caused by static field inhomogeneity and the inherent apparatus offset phase. Experiments are conducted using acetone and benzene with a medium-bore superconductive magnet operating at 0.5T. From these experiments, two chemical shift images are obtained. These images are then superimposed to produce a conventional density image. (author)

Random coil chemical shifts in acidic 8 M urea: Implementation of random coil shift data in NMRView

International Nuclear Information System (INIS)

Schwarzinger, Stephan; Kroon, Gerard J.A.; Foss, Ted R.; Wright, Peter E.; Dyson, H. Jane

2000-01-01

Studies of proteins unfolded in acid or chemical denaturant can help in unraveling events during the earliest phases of protein folding. In order for meaningful comparisons to be made of residual structure in unfolded states, it is necessary to use random coil chemical shifts that are valid for the experimental system under study. We present a set of random coil chemical shifts obtained for model peptides under experimental conditions used in studies of denatured proteins. This new set, together with previously published data sets, has been incorporated into a software interface for NMRView, allowing selection of the random coil data set that fits the experimental conditions best

Prediction of proton chemical shifts in RNA - Their use in structure refinement and validation

International Nuclear Information System (INIS)

Cromsigt, Jenny A.M.T.C.; Hilbers, Cees W.; Wijmenga, Sybren S.

2001-01-01

An analysis is presented of experimental versus calculated chemical shifts of the non-exchangeable protons for 28 RNA structures deposited in the Protein Data Bank, covering a wide range of structural building blocks. We have used existing models for ring-current and magnetic-anisotropy contributions to calculate the proton chemical shifts from the structures. Two different parameter sets were tried: (i) parameters derived by Ribas-Prado and Giessner-Prettre (GP set) [(1981) J. Mol. Struct.,76, 81-92.]; (ii) parameters derived by Case [(1995) J. Biomol. NMR, 6, 341-346]. Both sets lead to similar results. The detailed analysis was carried using the GP set. The root-mean-square-deviation between the predicted and observed chemical shifts of the complete database is 0.16 ppm with a Pearson correlation coefficient of 0.79. For protons in the usually well-defined A-helix environment these numbers are, 0.08 ppm and 0.96, respectively. As a result of this good correspondence, a reliable analysis could be made of the structural dependencies of the 1 H chemical shifts revealing their physical origin. For example, a down-field shift of either H2' or H3' or both indicates a high-syn/syn χ-angle. In an A-helix it is essentially the 5'-neighbor that affects the chemical shifts of H5, H6 and H8 protons. The H5, H6 and H8 resonances can therefore be assigned in an A-helix on the basis of their observed chemical shifts. In general, the chemical shifts were found to be quite sensitive to structural changes. We therefore propose that a comparison between calculated and observed 1 H chemical shifts is a good tool for validation and refinement of structures derived from NOEs and J-couplings

A procedure to validate and correct the {sup 13}C chemical shift calibration of RNA datasets

Energy Technology Data Exchange (ETDEWEB)

Aeschbacher, Thomas; Schubert, Mario, E-mail: schubert@mol.biol.ethz.ch; Allain, Frederic H.-T., E-mail: allain@mol.biol.ethz.ch [ETH Zuerich, Institute for Molecular Biology and Biophysics (Switzerland)

2012-02-15

Chemical shifts reflect the structural environment of a certain nucleus and can be used to extract structural and dynamic information. Proper calibration is indispensable to extract such information from chemical shifts. Whereas a variety of procedures exist to verify the chemical shift calibration for proteins, no such procedure is available for RNAs to date. We present here a procedure to analyze and correct the calibration of {sup 13}C NMR data of RNAs. Our procedure uses five {sup 13}C chemical shifts as a reference, each of them found in a narrow shift range in most datasets deposited in the Biological Magnetic Resonance Bank. In 49 datasets we could evaluate the {sup 13}C calibration and detect errors or inconsistencies in RNA {sup 13}C chemical shifts based on these chemical shift reference values. More than half of the datasets (27 out of those 49) were found to be improperly referenced or contained inconsistencies. This large inconsistency rate possibly explains that no clear structure-{sup 13}C chemical shift relationship has emerged for RNA so far. We were able to recalibrate or correct 17 datasets resulting in 39 usable {sup 13}C datasets. 6 new datasets from our lab were used to verify our method increasing the database to 45 usable datasets. We can now search for structure-chemical shift relationships with this improved list of {sup 13}C chemical shift data. This is demonstrated by a clear relationship between ribose {sup 13}C shifts and the sugar pucker, which can be used to predict a C2 Prime - or C3 Prime -endo conformation of the ribose with high accuracy. The improved quality of the chemical shift data allows statistical analysis with the potential to facilitate assignment procedures, and the extraction of restraints for structure calculations of RNA.

Protein backbone angle restraints from searching a database for chemical shift and sequence homology

Energy Technology Data Exchange (ETDEWEB)

Cornilescu, Gabriel; Delaglio, Frank; Bax, Ad [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

1999-03-15

Chemical shifts of backbone atoms in proteins are exquisitely sensitive to local conformation, and homologous proteins show quite similar patterns of secondary chemical shifts. The inverse of this relation is used to search a database for triplets of adjacent residues with secondary chemical shifts and sequence similarity which provide the best match to the query triplet of interest. The database contains 13C{alpha}, 13C{beta}, 13C', 1H{alpha} and 15N chemical shifts for 20 proteins for which a high resolution X-ray structure is available. The computer program TALOS was developed to search this database for strings of residues with chemical shift and residue type homology. The relative importance of the weighting factors attached to the secondary chemical shifts of the five types of resonances relative to that of sequence similarity was optimized empirically. TALOS yields the 10 triplets which have the closest similarity in secondary chemical shift and amino acid sequence to those of the query sequence. If the central residues in these 10 triplets exhibit similar {phi} and {psi} backbone angles, their averages can reliably be used as angular restraints for the protein whose structure is being studied. Tests carried out for proteins of known structure indicate that the root-mean-square difference (rmsd) between the output of TALOS and the X-ray derived backbone angles is about 15 deg. Approximately 3% of the predictions made by TALOS are found to be in error.

Optical chemical sensors for atmospheric pollutants based on nano porous materials: application to the formaldehyde and the other carbonyl compounds

International Nuclear Information System (INIS)

Paolacci, H.

2006-12-01

Formaldehyde, a well-identified indoor pollutant, was recently classified as carcinogenic. New regulations for the air quality are expected and therefore there is a need for low-cost sensors, sensitive and selective with a fast response time for the detection of formaldehyde at ppb level. In the present work, we had developed a chemical sensor based on nano-porous matrices doped with Fluoral-P and optical methods of detection. The nano-porous matrices, elaborated via the Sol-Gel process, display nano-pores whose cavity is tailored for the trapping of the targeted pollutant. They provide a first selectivity with the discrimination of the pollutants by their size. A second selectivity is obtained with a molecular probe, Fluoral-P, which reacts specifically with formaldehyde leading to the 3,5- di-acetyl-1,4-dihydro-lutidine (DDL). The kinetics of formation of DDL was studied as function of many parameters such as the concentration of Fluoral-P in the matrix, the pollutant content in gas mixture, the flow rate, the relative humidity of the gas mixtures and interference with other carbonylated compounds. The present chemical sensor can detect, via absorbance measurements, 2 ppb of formaldehyde within 30 min over a O to 60% relative humidity range. Moreover, to detect the total carbonylated compounds, we also explored the potentiality of a chemical sensor using, as a probe molecule, the 2'4-dinitro-phenyl-hydrazine which forms with these compounds the corresponding hydrazones derivatives. A patent was deposited for these two sensors. We have also developed a semi-miniaturized prototype for demonstration, using a flow cell, a miniaturized spectrophotometer, a light source and a lap-top. (author)

Benchmarking quantum mechanical calculations with experimental NMR chemical shifts of 2-HADNT

Science.gov (United States)

Liu, Yuemin; Junk, Thomas; Liu, Yucheng; Tzeng, Nianfeng; Perkins, Richard

2015-04-01

In this study, both GIAO-DFT and GIAO-MP2 calculations of nuclear magnetic resonance (NMR) spectra were benchmarked with experimental chemical shifts. The experimental chemical shifts were determined experimentally for carbon-13 (C-13) of seven carbon atoms for the TNT degradation product 2-hydroxylamino-4,6-dinitrotoluene (2-HADNT). Quantum mechanics GIAO calculations were implemented using Becke-3-Lee-Yang-Parr (B3LYP) and other six hybrid DFT methods (Becke-1-Lee-Yang-Parr (B1LYP), Becke-half-and-half-Lee-Yang-Parr (BH and HLYP), Cohen-Handy-3-Lee-Yang-Parr (O3LYP), Coulomb-attenuating-B3LYP (CAM-B3LYP), modified-Perdew-Wang-91-Lee-Yang-Parr (mPW1LYP), and Xu-3-Lee-Yang-Parr (X3LYP)) which use the same correlation functional LYP. Calculation results showed that the GIAO-MP2 method gives the most accurate chemical shift values, and O3LYP method provides the best prediction of chemical shifts among the B3LYP and other five DFT methods. Three types of atomic partial charges, Mulliken (MK), electrostatic potential (ESP), and natural bond orbital (NBO), were also calculated using MP2/aug-cc-pVDZ method. A reasonable correlation was discovered between NBO partial charges and experimental chemical shifts of carbon-13 (C-13).

Organocatalytic Hydrophosphonylation Reaction of Carbonyl Groups.

Science.gov (United States)

Herrera, Raquel P

2017-09-01

This revision is covering the limited examples reported for a pivotal strategy in the formation of C-P bonds such as the asymmetric organocatalytic hydrophosphonylation of carbonyl groups (Pudovik reaction). The scope and limitations, and the proposed mechanisms for the scarce different possibilities of asymmetric induction are also shown. The recent evolution and future trends of this undeveloped approach are commented. © 2017 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Relation between chemical shift artifact and infiltration on MR imaging of renal cell carcinoma

International Nuclear Information System (INIS)

Yoshigoe, Fukuo; Makino, Hideki; Yanada, Syuichi; Ohishi, Yukihiko; Mashima, Yasuoki; Yamada, Hideo.

1994-01-01

Retrospective study on the relation between existence of the interruption and disturbance of chemical shift artifact and tumor infiltration at the periphery of the kidney on MR imaging was evaluated in 28 cases with renal cell carcinoma. Judgement was possible in 9 out of the 11 cases with pathological stage below pT2 and 14 cases out of 17 pT3 cases. Judgement was impracticable in 5 cases because the peripheral fat tissue of the kidney was too less to observe chemical shift artifact and the tumor was spreading at the side opposite to the chemical shift artifact. Chemical shift artifact on MRI in this study correlated well with renal tumor infiltration. (author)

Database proton NMR chemical shifts for RNA signal assignment and validation

Energy Technology Data Exchange (ETDEWEB)

Barton, Shawn; Heng Xiao [University of Maryland, Baltimore County, Howard Hughes Medical Institute (United States); Johnson, Bruce A., E-mail: bruce@onemoonscientific.com [University of Maryland, Baltimore County, Department of Chemistry and Biochemistry (United States); Summers, Michael F., E-mail: summers@hhmi.umbc.edu [University of Maryland, Baltimore County, Howard Hughes Medical Institute (United States)

2013-01-15

The Biological Magnetic Resonance Data Bank contains NMR chemical shift depositions for 132 RNAs and RNA-containing complexes. We have analyzed the {sup 1}H NMR chemical shifts reported for non-exchangeable protons of residues that reside within A-form helical regions of these RNAs. The analysis focused on the central base pair within a stretch of three adjacent base pairs (BP triplets), and included both Watson-Crick (WC; G:C, A:U) and G:U wobble pairs. Chemical shift values were included for all 4{sup 3} possible WC-BP triplets, as well as 137 additional triplets that contain one or more G:U wobbles. Sequence-dependent chemical shift correlations were identified, including correlations involving terminating base pairs within the triplets and canonical and non-canonical structures adjacent to the BP triplets (i.e. bulges, loops, WC and non-WC BPs), despite the fact that the NMR data were obtained under different conditions of pH, buffer, ionic strength, and temperature. A computer program (RNAShifts) was developed that enables convenient comparison of RNA {sup 1}H NMR assignments with database predictions, which should facilitate future signal assignment/validation efforts and enable rapid identification of non-canonical RNA structures and RNA-ligand/protein interaction sites.

/sup 1/H-NMR chemical shift imaging suitable for low field systems

Energy Technology Data Exchange (ETDEWEB)

Yamamoto, Etsuji; Onodera, Takashi; Shiono, Hidemi; Kohno, Hideki

1986-12-01

An echo-time encoding proton NMR chemical shift imaging proposed by Dixon is extended to be applicable to low filed systems. The method utilizes the small phase angle between magnetic vectors of water and lipid protons to decrease the signal decays with spin-spin relaxation. The inevitable phase error caused by the static field inhomogeneity is corrected by using phase images of phantom measured under the same conditions as the actual measurements. The experiments were carried out using CuSO/sub 4/ doped water and vegetable oil at 0.5 T. Two chemical shift images could be clearly resolved with only one scan when the field inhomogeneity was larger than the chemical shift difference.

Line profile analyses of rhodium metal obtained by decomposition of rhodium carbonyl

International Nuclear Information System (INIS)

Chandra, D.; Mandalia, H.; Garner, M.L.; Blakely, M.K.; Lau, K.H.

1995-01-01

Metal carbonyls are important for chemical vapor deposition (CVD) of metals and alloys and formation of high surface area metallic particles which have potential applications as catalysts. Rhodium carbonyl [Rh 6 (CO) 16 ] produces high surface area metallic particles whose structure has been reported as monoclinic (I2/a) with lattice dimensions, a=17.00(±0.03)Angstrom, b=9.78(±0.02)Angstrom, c=17.53(±0.03)Angstrom and Β=121 degrees 45' ± 30' at room temperature. Generally, metal carbonyl crystals dissociate under vacuum as carbonyl gas and decompose to metallic crystals and carbon monoxide at higher temperatures. However, the behavior of rhodium carbonyl crystals is different; they decompose directly to metallic rhodium without the formation of rhodium carbonyl gas in vacuum. Several residual fine grains of rhodium metal are found after the decomposition in vacuum at relatively low temperatures. The metallic samples of rhodium were obtained from vapor pressure experiments using torsion Knudsen-effusion apparatus. X-ray diffraction analyses performed on these gains showed severely broadened Bragg reflections indicative of small particle size and/or lattice microgram. In this study, a comparison of lattice strains and domain sizes obtained by integral breadth and Fourier methods has been made. In addition a comparison of the lattice strains and domain sizes has been made between the Cauchy, Gaussian, Cauchy-Gaussian and Aqua integral breadth methods

Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts.

Science.gov (United States)

Boomsma, Wouter; Tian, Pengfei; Frellsen, Jes; Ferkinghoff-Borg, Jesper; Hamelryck, Thomas; Lindorff-Larsen, Kresten; Vendruscolo, Michele

2014-09-23

Methods of protein structure determination based on NMR chemical shifts are becoming increasingly common. The most widely used approaches adopt the molecular fragment replacement strategy, in which structural fragments are repeatedly reassembled into different complete conformations in molecular simulations. Although these approaches are effective in generating individual structures consistent with the chemical shift data, they do not enable the sampling of the conformational space of proteins with correct statistical weights. Here, we present a method of molecular fragment replacement that makes it possible to perform equilibrium simulations of proteins, and hence to determine their free energy landscapes. This strategy is based on the encoding of the chemical shift information in a probabilistic model in Markov chain Monte Carlo simulations. First, we demonstrate that with this approach it is possible to fold proteins to their native states starting from extended structures. Second, we show that the method satisfies the detailed balance condition and hence it can be used to carry out an equilibrium sampling from the Boltzmann distribution corresponding to the force field used in the simulations. Third, by comparing the results of simulations carried out with and without chemical shift restraints we describe quantitatively the effects that these restraints have on the free energy landscapes of proteins. Taken together, these results demonstrate that the molecular fragment replacement strategy can be used in combination with chemical shift information to characterize not only the native structures of proteins but also their conformational fluctuations.

CheShift-2 resolves a local inconsistency between two X-ray crystal structures

International Nuclear Information System (INIS)

Vila, Jorge A.; Sue, Shih-Che; Fraser, James S.; Scheraga, Harold A.; Dyson, H. Jane

2012-01-01

Since chemical shifts provide important and relatively accessible information about protein structure in solution, a Web server, CheShift-2, was developed for structure interrogation, based on a quantum mechanics database of 13 C α chemical shifts. We report the application of CheShift-2 to a local inconsistency between two X-ray crystal structures (PDB IDs 1IKN and 1NFI) of the complex between the p65/p50 heterodimer of NFκB and its inhibitor IκBα. The availability of NMR resonance assignments that included the region of the inconsistency provided an opportunity for independent validation of the CheShift-2 server. Application of the server showed that the 13 C α chemical shifts measured for the Gly270-Pro281 sequence close to the C-terminus of IκBα were unequivocally consistent with the backbone structure modeled in the 1IKN structure, and were inconsistent with the 1NFI structure. Previous NOE measurements had demonstrated that the position of a tryptophan ring in the region immediately N-terminal in this region was not consistent with either structure. Subsequent recalculation of the local structure in this region, based on the electron density of the deposited structure factors for 1IKN, confirmed that the local backbone structure was best modeled by 1IKN, but that the rotamer of Trp258 is consistent with the 1NFI structure, including the presence of a hydrogen bond between the ring NεH of Trp258 and the backbone carbonyl group of Gln278. The consensus between all of these measures suggests that the CheShift-2 server operates well under circumstances in which backbone chemical shifts are available but where local plasticity may render X-ray structural data ambiguous.

Protein Structure Validation and Refinement Using Chemical Shifts Derived from Quantum Mechanics

DEFF Research Database (Denmark)

Bratholm, Lars Andersen

to within 3 A. Furthermore, a fast quantum mechanics based chemical shift predictor was developed together with methodology for using chemical shifts in structure simulations. The developed predictor was used for renement of several protein structures and for reducing the computational cost of quantum...... mechanics / molecular mechanics (QM/MM) computations of chemical shieldings. Several improvements to the predictor is ongoing, where among other things, kernel based machine learning techniques have successfully been used to improve the quantum mechanical level of theory used in the predictions....

Improving 3D structure prediction from chemical shift data

Energy Technology Data Exchange (ETDEWEB)

Schot, Gijs van der [Utrecht University, Computational Structural Biology, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry (Netherlands); Zhang, Zaiyong [Technische Universitaet Muenchen, Biomolecular NMR and Munich Center for Integrated Protein Science, Department Chemie (Germany); Vernon, Robert [University of Washington, Department of Biochemistry (United States); Shen, Yang [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Vranken, Wim F. [VIB, Department of Structural Biology (Belgium); Baker, David [University of Washington, Department of Biochemistry (United States); Bonvin, Alexandre M. J. J., E-mail: a.m.j.j.bonvin@uu.nl [Utrecht University, Computational Structural Biology, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry (Netherlands); Lange, Oliver F., E-mail: oliver.lange@tum.de [Technische Universitaet Muenchen, Biomolecular NMR and Munich Center for Integrated Protein Science, Department Chemie (Germany)

2013-09-15

We report advances in the calculation of protein structures from chemical shift nuclear magnetic resonance data alone. Our previously developed method, CS-Rosetta, assembles structures from a library of short protein fragments picked from a large library of protein structures using chemical shifts and sequence information. Here we demonstrate that combination of a new and improved fragment picker and the iterative sampling algorithm RASREC yield significant improvements in convergence and accuracy. Moreover, we introduce improved criteria for assessing the accuracy of the models produced by the method. The method was tested on 39 proteins in the 50-100 residue size range and yields reliable structures in 70 % of the cases. All structures that passed the reliability filter were accurate (<2 A RMSD from the reference)

Chemical Mass Shifts in a Digital Linear Ion Trap as Analytical Identity of o-, m-, and p-Xylene

Science.gov (United States)

Sun, Lulu; Xue, Bing; Huang, Zhengxu; Cheng, Ping; Ma, Li; Ding, Li; Zhou, Zhen

2018-04-01

Chemical mass shifts between isomeric ions of o-, m-, and p-xylene were measured using a digital linear ion trap, and the directions and values of the shifts were found to be correlated to the collision cross sections of the isomers. Both forward and reverse scans were used and the chemical shifts for each pair of isomers in scans of opposite directions were in opposite signs. Using different voltage settings (namely the voltage dividing ratio-VDR) of the ion trap allows adding high order field components in the quadrupole field and results in larger chemical mass shifts. The differential chemical mass shift which combined the shifts from forward and reverse scans doubled the amount of chemical shift, e.g., 0.077 Th between o- and p-xylene, enough for identification of the type of isomer without using an additional ion mobility spectrometer. The feature of equal and opposite chemical mass shifts also allowed to null out the chemical mass shift by calculating the mean m/z value between the two opposite scans and remove or reduce the mass error caused by chemical mass shift. [Figure not available: see fulltext.

Chemical Mass Shifts in a Digital Linear Ion Trap as Analytical Identity of o-, m-, and p-Xylene.

Science.gov (United States)

Sun, Lulu; Xue, Bing; Huang, Zhengxu; Cheng, Ping; Ma, Li; Ding, Li; Zhou, Zhen

2018-07-01

Chemical mass shifts between isomeric ions of o-, m-, and p-xylene were measured using a digital linear ion trap, and the directions and values of the shifts were found to be correlated to the collision cross sections of the isomers. Both forward and reverse scans were used and the chemical shifts for each pair of isomers in scans of opposite directions were in opposite signs. Using different voltage settings (namely the voltage dividing ratio-VDR) of the ion trap allows adding high order field components in the quadrupole field and results in larger chemical mass shifts. The differential chemical mass shift which combined the shifts from forward and reverse scans doubled the amount of chemical shift, e.g., 0.077 Th between o- and p-xylene, enough for identification of the type of isomer without using an additional ion mobility spectrometer. The feature of equal and opposite chemical mass shifts also allowed to null out the chemical mass shift by calculating the mean m/z value between the two opposite scans and remove or reduce the mass error caused by chemical mass shift. Graphical Abstract ᅟ.

Stereospecific assignment of the asparagine and glutamine sidechain amide protons in proteins from chemical shift analysis

Energy Technology Data Exchange (ETDEWEB)

Harsch, Tobias; Schneider, Philipp; Kieninger, Bärbel; Donaubauer, Harald; Kalbitzer, Hans Robert, E-mail: hans-robert.kalbitzer@biologie.uni-regensburg.de [University of Regensburg, Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine (Germany)

2017-02-15

Side chain amide protons of asparagine and glutamine residues in random-coil peptides are characterized by large chemical shift differences and can be stereospecifically assigned on the basis of their chemical shift values only. The bimodal chemical shift distributions stored in the biological magnetic resonance data bank (BMRB) do not allow such an assignment. However, an analysis of the BMRB shows, that a substantial part of all stored stereospecific assignments is not correct. We show here that in most cases stereospecific assignment can also be done for folded proteins using an unbiased artificial chemical shift data base (UACSB). For a separation of the chemical shifts of the two amide resonance lines with differences ≥0.40 ppm for asparagine and differences ≥0.42 ppm for glutamine, the downfield shifted resonance lines can be assigned to H{sup δ21} and H{sup ε21}, respectively, at a confidence level >95%. A classifier derived from UASCB can also be used to correct the BMRB data. The program tool AssignmentChecker implemented in AUREMOL calculates the Bayesian probability for a given stereospecific assignment and automatically corrects the assignments for a given list of chemical shifts.

Deuterium isotope effects on 13C chemical shifts of 10-Hydroxybenzo[h]quinolines

DEFF Research Database (Denmark)

Hansen, Poul Erik; Kamounah, Fadhil S.; Gryko, Daniel T.

2013-01-01

Deuterium isotope effects on 13C-NMR chemical shifts are investigated in a series of 10-hydroxybenzo[h]quinolines (HBQ’s) The OH proton is deuteriated. The isotope effects on 13C chemical shifts in these hydrogen bonded systems are rather unusual. The formal four-bond effects are found to be nega...

Solvent Effects on Oxygen-17 Chemical Shifts in Amides. Quantitative Linear Solvation Shift Relationships

Science.gov (United States)

Díez, Ernesto; Fabián, Jesús San; Gerothanassis, Ioannis P.; Esteban, Angel L.; Abboud, José-Luis M.; Contreras, Ruben H.; de Kowalewski, Dora G.

1997-01-01

A multiple-linear-regression analysis (MLRA) has been carried out using the Kamlet-Abboud-Taft (KAT) solvatochromic parameters in order to elucidate and quantify the solvent effects on the17O chemical shifts ofN-methylformamide (NMF),N,N-dimethylformamide (DMF),N-methylacetamide (NMA), andN,N-dimethylacetamide (DMA). The chemical shifts of the four molecules show the same dependence (in ppm) on the solvent polarity-polarizability, i.e., -22π*. The influence of the solvent hydrogen-bond-donor (HBD) acidities is slightly larger for the acetamides NMA and DMA, i.e., -48α, than for the formamides NMF and DMF, i.e., -42α. The influence of the solvent hydrogen-bond-acceptor (HBA) basicities is negligible for the nonprotic molecules DMF and DMA but significant for the protic molecules NMF and NMA, i.e., -9β. The effect of substituting the N-H hydrogen by a methyl group amounts to -5.9 ppm in NMF and 5.4 ppm in NMA. The effect of substituting the O=C-H hydrogen amounts to 5.5 ppm in NMF and 16.8 ppm in DMF. The model of specific hydration sites of amides by I. P. Gerothanassis and C. Vakka [J. Org. Chem.59,2341 (1994)] is settled in a more quantitative basis and the model by M. I. Burgar, T. E. St. Amour, and D. Fiat [J. Phys. Chem.85,502 (1981)] is critically evaluated.17O hydration shifts have been calculated for formamide (FOR) by the ab initio LORG method at the 6-31G* level. For a formamide surrounded by the four in-plane molecules of water in the first hydration shell, the calculated17O shift change due to the four hydrogen bonds, -83.2 ppm, is smaller than the empirical hydration shift, -100 ppm. The17O shift change from each out-of-plane water molecule hydrogen-bonded to the amide oxygen is -18.0 ppm. These LORG results support the conclusion that no more than four water molecules are hydrogen-bonded to the amide oxygen in formamide.

Identify Beta-Hairpin Motifs with Quadratic Discriminant Algorithm Based on the Chemical Shifts.

Directory of Open Access Journals (Sweden)

Feng YongE

Full Text Available Successful prediction of the beta-hairpin motif will be helpful for understanding the of the fold recognition. Some algorithms have been proposed for the prediction of beta-hairpin motifs. However, the parameters used by these methods were primarily based on the amino acid sequences. Here, we proposed a novel model for predicting beta-hairpin structure based on the chemical shift. Firstly, we analyzed the statistical distribution of chemical shifts of six nuclei in not beta-hairpin and beta-hairpin motifs. Secondly, we used these chemical shifts as features combined with three algorithms to predict beta-hairpin structure. Finally, we achieved the best prediction, namely sensitivity of 92%, the specificity of 94% with 0.85 of Mathew's correlation coefficient using quadratic discriminant analysis algorithm, which is clearly superior to the same method for the prediction of beta-hairpin structure from 20 amino acid compositions in the three-fold cross-validation. Our finding showed that the chemical shift is an effective parameter for beta-hairpin prediction, suggesting the quadratic discriminant analysis is a powerful algorithm for the prediction of beta-hairpin.

Cytoprotective Effects of Pumpkin (Cucurbita Moschata) Fruit Extract against Oxidative Stress and Carbonyl Stress.

Science.gov (United States)

Shayesteh, Reyhaneh; Kamalinejad, Mohammad; Adiban, Hasan; Kardan, Azin; Keyhanfar, Fariborz; Eskandari, Mohammad Reza

2017-10-01

Background Diabetes mellitus is a chronic endocrine disorder that is associated with significant mortality and morbidity due to microvascular and macrovascular complications. Diabetes complications accompanied with oxidative stress and carbonyl stress in different organs of human body because of the increased generation of free radicals and impaired antioxidant defense systems. In the meantime, reactive oxygen species (ROS) and reactive carbonyl species (RCS) have key mediatory roles in the development and progression of diabetes complications. Therapeutic strategies have recently focused on preventing such diabetes-related abnormalities using different natural and chemical compounds. Pumpkin ( Cucurbita moschata ) is one of the most important vegetables in the world with a broad-range of pharmacological activities such as antihyperglycemic effect. Methods In the present study, the cytoprotective effects of aqueous extract of C. moschata fruit on hepatocyte cytotoxicity induced by cumene hydroperoxide (oxidative stress model) or glyoxal (carbonylation model) were investigated using freshly isolated rat hepatocytes. Results The extract of C. moschata (50 μg/ml) excellently prevented oxidative and carbonyl stress markers, including hepatocyte lysis, ROS production, lipid peroxidation, glutathione depletion, mitochondrial membrane potential collapse, lysosomal damage, and cellular proteolysis. In addition, protein carbonylation was prevented by C. moschata in glyoxal-induced carbonyl stress. Conclusion It can be concluded that C. moschata has cytoprotective effects in oxidative stress and carbonyl stress models and this valuable vegetable can be considered as a suitable herbal product for the prevention of toxic subsequent of oxidative stress and carbonyl stress seen in chronic hyperglycemia. © Georg Thieme Verlag KG Stuttgart · New York.

Identification of helix capping and {beta}-turn motifs from NMR chemical shifts

Energy Technology Data Exchange (ETDEWEB)

Shen Yang; Bax, Ad, E-mail: bax@nih.gov [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

2012-03-15

We present an empirical method for identification of distinct structural motifs in proteins on the basis of experimentally determined backbone and {sup 13}C{sup {beta}} chemical shifts. Elements identified include the N-terminal and C-terminal helix capping motifs and five types of {beta}-turns: I, II, I Prime , II Prime and VIII. Using a database of proteins of known structure, the NMR chemical shifts, together with the PDB-extracted amino acid preference of the helix capping and {beta}-turn motifs are used as input data for training an artificial neural network algorithm, which outputs the statistical probability of finding each motif at any given position in the protein. The trained neural networks, contained in the MICS (motif identification from chemical shifts) program, also provide a confidence level for each of their predictions, and values ranging from ca 0.7-0.9 for the Matthews correlation coefficient of its predictions far exceed those attainable by sequence analysis. MICS is anticipated to be useful both in the conventional NMR structure determination process and for enhancing on-going efforts to determine protein structures solely on the basis of chemical shift information, where it can aid in identifying protein database fragments suitable for use in building such structures.

Identification of helix capping and β-turn motifs from NMR chemical shifts

International Nuclear Information System (INIS)

Shen Yang; Bax, Ad

2012-01-01

We present an empirical method for identification of distinct structural motifs in proteins on the basis of experimentally determined backbone and 13 C β chemical shifts. Elements identified include the N-terminal and C-terminal helix capping motifs and five types of β-turns: I, II, I′, II′ and VIII. Using a database of proteins of known structure, the NMR chemical shifts, together with the PDB-extracted amino acid preference of the helix capping and β-turn motifs are used as input data for training an artificial neural network algorithm, which outputs the statistical probability of finding each motif at any given position in the protein. The trained neural networks, contained in the MICS (motif identification from chemical shifts) program, also provide a confidence level for each of their predictions, and values ranging from ca 0.7–0.9 for the Matthews correlation coefficient of its predictions far exceed those attainable by sequence analysis. MICS is anticipated to be useful both in the conventional NMR structure determination process and for enhancing on-going efforts to determine protein structures solely on the basis of chemical shift information, where it can aid in identifying protein database fragments suitable for use in building such structures.

Effect of carbonyl iron particles composition on the physical characteristics of MR grease

Energy Technology Data Exchange (ETDEWEB)

Mohamad, Norzilawati, E-mail: mnorzilawati@gmail.com; Mazlan, Saiful Amri, E-mail: amri.kl@utm.my [Vehicle System Engineering, Malaysia – Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra (Jalan Semarak), Kuala Lumpur, 54000 (Malaysia); Ubaidillah, E-mail: ubaidillah@uns.ac.id [Vehicle System Engineering, Malaysia – Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra (Jalan Semarak), Kuala Lumpur, 54000 (Malaysia); Mechanical Engineering Department, Faculty of Engineering, Universitas Sebelas Maret, Jl. Ir. Sutami 36A, Kentingan, Surakarta, 57126, Central Java, Surakarta (Indonesia)

2016-03-29

Magnetorheological (MR) grease is an extension of the study of magnetorheological materials. The MR grease can help to reduce the particles sedimentation problem occurred in the MR fluids. Within this study, an effort has been taken to investigate the effect of different weight compositions of carbonyl iron particles on the physical and chemical characteristics of the MR grease under off-state condition (no magnetic field). The MR grease is prepared by mixing carbonyl iron particles having a size range of 1 to 10 µm with commercial NPC Highrex HD-3 grease. Characterizations of MR grease are investigated using Vibrating Sample Magnetometer (VSM), Environmental Scanning Electron Microscopy (ESEM), Differential Scanning Calorimeter (DSC) and rheometer. The dependency of carbonyl iron particles weight towards the magnetic properties of MR grease and other characterizations are investigated.

Chemical shift MRI can aid in the diagnosis of indeterminate skeletal lesions of the spine

Energy Technology Data Exchange (ETDEWEB)

Douis, H. [University Hospital Birmingham, Department of Radiology, Birmingham (United Kingdom); Royal Orthopaedic Hospital, Department of Radiology, Birmingham (United Kingdom); Davies, A.M. [Royal Orthopaedic Hospital, Department of Radiology, Birmingham (United Kingdom); Jeys, L. [Royal Orthopaedic Hospital, Department of Orthopaedic Oncology, Birmingham (United Kingdom); Sian, P. [Royal Orthopaedic Hospital, Department of Spinal Surgery and Spinal Oncology, Birmingham (United Kingdom)

2016-04-15

To evaluate the role of chemical shift MRI in the characterisation of indeterminate skeletal lesions of the spine as benign or malignant. Fifty-five patients (mean age 54.7 years) with 57 indeterminate skeletal lesions of the spine were included in this retrospective study. In addition to conventional MRI at 3 T which included at least sagittal T1WI and T2WI/STIR sequences, patients underwent chemical shift MRI. A cut-off value with a signal drop-out of 20 % was used to differentiate benign lesions from malignant lesions (signal drop-out <20 % being malignant). There were 45 benign lesions and 12 malignant lesions. Chemical shift imaging correctly diagnosed 33 of 45 lesions as benign and 11 of 12 lesions as malignant. In contrast, there were 12 false positive cases and 1 false negative case based on chemical shift MRI. This yielded a sensitivity of 91.7 %, a specificity of 73.3 %, a negative predictive value of 97.1 %, a positive predictive value of 47.8 % and a diagnostic accuracy of 82.5 %. Chemical shift MRI can aid in the characterisation of indeterminate skeletal lesions of the spine in view of its high sensitivity in diagnosing malignant lesions. Chemical shift MRI can potentially avoid biopsy in a considerable percentage of patients with benign skeletal lesions of the spine. (orig.)

Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution

DEFF Research Database (Denmark)

Kjærgaard, Magnus; Poulsen, Flemming Martin

2011-01-01

Random coil chemical shifts are necessary for secondary chemical shift analysis, which is the main NMR method for identification of secondary structure in proteins. One of the largest challenges in the determination of random coil chemical shifts is accounting for the effect of neighboring residues....... The contributions from the neighboring residues are typically removed by using neighbor correction factors determined based on each residue's effect on glycine chemical shifts. Due to its unusual conformational freedom, glycine may be particularly unrepresentative for the remaining residue types. In this study, we...... in the conformational ensemble are an important source of neighbor effects in disordered proteins. Glutamine derived random coil chemical shifts and correction factors modestly improve our ability to predict (13)C chemical shifts of intrinsically disordered proteins compared to existing datasets, and may thus improve...

Conformationally selective multidimensional chemical shift ranges in proteins from a PACSY database purged using intrinsic quality criteria

International Nuclear Information System (INIS)

Fritzsching, Keith J.; Hong, Mei; Schmidt-Rohr, Klaus

2016-01-01

We have determined refined multidimensional chemical shift ranges for intra-residue correlations ( 13 C– 13 C, 15 N– 13 C, etc.) in proteins, which can be used to gain type-assignment and/or secondary-structure information from experimental NMR spectra. The chemical-shift ranges are the result of a statistical analysis of the PACSY database of >3000 proteins with 3D structures (1,200,207 13 C chemical shifts and >3 million chemical shifts in total); these data were originally derived from the Biological Magnetic Resonance Data Bank. Using relatively simple non-parametric statistics to find peak maxima in the distributions of helix, sheet, coil and turn chemical shifts, and without the use of limited “hand-picked” data sets, we show that ∼94 % of the 13 C NMR data and almost all 15 N data are quite accurately referenced and assigned, with smaller standard deviations (0.2 and 0.8 ppm, respectively) than recognized previously. On the other hand, approximately 6 % of the 13 C chemical shift data in the PACSY database are shown to be clearly misreferenced, mostly by ca. −2.4 ppm. The removal of the misreferenced data and other outliers by this purging by intrinsic quality criteria (PIQC) allows for reliable identification of secondary maxima in the two-dimensional chemical-shift distributions already pre-separated by secondary structure. We demonstrate that some of these correspond to specific regions in the Ramachandran plot, including left-handed helix dihedral angles, reflect unusual hydrogen bonding, or are due to the influence of a following proline residue. With appropriate smoothing, significantly more tightly defined chemical shift ranges are obtained for each amino acid type in the different secondary structures. These chemical shift ranges, which may be defined at any statistical threshold, can be used for amino-acid type assignment and secondary-structure analysis of chemical shifts from intra-residue cross peaks by inspection or by using a

Conformationally selective multidimensional chemical shift ranges in proteins from a PACSY database purged using intrinsic quality criteria

Energy Technology Data Exchange (ETDEWEB)

Fritzsching, Keith J., E-mail: kfritzsc@brandeis.edu [Brandeis University, Department of Chemistry (United States); Hong, Mei [Massachusetts Institute of Technology, Department of Chemistry (United States); Schmidt-Rohr, Klaus, E-mail: srohr@brandeis.edu [Brandeis University, Department of Chemistry (United States)

2016-02-15

We have determined refined multidimensional chemical shift ranges for intra-residue correlations ({sup 13}C–{sup 13}C, {sup 15}N–{sup 13}C, etc.) in proteins, which can be used to gain type-assignment and/or secondary-structure information from experimental NMR spectra. The chemical-shift ranges are the result of a statistical analysis of the PACSY database of >3000 proteins with 3D structures (1,200,207 {sup 13}C chemical shifts and >3 million chemical shifts in total); these data were originally derived from the Biological Magnetic Resonance Data Bank. Using relatively simple non-parametric statistics to find peak maxima in the distributions of helix, sheet, coil and turn chemical shifts, and without the use of limited “hand-picked” data sets, we show that ∼94 % of the {sup 13}C NMR data and almost all {sup 15}N data are quite accurately referenced and assigned, with smaller standard deviations (0.2 and 0.8 ppm, respectively) than recognized previously. On the other hand, approximately 6 % of the {sup 13}C chemical shift data in the PACSY database are shown to be clearly misreferenced, mostly by ca. −2.4 ppm. The removal of the misreferenced data and other outliers by this purging by intrinsic quality criteria (PIQC) allows for reliable identification of secondary maxima in the two-dimensional chemical-shift distributions already pre-separated by secondary structure. We demonstrate that some of these correspond to specific regions in the Ramachandran plot, including left-handed helix dihedral angles, reflect unusual hydrogen bonding, or are due to the influence of a following proline residue. With appropriate smoothing, significantly more tightly defined chemical shift ranges are obtained for each amino acid type in the different secondary structures. These chemical shift ranges, which may be defined at any statistical threshold, can be used for amino-acid type assignment and secondary-structure analysis of chemical shifts from intra

Mechanistic differences between methanol and dimethyl ether carbonylation in side pockets and large channels of mordenite.

Science.gov (United States)

Boronat, Mercedes; Martínez, Cristina; Corma, Avelino

2011-02-21

The activity and selectivity towards carbonylation presented by Brønsted acid sites located inside the 8MR pockets or in the main 12MR channels of mordenite is studied by means of quantum-chemical calculations, and the mechanistic differences between methanol and DME carbonylation are investigated. The selectivity towards carbonylation is higher inside the 8MR pockets, where the competitive formation of DME and hydrocarbons that finally leads to catalyst deactivation is sterically impeded. Moreover, inclusion of dispersion interactions in the calculations leads to agreement between the calculated activation barriers for the rate determining step and the experimentally observed higher reactivity of methoxy groups located inside the 8MR channels.

DFT/GIAO calculations of the relative contributions of hyperconjugation to the chemical shifts of ethanol

International Nuclear Information System (INIS)

Carneiro, J. Walkimar de M.; Dias, Jacques F.; Seidl, Peter R.; Tostes, J. Glauco R.

2002-01-01

Our previous DFT/GIAO calculations on different types of alcohols reveal that the rotation of the hydroxyl group can affect the chemical shift of carbons and hydrogens close to the substituent in different ways. Besides the steric and electrostatic effects that have been widely studied, hyperconjugation with the lone pairs on oxygen of the hydroxyl group leads to changes in bond lengths and angles as well as to different charge distributions. As all three of these factors also affect chemical shifts, we undertook a systematic investigation of their relative contributions to the chemical shifts of ethanol, a molecule in which there is minimum interference among these factors. Calculations by the B3LYP method at the 6-31G(d) level for ethanol conformers corresponding to a rotation around the carbon-oxygen bond at 30 dec increments are used to show how relative contributions vary with the dihedral angle formed between the carbon-carbon and oxygen-hydrogen bonds (C-C-O-H). Largest contributions to carbon chemical shifts can be attributed to changes in bond lengths while for hydrogen chemical shifts also contribute significantly differences in charge distribution. (author)

Weak carbonyl-methyl intermolecular interactions in acetone clusters explored by IR plus VUV spectroscopy

International Nuclear Information System (INIS)

Guan, Jiwen; Hu, Yongjun; Xie, Min; Bernstein, Elliot R.

2012-01-01

Highlights: ► The carbonyl overtone of acetone clusters is observed by IR-VUV spectroscopy. ► Acetone molecules in the dimer are stacked with an antiparallel way. ► The structure of the acetone trimer and the tetramer are the cyclic structures. ► The carbonyl groups would interact with the methyl groups in acetone clusters. ► These weak interactions are further confirmed by H/D substitution experiment. -- Abstract: Size-selected IR–VUV spectroscopy is employed to detect vibrational characteristics in the region 2850 ∼ 3550 cm −1 of neutral acetone and its clusters (CH 3 COCH 3 ) n (n = 1–4). Features around 3440 cm −1 in the spectra of acetone monomer and its clusters are assigned to the carbonyl stretch (CO) overtone. These features red-shift from 3455 to 3433 cm −1 as the size of the clusters increases from the monomer to the tetramer. Based on calculations, the experimental IR spectra in the C=O overtone region suggest that the dominant structures for the acetone trimer and tetramer should be cyclic in the supersonic expansion sample. This study also suggests that the carbonyl groups interact with the methyl groups in the acetone clusters. These weak interactions are further confirmed by the use of deuterium substitution.

Anisotropy of the fluorine chemical shift tensor in UF6

International Nuclear Information System (INIS)

Rigny, P.

1965-04-01

An 19 F magnetic resonance study of polycrystalline UF 6 is presented. The low temperature complex line can be analyzed as the superposition of two distinct lines, which is attributed to a distortion of the UF 6 octahedron in the solid. The shape of the two components is studied. Their width is much larger than the theoretical dipolar width, and must be explained by large anisotropies of the fluorine chemical shift tensors. The resulting shape functions of the powder spectra are determined. The values of the parameters of the chemical shift tensors yield estimates of the characters of the U-F bonds, and this gives some information on the ground state electronic wave function of the UF 6 molecule in the solid. (author) [fr

Prediction of hydrogen and carbon chemical shifts from RNA using database mining and support vector regression

Energy Technology Data Exchange (ETDEWEB)

Brown, Joshua D.; Summers, Michael F. [University of Maryland Baltimore County, Howard Hughes Medical Institute (United States); Johnson, Bruce A., E-mail: bruce.johnson@asrc.cuny.edu [University of Maryland Baltimore County, Department of Chemistry and Biochemistry (United States)

2015-09-15

The Biological Magnetic Resonance Data Bank (BMRB) contains NMR chemical shift depositions for over 200 RNAs and RNA-containing complexes. We have analyzed the {sup 1}H NMR and {sup 13}C chemical shifts reported for non-exchangeable protons of 187 of these RNAs. Software was developed that downloads BMRB datasets and corresponding PDB structure files, and then generates residue-specific attributes based on the calculated secondary structure. Attributes represent properties present in each sequential stretch of five adjacent residues and include variables such as nucleotide type, base-pair presence and type, and tetraloop types. Attributes and {sup 1}H and {sup 13}C NMR chemical shifts of the central nucleotide are then used as input to train a predictive model using support vector regression. These models can then be used to predict shifts for new sequences. The new software tools, available as stand-alone scripts or integrated into the NMR visualization and analysis program NMRViewJ, should facilitate NMR assignment and/or validation of RNA {sup 1}H and {sup 13}C chemical shifts. In addition, our findings enabled the re-calibration a ring-current shift model using published NMR chemical shifts and high-resolution X-ray structural data as guides.

Skeletal and chlorine effects on 13C-NMR chemical shifts of chlorinated polycyclic systems

Directory of Open Access Journals (Sweden)

Costa V.E.U.

1999-01-01

Full Text Available In order to establish a comparative analysis of chemical shifts caused by ring compression effects or by the presence of a chlorine atom on strained chlorinated carbons, a series of the chlorinated and dechlorinated polycyclic structures derived from "aldrin" (5 and "isodrin" (14 was studied. Compounds were classified in four different groups, according to their conformation and number of ring such as: endo-exo and endo-endo tetracyclics, pentacyclics and hexacyclics. The 13C chemical shift comparison between the chlorinated and dechlorinated compounds showed that when C-9 and C-10 are olefinic carbons, it occurs a shielding of 0.5-2.4 ppm for endo-endo tetracyclics and of 4.7-7.6 ppm for endo-exo tetracyclic. The chemical shift variation for C-11 reaches 49-53 ppm for endo-exo and endo-endo tetracyclics, 54 ppm for pentacyclic and 56-59 ppm for hexacyclic compounds. From these data, it was possible to observe the influence of ring compression on the chemical shifts.

Carbonyl Emissions from Gasoline and Diesel Motor Vehicles

Energy Technology Data Exchange (ETDEWEB)

Destaillats, Hugo; Jakober, Chris A.; Robert, Michael A.; Riddle, Sarah G.; Destaillats, Hugo; Charles, M. Judith; Green, Peter G.; Kleeman, Michael J.

2007-12-01

Carbonyls from gasoline powered light-duty vehicles (LDVs) and heavy-duty diesel powered vehicles (HDDVs) operated on chassis dynamometers were measured using an annular denuder-quartz filter-polyurethane foam sampler with O-(2,3,4,5,6-pentafluorobenzyl)hydroxylamine derivatization and chromatography-mass spectrometry analyses. Two internal standards were utilized based on carbonyl recovery, 4-fluorobenzaldehyde forcarbonyls and 6-fluoro-4-chromanone for>_C8 compounds. Gas- and particle-phase emissions for 39 aliphatic and 20 aromatic carbonyls ranged from 0.1 ? 2000 ?g/L fuel for LDVs and 1.8 - 27000 mu g/L fuel for HDDVs. Gas-phase species accounted for 81-95percent of the total carbonyls from LDVs and 86-88percent from HDDVs. Particulate carbonyls emitted from a HDDV under realistic driving conditions were similar to concentrations measured in a diesel particulate matter (PM) standard reference material. Carbonyls accounted for 19percent of particulate organic carbon (POC) emissions from low-emission LDVs and 37percent of POC emissions from three-way catalyst equipped LDVs. This identifies carbonyls as one of the largest classes of compounds in LDV PM emissions. The carbonyl fraction of HDDV POC was lower, 3.3-3.9percent depending upon operational conditions. Partitioning analysis indicates the carbonyls had not achieved equilibrium between the gas- and particle-phase under the dilution factors of 126-584 used in the current study.

SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network

International Nuclear Information System (INIS)

Shen Yang; Bax, Ad

2010-01-01

NMR chemical shifts provide important local structural information for proteins and are key in recently described protein structure generation protocols. We describe a new chemical shift prediction program, SPARTA+, which is based on artificial neural networking. The neural network is trained on a large carefully pruned database, containing 580 proteins for which high-resolution X-ray structures and nearly complete backbone and 13 C β chemical shifts are available. The neural network is trained to establish quantitative relations between chemical shifts and protein structures, including backbone and side-chain conformation, H-bonding, electric fields and ring-current effects. The trained neural network yields rapid chemical shift prediction for backbone and 13 C β atoms, with standard deviations of 2.45, 1.09, 0.94, 1.14, 0.25 and 0.49 ppm for δ 15 N, δ 13 C', δ 13 C α , δ 13 C β , δ 1 H α and δ 1 H N , respectively, between the SPARTA+ predicted and experimental shifts for a set of eleven validation proteins. These results represent a modest but consistent improvement (2-10%) over the best programs available to date, and appear to be approaching the limit at which empirical approaches can predict chemical shifts.

Enhanced antioxidation and microwave absorbing properties of SiO2-coated flaky carbonyl iron particles

Science.gov (United States)

Zhou, Yingying; Xie, Hui; Zhou, Wancheng; Ren, Zhaowen

2018-01-01

SiO2 was successfully coated on the surface of flaky carbonyl iron particles using a chemical bath deposition method in the presence of 3-aminopropyl triethoxysilane (APTES). The morphologies, composition, valence states of elements, as well as antioxidation and electromagnetic properties of the samples were characterized by scanning electron microscope (SEM), energy dispersive spectrometer (EDS), X-ray photoelectron spectroscopy (XPS), thermogravimetric (TG) and microwave network analyzer. TG curve shows the obvious weight gain of carbonyl iron was deferred to 360 °C after SiO2-coated, which can be ascribed to the exits of SiO2 overlayer. Compared with the raw carbonyl iron, SiO2-coated sample shows good wave absorption performance due to its impedance matching. The electromagnetic properties of raw and SiO2-coated carbonyl iron particles were characterized in X band before and after heat treatment at 250 °C for 10 h. It was established that SiO2-coated carbonyl iron demonstrate good thermal stability, indicating SiO2-coating is useful in the usage of microwave absorbers operating at temperature up to 250 °C.

Cyclohexanecarbonitriles: Assigning Configurations at Quaternary Centers From 13C NMR CN Chemical Shifts.1

Science.gov (United States)

Wei, Guoqing

2009-01-01

13C NMR chemical shifts of the nitrile carbon in cyclohexanecarbonitriles directly correlate with the configuration of the quaternary, nitrile-bearing stereocenter. Comparing 13C NMR chemical shifts for over 200 cyclohexanecarbonitriles reveals that equatorially oriented nitriles resonate 3.3 ppm downfield, on average, from their axial counterparts. Pairs of axial/equatorial diastereomers varying only at the nitrile-bearing carbon consistently exhibit downfield shifts of δ 0.4–7.2 for the equatorial nitrile carbon, even in angularly substituted decalins and hydrindanes. PMID:19348434

Electromagnetic absorbing property of the flaky carbonyl iron particles by chemical corrosion process

Energy Technology Data Exchange (ETDEWEB)

Zheng, Dianliang, E-mail: 272895980@qq.com [College of Aeronautical Engineering, Jilin Institute of Chemical Technology, Jilin 132022 (China); Liu, Ting; Zhou, Li [College of Aeronautical Engineering, Jilin Institute of Chemical Technology, Jilin 132022 (China); Xu, Yonggang [Science and Technology on Electromagnetic Scattering Laboratory, Shanghai 200438 (China)

2016-12-01

The flaky carbonyl iron particles (CIPs) were prepared using a milling process at the first step, then the chemical corrosion process was done to optimize the particle shape. The particle morphology was characterized by the scanning electron microscopy, the static magnetic property was evaluated on a vibrating sample magnetometer and X-ray diffraction (XRD) patterns were done to analyze the particle crystal grain structure. The complex permittivity and permeability were measured using a vector network analyzer in the frequency range of 2–18 GHz and the reflection loss (RL) was calculated. The results showed that the saturation magnetization value of the CIPs decreased as the CIPs was corroded to the small flakes in chemical corrosion process. The diffraction peaks of the single α-Fe existed in the XRD pattern of CIPs, and the characteristic peaks was more obvious and the intensity of the diffraction pattern was lower by corrosion. The permittivity and the permeability of the corroded milling CIPs was a little larger than the milling CIPs, it was due to the larger aspect ratio based on the fitting calculation process. At thickness 0.6 mm and 0.8 mm, the corroded milling CIPs composite had the better absorbing property than the other two samples. The frequency band (RL<−5 dB) could be widened to 8.96–18 GHz at 0.6 mm and 5.92–18 GHz at 0.8 mm, and RL less than −8 dB began to exist in 8.96–14.72 GHz at 0.8 mm. - Graphical abstract: The property of absorber using corrosion process could be enhanced. - Highlights: • The chemical corrosion process was done to optimize the particle shape. • The permittivity and permeability of corroded milling CIPs increased. • The aspect ratio of flaky CIPs increased in the corrosion process. • The corroded milling CIPs composite had the better absorbing property.

THE METAL CARBONYLS.

Science.gov (United States)

Blanchard, A A

1941-10-03

When the metal carbonyls were first discovered, their properties were startling because they seemed to violate nearly all the previously recognized generalizations of chemistry. Even to-day the existence of the carbonyls is not particularly emphasized in elementary courses of chemistry because it is rather hard to reconcile them with the first presentations of the generalizations of chemistry. Nevertheless, as the student progresses deeper into the knowledge of chemistry it becomes desirable to include the knowledge of the carbonyls both because they become more comprehensible when viewed in the light of Werner's system of coordination and because they themselves contribute to the comprehension of the Werner theory. As long ago as 1931, Reiff in his discussion of cobalt nitrosyl carbonyl recognized the correlation between the effective atomic number and the volatility of carbonyls. A more recent study of charged Werner coordination complexes, that is, of complex ions, has shown a similar role of the effective atomic number. We are standing on fairly firm ground when we point out the correlation between E.A.N. and the volatility of the carbonyl complexes and the existence of complex ions. Be it noted that we have made no postulates as to the arrangement of the electrons in quantum levels. In the inert gases the outer principal quantum group is supposed always to contain eight electrons. In the carbonyls and other Werner complexes there is no compelling reason to suppose that the electrons in the coordinating layer, be this layer of eight, ten, twelve or sixteen electrons, are not all at the same energy level. Although we have confined our discussion almost exclusively to the property of volatility, the carbonyls are very interesting from the standpoint of several other properties, for example, magnetic susceptibility and dielectric constant. Enthusiasts in the interpretation of such properties try to draw conclusions as to the condition of the electrons, sometimes

1H NMR spectra part 31: 1H chemical shifts of amides in DMSO solvent.

Science.gov (United States)

Abraham, Raymond J; Griffiths, Lee; Perez, Manuel

2014-07-01

The (1)H chemical shifts of 48 amides in DMSO solvent are assigned and presented. The solvent shifts Δδ (DMSO-CDCl3 ) are large (1-2 ppm) for the NH protons but smaller and negative (-0.1 to -0.2 ppm) for close range protons. A selection of the observed solvent shifts is compared with calculated shifts from the present model and from GIAO calculations. Those for the NH protons agree with both calculations, but other solvent shifts such as Δδ(CHO) are not well reproduced by the GIAO calculations. The (1)H chemical shifts of the amides in DMSO were analysed using a functional approach for near ( ≤ 3 bonds removed) protons and the electric field, magnetic anisotropy and steric effect of the amide group for more distant protons. The chemical shifts of the NH protons of acetanilide and benzamide vary linearly with the π density on the αN and βC atoms, respectively. The C=O anisotropy and steric effect are in general little changed from the values in CDCl3. The effects of substituents F, Cl, Me on the NH proton shifts are reproduced. The electric field coefficient for the protons in DMSO is 90% of that in CDCl3. There is no steric effect of the C=O oxygen on the NH proton in an NH…O=C hydrogen bond. The observed deshielding is due to the electric field effect. The calculated chemical shifts agree well with the observed shifts (RMS error of 0.106 ppm for the data set of 257 entries). Copyright © 2014 John Wiley & Sons, Ltd.

Characterization of the conformational equilibrium between the two major substates of RNase A using NMR chemical shifts.

Science.gov (United States)

Camilloni, Carlo; Robustelli, Paul; De Simone, Alfonso; Cavalli, Andrea; Vendruscolo, Michele

2012-03-07

Following the recognition that NMR chemical shifts can be used for protein structure determination, rapid advances have recently been made in methods for extending this strategy for proteins and protein complexes of increasing size and complexity. A remaining major challenge is to develop approaches to exploit the information contained in the chemical shifts about conformational fluctuations in native states of proteins. In this work we show that it is possible to determine an ensemble of conformations representing the free energy surface of RNase A using chemical shifts as replica-averaged restraints in molecular dynamics simulations. Analysis of this surface indicates that chemical shifts can be used to characterize the conformational equilibrium between the two major substates of this protein. © 2012 American Chemical Society

Protein Carbonylation and Adipocyte Mitochondrial Function*

Science.gov (United States)

Curtis, Jessica M.; Hahn, Wendy S.; Stone, Matthew D.; Inda, Jacob J.; Droullard, David J.; Kuzmicic, Jovan P.; Donoghue, Margaret A.; Long, Eric K.; Armien, Anibal G.; Lavandero, Sergio; Arriaga, Edgar; Griffin, Timothy J.; Bernlohr, David A.

2012-01-01

Carbonylation is the covalent, non-reversible modification of the side chains of cysteine, histidine, and lysine residues by lipid peroxidation end products such as 4-hydroxy- and 4-oxononenal. In adipose tissue the effects of such modifications are associated with increased oxidative stress and metabolic dysregulation centered on mitochondrial energy metabolism. To address the role of protein carbonylation in the pathogenesis of mitochondrial dysfunction, quantitative proteomics was employed to identify specific targets of carbonylation in GSTA4-silenced or overexpressing 3T3-L1 adipocytes. GSTA4-silenced adipocytes displayed elevated carbonylation of several key mitochondrial proteins including the phosphate carrier protein, NADH dehydrogenase 1α subcomplexes 2 and 3, translocase of inner mitochondrial membrane 50, and valyl-tRNA synthetase. Elevated protein carbonylation is accompanied by diminished complex I activity, impaired respiration, increased superoxide production, and a reduction in membrane potential without changes in mitochondrial number, area, or density. Silencing of the phosphate carrier or NADH dehydrogenase 1α subcomplexes 2 or 3 in 3T3-L1 cells results in decreased basal and maximal respiration. These results suggest that protein carbonylation plays a major instigating role in cytokine-dependent mitochondrial dysfunction and may be linked to the development of insulin resistance in the adipocyte. PMID:22822087

Protein carbonylation and adipocyte mitochondrial function.

Science.gov (United States)

Curtis, Jessica M; Hahn, Wendy S; Stone, Matthew D; Inda, Jacob J; Droullard, David J; Kuzmicic, Jovan P; Donoghue, Margaret A; Long, Eric K; Armien, Anibal G; Lavandero, Sergio; Arriaga, Edgar; Griffin, Timothy J; Bernlohr, David A

2012-09-21

Carbonylation is the covalent, non-reversible modification of the side chains of cysteine, histidine, and lysine residues by lipid peroxidation end products such as 4-hydroxy- and 4-oxononenal. In adipose tissue the effects of such modifications are associated with increased oxidative stress and metabolic dysregulation centered on mitochondrial energy metabolism. To address the role of protein carbonylation in the pathogenesis of mitochondrial dysfunction, quantitative proteomics was employed to identify specific targets of carbonylation in GSTA4-silenced or overexpressing 3T3-L1 adipocytes. GSTA4-silenced adipocytes displayed elevated carbonylation of several key mitochondrial proteins including the phosphate carrier protein, NADH dehydrogenase 1α subcomplexes 2 and 3, translocase of inner mitochondrial membrane 50, and valyl-tRNA synthetase. Elevated protein carbonylation is accompanied by diminished complex I activity, impaired respiration, increased superoxide production, and a reduction in membrane potential without changes in mitochondrial number, area, or density. Silencing of the phosphate carrier or NADH dehydrogenase 1α subcomplexes 2 or 3 in 3T3-L1 cells results in decreased basal and maximal respiration. These results suggest that protein carbonylation plays a major instigating role in cytokine-dependent mitochondrial dysfunction and may be linked to the development of insulin resistance in the adipocyte.

Sequential nearest-neighbor effects on computed {sup 13}C{sup {alpha}} chemical shifts

Energy Technology Data Exchange (ETDEWEB)

Vila, Jorge A. [Cornell University, Baker Laboratory of Chemistry and Chemical Biology (United States); Serrano, Pedro; Wuethrich, Kurt [The Scripps Research Institute, Department of Molecular Biology (United States); Scheraga, Harold A., E-mail: has5@cornell.ed [Cornell University, Baker Laboratory of Chemistry and Chemical Biology (United States)

2010-09-15

To evaluate sequential nearest-neighbor effects on quantum-chemical calculations of {sup 13}C{sup {alpha}} chemical shifts, we selected the structure of the nucleic acid binding (NAB) protein from the SARS coronavirus determined by NMR in solution (PDB id 2K87). NAB is a 116-residue {alpha}/{beta} protein, which contains 9 prolines and has 50% of its residues located in loops and turns. Overall, the results presented here show that sizeable nearest-neighbor effects are seen only for residues preceding proline, where Pro introduces an overestimation, on average, of 1.73 ppm in the computed {sup 13}C{sup {alpha}} chemical shifts. A new ensemble of 20 conformers representing the NMR structure of the NAB, which was calculated with an input containing backbone torsion angle constraints derived from the theoretical {sup 13}C{sup {alpha}} chemical shifts as supplementary data to the NOE distance constraints, exhibits very similar topology and comparable agreement with the NOE constraints as the published NMR structure. However, the two structures differ in the patterns of differences between observed and computed {sup 13}C{sup {alpha}} chemical shifts, {Delta}{sub ca,i}, for the individual residues along the sequence. This indicates that the {Delta}{sub ca,i} -values for the NAB protein are primarily a consequence of the limited sampling by the bundles of 20 conformers used, as in common practice, to represent the two NMR structures, rather than of local flaws in the structures.

Radical carbonylations using a continuous microflow system

Directory of Open Access Journals (Sweden)

Takahide Fukuyama

2009-07-01

Full Text Available Radical-based carbonylation reactions of alkyl halides were conducted in a microflow reactor under pressurized carbon monoxide gas. Good to excellent yields of carbonylated products were obtained via radical formylation, carbonylative cyclization and three-component coupling reactions, using tributyltin hydride or TTMSS as a radical mediator.

Intermolecular Interactions in Crystalline Theobromine as Reflected in Electron Deformation Density and (13)C NMR Chemical Shift Tensors.

Science.gov (United States)

Bouzková, Kateřina; Babinský, Martin; Novosadová, Lucie; Marek, Radek

2013-06-11

An understanding of the role of intermolecular interactions in crystal formation is essential to control the generation of diverse crystalline forms which is an important concern for pharmaceutical industry. Very recently, we reported a new approach to interpret the relationships between intermolecular hydrogen bonding, redistribution of electron density in the system, and NMR chemical shifts (Babinský et al. J. Phys. Chem. A, 2013, 117, 497). Here, we employ this approach to characterize a full set of crystal interactions in a sample of anhydrous theobromine as reflected in (13)C NMR chemical shift tensors (CSTs). The important intermolecular contacts are identified by comparing the DFT-calculated NMR CSTs for an isolated theobromine molecule and for clusters composed of several molecules as selected from the available X-ray diffraction data. Furthermore, electron deformation density (EDD) and shielding deformation density (SDD) in the proximity of the nuclei involved in the proposed interactions are calculated and visualized. In addition to the recently reported observations for hydrogen bonding, we focus here particularly on the stacking interactions. Although the principal relations between the EDD and CST for hydrogen bonding (HB) and stacking interactions are similar, the real-space consequences are rather different. Whereas the C-H···X hydrogen bonding influences predominantly and significantly the in-plane principal component of the (13)C CST perpendicular to the HB path and the C═O···H hydrogen bonding modulates both in-plane components of the carbonyl (13)C CST, the stacking modulates the out-of-plane electron density resulting in weak deshielding (2-8 ppm) of both in-plane principal components of the CST and weak shielding (∼ 5 ppm) of the out-of-plane component. The hydrogen-bonding and stacking interactions may add to or subtract from one another to produce total values observed experimentally. On the example of theobromine, we demonstrate

Isotope effects on chemical shifts in tautomeric systems with double proton transfer. Citronin

International Nuclear Information System (INIS)

Hansen, P.E.; Langgard, M.; Bolvig, S.

1998-01-01

Primary and secondary deuterium isotope effects on 1 H and 13 C chemical shifts are measured in citrinin, a tautomeric compound with an unusual doubly intramolecularly hydrogen bonded structure. The isotope effects are to a large extent dominated by equilibrium contributions and deuteration leads to more of the deuterated enol forms rather than the deuterated acid form. 1 H 13 C and 17 O nuclear shieldings are calculated using density functional ab initio methods. A very good correlation between calculated nuclear shieldings and experimental 1 H and 13 C chemical shifts is obtained. The tautomeric equilibrium can be analyzed based on the isotope effects on B-6 and C-8 carbons and shows an increase in the o-quinone form on lowering the temperature. Furthermore, upon deuteration the largest equilibrium shift is found for deuteration at OH-8 and the shift in the tautomeric equilibrium upon deuteration at OH-8 and the shift in the tautomeric equilibrium upon deuteration is increasing at lower temperature. (author)

SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network

Energy Technology Data Exchange (ETDEWEB)

Shen Yang; Bax, Ad, E-mail: bax@nih.go [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

2010-09-15

NMR chemical shifts provide important local structural information for proteins and are key in recently described protein structure generation protocols. We describe a new chemical shift prediction program, SPARTA+, which is based on artificial neural networking. The neural network is trained on a large carefully pruned database, containing 580 proteins for which high-resolution X-ray structures and nearly complete backbone and {sup 13}C{sup {beta}} chemical shifts are available. The neural network is trained to establish quantitative relations between chemical shifts and protein structures, including backbone and side-chain conformation, H-bonding, electric fields and ring-current effects. The trained neural network yields rapid chemical shift prediction for backbone and {sup 13}C{sup {beta}} atoms, with standard deviations of 2.45, 1.09, 0.94, 1.14, 0.25 and 0.49 ppm for {delta}{sup 15}N, {delta}{sup 13}C', {delta}{sup 13}C{sup {alpha}}, {delta}{sup 13}C{sup {beta}}, {delta}{sup 1}H{sup {alpha}} and {delta}{sup 1}H{sup N}, respectively, between the SPARTA+ predicted and experimental shifts for a set of eleven validation proteins. These results represent a modest but consistent improvement (2-10%) over the best programs available to date, and appear to be approaching the limit at which empirical approaches can predict chemical shifts.

The interplay between transient a-helix formation and side chain rotamer distributions in disordered proteins probed by methyl chemical shifts

DEFF Research Database (Denmark)

Kjærgaard, Magnus; Iesmantavicius, Vytautas; Poulsen, Flemming M

2011-01-01

and retinoid receptors (ACTR). We find that small differences in the methyl carbon chemical shifts due to the ¿-gauche effect may provide information about the side chain rotamer distributions. However, the effects of neighboring residues on the methyl group chemical shifts obscure the direct observation...... of ¿-gauche effect. To overcome this, we reference the chemical shifts to those in a more disordered state resulting in residue specific random coil chemical shifts. The (13)C secondary chemical shifts of the methyl groups of valine, leucine, and isoleucine show sequence specific effects, which allow...

What can we learn by computing 13Cα chemical shifts for X-ray protein models?

International Nuclear Information System (INIS)

Arnautova, Yelena A.; Vila, Jorge A.; Martin, Osvaldo A.; Scheraga, Harold A.

2009-01-01

The room-temperature X-ray structures of two proteins, solved at 1.8 and 1.9 Å resolution, are used to investigate whether a set of conformations, rather than a single X-ray structure, provides better agreement with both the X-ray data and the observed 13 C α chemical shifts in solution. The room-temperature X-ray structures of ubiquitin and of the RNA-binding domain of nonstructural protein 1 of influenza A virus solved at 1.8 and 1.9 Å resolution, respectively, were used to investigate whether a set of conformations rather than a single X-ray structure provides better agreement with both the X-ray data and the observed 13 C α chemical shifts in solution. For this purpose, a set of new conformations for each of these proteins was generated by fitting them to the experimental X-ray data deposited in the PDB. For each of the generated structures, which show R and R free factors similar to those of the deposited X-ray structure, the 13 C α chemical shifts of all residues in the sequence were computed at the DFT level of theory. The sets of conformations were then evaluated by their ability to reproduce the observed 13 C α chemical shifts by using the conformational average root-mean-square-deviation (ca-r.m.s.d.). For ubiquitin, the computed set of conformations is a better representation of the observed 13 C α chemical shifts in terms of the ca-r.m.s.d. than a single X-ray-derived structure. However, for the RNA-binding domain of nonstructural protein 1 of influenza A virus, consideration of an ensemble of conformations does not improve the agreement with the observed 13 C α chemical shifts. Whether an ensemble of conformations rather than any single structure is a more accurate representation of a protein structure in the crystal as well as of the observed 13 C α chemical shifts is determined by the dispersion of coordinates, in terms of the all-atom r.m.s.d. among the generated models; these generated models satisfy the experimental X-ray data with

Conformational analysis of the chemical shifts for molecules containing diastereotopic methylene protons

Science.gov (United States)

Borowski, Piotr

2012-01-01

Quantum chemistry SCF/GIAO calculations were carried out on a set of compounds containing diastereotopic protons. Five molecules, including recently synthesized 1,3-di(2,3-epoxypropoxy)benzene, containing the chiral or pro-chiral center and the neighboring methylene group, were chosen. The rotational averages (i.e. normalized averages with respect to the rotation about the torsional angle τ with the exponential energy weight at temperature T) calculated individually for each of the methylene protons in 1,3-di(2,3-epoxypropoxy)benzene differ by ca. 0.6 ppm, which is significantly less than the value calculated for the lowest energy conformer. This value turned out to be low enough to guarantee the proper ordering of theoretical chemical shifts, supporting the interpretation of the 1H NMR spectrum of this important compound. The rotational averages of chemical shifts for methylene protons for a given type of conformer are shown to be essentially equal to the Boltzmann averages (here, the population-weighted averages for the individual conformers representing minima on the E( τ) cross-section). The calculated Boltzmann averages in the representative conformational space may exhibit completely different ordering as compared to the chemical shifts calculated for the lowest-energy conformer. This is especially true in the case of molecules, for which no significant steric effects are present. In this case, only Boltzmann averages account for the experimental pattern of proton signals. In addition, better overall agreement with experiment (lower value of the root-mean-square deviation between calculated and measured chemical shifts) is typically obtained when Boltzmann averages are used.

Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology

International Nuclear Information System (INIS)

Shen Yang; Bax, Ad

2007-01-01

Chemical shifts of nuclei in or attached to a protein backbone are exquisitely sensitive to their local environment. A computer program, SPARTA, is described that uses this correlation with local structure to predict protein backbone chemical shifts, given an input three-dimensional structure, by searching a newly generated database for triplets of adjacent residues that provide the best match in φ/ψ/χ 1 torsion angles and sequence similarity to the query triplet of interest. The database contains 15 N, 1 H N , 1 H α , 13 C α , 13 C β and 13 C' chemical shifts for 200 proteins for which a high resolution X-ray (≤2.4 A) structure is available. The relative importance of the weighting factors for the φ/ψ/χ 1 angles and sequence similarity was optimized empirically. The weighted, average secondary shifts of the central residues in the 20 best-matching triplets, after inclusion of nearest neighbor, ring current, and hydrogen bonding effects, are used to predict chemical shifts for the protein of known structure. Validation shows good agreement between the SPARTA-predicted and experimental shifts, with standard deviations of 2.52, 0.51, 0.27, 0.98, 1.07 and 1.08 ppm for 15 N, 1 H N , 1 H α , 13 C α , 13 C β and 13 C', respectively, including outliers

Implementation of the NMR CHEmical Shift Covariance Analysis (CHESCA): A Chemical Biologist's Approach to Allostery.

Science.gov (United States)

Boulton, Stephen; Selvaratnam, Rajeevan; Ahmed, Rashik; Melacini, Giuseppe

2018-01-01

Mapping allosteric sites is emerging as one of the central challenges in physiology, pathology, and pharmacology. Nuclear Magnetic Resonance (NMR) spectroscopy is ideally suited to map allosteric sites, given its ability to sense at atomic resolution the dynamics underlying allostery. Here, we focus specifically on the NMR CHEmical Shift Covariance Analysis (CHESCA), in which allosteric systems are interrogated through a targeted library of perturbations (e.g., mutations and/or analogs of the allosteric effector ligand). The atomic resolution readout for the response to such perturbation library is provided by NMR chemical shifts. These are then subject to statistical correlation and covariance analyses resulting in clusters of allosterically coupled residues that exhibit concerted responses to the common set of perturbations. This chapter provides a description of how each step in the CHESCA is implemented, starting from the selection of the perturbation library and ending with an overview of different clustering options.

Proton chemical shift imaging after myocardial infarction

International Nuclear Information System (INIS)

Bouchard, A.; Doyle, M.; Pohost, G.M.

1989-01-01

The present study was undertaken to test whether chemical shift imaging could detect spatially the lipids known to accumulate in myocardium after an ischemic insult. Seven dogs underwent a 24-hour coronary artery occlusion. Hearts were removed and imaged ex vivo by the Dixon method (1.5 T), and myocardial samples were obtained for high-resolution H-1 spectroscopy. Lipid images revealed regions of increased signal intensity in the periphery f the myocardial infarction. The zones of high lipid signal corresponded to zones with elevated mobile lipids as detected by H-1 spectroscopy

Accuracy and precision of protein–ligand interaction kinetics determined from chemical shift titrations

International Nuclear Information System (INIS)

Markin, Craig J.; Spyracopoulos, Leo

2012-01-01

NMR-monitored chemical shift titrations for the study of weak protein–ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K D ) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K D value of a 1:1 protein–ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125–138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of 1 H– 15 N 2D HSQC NMR spectra acquired using precise protein–ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k off ). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k off ∼ 3,000 s −1 in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k off from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k off values over a wide range, from 100 to 15,000 s −1 . The validity of line shape analysis for k off values approaching intermediate exchange (∼100 s −1 ), may be facilitated by more accurate K D measurements from NMR

Accuracy and precision of protein-ligand interaction kinetics determined from chemical shift titrations.

Science.gov (United States)

Markin, Craig J; Spyracopoulos, Leo

2012-12-01

NMR-monitored chemical shift titrations for the study of weak protein-ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K ( D )) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K ( D ) value of a 1:1 protein-ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125-138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of (1)H-(15)N 2D HSQC NMR spectra acquired using precise protein-ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k ( off )). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k ( off ) ~ 3,000 s(-1) in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k ( off ) from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k ( off ) values over a wide range, from 100 to 15,000 s(-1). The validity of line shape analysis for k ( off ) values approaching intermediate exchange (~100 s(-1)), may be facilitated by more accurate K ( D ) measurements

Glucosinolates and isothiocyanates from broccoliseed extractsuppressproteinglycationand carbonylation

Directory of Open Access Journals (Sweden)

Marina Hirano,

2018-01-01

Full Text Available Background: Glucosinolates from brassica plants are hydrolyzed by internal or salivary myrosinase to produce isothiocyanates. Glucoraphanin, a major glucosinolate in broccoli, is hydrolyzed to sulforaphane (SFN, which exhibits antitumor and detoxification activities. Regarding the influence of broccoli and its constituents on the skin, a few studies have reported anti-inflammatory and antioxidant effects. Recently, advanced glycation end products (AGEs and carbonyl proteins have been reported to accelerate skin aging. Objective: We evaluated the effects of broccoli seed extract (BSE and glucosinolates on protein glycation and carbonylation in vitro. Methods: To evaluate the effects of BSE and its constituents, protein glycation and carbonylation were induced by mixing fructose with bovine serum albumin (BSA and then measuring production of AGEs, fructosamine, and carbonyl proteins (CP. Production of CP after mixing fatty acids with BSA was also assessed. Furthermore, the effect of BSE and its constituents on CP production by human fibroblasts (TIG103 was examined. Results: BSE suppressed the production of AGEs, fructosamine, and CP after mixing fructose and BSA. BSE also suppressed production of CP when oxidized linoleic acid was mixed with BSA. Isothiocyanates, including SFN and iberin, suppressed fructose-based CP production, but SFN had no effect on CP production stimulated by oxidized linoleic acid. In contrast, glucosinolates from BSE did not suppress fructose-based CP production, but suppressed CP production due to oxidized linoleic acid. Among the glucosinolates in BSE, glucoberteroin showed the strongest suppression of CP production. CP production in fibroblasts was also suppressed by glucosinolates, including glucoiberin and glucoberteroin. Conclusions: BSE demonstrated anti-glycation and anti-carbonylation effects on protein reactions with fructose and oxidized fatty acids. Isothiocyanates suppressed protein carbonylation induced by

Chemical shift-based identification of monosaccharide spin-systems with NMR spectroscopy to complement untargeted glycomics.

Science.gov (United States)

Klukowski, Piotr; Schubert, Mario

2018-06-15

A better understanding of oligosaccharides and their wide-ranging functions in almost every aspect of biology and medicine promises to uncover hidden layers of biology and will support the development of better therapies. Elucidating the chemical structure of an unknown oligosaccharide is still a challenge. Efficient tools are required for non-targeted glycomics. Chemical shifts are a rich source of information about the topology and configuration of biomolecules, whose potential is however not fully explored for oligosaccharides. We hypothesize that the chemical shifts of each monosaccharide are unique for each saccharide type with a certain linkage pattern, so that correlated data measured by NMR spectroscopy can be used to identify the chemical nature of a carbohydrate. We present here an efficient search algorithm, GlycoNMRSearch, that matches either a subset or the entire set of chemical shifts of an unidentified monosaccharide spin system to all spin systems in an NMR database. The search output is much more precise than earlier search functions and highly similar matches suggest the chemical structure of the spin system within the oligosaccharide. Thus searching for connected chemical shift correlations within all electronically available NMR data of oligosaccharides is a very efficient way of identifying the chemical structure of unknown oligosaccharides. With an improved database in the future, GlycoNMRSearch will be even more efficient deducing chemical structures of oligosaccharides and there is a high chance that it becomes an indispensable technique for glycomics. The search algorithm presented here, together with a graphical user interface, is available at http://glyconmrsearch.santos.pwr.edu.pl. Supplementary data are available at Bioinformatics online.

Elucidation of the substitution pattern of 9,10-anthraquinones through the chemical shifts of peri-hydroxyl protons

DEFF Research Database (Denmark)

Schripsema, Jan; Danigno, Denise

1996-01-01

In 9,10-anthraquinones the chemical shift of a peri-hydroxyl proton is affected by the substituents in the other benzenoid ring. These effects are additive. They are useful for the determination of substitution patterns and have been used to revise the structures of six previously reported...... anthraquinones containing methoxyl, hydroxyl, methylenedioxy and beta-methyl substituents. Because the chemical shifts of the other protons are hardly affected by substitutions in the other ring, the characteristic chemical shifts for a wide variety of substitution patterns could be derived....

Mechanofluorochromic Carbon Nanodots: Controllable Pressure-Triggered Blue- and Red-Shifted Photoluminescence.

Science.gov (United States)

Liu, Cui; Xiao, Guanjun; Yang, Mengli; Zou, Bo; Zhang, Zhi-Ling; Pang, Dai-Wen

2018-02-12

Mechanofluorochromic materials, which change their photoluminescence (PL) colors in responding to mechanical stimuli, can be used as mechanosensors, security papers, and photoelectronic devices. However, traditional mechanofluorochromic materials can only be adjusted to a monotone direction upon the external stimuli. Controllable pressure-triggered blue- and red-shifted PL is reported for C-dots. The origin of mechanofluorochromism (MFC) in C-dots is interpreted based on structure-property relationships. The carbonyl group and the π-conjugated system play key roles in the PL change of C-dots under high pressure. As the pressure increases, the enhanced π-π stacking of the π-conjugated system causes the red-shift of PL, while the conversion of carbonyl groups eventually induces a blue-shift. Together with their low toxicity, good hydrophilicity, and small size, the tunable MFC property would boost various potential applications of C-dots. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Vanadium NMR Chemical Shifts of (Imido)vanadium(V) Dichloride Complexes with Imidazolin-2-iminato and Imidazolidin-2-iminato Ligands: Cooperation with Quantum-Chemical Calculations and Multiple Linear Regression Analyses.

Science.gov (United States)

Yi, Jun; Yang, Wenhong; Sun, Wen-Hua; Nomura, Kotohiro; Hada, Masahiko

2017-11-30

The NMR chemical shifts of vanadium ( 51 V) in (imido)vanadium(V) dichloride complexes with imidazolin-2-iminato and imidazolidin-2-iminato ligands were calculated by the density functional theory (DFT) method with GIAO. The calculated 51 V NMR chemical shifts were analyzed by the multiple linear regression (MLR) analysis (MLRA) method with a series of calculated molecular properties. Some of calculated NMR chemical shifts were incorrect using the optimized molecular geometries of the X-ray structures. After the global minimum geometries of all of the molecules were determined, the trend of the observed chemical shifts was well reproduced by the present DFT method. The MLRA method was performed to investigate the correlation between the 51 V NMR chemical shift and the natural charge, band energy gap, and Wiberg bond index of the V═N bond. The 51 V NMR chemical shifts obtained with the present MLR model were well reproduced with a correlation coefficient of 0.97.

A Moessbauer effect study of the bonding in several organoiron carbonyl clusters

International Nuclear Information System (INIS)

Long, G.J.; O'Brien, J.F.

1988-01-01

After a brief review of the applications of the Moessbauer effect to cyclopentadienyl containing compounds, the chemistry and spectral properties of the various iron carbonyl complexes are described. The electronic properties of a series of trinuclear and tetranuclear organoiron clusters have been investigated through Fenske-Hall self-consistent field molecular orbital calculations, and the results are compared with the Moessbauer effect isomer shifts. A linear correlation is found between the Slater effective nuclear charge, as calculated from the Fenske-Hall partial orbital occupancy factors, and the isomer shift. In these compounds the 4s orbital populations are rather constant. However, the cis and trans isomers of [CpFe(CO) 2 ] 2 have a significantly lower 4s orbital populations. In this case, the reduced 4s population must be accounted for by adding it to the effective nuclear charge to obtain a good correlation with the isomer shift. (orig.)

Evaluation of the application of chemical shift for the detection of lipid in brain lesion

Energy Technology Data Exchange (ETDEWEB)

Lim, C.J. [Department of Biomedical Imaging, Faculty of Medicine, University of Malaya Medical Centre, Kuala Lumpur (Malaysia); Ng, K.H., E-mail: ngkh@um.edu.m [Department of Biomedical Imaging, Faculty of Medicine, University of Malaya Medical Centre, Kuala Lumpur (Malaysia); Ramli, N.; Azman, R.R. [Department of Biomedical Imaging, Faculty of Medicine, University of Malaya Medical Centre, Kuala Lumpur (Malaysia)

2011-02-15

Non-invasive detection of the presence of lipids is particularly important in staging of intracranial tumours. Presence of lipid peak in aggressive intracranial tumours has been reported widely using MR spectroscopy. However this method has limitation due to long imaging time and artefacts formed by adjacent bones. Chemical shift MR imaging (with has shorter imaging time) is an alternative method that had been used to detect presence of lipid in vivo by means of signal intensity loss. The purpose of this study was to evaluate gradient echo in- and opposed-phase chemical shift pulse sequences for detection of lipid elements in brain lesion. Ten cylindered phantoms measuring 3 x 3 cm were filled with various mixtures of lipid and water: 0-90% lipid, in 10% step by weight. The gradient echo in- and opposed-phase chemical shift sequences were performed using a 1.5 T MRI (Magnetom Vision, Siemens) with a head coil. In addition, we performed MRI and chemical shift studies on 32 patients with brain lesion. We then analysed the association between out of phase intensity value and classification of the lesions. For phantom containing 50% lipid, maximum signal loss on opposed-phase images was observed. There were significant differences between in- and opposed-phase lipid-water phantom images (P = 0.0054). Most of the benign lesions fall into the positive out of phase intensity value, and malignant lesions fall into negative out of phase intensity value. We conclude that chemical shift artefact can be applied in detecting and characterising lipid elements in brain lesion.

Evaluation of the application of chemical shift for the detection of lipid in brain lesion

International Nuclear Information System (INIS)

Lim, C.J.; Ng, K.H.; Ramli, N.; Azman, R.R.

2011-01-01

Non-invasive detection of the presence of lipids is particularly important in staging of intracranial tumours. Presence of lipid peak in aggressive intracranial tumours has been reported widely using MR spectroscopy. However this method has limitation due to long imaging time and artefacts formed by adjacent bones. Chemical shift MR imaging (with has shorter imaging time) is an alternative method that had been used to detect presence of lipid in vivo by means of signal intensity loss. The purpose of this study was to evaluate gradient echo in- and opposed-phase chemical shift pulse sequences for detection of lipid elements in brain lesion. Ten cylindered phantoms measuring 3 x 3 cm were filled with various mixtures of lipid and water: 0-90% lipid, in 10% step by weight. The gradient echo in- and opposed-phase chemical shift sequences were performed using a 1.5 T MRI (Magnetom Vision, Siemens) with a head coil. In addition, we performed MRI and chemical shift studies on 32 patients with brain lesion. We then analysed the association between out of phase intensity value and classification of the lesions. For phantom containing 50% lipid, maximum signal loss on opposed-phase images was observed. There were significant differences between in- and opposed-phase lipid-water phantom images (P = 0.0054). Most of the benign lesions fall into the positive out of phase intensity value, and malignant lesions fall into negative out of phase intensity value. We conclude that chemical shift artefact can be applied in detecting and characterising lipid elements in brain lesion.

Validation of protein carbonyl measurement: A multi-centre study

Directory of Open Access Journals (Sweden)

Edyta Augustyniak

2015-04-01

Full Text Available Protein carbonyls are widely analysed as a measure of protein oxidation. Several different methods exist for their determination. A previous study had described orders of magnitude variance that existed when protein carbonyls were analysed in a single laboratory by ELISA using different commercial kits. We have further explored the potential causes of variance in carbonyl analysis in a ring study. A soluble protein fraction was prepared from rat liver and exposed to 0, 5 and 15 min of UV irradiation. Lyophilised preparations were distributed to six different laboratories that routinely undertook protein carbonyl analysis across Europe. ELISA and Western blotting techniques detected an increase in protein carbonyl formation between 0 and 5 min of UV irradiation irrespective of method used. After irradiation for 15 min, less oxidation was detected by half of the laboratories than after 5 min irradiation. Three of the four ELISA carbonyl results fell within 95% confidence intervals. Likely errors in calculating absolute carbonyl values may be attributed to differences in standardisation. Out of up to 88 proteins identified as containing carbonyl groups after tryptic cleavage of irradiated and control liver proteins, only seven were common in all three liver preparations. Lysine and arginine residues modified by carbonyls are likely to be resistant to tryptic proteolysis. Use of a cocktail of proteases may increase the recovery of oxidised peptides. In conclusion, standardisation is critical for carbonyl analysis and heavily oxidised proteins may not be effectively analysed by any existing technique.

Gas/particle partitioning of carbonyls in the photooxidation of isoprene and 1,3,5-trimethylbenzene

Directory of Open Access Journals (Sweden)

R. M. Healy

2008-06-01

Full Text Available A new denuder-filter sampling technique has been used to investigate the gas/particle partitioning behaviour of the carbonyl products from the photooxidation of isoprene and 1,3,5-trimethylbenzene. A series of experiments was performed in two atmospheric simulation chambers at atmospheric pressure and ambient temperature in the presence of NO_x and at a relative humidity of approximately 50%. The denuder and filter were both coated with the derivatizing agent O-(2,3,4,5,6-pentafluorobenzyl-hydroxylamine (PFBHA to enable the efficient collection of gas- and particle-phase carbonyls respectively. The tubes and filters were extracted and carbonyls identified as their oxime derivatives by GC-MS. The carbonyl products identified in the experiments accounted for around 5% and 10% of the mass of secondary organic aerosol formed from the photooxidation of isoprene and 1,3,5-trimethylbenzene respectively.

Experimental gas/particle partitioning coefficients were determined for a wide range of carbonyl products formed from the photooxidation of isoprene and 1,3,5-trimethylbenzene and compared with the theoretical values based on standard absorptive partitioning theory. Photooxidation products with a single carbonyl moiety were not observed in the particle phase, but dicarbonyls, and in particular, glyoxal and methylglyoxal, exhibited gas/particle partitioning coefficients several orders of magnitude higher than expected theoretically. These findings support the importance of heterogeneous and particle-phase chemical reactions for SOA formation and growth during the atmospheric degradation of anthropogenic and biogenic hydrocarbons.

Molybdenum-95 nuclear magnetic resonance of a series of phosphine and phosphite substituted molybdenum carbonyls Mo(CO)sub(6-n)Lsub(n)(n = 1,2,3,4,5)

International Nuclear Information System (INIS)

Jaitner, P.; Wohlgenannt, W.

1982-01-01

Molybdenum-95 NMR spectra of a series of phosphine and phosphite substituted molybdenum carbonyls Mo(CO)sub(6-n)Lsub(n)n[L = P(OCH 3 ) 3 n = 1,2,3,4,5, L = P(OC 2 H 5 ) 3 n = 1,2,3, L = P(C 6 H 5 ) 3 n = 1] including isomers (cis, trans, fac, mer) are reported. A large range of chemical shifts is found for the title compounds. The coupling constants 1 J( 95 Mo- 31 P) are derived either from 95 Mo-NMR spectra or 31 P-NMR spectra. Syntheses of the measured compounds were performed by thermal or photochemical ligand sustitution. (Author)

Accuracy and precision of protein-ligand interaction kinetics determined from chemical shift titrations

Energy Technology Data Exchange (ETDEWEB)

Markin, Craig J.; Spyracopoulos, Leo, E-mail: leo.spyracopoulos@ualberta.ca [University of Alberta, Department of Biochemistry (Canada)

2012-12-15

NMR-monitored chemical shift titrations for the study of weak protein-ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K{sub D}) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K{sub D} value of a 1:1 protein-ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125-138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of {sup 1}H-{sup 15}N 2D HSQC NMR spectra acquired using precise protein-ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k{sub off}). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k{sub off} {approx} 3,000 s{sup -1} in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k{sub off} from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k{sub off} values over a wide range, from 100 to 15,000 s{sup -1}. The validity of line shape analysis for k{sub off} values approaching intermediate exchange ({approx}100 s{sup -1}), may be facilitated by

An extrapolation scheme for solid-state NMR chemical shift calculations

Science.gov (United States)

Nakajima, Takahito

2017-06-01

Conventional quantum chemical and solid-state physical approaches include several problems to accurately calculate solid-state nuclear magnetic resonance (NMR) properties. We propose a reliable computational scheme for solid-state NMR chemical shifts using an extrapolation scheme that retains the advantages of these approaches but reduces their disadvantages. Our scheme can satisfactorily yield solid-state NMR magnetic shielding constants. The estimated values have only a small dependence on the low-level density functional theory calculation with the extrapolation scheme. Thus, our approach is efficient because the rough calculation can be performed in the extrapolation scheme.

Carbonyl-Olefin Exchange Reaction: Present State and Outlook

Science.gov (United States)

Kalinova, Radostina; Jossifov, Christo

The carbonyl-olefin exchange reaction (COER) is a new reaction between carbonyl group and olefin double bond, which has a formal similarity with the olefin metathesis (OM) - one carbon atom in the latter is replaced with an oxygen atom. Till now the new reaction is performed successfully only when the two functional groups (carbonyl group and olefin double bond) are in one molecule and are conjugated. The α, β-unsaturated carbonyl compounds (substituted propenones) are the compounds with such a structure. They polymerize giving substituted polyacetylenes. The chain propagation step of this polymerization is in fact the COER. The question arises: is it possible the COER to take place when the two functional groups are not in one molecule and are not conjugated, and could this reaction became an alternative of the existing carbonyl olefination reactions?

Gas-phase chemistry of Mo, Ru, W, and Os metal carbonyl complexes

International Nuclear Information System (INIS)

Wang, Y.; Qin, Z.; Fan, F.L.

2014-01-01

Metal carbonyl complexes were used for studying the gas-phase chemical behavior of Mo, Ru, W and Os isotopes with an on-line low temperature isothermal gas chromatography apparatus. Short-lived Mo and Ru isotopes were produced by a 252 Cf spontaneous fission source. Short-lived nuclides of W and Os were produced using the heavy ion reactions 19 F + 159 Tb and 165 Ho, respectively. Short-lived products were thermalized in a recoil chamber filled with a gas mixture of helium and carbon monoxide. The carbonyls formed were then transported through capillaries to an isothermal chromatography column for study of the adsorption behavior as a function of temperature. On-line isothermal chromatography (IC) experiments on Teflon (PTFE) and quartz surfaces showed that short-lived isotopes of the listed elements can form carbonyl complexes which are very volatile and interact most likely in physical sorption processes. Deduced adsorption enthalpies of Mo and Ru carbonyls were -38 ± 2 kJ/mol and -36 ± 2 kJ/mol, respectively. These values are in good agreement with literature data, partly obtained with different chromatographic techniques. A validation of the applied Monte Carlo model to deduce adsorption enthalpies with Mo isotopes of different half-lives proved the validity of the underlying adsorption model. The investigations using a gas-jet system coupled to a heavy ion accelerator without any preseparator clearly showed the limitations of the approach. The He and CO gas mixture, which was directly added into the chamber, will result in decomposition of CO gas and produce some aerosol particles. After the experiment of 173 W and 179 Os in the heavy ion experiments, the Teflon column was covered by a yellowish deposit; the adsorption enthalpy of W and Os carbonyls could therefore not be properly deduced using Monte Carlo simulations. (orig.)

Carbonyl compounds in gas and particle phases of mainstream cigarette smoke

International Nuclear Information System (INIS)

Pang, Xiaobing; Lewis, Alastair C.

2011-01-01

Carbonyl compounds (carbonyls) are important constituents of cigarette smoke and some are toxic and may be carcinogenic or mutagenic to humans. In this study carbonyl emissions in the gas and particle phases of mainstream cigarette smoke were assessed by GC-MS with pentafluorophenyl hydrazine (PFPH) derivatization. Seven brands of cigarettes and one brand of cigar common in the UK market and having differing nicotine, tar and carbon monoxide yields were investigated. Sixteen carbonyl components were identified in gaseous emissions and twenty in the particle phase. In the gaseous emissions, acetaldehyde presented as the predominant species, followed by formaldehyde, 2-propenal, and pentanal. In the particulate emissions, 1-hydroxy-2-propanone was the most abundant followed by formaldehyde, benzaldehyde, and 2,5-dimethylbenzaldehyde. Significant differences were found in carbonyl emissions among the brands of cigarettes. The gaseous carbonyl emissions varied in the range of 216-405 μg cigarette -1 (μg cig -1 ) and the particulate carbonyl emissions varied in the range of 23-127 μg cig -1 . Positive correlations were found between the total emission of carbonyls, tar yield and carbon monoxide yield. Similar gas/particle (G/P) partitioning ratios of carbonyls were found among all cigarettes, which implies that G/P partitions of carbonyls in smoke mainly depend on the physical properties of the carbonyls. The gaseous carbonyl emissions were enhanced by 40% to 130% when some of the water, accounting for 8-12% of cigarettes in mass, was removed from the tobacco. Non-filtered cigarettes showed significantly higher carbonyl emissions compared to their filtered equivalents. Carbonyl particulate accounted for 11-19% by mass of total particulate matter from tobacco smoke. The cigar generated 806 μg cig -1 gaseous and 141 μg cig -1 particulate carbonyls, which is 2-4 times greater than the cigarettes. - Highlights: → Carbonyl emission factors in both gas (16 species) and

Carbonyl compounds in gas and particle phases of mainstream cigarette smoke

Energy Technology Data Exchange (ETDEWEB)

Pang, Xiaobing, E-mail: pangxbyuanj@gmail.com [Department of Chemistry, University of York, Heslington, York, YO10 5DD (United Kingdom); Lewis, Alastair C., E-mail: ally.lewis@york.ac.uk [National Centre for Atmospheric Science, University of York, Heslington, York, YO10 5DD (United Kingdom)

2011-11-01

Carbonyl compounds (carbonyls) are important constituents of cigarette smoke and some are toxic and may be carcinogenic or mutagenic to humans. In this study carbonyl emissions in the gas and particle phases of mainstream cigarette smoke were assessed by GC-MS with pentafluorophenyl hydrazine (PFPH) derivatization. Seven brands of cigarettes and one brand of cigar common in the UK market and having differing nicotine, tar and carbon monoxide yields were investigated. Sixteen carbonyl components were identified in gaseous emissions and twenty in the particle phase. In the gaseous emissions, acetaldehyde presented as the predominant species, followed by formaldehyde, 2-propenal, and pentanal. In the particulate emissions, 1-hydroxy-2-propanone was the most abundant followed by formaldehyde, benzaldehyde, and 2,5-dimethylbenzaldehyde. Significant differences were found in carbonyl emissions among the brands of cigarettes. The gaseous carbonyl emissions varied in the range of 216-405 {mu}g cigarette{sup -1} ({mu}g cig{sup -1}) and the particulate carbonyl emissions varied in the range of 23-127 {mu}g cig{sup -1}. Positive correlations were found between the total emission of carbonyls, tar yield and carbon monoxide yield. Similar gas/particle (G/P) partitioning ratios of carbonyls were found among all cigarettes, which implies that G/P partitions of carbonyls in smoke mainly depend on the physical properties of the carbonyls. The gaseous carbonyl emissions were enhanced by 40% to 130% when some of the water, accounting for 8-12% of cigarettes in mass, was removed from the tobacco. Non-filtered cigarettes showed significantly higher carbonyl emissions compared to their filtered equivalents. Carbonyl particulate accounted for 11-19% by mass of total particulate matter from tobacco smoke. The cigar generated 806 {mu}g cig{sup -1} gaseous and 141 {mu}g cig{sup -1} particulate carbonyls, which is 2-4 times greater than the cigarettes. - Highlights: {yields} Carbonyl

Optimized biotin-hydrazide enrichment and mass spectrometry analysis of peptide carbonyls

DEFF Research Database (Denmark)

Havelund, Jesper F.; Wojdyla, K; Jensen, O. N.

Irreversible cell damage through protein carbonylation is the result of reaction with reactive oxygen species (ROS) and has been coupled to many diseases. The precise molecular consequences of protein carbonylation, however, are still not clear. The localization of the carbonylated amino acid is ...... modifications are isobaric to carbonylation and it is often challenging to detect the weaker signal from carbonylated peptides necessitating enrichment step. We here present an optimized method for the enrichment of carbonylated peptides....

Ambient levels of carbonyl compounds and their sources in Guangzhou, China

Science.gov (United States)

Feng, Yanli; Wen, Sheng; Chen, Yingjun; Wang, Xinming; Lü, Huixiong; Bi, Xinhui; Sheng, Guoying; Fu, Jiamo

Ambient levels of carbonyl compounds and their possible sources, vehicular exhaust and cooking exhaust, were studied at seven places in Guangzhou, including five districts (a residential area, an industrial area, a botanical garden, a downtown area and a semi-rural area), a bus station and a restaurant during the period of June-September 2003. Nineteen carbonyl compounds were identified in the ambient air, of which acetone was the most abundant carbonyl, followed by formaldehyde and acetaldehyde. Only little changes were found in carbonyl concentration levels in the five different districts because of their dispersion and mixture in the atmosphere in summer. The lower correlations between the carbonyls' concentrations might result from the mixture of carbonyls derived from different sources, including strong photochemical reactions at noon in summer. Formaldehyde and acetaldehyde were the main carbonyls in bus station, while straight-chain carbonyls were comparatively abundant in cooking exhaust. Besides vehicular exhaust, cooking might be another major source of carbonyl compounds in Guangzhou City, especially for high molecular weight carbonyls.

Experimental and DFT evaluation of the 1H and 13C NMR chemical shifts for calix[4]arenes

Science.gov (United States)

Guzzo, Rodrigo N.; Rezende, Michelle Jakeline Cunha; Kartnaller, Vinicius; Carneiro, José Walkimar de M.; Stoyanov, Stanislav R.; Costa, Leonardo Moreira da

2018-04-01

The density functional theory is employed to determine the efficiency of 11 exchange-correlation (XC) functionals to compute the 1H and 13C NMR chemical shifts of p-tert-butylcalix[4]arene (ptcx4, R1 = C(CH3)3) and congeners using the 6-31G(d,p) basis set. The statistical analysis shows that B3LYP, B3PW91 and PBE1PBE are the best XC functionals for the calculation of 1H chemical shifts. Moreover, the best results for the 13C chemical shifts are obtained using the LC-WPBE, M06-2X and wB97X-D functionals. The performance of these XC functionals is tested for three other calix[4]arenes: p-sulfonic acid calix[4]arene (sfxcx4 - R1 = SO3H), p-nitro-calix[4]arene (ncx4, R1 = NO2) and calix[4]arene (cx4 - R1 = H). For 1H chemical shifts B3LYP, B3PW91 and PBE1PBE yield similar results, although B3PW91 shows more consistency in the calculated error for the different structures. For 13C NMR chemical shifts, the XC functional that stood out as best is LC-WPBE. Indeed, the three functionals selected for each of 1H and 13C show good accuracy and can be used in future studies involving the prediction of 1H and 13C chemical shifts for this type of compounds.

Investigation of DOTA-Metal Chelation Effects on the Chemical Shift of ¹²⁹ Xe

Energy Technology Data Exchange (ETDEWEB)

Jeong, K; Slack, CC; Vassiliou, CC; Dao, P; Gomes, MD; Kennedy, DJ; Truxal, AE; Sperling, LJ; Francis, MB; Wemmer, DE; Pines, A

2015-09-17

Recent work has shown that xenon chemical shifts in cryptophane-cage sensors are affected when tethered chelators bind to metals. Here in this paper, we explore the xenon shifts in response to a wide range of metal ions binding to diastereomeric forms of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) linked to cryptophane-A. The shifts induced by the binding of Ca²⁺, Cu²⁺, Ce³⁺, Zn²⁺, Cd²⁺, Ni²⁺, Co²⁺, Cr²⁺, Fe³⁺, and Hg²⁺ are distinct. In addition, the different responses of the diastereomers for the same metal ion indicate that shifts are affected by partial folding with a correlation between the expected coordination number of the metal in the DOTA complex and the chemical shift of ¹²⁹Xe. Lastly, these sensors may be used to detect and quantify many important metal ions, and a better understanding of the basis for the induced shifts could enhance future designs.

Carbonyl complexes of rhodium with N-donor ligands: factors determining the formation of terminal versus bridging carbonyls

NARCIS (Netherlands)

Dzik, W.I.; Creusen, C.; de Gelder, R.; Peters, T.P.J.; Smits, J.M.M.; de Bruin, B.

2010-01-01

Cationic rhodium carbonyl complexes supported by a series of different N-3- and N-4-donor ligands were prepared, and their ability to form carbonyl-bridged species was evaluated. Complex [Rh(K3-bpa)(cod)r (1(+)) (bpa = bis(2-picolyBamine, cod = cis,cis-1,5-cyclooctadiene) reacts with I bar of CO to

Pressure-dependent {sup 13}C chemical shifts in proteins: origins and applications

Energy Technology Data Exchange (ETDEWEB)

Wilton, David J. [University of Sheffield, Department of Molecular Biology and Biotechnology (United Kingdom); Kitahara, Ryo [Ritsumeikan University, College of Pharmaceutical Sciences (Japan); Akasaka, Kazuyuki [Kinki University, Department of Biotechnological Science, School of Biology-Oriented Science and Technology (Japan); Williamson, Mike P. [University of Sheffield, Department of Molecular Biology and Biotechnology (United Kingdom)], E-mail: m.williamson@sheffield.ac.uk

2009-05-15

Pressure-dependent {sup 13}C chemical shifts have been measured for aliphatic carbons in barnase and Protein G. Up to 200 MPa (2 kbar), most shift changes are linear, demonstrating pressure-independent compressibilities. CH{sub 3}, CH{sub 2} and CH carbon shifts change on average by +0.23, -0.09 and -0.18 ppm, respectively, due to a combination of bond shortening and changes in bond angles, the latter matching one explanation for the {gamma}-gauche effect. In addition, there is a residue-specific component, arising from both local compression and conformational change. To assess the relative magnitudes of these effects, residue-specific shift changes for protein G were converted into structural restraints and used to calculate the change in structure with pressure, using a genetic algorithm to convert shift changes into dihedral angle restraints. The results demonstrate that residual {sup 13}C{alpha} shifts are dominated by dihedral angle changes and can be used to calculate structural change, whereas {sup 13}C{beta} shifts retain significant dependence on local compression, making them less useful as structural restraints.

Spin-echo based diagonal peak suppression in solid-state MAS NMR homonuclear chemical shift correlation spectra

Science.gov (United States)

Wang, Kaiyu; Zhang, Zhiyong; Ding, Xiaoyan; Tian, Fang; Huang, Yuqing; Chen, Zhong; Fu, Riqiang

2018-02-01

The feasibility of using the spin-echo based diagonal peak suppression method in solid-state MAS NMR homonuclear chemical shift correlation experiments is demonstrated. A complete phase cycling is designed in such a way that in the indirect dimension only the spin diffused signals are evolved, while all signals not involved in polarization transfer are refocused for cancellation. A data processing procedure is further introduced to reconstruct this acquired spectrum into a conventional two-dimensional homonuclear chemical shift correlation spectrum. A uniformly 13C, 15N labeled Fmoc-valine sample and the transmembrane domain of a human protein, LR11 (sorLA), in native Escherichia coli membranes have been used to illustrate the capability of the proposed method in comparison with standard 13C-13C chemical shift correlation experiments.

Spatiotemporal distribution of carbonyl compounds in China

International Nuclear Information System (INIS)

Ho, K.F.; Ho, Steven Sai Hang; Huang, R.-J.; Dai, W.T.; Cao, J.J.; Tian, Linwei; Deng, W.J.

2015-01-01

A sampling campaign was carried out at nine Chinese cities in 2010/2011. Fifteen monocarbonyls (C#= 1–9) were quantified. Temperature is the rate-determining factor of the summertime carbonyl levels. The carbonyl emissions in winter are mainly driven by the primary anthropogenic sources like automobile. A molar ratio of propionaldehyde to nonaldehyde is a barometer of the impact of atmospheric vegetation emission which suggesting that strong vegetation emissions exist in summer and high propionaldehyde abundance is caused by fossil fuel combustion in winter. Potential health risk assessment of formaldehyde and acetaldehyde was conducted and the highest cumulative risks were observed at Chengdu in summer and Wuhan in winter. Because of the strong photochemical reaction and large amount of anthropogenic emissions, high concentrations of carbonyl compounds were observed in Chengdu. The use of ethanol-blended gasoline in Wuhan is the key reason of acetaldehyde emission and action should be taken to avoid potential health risks. - Highlights: • A national wide survey of ambient carbonyl compounds were conducted in China. • Using ethanol-blended gasoline can lead to higher cancer risks. • High concentrations of HMW carbonyls (C6, C7, C8 and C9) were observed in all cities. • HMW carbonyls (C6–C9) species show a very consistent seasonal variation. • C 3 /C 9 acts as an indicator for the impact of vegetation emission in the atmosphere. - Capsule abstract: Strong vegetation emission occurs in summer atmosphere and high acetaldehyde emission due to ethanol-blended gasoline consumption in 9 Chinese cities is discouraged

Recent Developments in Carbonylation Chemistry Using [13 C]CO, [11 C]CO and [14 C]CO.

Science.gov (United States)

Nielsen, Dennis U; Neumann, Karoline T; Lindhardt, Anders T; Skrydstrup, Troels

2018-06-01

Carbon monoxide represents the most important C1-building block for the chemical industry, both for the production of bulk and fine chemicals, but also for synthetic fuels. Yet, its toxicity and subsequently its cautious handling has limited its applications in medicinal chemistry research and in particular for the synthesis of pharmaceutically relevant molecules. Recent years have nevertheless witnessed a considerable headway on the development of carbon monoxide surrogates and reactor systems, which provide an ideal setting for performing carbonylation chemistry with stoichiometric and sub-stoichiometric carbon monoxide. Such set-ups are particularly ideal for the introduction of isotope labels such as carbon-11, carbon-13 and carbon-14 into bioactive compounds. This review summarizes this growing field and examines the large number of carbonylation reactions that can be exploited for the introduction of a carbon isotope. This article is protected by copyright. All rights reserved.

Physical basis of the effect of hemoglobin on the 31P NMR chemical shifts of various phosphoryl compounds

International Nuclear Information System (INIS)

Kirk, K.; Kuchel, P.W.

1988-01-01

The marked difference between the intra- and extracellular 31 P NMR chemical shifts of various phosphoryl compounds when added to a red cell suspension may be largely understood in terms of the effects of hemoglobin on the 31 P NMR chemical shifts. The presence of [oxy- or (carbonmonoxy)-] hemoglobin inside the red cell causes the bulk magnetic susceptibility of the cell cytoplasm to be significantly less than that of the external solution. This difference is sufficient to account for the difference in the intra- and extracellular chemical shifts of the two phosphate esters trimethyl phosphate and triethyl phosphate. However, in the case of the compounds dimethyl methylphosphonate, diethyl methylphosphonate, and trimethylphosphine oxide as well as the hypophosphite, phenylphosphinate, and diphenylphosphinate ions, hemoglobin exerts an additional, much larger, effect, causing the 31 P NMR resonances to shift to lower frequency in a manner that cannot be accounted for in terms of magnetic susceptibility. Lysozyme is a protein structurally unrelated to hemoglobin and was shown to cause similar shifts to lower frequency of the resonances of these six compounds; this suggests that the mechanism may involve a property of proteins in general and not a specific property of hemoglobin. The effect of different solvents on the chemical shifts of the eight phosphoryl compounds provided an insight into the possible physical basis of the effect. It is proposed that, in addition to magnetic susceptibility effects, hemoglobin exerts its influence on phosphoryl chemical shifts by disrupting the hydrogen bonding of the phosphoryl group to solvent water

Reactions of laser-ablated Co, Rh, and Ir with CO: Infrared spectra and density functional calculations of the metal carbonyl molecules, cations and anions in solid neon

International Nuclear Information System (INIS)

Zhou, M.; Andrews, L.

1999-01-01

Laser ablation produces metal atoms, cations, and electrons for reaction with CO during condensation in excess neon at 4 K. Infrared spectra are observed for the metal carbonyls, cations, and anions, which are identified from isotopic shifts ( 13 CO, C 18 O) and splittings using mixed isotopic precursors. Density functional calculations with pseudopotentials for Rh and Ir predict the observed carbonyl stretching frequencies within 1--2%. This characterization of the simple RhCO + , RhCO, and RhCO - (and Ir) species over a 350 cm -1 range provides a scale for comparison of larger catalytically active Rh and Ir carbonyl complexes in solution and on surfaces to estimate charge on the metal center. This work provides the first spectroscopic characterization of Rh and Ir carbonyl cations and anions except for the stable tetracarbonyl anions in solution

Tandem pseudopericyclic reactions: [1,5]-X sigmatropic shift/6pi-electrocyclic ring closure converting N-(2-X-carbonyl)phenyl ketenimines into 2-X-quinolin-4(3H)-ones.

Science.gov (United States)

Alajarín, Mateo; Ortín, María-Mar; Sanchez-Andrada, Pilar; Vidal, Angel

2006-10-13

N-(2-X-Carbonyl)phenyl ketenimines undergo, under mild thermal conditions, [1,5]-migration of the X group from the carbonyl carbon to the electron-deficient central carbon atom of the ketenimine fragment, followed by a 6pi-electrocyclic ring closure of the resulting ketene to provide 2-X-substituted quinolin-4(3H)-ones in a sequential one-pot manner. The X groups tested are electron-donor groups, such as alkylthio, arylthio, arylseleno, aryloxy, and amino. When involving alkylthio, arylthio, and arylseleno groups, the complete transformation takes place in refluxing toluene, whereas for aryloxy and amino groups the starting ketenimines must be heated at 230 degrees C in a sealed tube in the absence of solvent. The mechanism for the conversion of these ketenimines into quinolin-4(3H)-ones has been studied by ab initio and DFT calculations, using as model compounds N-(2-X-carbonyl)vinyl ketenimines bearing different X groups (X = F, Cl, OH, SH, NH(2), and PH(2)) converting into 4(3H)-pyridones. This computational study afforded two general reaction pathways for the first step of the sequence, the [1,5]-X shift, depending on the nature of X. When X is F, Cl, OH, or SH, the migration occurs in a concerted mode, whereas when X is NH(2) or PH(2), it involves a two-step sequence. The order of migratory aptitudes of the X substituents at the acyl group is predicted to be PH(2) > Cl > SH > NH(2) > F> OH. The second step of the full transformation, the 6pi-electrocyclic ring closure, is calculated to be concerted and with low energy barriers in all the cases. We have included in the calculations an alternative mode of cyclization of the N-(2-X-carbonyl)vinyl ketenimines, the 6pi-electrocyclic ring closure leading to 1,3-oxazines that involves its 1-oxo-5-aza-1,3,5-hexatrienic system. Additionally, the pseudopericyclic topology of the transition states for some of the [1,5]-X migrations (X = F, Cl, OH, SH), for the 6pi-electrocyclization of the ketene intermediates to the 4

Ruthenium(ii)-catalyzed olefination via carbonyl reductive cross-coupling.

Science.gov (United States)

Wei, Wei; Dai, Xi-Jie; Wang, Haining; Li, Chenchen; Yang, Xiaobo; Li, Chao-Jun

2017-12-01

Natural availability of carbonyl groups offers reductive carbonyl coupling tremendous synthetic potential for efficient olefin synthesis, yet the catalytic carbonyl cross-coupling remains largely elusive. We report herein such a reaction, mediated by hydrazine under ruthenium(ii) catalysis. This method enables facile and selective cross-couplings of two unsymmetrical carbonyl compounds in either an intermolecular or intramolecular fashion. Moreover, this chemistry accommodates a variety of substrates, proceeds under mild reaction conditions with good functional group tolerance, and generates stoichiometric benign byproducts. Importantly, the coexistence of KO t Bu and bidentate phosphine dmpe is vital to this transformation.

Time and dose effects of cigarette smoke and acrolein on protein carbonyl formation in HaCaT keratinocytes.

Science.gov (United States)

Avezov, K; Reznick, A Z; Aizenbud, D

2015-01-01

Cigarette smoke (CS) is an important environmental source of human exposure to a highly toxic and chemically active α,β-unsaturated aldehyde: acrolein. It is capable of causing protein carbonylation and dysfunction, especially in oral tissues of smokers, constantly exposed to CS toxic constituents. The foremost damage is considered to be cumulative, but even a short exposure can be potentially harmful. The objectives of the current study were to examine the short time and dose effects of direct CS and acrolein exposure on intracellular protein carbonylation in epithelial cells. HaCaT-keratinocytes were exposed to different doses of acrolein and whole phase CS using a unique smoking simulator apparatus that mimics the exposure in smokers. The rate of intracellular protein carbonyl modification was examined 10-60 min after the exposure by Western blot. In addition, the effect of pre-incubation with a thiol scavenger N-acetylcysteine (NAC) was also assessed. We found that intracellular protein carbonyls increased as fast as 10 min after CS exposure and their concentration doubled after 20 min, with a slight elevation afterwards. Also, carbonyl levels increased gradually as CS and acrolein doses were elevated. Addition of 1 mM NAC neutralized part of the damage. We conclude that CS and acrolein intracellular protein carbonylation is dose- and time- dependent. Even a short time exposure to CS and its aldehydic constituents can be potentially harmful.

Binding energies and chemical shifts of least bound core electron excitations in cubic Asub(N)Bsub(8-N) semiconductors

International Nuclear Information System (INIS)

Bechstedt, F.; Enderlein, R.; Wischnewski, R.

1981-01-01

Core electron binding energies Esup(B) with respect to the vacuum level and their chemical shifts are calculated for the least bound core levels of cations and anions of cubic Asub(N)Bsub(8-N) semiconductors. Starting from the HF-binding energy of the free atom absolute values of Esup(B) are obtained by adding core level shifts and relaxation energies. Core level shifts are calculated by means of an electrostatic model with ionic and bond charges according to Phillips' bond charge model. For the calculation of relaxation energies the linear dielectric theory of electronic polarization is applied. Valence and core electrons, and diagonal and non-diagonal screening are taken into account. The theoretical results for chemical shifts of binding energies are compared with experimental values from XPS-measurements corrected by work function data. Good agreement is obtained in all cases within the error limit of about one eV. Chemical and atomic trends of core level shifts, relaxation energies, and binding energies are discussed in terms of changes of atomic and solid state parameters. Chemical shifts and relaxation energies are predicted for various ternary Asub(N)Bsub(8-N) compounds. (author)

High throughput assay for evaluation of reactive carbonyl scavenging capacity.

Science.gov (United States)

Vidal, N; Cavaille, J P; Graziani, F; Robin, M; Ouari, O; Pietri, S; Stocker, P

2014-01-01

Many carbonyl species from either lipid peroxidation or glycoxidation are extremely reactive and can disrupt the function of proteins and enzymes. 4-hydroxynonenal and methylglyoxal are the most abundant and toxic lipid-derived reactive carbonyl species. The presence of these toxics leads to carbonyl stress and cause a significant amount of macromolecular damages in several diseases. Much evidence indicates trapping of reactive carbonyl intermediates may be a useful strategy for inhibiting or decreasing carbonyl stress-associated pathologies. There is no rapid and convenient analytical method available for the assessment of direct carbonyl scavenging capacity, and a very limited number of carbonyl scavengers have been identified to date, their therapeutic potential being highlighted only recently. In this context, we have developed a new and rapid sensitive fluorimetric method for the assessment of reactive carbonyl scavengers without involvement glycoxidation systems. Efficacy of various thiol- and non-thiol-carbonyl scavenger pharmacophores was tested both using this screening assay adapted to 96-well microplates and in cultured cells. The scavenging effects on the formation of Advanced Glycation End-product of Bovine Serum Albumin formed with methylglyoxal, 4-hydroxynonenal and glucose-glycated as molecular models were also examined. Low molecular mass thiols with an α-amino-β-mercaptoethane structure showed the highest degree of inhibitory activity toward both α,β-unsaturated aldehydes and dicarbonyls. Cysteine and cysteamine have the best scavenging ability toward methylglyoxal. WR-1065 which is currently approved for clinical use as a protective agent against radiation and renal toxicity was identified as the best inhibitor of 4-hydroxynonenal.

High throughput assay for evaluation of reactive carbonyl scavenging capacity

Directory of Open Access Journals (Sweden)

N. Vidal

2014-01-01

Full Text Available Many carbonyl species from either lipid peroxidation or glycoxidation are extremely reactive and can disrupt the function of proteins and enzymes. 4-hydroxynonenal and methylglyoxal are the most abundant and toxic lipid-derived reactive carbonyl species. The presence of these toxics leads to carbonyl stress and cause a significant amount of macromolecular damages in several diseases. Much evidence indicates trapping of reactive carbonyl intermediates may be a useful strategy for inhibiting or decreasing carbonyl stress-associated pathologies. There is no rapid and convenient analytical method available for the assessment of direct carbonyl scavenging capacity, and a very limited number of carbonyl scavengers have been identified to date, their therapeutic potential being highlighted only recently. In this context, we have developed a new and rapid sensitive fluorimetric method for the assessment of reactive carbonyl scavengers without involvement glycoxidation systems. Efficacy of various thiol- and non-thiol-carbonyl scavenger pharmacophores was tested both using this screening assay adapted to 96-well microplates and in cultured cells. The scavenging effects on the formation of Advanced Glycation End-product of Bovine Serum Albumin formed with methylglyoxal, 4-hydroxynonenal and glucose-glycated as molecular models were also examined. Low molecular mass thiols with an α-amino-β-mercaptoethane structure showed the highest degree of inhibitory activity toward both α,β-unsaturated aldehydes and dicarbonyls. Cysteine and cysteamine have the best scavenging ability toward methylglyoxal. WR-1065 which is currently approved for clinical use as a protective agent against radiation and renal toxicity was identified as the best inhibitor of 4-hydroxynonenal.

Catalytic performance of heterogeneous Rh/C3N4 for the carbonylation of methanol

Science.gov (United States)

Budiman, Anatta Wahyu; Choi, Myoung Jae; Nur, Adrian

2018-02-01

The excess of water in homogeneous the carbonylation of methanol system could increase the amount of by-products formed through water-gas shift reaction and could accelerate the rusting of equipment. Many scientists tried to decrease the content of water in the carbonylation of methanol system by using lithium and iodide promoter that results a moderate catalytic activity in the water content at 2wt%. The heterogenized catalyst offers several distinct advantages such as it was enables increased catalyst concentration in the reaction mixture, which is directly proportional to acetic acid production rate, without the addition of an alkali iodide salt promoter. The heterogeneous catalyst also results in reduced by-product formation. This study is aimed to produce a novel catalyst (Rh/C3N4) with a high selectivity of acetic acid in a relatively lower water and halide content. This novel catalyst performs high conversion and selectivity of acetic acid as the result of the strong ionic bonding of melamine and rhodium complex species that was caused by the presence of methyl iodide species. The CO2 in feed gas significantly decreases the catalytic activity of Rh-melamine because of its inert characteristics. The kinetic test was performed as that the first order kinetic equation. The kinetic tests revealed the reaction route of the the carbonylation of methanol in this system was performed trough the methyl acetate.

A method of detecting carbonyl compounds in tree leaves in China.

Science.gov (United States)

Huang, Juan; Feng, Yanli; Fu, Jiamo; Sheng, Guoying

2010-06-01

Carbonyl compounds have been paid more and more attention because some carbonyl species have been proven to be carcinogenic or a risk for human health. Plant leaves are both an important emission source and an important sink of carbonyl compounds. But the research on carbonyl compounds from plant leaves is very scarce. In order to make an approach to the emission mechanism of plant leaves, a new method was established to extract carbonyl compounds from fresh plant leaves. The procedure combining derivatization with ultrasonication was developed for the fast extraction of carbonyl compounds from tree leaves. Fresh leaves (Metasequoia glyptostroboides), were selected and extracted by this method. Seven carbonyl compounds, including formaldehyde, acetaldehyde, acetone, acrolein, p-tolualdehyde, m/o-tolualdehyde, and hexaldehyde were determined and quantified. The most common carbonyl species of the four tree leaves were formaldehyde, acrolein, and m/o-tolualdehyde. They accounted for 67.3% in cedar, 50.8% in sweet olive, 45.8% in dawn redwood, and 44.6% in camphor tree, respectively. Camphor tree had the highest leaf level of m/o-tolualdehyde with 15.0 +/- 3.4 microg g(-1)(fresh leaf weight), which indicated that camphor tree may be a bioindicator of the level of tolualdehyde or xylene in the atmosphere. By analyzing carbonyl compounds from different tree leaves, it is not only helpful for further studying the relationship between sink and emission of carbonyls from plants, but also helpful for exploring optimum plant population in urban greening.

Pattern of occurrence and occupancy of carbonylation sites in proteins

DEFF Research Database (Denmark)

Rao, R Shyama Prasad; Møller, Ian Max

2011-01-01

sites. Comparison of metal-catalyzed oxidation of two closely related proteins indicates that this type of carbonylation might not be very specific in proteins. Interestingly, carbonylated sites show a very strong tendency to cluster together in the protein primary sequence hinting at some sort......Proteins are targets for modification by reactive oxygen species, and carbonylation is an important irreversible modification that increases during oxidative stress. While information on protein carbonylation is accumulating, its pattern is not yet understood. We have made a meta...

Determination of Carbonyl Compounds in Exhaled Cigarette Smoke

Directory of Open Access Journals (Sweden)

Moldoveanu S

2014-12-01

Full Text Available This paper presents the findings on a quantitative evaluation of carbonyl levels in exhaled cigarette smoke from human subjects. The cigarettes evaluated include products with 5.0 mg ‘tar’, 10.6 mg ‘tar’ and 16.2 mg ‘tar’, where ‘tar’ is defined as the weight of total wet particulate matter (TPM minus the weight of nicotine and water, and the cigarettes are smoked following U.S. Federal Trade Commission (FTC recommendations. The measured levels of carbonyls in the exhaled smoke were compared with calculated yields of carbonyls in the inhaled smoke and a retention efficiency was obtained. The number of human subjects included a total of ten smokers for the 10.6 mg ‘tar’, five for the 16.2 mg ‘tar’, and five for the 5.0 mg ‘tar’ product, each subject smoking three cigarettes. The analyzed carbonyl compounds included several aldehydes (formaldehyde, acetaldehyde, acrolein, propionaldehyde, crotonaldehyde and n-butyraldehyde, and two ketones (acetone and 2-butanone. The smoke collection from the human subjects was vacuum assisted. Exhaled smoke was collected on Cambridge pads pretreated with a solution of dinitrophenylhydrazine (DNPH followed by high performance liquid chromatography (HPLC analysis of the dinitrophenylhydrazones of the carbonyl compounds. The cigarette butts from the smokers were collected and analyzed for nicotine. The nicotine levels for the cigarette butts from the smokers were used to calculate the level of carbonyls in the inhaled smoke, based on calibration curves. These were generated separately by analyzing the carbonyls in smoke and the nicotine in the cigarette butts obtained by machine smoking under different puffing regimes. The comparison of the level of carbonyl compounds in exhaled smoke with that from the inhaled smoke showed high retention of all the carbonyls. The retention of aldehydes was above 95% for all three different ‘tar’ levels cigarettes. The ketones were retained with a

Fragment-based {sup 13}C nuclear magnetic resonance chemical shift predictions in molecular crystals: An alternative to planewave methods

Energy Technology Data Exchange (ETDEWEB)

Hartman, Joshua D.; Beran, Gregory J. O., E-mail: gregory.beran@ucr.edu [Department of Chemistry, University of California, Riverside, California 92521 (United States); Monaco, Stephen; Schatschneider, Bohdan [The Pennsylvania State University, The Eberly Campus, 2201 University Dr, Lemont Furnace, Pennsylvania 15456 (United States)

2015-09-14

We assess the quality of fragment-based ab initio isotropic {sup 13}C chemical shift predictions for a collection of 25 molecular crystals with eight different density functionals. We explore the relative performance of cluster, two-body fragment, combined cluster/fragment, and the planewave gauge-including projector augmented wave (GIPAW) models relative to experiment. When electrostatic embedding is employed to capture many-body polarization effects, the simple and computationally inexpensive two-body fragment model predicts both isotropic {sup 13}C chemical shifts and the chemical shielding tensors as well as both cluster models and the GIPAW approach. Unlike the GIPAW approach, hybrid density functionals can be used readily in a fragment model, and all four hybrid functionals tested here (PBE0, B3LYP, B3PW91, and B97-2) predict chemical shifts in noticeably better agreement with experiment than the four generalized gradient approximation (GGA) functionals considered (PBE, OPBE, BLYP, and BP86). A set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided based on these benchmark calculations. Statistical cross-validation procedures are used to demonstrate the robustness of these fits.

Protein carbonylation sites in bovine raw milk and processed milk products.

Science.gov (United States)

Milkovska-Stamenova, Sanja; Mnatsakanyan, Ruzanna; Hoffmann, Ralf

2017-08-15

During thermal treatment of milk, proteins are oxidized, which may reduce the nutritional value of milk, abolish protein functions supporting human health, especially important for newborns, and yield potentially harmful products. The side chains of several amino acids can be oxidized to reactive carbonyls, which are often used to monitor oxidative stress in organisms. Here we mapped protein carbonylation sites in raw milk and different brands of pasteurized, ultra high temperature (UHT) treated milk, and infant formulas (IFs) after digesting the precipitated proteins with trypsin. Reactive carbonyls were derivatized with O-(biotinylcarbazoylmethyl)hydroxylamine to enrich the modified peptides by avidin-biotin affinity chromatography and analyze them by nanoRP-UPLC-ESI-MS. Overall, 53 unique carbonylated peptides (37 carbonylation sites, 15 proteins) were identified. Most carbonyls were derived from dicarbonyls (mainly glyoxal). The number of carbonylation sites increased with the harsher processing from raw milk (4) to pasteurized (16) and UHT milk (16) and to IF (24). Copyright © 2017 Elsevier Ltd. All rights reserved.

Carbon 13 nuclear magnetic resonance chemical shifts empiric calculations of polymers by multi linear regression and molecular modeling

International Nuclear Information System (INIS)

Da Silva Pinto, P.S.; Eustache, R.P.; Audenaert, M.; Bernassau, J.M.

1996-01-01

This work deals with carbon 13 nuclear magnetic resonance chemical shifts empiric calculations by multi linear regression and molecular modeling. The multi linear regression is indeed one way to obtain an equation able to describe the behaviour of the chemical shift for some molecules which are in the data base (rigid molecules with carbons). The methodology consists of structures describer parameters definition which can be bound to carbon 13 chemical shift known for these molecules. Then, the linear regression is used to determine the equation significant parameters. This one can be extrapolated to molecules which presents some resemblances with those of the data base. (O.L.). 20 refs., 4 figs., 1 tab

Cα and Cβ Carbon-13 Chemical Shifts in Proteins From an Empirical Database

International Nuclear Information System (INIS)

Iwadate, Mitsuo; Asakura, Tetsuo; Williamson, Michael P.

1999-01-01

We have constructed an extensive database of 13C Cα and Cβ chemical shifts in proteins of solution, for proteins of which a high-resolution crystal structure exists, and for which the crystal structure has been shown to be essentially identical to the solution structure. There is no systematic effect of temperature, reference compound, or pH on reported shifts, but there appear to be differences in reported shifts arising from referencing differences of up to 4.2 ppm. The major factor affecting chemical shifts is the backbone geometry, which causes differences of ca. 4 ppm between typical α- helix and β-sheet geometries for Cα, and of ca. 2 ppm for Cβ. The side-chain dihedral angle χ1 has an effect of up to 0.5 ppm on the Cα shift, particularly for amino acids with branched side-chains at Cβ. Hydrogen bonding to main-chain atoms has an effect of up to 0.9 ppm, which depends on the main- chain conformation. The sequence of the protein and ring-current shifts from aromatic rings have an insignificant effect (except for residues following proline). There are significant differences between different amino acid types in the backbone geometry dependence; the amino acids can be grouped together into five different groups with different φ,ψ shielding surfaces. The overall fit of individual residues to a single non-residue-specific surface, incorporating the effects of hydrogen bonding and χ1 angle, is 0.96 ppm for both Cα and Cβ. The results from this study are broadly similar to those from ab initio studies, but there are some differences which could merit further attention

Composition tunable cobalt–nickel and cobalt–iron alloy nanoparticles below 10 nm synthesized using acetonated cobalt carbonyl

International Nuclear Information System (INIS)

Schooneveld, Matti M. van; Campos-Cuerva, Carlos; Pet, Jeroen; Meeldijk, Johannes D.; Rijssel, Jos van; Meijerink, Andries; Erné, Ben H.; Groot, Frank M. F. de

2012-01-01

A general organometallic route has been developed to synthesize Co x Ni 1−x and Co x Fe 1−x alloy nanoparticles with a fully tunable composition and a size of 4–10 nm with high yield. In contrast to previously reported synthesis methods using dicobalt octacarbonyl (Co 2 (CO) 8 ), here the cobalt–cobalt bond in the carbonyl complex is first broken with anhydrous acetone. The acetonated compound, in the presence of iron carbonyl or nickel acetylacetonate, is necessary to obtain small composition tunable alloys. This new route and insights will provide guidelines for the wet-chemical synthesis of yet unmade bimetallic alloy nanoparticles.

Catalyst Initiation in the Oscillatory Carbonylation Reaction

Directory of Open Access Journals (Sweden)

Katarina Novakovic

2011-01-01

Full Text Available Palladium(II iodide is used as a catalyst in the phenylacetylene oxidative carbonylation reaction that has demonstrated oscillatory behaviour in both pH and heat of reaction. In an attempt to extract the reaction network responsible for the oscillatory nature of this reaction, the system was divided into smaller parts and they were studied. This paper focuses on understanding the reaction network responsible for the initial reactions of palladium(II iodide within this oscillatory reaction. The species researched include methanol, palladium(II iodide, potassium iodide, and carbon monoxide. Several chemical reactions were considered and applied in a modelling study. The study revealed the significant role played by traces of water contained in the standard HPLC grade methanol used.

The 40th anniversary of the discovery of NMR-chemical shift and nuclear spin-spin coupling

International Nuclear Information System (INIS)

Zhu Zhenghe; Gou Qingquan

1989-01-01

After the discovery of NMR Phenomenon in the physics laboratories of E.M.Purcell at Harvard and F.Bloch at Stanford in 1946, W.G.Proctor and F.C.Yu made the successful discovery of NMR-chemical shift and nuclear spin-spin coupling at Stanford in 1950, Which brought NMR spectroscopy from the physics laboratory to the laboratories of many different fields. This is worth memorizing. Retrospecting the past 40 years, it is sure that chemical shift theory will be much more prosperous prospects

Chemical Shifts of the Carbohydrate Binding Domain of Galectin-3 from Magic Angle Spinning NMR and Hybrid Quantum Mechanics/Molecular Mechanics Calculations.

Science.gov (United States)

Kraus, Jodi; Gupta, Rupal; Yehl, Jenna; Lu, Manman; Case, David A; Gronenborn, Angela M; Akke, Mikael; Polenova, Tatyana

2018-03-22

Magic angle spinning NMR spectroscopy is uniquely suited to probe the structure and dynamics of insoluble proteins and protein assemblies at atomic resolution, with NMR chemical shifts containing rich information about biomolecular structure. Access to this information, however, is problematic, since accurate quantum mechanical calculation of chemical shifts in proteins remains challenging, particularly for 15 N H . Here we report on isotropic chemical shift predictions for the carbohydrate recognition domain of microcrystalline galectin-3, obtained from using hybrid quantum mechanics/molecular mechanics (QM/MM) calculations, implemented using an automated fragmentation approach, and using very high resolution (0.86 Å lactose-bound and 1.25 Å apo form) X-ray crystal structures. The resolution of the X-ray crystal structure used as an input into the AF-NMR program did not affect the accuracy of the chemical shift calculations to any significant extent. Excellent agreement between experimental and computed shifts is obtained for 13 C α , while larger scatter is observed for 15 N H chemical shifts, which are influenced to a greater extent by electrostatic interactions, hydrogen bonding, and solvation.

Metal-Diazo Radicals of α-Carbonyl Diazomethanes

Science.gov (United States)

Li, Feifei; Xiao, Longqiang; Liu, Lijian

2016-03-01

Metal-diazo radicals of α-carbonyl diazomethanes are new members of the radical family and are precursors to metal-carbene radicals. Herein, using electron paramagnetic resonance spectroscopy with spin-trapping, we detect diazo radicals of α-carbonyl diazomethanes, induced by [RhICl(cod)]2, [CoII(por)] and PdCl2, at room temperature. The unique quintet signal of the Rh-diazo radical was observed in measurements of α-carbonyl diazomethane adducts of [RhICl(cod)]2 in the presence of 5,5-dimethyl-pyrroline-1-N-oxide (DMPO). DFT calculations indicated that 97.2% of spin density is localized on the diazo moiety. Co- and Pd-diazo radicals are EPR silent but were captured by DMPO to form spin adducts of DMPO-N• (triplet-of-sextets signal). The spin-trapping also provides a powerful tool for detection of metal-carbene radicals, as evidenced by the DMPO-trapped carbene radicals (DMPO-C•, sextet signal) and 2-methyl-2-nitrosopropane-carbene adducts (MNP-C•, doublet-of-triplets signal). The transformation of α-carbonyl diazomethanes to metal-carbene radicals was confirmed to be a two-step process via metal-diazo radicals.

H-1 chemical shift imaging characterization of human brain tumor and edema

NARCIS (Netherlands)

Sijens, PE; Oudkerk, M

Longitudinal (T1) and transverse (T2) relaxation times of metabolites in human brain tumor, peritumoral edema, and unaffected brain tissue were assessed from point resolved spectroscopy (PRESS) H-1 chemical shift imaging results at different repetition times (TR = 1500 and 5000 ms; T1: n = 19) and

PACSY, a relational database management system for protein structure and chemical shift analysis.

Science.gov (United States)

Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo; Lee, Weontae; Markley, John L

2012-10-01

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu.

PACSY, a relational database management system for protein structure and chemical shift analysis

Energy Technology Data Exchange (ETDEWEB)

Lee, Woonghee, E-mail: whlee@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison, and Biochemistry Department (United States); Yu, Wookyung [Center for Proteome Biophysics, Pusan National University, Department of Physics (Korea, Republic of); Kim, Suhkmann [Pusan National University, Department of Chemistry and Chemistry Institute for Functional Materials (Korea, Republic of); Chang, Iksoo [Center for Proteome Biophysics, Pusan National University, Department of Physics (Korea, Republic of); Lee, Weontae, E-mail: wlee@spin.yonsei.ac.kr [Yonsei University, Structural Biochemistry and Molecular Biophysics Laboratory, Department of Biochemistry (Korea, Republic of); Markley, John L., E-mail: markley@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison, and Biochemistry Department (United States)

2012-10-15

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.eduhttp://pacsy.nmrfam.wisc.edu.

PACSY, a relational database management system for protein structure and chemical shift analysis

Science.gov (United States)

Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo

2012-01-01

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu. PMID:22903636

PACSY, a relational database management system for protein structure and chemical shift analysis

International Nuclear Information System (INIS)

Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo; Lee, Weontae; Markley, John L.

2012-01-01

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.eduhttp://pacsy.nmrfam.wisc.edu.

Preparation and microwave shielding property of silver-coated carbonyl iron powder

International Nuclear Information System (INIS)

Cao, Xiao Guo; Ren, Hao; Zhang, Hai Yan

2015-01-01

Highlights: • The silver-coated carbonyl iron powder is prepared by the electroless plating process. • The silver-coated carbonyl iron powder is a new kind of conductive filler. • The reflection and absorption dominate the shielding mechanism of the prepared powder. • Increasing the thickness of electroconductive adhesive will increase the SE. - Abstract: Electroless silver coating of carbonyl iron powder is demonstrated in the present investigation. The carbonyl iron powders are characterized by scanning electron microscope (SEM), energy dispersive X-ray spectroscopy (EDX), and X-ray diffraction analysis (XRD) before and after the coating process. The relatively uniform and continuous silver coating is obtained under the given coating conditions. In this paper, the electromagnetic interference (EMI) shielding mechanism of the silver-coated carbonyl iron powder is suggested. The reflection of silver coating and absorption of carbonyl iron powder dominate the shielding mechanism of the silver-coated carbonyl iron powder. The silver-coated carbonyl iron powders are used as conductive filler in electroconductive adhesive for electromagnetic interference shielding applications. The effect of the thickness of electroconductive adhesive on the shielding effectiveness (SE) is investigated. The results indicate that the SE increases obviously with the increase of the thickness of electroconductive adhesive. The SE of the electroconductive adhesive with 0.35 mm thickness is above 38 dB across the tested frequency range

Dansyl labeling and bidimensional mass spectrometry to investigate protein carbonylation.

Science.gov (United States)

Palmese, Angelo; De Rosa, Chiara; Marino, Gennaro; Amoresano, Angela

2011-01-15

Carbonylation is a non-enzymatic irreversible post-translational modification. The adduction of carbonyl groups to proteins is due to the presence of excess of ROS in cells. Carbonylation of specific amino acid side chains is one of the most abundant consequences of oxidative stress; therefore, the determination of carbonyl groups content in proteins is regarded as a reliable way to estimate the cellular damage caused by oxidative stress. This paper reports a novel RIGhT (Reporter Ion Generating Tag) (A. Amoresano, G. Monti, C. Cirulli, G. Marino. Rapid Commun. Mass Spectrom. 2006, 20, 1400) approach for selective labeling of carbonyl groups in proteins using dansylhydrazide, coupled with selective analysis by bidimensional mass spectrometry. We first applied this approach to ribonuclease A and lysozyme as model proteins. According to the so-called 'gel-free procedures', the analysis is carried out at the level of peptides following tryptic digest of the whole protein mixture. Modified RNaseA was analyzed in combined MS(2) and MS(3) scan mode, to specifically select the dansylated species taking advantage of the dansyl-specific fragmentation pathways. This combination allowed us to obtain a significant increase in signal/noise ratio and a significant increase in sensitivity of analysis, due to the reduction of duty cycle of the mass spectrometer. The unique signal obtained was correlated to peptide 1-10 of RNaseA carbonylated and labeled by dansylhydrazide. This strategy represents the first method leading to the direct identification of the carbonylation sites in proteins, thus indicating the feasibility of this strategy to investigate protein carbonylation in a proteomic approach. Copyright © 2010 John Wiley & Sons, Ltd.

New method to determine the total carbonyl functional group content in extractable particulate organic matter by tandem mass spectrometry.

Science.gov (United States)

Dron, J; Zheng, W; Marchand, N; Wortham, H

2008-08-01

A functional group analysis method was developed to determine the quantitative content of carbonyl functional groups in atmospheric particulate organic matter (POM) using constant neutral loss scanning-tandem mass spectrometry (CNLS-MS/MS). The neutral loss method consists in monitoring the loss of a neutral fragment produced by the fragmentation of a precursor ion in a collision cell. The only ions detected are the daughter ions resulting from the loss of the neutral fragment under study. Then, scanning the loss of a neutral fragment characteristic of a functional group enables the selective detection of the compounds bearing the chemical function under study within a complex mixture. The selective detection of carbonyl functional groups was achieved after derivatization with pentafluorophenylhydrazine (PFPH) by monitoring the neutral loss of C(6)F(5)N (181 amu), which was characteristic of a large panel of derivatized carbonyl compounds. The method was tested on 25 reference mixtures of different composition, all containing 24 carbonyl compounds at randomly determined concentrations. The repeatability and calibration tests were satisfying as they resulted in a relative standard deviation below 5% and a linear range between 0.01 and 0.65 mM with a calculated detection limit of 0.0035 mM. Also, the relative deviation induced by changing the composition of the mixture while keeping the total concentration of carbonyl functional groups constant was less than 20%. These reliability experiments demonstrate the high robustness of the developed procedure for accurate carbonyl functional group measurement, which was applied to atmospheric POM samples. Copyright (c) 2008 John Wiley & Sons, Ltd.

Sensitivity of ab Initio vs Empirical Methods in Computing Structural Effects on NMR Chemical Shifts for the Example of Peptides.

Science.gov (United States)

Sumowski, Chris Vanessa; Hanni, Matti; Schweizer, Sabine; Ochsenfeld, Christian

2014-01-14

The structural sensitivity of NMR chemical shifts as computed by quantum chemical methods is compared to a variety of empirical approaches for the example of a prototypical peptide, the 38-residue kaliotoxin KTX comprising 573 atoms. Despite the simplicity of empirical chemical shift prediction programs, the agreement with experimental results is rather good, underlining their usefulness. However, we show in our present work that they are highly insensitive to structural changes, which renders their use for validating predicted structures questionable. In contrast, quantum chemical methods show the expected high sensitivity to structural and electronic changes. This appears to be independent of the quantum chemical approach or the inclusion of solvent effects. For the latter, explicit solvent simulations with increasing number of snapshots were performed for two conformers of an eight amino acid sequence. In conclusion, the empirical approaches neither provide the expected magnitude nor the patterns of NMR chemical shifts determined by the clearly more costly ab initio methods upon structural changes. This restricts the use of empirical prediction programs in studies where peptide and protein structures are utilized for the NMR chemical shift evaluation such as in NMR refinement processes, structural model verifications, or calculations of NMR nuclear spin relaxation rates.

Modelling the acid/base 1H NMR chemical shift limits of metabolites in human urine.

Science.gov (United States)

Tredwell, Gregory D; Bundy, Jacob G; De Iorio, Maria; Ebbels, Timothy M D

2016-01-01

Despite the use of buffering agents the 1 H NMR spectra of biofluid samples in metabolic profiling investigations typically suffer from extensive peak frequency shifting between spectra. These chemical shift changes are mainly due to differences in pH and divalent metal ion concentrations between the samples. This frequency shifting results in a correspondence problem: it can be hard to register the same peak as belonging to the same molecule across multiple samples. The problem is especially acute for urine, which can have a wide range of ionic concentrations between different samples. To investigate the acid, base and metal ion dependent 1 H NMR chemical shift variations and limits of the main metabolites in a complex biological mixture. Urine samples from five different individuals were collected and pooled, and pre-treated with Chelex-100 ion exchange resin. Urine samples were either treated with either HCl or NaOH, or were supplemented with various concentrations of CaCl 2 , MgCl 2 , NaCl or KCl, and their 1 H NMR spectra were acquired. Nonlinear fitting was used to derive acid dissociation constants and acid and base chemical shift limits for peaks from 33 identified metabolites. Peak pH titration curves for a further 65 unidentified peaks were also obtained for future reference. Furthermore, the peak variations induced by the main metal ions present in urine, Na + , K + , Ca 2+ and Mg 2+ , were also measured. These data will be a valuable resource for 1 H NMR metabolite profiling experiments and for the development of automated metabolite alignment and identification algorithms for 1 H NMR spectra.

Quantum-Chemical Approach to NMR Chemical Shifts in Paramagnetic Solids Applied to LiFePO4 and LiCoPO4.

Science.gov (United States)

Mondal, Arobendo; Kaupp, Martin

2018-04-05

A novel protocol to compute and analyze NMR chemical shifts for extended paramagnetic solids, accounting comprehensively for Fermi-contact (FC), pseudocontact (PC), and orbital shifts, is reported and applied to the important lithium ion battery cathode materials LiFePO 4 and LiCoPO 4 . Using an EPR-parameter-based ansatz, the approach combines periodic (hybrid) DFT computation of hyperfine and orbital-shielding tensors with an incremental cluster model for g- and zero-field-splitting (ZFS) D-tensors. The cluster model allows the use of advanced multireference wave function methods (such as CASSCF or NEVPT2). Application of this protocol shows that the 7 Li shifts in the high-voltage cathode material LiCoPO 4 are dominated by spin-orbit-induced PC contributions, in contrast with previous assumptions, fundamentally changing interpretations of the shifts in terms of covalency. PC contributions are smaller for the 7 Li shifts of the related LiFePO 4 , where FC and orbital shifts dominate. The 31 P shifts of both materials finally are almost pure FC shifts. Nevertheless, large ZFS contributions can give rise to non-Curie temperature dependences for both 7 Li and 31 P shifts.

Electromagnetic properties of carbonyl iron and their microwave ...

Indian Academy of Sciences (India)

Administrator

The aim of this paper is to develop a novel thin micro- wave absorber with good absorbing performance in wide bandwidth and lightweight. So we investigated the micro- wave absorbing characterization of silicone rubber using carbonyl iron as filler. Carbonyl iron can be widely used in the field of electromagnetic shielding ...

Relativistic Spin-Orbit Heavy Atom on the Light Atom NMR Chemical Shifts: General Trends Across the Periodic Table Explained.

Science.gov (United States)

Vícha, Jan; Komorovsky, Stanislav; Repisky, Michal; Marek, Radek; Straka, Michal

2018-05-10

The importance of relativistic effects on the NMR parameters in heavy-atom (HA) compounds, particularly the SO-HALA (Spin-Orbit Heavy Atom on the Light Atom) effect on NMR chemical shifts, has been known for about 40 years. Yet, a general correlation between the electronic structure and SO-HALA effect has been missing. By analyzing 1 H NMR chemical shifts of the sixth-period hydrides (Cs-At), we discovered general electronic-structure principles and mechanisms that dictate the size and sign of the SO-HALA NMR chemical shifts. In brief, partially occupied HA valence shells induce relativistic shielding at the light atom (LA) nuclei, while empty HA valence shells induce relativistic deshielding. In particular, the LA nucleus is relativistically shielded in 5d 2 -5d 8 and 6p 4 HA hydrides and deshielded in 4f 0 , 5d 0 , 6s 0 , and 6p 0 HA hydrides. This general and intuitive concept explains periodic trends in the 1 H NMR chemical shifts along the sixth-period hydrides (Cs-At) studied in this work. We present substantial evidence that the introduced principles have a general validity across the periodic table and can be extended to nonhydride LAs. The decades-old question of why compounds with occupied frontier π molecular orbitals (MOs) cause SO-HALA shielding at the LA nuclei, while the frontier σ MOs cause deshielding is answered. We further derive connection between the SO-HALA NMR chemical shifts and Spin-Orbit-induced Electron Deformation Density (SO-EDD), a property that can be obtained easily from differential electron densities and can be represented graphically. SO-EDD provides an intuitive understanding of the SO-HALA effect in terms of the depletion/concentration of the electron density at LA nuclei caused by spin-orbit coupling due to HA in the presence of a magnetic field. Using an analogy between the SO-EDD concept and arguments from classic NMR theory, the complex question of the SO-HALA NMR chemical shifts becomes easily understandable for a wide

TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts

Energy Technology Data Exchange (ETDEWEB)

Shen Yang; Delaglio, Frank [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Cornilescu, Gabriel [National Magnetic Resonance Facility (United States); Bax, Ad [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)], E-mail: bax@nih.gov

2009-08-15

NMR chemical shifts in proteins depend strongly on local structure. The program TALOS establishes an empirical relation between {sup 13}C, {sup 15}N and {sup 1}H chemical shifts and backbone torsion angles {phi} and {psi} (Cornilescu et al. J Biomol NMR 13 289-302, 1999). Extension of the original 20-protein database to 200 proteins increased the fraction of residues for which backbone angles could be predicted from 65 to 74%, while reducing the error rate from 3 to 2.5%. Addition of a two-layer neural network filter to the database fragment selection process forms the basis for a new program, TALOS+, which further enhances the prediction rate to 88.5%, without increasing the error rate. Excluding the 2.5% of residues for which TALOS+ makes predictions that strongly differ from those observed in the crystalline state, the accuracy of predicted {phi} and {psi} angles, equals {+-}13{sup o}. Large discrepancies between predictions and crystal structures are primarily limited to loop regions, and for the few cases where multiple X-ray structures are available such residues are often found in different states in the different structures. The TALOS+ output includes predictions for individual residues with missing chemical shifts, and the neural network component of the program also predicts secondary structure with good accuracy.

Observations and Explicit Modeling of Summertime Carbonyl Formation in Beijing: Identification of Key Precursor Species and Their Impact on Atmospheric Oxidation Chemistry

Science.gov (United States)

Yang, Xue; Xue, Likun; Wang, Tao; Wang, Xinfeng; Gao, Jian; Lee, Shuncheng; Blake, Donald R.; Chai, Fahe; Wang, Wenxing

2018-01-01

Carbonyls are an important group of volatile organic compounds (VOCs) that play critical roles in tropospheric chemistry. To better understand the formation mechanisms of carbonyl compounds, extensive measurements of carbonyls and related parameters were conducted in Beijing in summer 2008. Formaldehyde (11.17 ± 5.32 ppbv), acetone (6.98 ± 3.01 ppbv), and acetaldehyde (5.27 ± 2.24 ppbv) were the most abundant carbonyl species. Two dicarbonyls, glyoxal (0.68 ± 0.26 ppbv) and methylglyoxal (MGLY; 1.10 ± 0.44 ppbv), were also present in relatively high concentrations. An observation-based chemical box model was used to simulate the in situ production of formaldehyde, acetaldehyde, glyoxal, and MGLY and quantify their contributions to ozone formation and ROx budget. All four carbonyls showed similar formation mechanisms but exhibited different precursor distributions. Alkenes (mainly isoprene and ethene) were the dominant precursors of formaldehyde, while both alkenes (e.g., propene, i-butene, and cis-2-pentene) and alkanes (mainly i-pentane) were major precursors of acetaldehyde. For dicarbonyls, both isoprene and aromatic VOCs were the dominant parent hydrocarbons of glyoxal and MGLY. Photolysis of oxygenated VOCs was the dominant source of ROx radicals (approximately >80% for HO2 and approximately >70% for RO2) in Beijing. Ozone production occurred under a mixed-control regime with carbonyls being the key VOC species. Overall, this study provides some new insights into the formation mechanisms of carbonyls, especially their parent hydrocarbon species, and underlines the important role of carbonyls in radical chemistry and ozone pollution in Beijing. Reducing the emissions of alkenes and aromatics would be an effective way to mitigate photochemical pollution in Beijing.

A comparison of chemical shift sensitivity of trifluoromethyl tags: optimizing resolution in {sup 19}F NMR studies of proteins

Energy Technology Data Exchange (ETDEWEB)

Ye, Libin; Larda, Sacha Thierry; Frank Li, Yi Feng [University of Toronto, UTM, Department of Chemistry (Canada); Manglik, Aashish [Stanford University School of Medicine, Department of Molecular and Cellular Physiology (United States); Prosser, R. Scott, E-mail: scott.prosser@utoronto.ca [University of Toronto, UTM, Department of Chemistry (Canada)

2015-05-15

The elucidation of distinct protein conformers or states by fluorine ({sup 19}F) NMR requires fluorinated moieties whose chemical shifts are most sensitive to subtle changes in the local dielectric and magnetic shielding environment. In this study we evaluate the effective chemical shift dispersion of a number of thiol-reactive trifluoromethyl probes [i.e. 2-bromo-N-(4-(trifluoromethyl)phenyl)acetamide (BTFMA), N-(4-bromo-3-(trifluoromethyl)phenyl)acetamide (3-BTFMA), 3-bromo-1,1,1-trifluoropropan-2-ol (BTFP), 1-bromo-3,3,4,4,4-pentafluorobutan-2-one (BPFB), 3-bromo-1,1,1-trifluoropropan-2-one (BTFA), and 2,2,2-trifluoroethyl-1-thiol (TFET)] under conditions of varying polarity. In considering the sensitivity of the {sup 19}F NMR chemical shift to the local environment, a series of methanol/water mixtures were prepared, ranging from relatively non-polar (MeOH:H{sub 2}O = 4) to polar (MeOH:H{sub 2}O = 0.25). {sup 19}F NMR spectra of the tripeptide, glutathione ((2S)-2-amino-4-{[(1R)-1-[(carboxymethyl)carbamoyl] -2-sulfanylethyl]carbamoyl}butanoic acid), conjugated to each of the above trifluoromethyl probes, revealed that the BTFMA tag exhibited a significantly greater range of chemical shift as a function of solvent polarity than did either BTFA or TFET. DFT calculations using the B3LYP hybrid functional and the 6-31G(d,p) basis set, confirmed the observed trend in chemical shift dispersion with solvent polarity.

Rh(I) -Catalyzed Intramolecular Carbonylative C-H/C-I Coupling of 2-Iodobiphenyls Using Furfural as a Carbonyl Source.

Science.gov (United States)

Furusawa, Takuma; Morimoto, Tsumoru; Nishiyama, Yasuhiro; Tanimoto, Hiroki; Kakiuchi, Kiyomi

2016-08-19

Synthesis of fluoren-9-ones by a Rh-catalyzed intramolecular C-H/C-I carbonylative coupling of 2-iodobiphenyls using furfural as a carbonyl source is presented. The findings indicate that the rate-determining step is not a C-H bond cleavage but, rather, the oxidative addition of the C-I bond to a Rh(I) center. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Phenolic carbonyls undergo rapid aqueous photodegradation to form low-volatility, light-absorbing products

Science.gov (United States)

Smith, Jeremy D.; Kinney, Haley; Anastasio, Cort

2016-02-01

We investigated the aqueous photochemistry of six phenolic carbonyls - vanillin, acetovanillone, guaiacyl acetone, syringaldehyde, acetosyringone, and coniferyl aldehyde - that are emitted from wood combustion. The phenolic carbonyls absorb significant amounts of solar radiation and decay rapidly via direct photodegradation, with lifetimes (τ) of 13-140 min under Davis, CA winter solstice sunlight at midday (solar zenith angle = 62°). The one exception is guaiacyl acetone, where the carbonyl group is not directly connected to the aromatic ring: This species absorbs very little sunlight and undergoes direct photodegradation very slowly (τ > 103 min). We also found that the triplet excited states (3C*) of the phenolic carbonyls rapidly oxidize syringol (a methoxyphenol without a carbonyl group), on timescales of 1-5 h for solutions containing 5 μM phenolic carbonyl. The direct photodegradation of the phenolic carbonyls, and the oxidation of syringol by 3C*, both efficiently produce low volatility products, with SOA mass yields ranging from 80 to 140%. Contrary to most aliphatic carbonyls, under typical fog conditions we find that the primary sink for the aromatic phenolic carbonyls is direct photodegradation in the aqueous phase. In areas of significant wood combustion, phenolic carbonyls appear to be small but significant sources of aqueous SOA: over the course of a few hours, nearly all of the phenolic carbonyls will be converted to SOA via direct photodegradation, enhancing the POA mass from wood combustion by approximately 3-5%.

Quantitative chemical shift-encoded MRI is an accurate method to quantify hepatic steatosis.

Science.gov (United States)

Kühn, Jens-Peter; Hernando, Diego; Mensel, Birger; Krüger, Paul C; Ittermann, Till; Mayerle, Julia; Hosten, Norbert; Reeder, Scott B

2014-06-01

To compare the accuracy of liver fat quantification using a three-echo chemical shift-encoded magnetic resonance imaging (MRI) technique without and with correction for confounders with spectroscopy (MRS) as the reference standard. Fifty patients (23 women, mean age 56.6 ± 13.2 years) with fatty liver disease were enrolled. Patients underwent T2-corrected single-voxel MRS and a three-echo chemical shift-encoded gradient echo (GRE) sequence at 3.0T. MRI fat fraction (FF) was calculated without and with T2* and T1 correction and multispectral modeling of fat and compared with MRS-FF using linear regression. The spectroscopic range of liver fat was 0.11%-38.7%. Excellent correlation between MRS-FF and MRI-FF was observed when using T2* correction (R(2)  = 0.96). With use of T2* correction alone, the slope was significantly different from 1 (1.16 ± 0.03, P fat were addressed, the results showed equivalence between fat quantification using MRI and MRS (slope: 1.02 ± 0.03, P = 0.528; intercept: 0.26% ± 0.46%, P = 0.572). Complex three-echo chemical shift-encoded MRI is equivalent to MRS for quantifying liver fat, but only with correction for T2* decay and T1 recovery and use of spectral modeling of fat. This is necessary because T2* decay, T1 recovery, and multispectral complexity of fat are processes which may otherwise bias the measurements. Copyright © 2013 Wiley Periodicals, Inc.

Chemical shift of Mn and Cr K-edges in X-ray absorption

Indian Academy of Sciences (India)

... Lecture Workshops · Refresher Courses · Symposia · Live Streaming. Home; Journals; Bulletin of Materials Science; Volume 36; Issue 6. Chemical shift of Mn and Cr K-edges in X-ray absorption spectroscopy with synchrotron radiation. D Joseph A K Yadav S N Jha D Bhattacharyya. Volume 36 Issue 6 November 2013 pp ...

Accumulation of carbonyls accelerates the formation of pentosidine, an advanced glycation end product: carbonyl stress in uremia.

Science.gov (United States)

Miyata, T; Ueda, Y; Yamada, Y; Izuhara, Y; Wada, T; Jadoul, M; Saito, A; Kurokawa, K; van Ypersele de Strihou, C

1998-12-01

Advanced glycation end product (AGE) formation is related to hyperglycemia in diabetes but not in uremia, because plasma AGE levels do not differ between diabetic and nondiabetic hemodialysis patients. The mechanism of this phenomenon remains elusive. Previously, it was suggested that elevation of AGE levels in uremia might result from the accumulation of unknown AGE precursors. The present study evaluates the in vitro generation of pentosidine, a well identified AGE structure. Plasma samples from healthy subjects and nondiabetic hemodialysis patients were incubated under air for several weeks. Pentosidine levels were determined at intervals by HPLC assay. Pentosidine rose to a much larger extent in uremic than in control plasma. Pentosidine yield, i.e., the change in pentosidine level between 0 and 4 wk divided by 28 d, averaged 0.172 nmol/ml per d in uremic versus 0.072 nmol/ml per d in control plasma (P aminoguanidine and OPB-9195, which inhibit the Maillard reaction, lowered pentosidine yield in both uremic and control plasma. When ultrafiltrated plasma was exposed to 2,4-dinitrophenylhydrazine, the yield of hydrazones, formed by interaction with carbonyl groups, was markedly higher in uremic than in control plasma. These observations strongly suggest that the pentosidine precursors accumulated in uremic plasma are carbonyl compounds. These precursors are unrelated to glucose or ascorbic acid, whose concentration is either normal or lowered in uremic plasma. They are also unrelated to 3-deoxyglucosone, a glucose-derived dicarbonyl compound whose level is raised in uremic plasma: Its addition to normal plasma fails to increase pentosidine yield. This study reports an elevated level of reactive carbonyl compounds ("carbonyl stress") in uremic plasma. Most have a lower than 5000 Da molecular weight and are thus partly removed by hemodialysis. Their effect on pentosidine generation can be inhibited by aminoguanidine or OPB-9195. Carbonyl stress might contribute to

Determination of Carbonyl Functional Groups in Bio-oils by Potentiometric Titration: The Faix Method.

Science.gov (United States)

Black, Stuart; Ferrell, Jack R

2017-02-07

Carbonyl compounds present in bio-oils are known to be responsible for bio-oil property changes upon storage and during upgrading. Specifically, carbonyls cause an increase in viscosity (often referred to as 'aging') during storage of bio-oils. As such, carbonyl content has previously been used as a method of tracking bio-oil aging and condensation reactions with less variability than viscosity measurements. Additionally, carbonyls are also responsible for coke formation in bio-oil upgrading processes. Given the importance of carbonyls in bio-oils, accurate analytical methods for their quantification are very important for the bio-oil community. Potentiometric titration methods based on carbonyl oximation have long been used for the determination of carbonyl content in pyrolysis bio-oils. Here, we present a modification of the traditional carbonyl oximation procedures that results in less reaction time, smaller sample size, higher precision, and more accurate carbonyl determinations. While traditional carbonyl oximation methods occur at room temperature, the Faix method presented here occurs at an elevated temperature of 80 °C.

Assignment of protein backbone resonances using connectivity, torsion angles and 13Cα chemical shifts

International Nuclear Information System (INIS)

Morris, Laura C.; Valafar, Homayoun; Prestegard, James H.

2004-01-01

A program is presented which will return the most probable sequence location for a short connected set of residues in a protein given just 13 C α chemical shifts (δ( 13 C α )) and data restricting the φ and ψ backbone angles. Data taken from both the BioMagResBank and the Protein Data Bank were used to create a probability density function (PDF) using a multivariate normal distribution in δ( 13 C α ), φ, and ψ space for each amino acid residue. Extracting and combining probabilities for particular amino acid residues in a short proposed sequence yields a score indicative of the correctness of the proposed assignment. The program is illustrated using several proteins for which structure and 13 C α chemical shift data are available

Protein carbonylation and metal-catalyzed protein oxidation in a cellular perspective

DEFF Research Database (Denmark)

Møller, Ian Max; Rogowska-Wrzesinska, Adelina; Rao, R S P

2011-01-01

Proteins can become oxidatively modified in many different ways, either by direct oxidation of amino acid side chains and protein backbone or indirectly by conjugation with oxidation products of polyunsaturated fatty acids and carbohydrates. While reversible oxidative modifications are thought...... to be relevant in physiological processes, irreversible oxidative modifications are known to contribute to cellular damage and disease. The most well-studied irreversible protein oxidation is carbonylation. In this work we first examine how protein carbonylation occurs via metal-catalyzed oxidation (MCO) in vivo...... and in vitro with an emphasis on cellular metal ion homeostasis and metal binding. We then review proteomic methods currently used for identifying carbonylated proteins and their sites of modification. Finally, we discuss the identified carbonylated proteins and the pattern of carbonylation sites in relation...

Stereoelectronic effects on 1H nuclear magnetic resonance chemical shifts in methoxybenzenes

DEFF Research Database (Denmark)

Lambert, Maja; Olsen, Lars; Jaroszewski, Jerzy W

2006-01-01

the Ar-OCH3 torsion out of the ring plane, resulting in large stereoelectronic effects on the chemical shift of Hpara. Conformational searches and geometry optimizations for 3-16 at the B3LYP/6-31G** level, followed by B3LYP/6-311++G(2d,2p) calculations for all low-energy conformers, gave excellent...

Chemical shift-selective snapshot FLASH MR imaging in combination with inversion-recovery T1 contrast at different field strengths

International Nuclear Information System (INIS)

Matthaei, D.; Haase, A.; Henrich, D.; Duhmke, E.

1991-01-01

With fast MR imaging, chemical shift contract becomes available to the clinician in seconds. The purpose of this paper is to evaluate the combination of chemical shift selective (CHESS) MR imaging using the snapshot FLASH MR method with the inversion-recovery technique and to obtain information concerning the signal-to-noise and chemical shift with the presaturation method at different field strengths. Investigations with volunteers and experimental animals were done at 2 and 3 T (whole body) and in a 4.7-T animal image. For the inversion-recovery experiments, saturation was done before every snapshot FLASH image. With increasing field strength due to signal-to-noise and chemical shift advantages, the method performs better. Increasing T1 values are also important at high field strengths. The combined technique is useful only for T1 water images with fat saturation. It also allows fast quantification of T1 in water-containing organs and pathologic processes. At high field strengths, fast CHESS and T1 imaging promise fast quantitative information. This is a possible argument for clinical high-field-strength MR imagining along with MR spectroscopy

Millimeter wave spectra of carbonyl cyanide ⋆

Science.gov (United States)

Bteich, S.B.; Tercero, B.; Cernicharo, J.; Motiyenko, R.A.; Margulès, L.; Guillemin, J.-C.

2016-01-01

Context More than 30 cyanide derivatives of simple organic molecules have been detected in the interstellar medium, but only one dicarbonitrile has been found and that very recently. There is still a lack of high-resolution spectroscopic data particularly for dinitriles derivatives. The carbonyl cyanide molecule is a new and interesting candidate for astrophysical detection. It could be formed by the reaction of CO and CN radicals, or by substitution of the hydrogen atom by a cyano group in cyanoformaldehyde, HC(=O)CN, that has already been detected in the interstellar medium. Aims The available data on the rotational spectrum of carbonyl cyanide is limited in terms of quantum number values and frequency range, and does not allow accurate extrapolation of the spectrum into the millimeter-wave range. To provide a firm basis for astrophysical detection of carbonyl cyanide we studied its millimeter-wave spectrum. Methods The rotational spectrum of carbonyl cyanide was measured in the frequency range 152 - 308 GHz and analyzed using Watson’s A- and S-reduction Hamiltonians. Results The ground and first excited state of v5 vibrational mode were assigned and analyzed. More than 1100 distinct frequency lines of the ground state were fitted to produce an accurate set of rotational and centrifugal distortion constants up to the eighth order. The frequency predictions based on these constants should be accurate enough for astrophysical searches in the frequency range up to 500 GHz and for transition involving energy levels with J ≤ 100 and Ka ≤ 42. Based on the results we searched for interstellar carbonyl cyanide in available observational data without success. Thus, we derived upper limits to its column density in different sources. PMID:27738349

Calculation of NMR chemical shifts. 7. Gauge-invariant INDO method

Science.gov (United States)

Fukui, H.; Miura, K.; Hirai, A.

A gauge-invariant INDO method based on the coupled Hartree-Fuck perturbation theory is presented and applied to the calculation of 1H and 13C chemical shifts of hydrocarbons including ring compounds. Invariance of the diamagnetic and paramagnetic shieldings with respect to displacement of the coordinate origin is discussed. Comparison between calculated and experimental results exhibits fairly good agreement, provided that the INDO parameters of Ellis et al. (J. Am. Chem. Soc.94, 4069 (1972)) are used with the inclusion of all multicenter one-electron integrals.

Rapid Determination of Six Low Molecular Carbonyl Compounds in Tobacco Smoke by the APCI-MS/MS Coupled to Data Mining

Directory of Open Access Journals (Sweden)

Wuduo Zhao

2017-01-01

Full Text Available A simple method was established for the rapid determination of low molecular carbonyl compounds by the combination of atmospheric pressure chemical ionization tandem mass spectrometry (APCI-MS/MS and data mining. The ionization was carried out in positive mode, and six low molecular carbonyl compounds of acrolein, acetone, propionaldehyde, crotonaldehyde, butanone, and butyraldehyde were analyzed by both full scan mode and daughter scan mode. To overcome the quantitative difficulties from isomer of acetone/propionaldehyde and butanone/butyraldehyde, the quantitation procedure was performed with the characteristic ion of [CH3O]+ under CID energy of 5 and 15 eV. Subsequently, the established method was successfully applied to analysis of six low molecular carbonyl compounds in tobacco smoke with analytical period less than four minutes. The contents of acrolein, acetone, propionaldehyde, crotonaldehyde, butanone, and butyraldehyde for a cigarette were about 63±5.8, 325±82, 55±9.7, 11±1.4, 67±5.9, and 12±1.8 μg/cig, respectively. The experimental results indicated that the established method had the potential application in rapid determination of low molecular carbonyl compounds.

Determination of the bonding of alkyl monolayers to the Si(111) surface using chemical-shift, scanned-energy photoelectron diffraction

Energy Technology Data Exchange (ETDEWEB)

Terry, J.; Linford, M.R.; Wigren, C.; Cao, R.; Pianetta, P.; Chidsey, C.E. [Stanford University, Stanford, California 94309 (United States)

1997-08-01

The bonding of alkyl monolayers to Si(111) surfaces has been studied by conventional x-ray photoelectron spectroscopy (XPS) and chemical-shift, scanned-energy photoelectron diffraction (PED) using synchrotron radiation. Two very different wet-chemical methods have been used to prepare the alkyl monolayers: (i) olefin insertion into the H{endash}Si bond on the H{endash}Si(111) surface, and (ii) replacement of Cl on the Cl{endash}Si(111) surface by an alkyl group from an alkyllithium reagent. In both cases, XPS has revealed a C 1s signal chemically shifted to lower binding energy, which we have assigned to carbon bonded to silicon. PED has shown that both preparative methods result in carbon bonded in an atop site with the expected C{endash}Si bond length of 1.85{plus_minus}0.05{Angstrom}. Chemical-shift, scanned-energy photoelectron diffraction is a particularly valuable probe of local structure at surfaces that contain the same element in multiple, chemically distinct environments. {copyright} {ital 1997 American Institute of Physics.}

Determination of the bonding of alkyl monolayers to the Si(111) surface using chemical-shift, scanned-energy photoelectron diffraction

International Nuclear Information System (INIS)

Terry, J.; Linford, M.R.; Wigren, C.; Cao, R.; Pianetta, P.; Chidsey, C.E.

1997-01-01

The bonding of alkyl monolayers to Si(111) surfaces has been studied by conventional x-ray photoelectron spectroscopy (XPS) and chemical-shift, scanned-energy photoelectron diffraction (PED) using synchrotron radiation. Two very different wet-chemical methods have been used to prepare the alkyl monolayers: (i) olefin insertion into the H endash Si bond on the H endash Si(111) surface, and (ii) replacement of Cl on the Cl endash Si(111) surface by an alkyl group from an alkyllithium reagent. In both cases, XPS has revealed a C 1s signal chemically shifted to lower binding energy, which we have assigned to carbon bonded to silicon. PED has shown that both preparative methods result in carbon bonded in an atop site with the expected C endash Si bond length of 1.85±0.05 Angstrom. Chemical-shift, scanned-energy photoelectron diffraction is a particularly valuable probe of local structure at surfaces that contain the same element in multiple, chemically distinct environments. copyright 1997 American Institute of Physics

Emissions of carbonyl compounds from various cookstoves in China

International Nuclear Information System (INIS)

Zhang, J.; Smith, K.R.; Univ. of California, Berkeley, CA

1999-01-01

This paper presents a new database of carbonyl emission factors for commonly used cookstoves in China. The emission factors, reported both on a fuel-mass basis (mg/kg) and on a defined cooking-task basis (mg/task), were determined using a carbon balance approach for 22 types of fuel/stove combinations. These include various stoves using different species of crop residues and wood, kerosene, and several types of coals and gases. The results show that all the tested cookstoves produced formaldehyde and acetaldehyde and that the vast majority of the biomass stoves produced additional carbonyl compounds such as acetone, acrolein, propionaldehyde, crotonaldehyde, 2-butanone, isobutyraldehyde, butyraldehyde, isovaleraldehyde, valeraldehyde, hexaldehyde, benzaldehyde, o-tolualdehyde, m,p-tolualdehyde, and 2,4-dimethylbenzaldehyde. Carbonyls other than formaldehyde and acetaldehyde, however, were rarely generated by burning coal, coal gas, and natural gas. Kerosene and LPG stoves generated more carbonyl compounds than coal, coal gas, and natural gas stoves, but less than biomass stoves. Indoor levels of carbonyl compounds for typical village houses during cooking hours, estimated using a mass balance model and the measured emission factors, can be high enough to cause acute health effects documented for formaldehyde exposure, depending upon house parameters and individuals' susceptibility

Solvation effects on chemical shifts by embedded cluster integral equation theory.

Science.gov (United States)

Frach, Roland; Kast, Stefan M

2014-12-11

The accurate computational prediction of nuclear magnetic resonance (NMR) parameters like chemical shifts represents a challenge if the species studied is immersed in strongly polarizing environments such as water. Common approaches to treating a solvent in the form of, e.g., the polarizable continuum model (PCM) ignore strong directional interactions such as H-bonds to the solvent which can have substantial impact on magnetic shieldings. We here present a computational methodology that accounts for atomic-level solvent effects on NMR parameters by extending the embedded cluster reference interaction site model (EC-RISM) integral equation theory to the prediction of chemical shifts of N-methylacetamide (NMA) in aqueous solution. We examine the influence of various so-called closure approximations of the underlying three-dimensional RISM theory as well as the impact of basis set size and different treatment of electrostatic solute-solvent interactions. We find considerable and systematic improvement over reference PCM and gas phase calculations. A smaller basis set in combination with a simple point charge model already yields good performance which can be further improved by employing exact electrostatic quantum-mechanical solute-solvent interaction energies. A larger basis set benefits more significantly from exact over point charge electrostatics, which can be related to differences of the solvent's charge distribution.

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

DFT global chemical reactivity descriptors (chemical hardness, total energy, electronic chemical potential, and electrophilicity) are calculated for the isomers and used to predict their relative stability and reactivity. The chemical reactivity indices are found to be related to the bond angle defined by the cis carbonyls and the ...

Benchmark fragment-based 1H, 13C, 15N and 17O chemical shift predictions in molecular crystals†

Science.gov (United States)

Hartman, Joshua D.; Kudla, Ryan A.; Day, Graeme M.; Mueller, Leonard J.; Beran, Gregory J. O.

2016-01-01

The performance of fragment-based ab initio 1H, 13C, 15N and 17O chemical shift predictions is assessed against experimental NMR chemical shift data in four benchmark sets of molecular crystals. Employing a variety of commonly used density functionals (PBE0, B3LYP, TPSSh, OPBE, PBE, TPSS), we explore the relative performance of cluster, two-body fragment, and combined cluster/fragment models. The hybrid density functionals (PBE0, B3LYP and TPSSh) generally out-perform their generalized gradient approximation (GGA)-based counterparts. 1H, 13C, 15N, and 17O isotropic chemical shifts can be predicted with root-mean-square errors of 0.3, 1.5, 4.2, and 9.8 ppm, respectively, using a computationally inexpensive electrostatically embedded two-body PBE0 fragment model. Oxygen chemical shieldings prove particularly sensitive to local many-body effects, and using a combined cluster/fragment model instead of the simple two-body fragment model decreases the root-mean-square errors to 7.6 ppm. These fragment-based model errors compare favorably with GIPAW PBE ones of 0.4, 2.2, 5.4, and 7.2 ppm for the same 1H, 13C, 15N, and 17O test sets. Using these benchmark calculations, a set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided and their robustness assessed using statistical cross-validation. We demonstrate the utility of these approaches and the reported scaling parameters on applications to 9-tertbutyl anthracene, several histidine co-crystals, benzoic acid and the C-nitrosoarene SnCl2(CH3)2(NODMA)2. PMID:27431490

Benchmark fragment-based (1)H, (13)C, (15)N and (17)O chemical shift predictions in molecular crystals.

Science.gov (United States)

Hartman, Joshua D; Kudla, Ryan A; Day, Graeme M; Mueller, Leonard J; Beran, Gregory J O

2016-08-21

The performance of fragment-based ab initio(1)H, (13)C, (15)N and (17)O chemical shift predictions is assessed against experimental NMR chemical shift data in four benchmark sets of molecular crystals. Employing a variety of commonly used density functionals (PBE0, B3LYP, TPSSh, OPBE, PBE, TPSS), we explore the relative performance of cluster, two-body fragment, and combined cluster/fragment models. The hybrid density functionals (PBE0, B3LYP and TPSSh) generally out-perform their generalized gradient approximation (GGA)-based counterparts. (1)H, (13)C, (15)N, and (17)O isotropic chemical shifts can be predicted with root-mean-square errors of 0.3, 1.5, 4.2, and 9.8 ppm, respectively, using a computationally inexpensive electrostatically embedded two-body PBE0 fragment model. Oxygen chemical shieldings prove particularly sensitive to local many-body effects, and using a combined cluster/fragment model instead of the simple two-body fragment model decreases the root-mean-square errors to 7.6 ppm. These fragment-based model errors compare favorably with GIPAW PBE ones of 0.4, 2.2, 5.4, and 7.2 ppm for the same (1)H, (13)C, (15)N, and (17)O test sets. Using these benchmark calculations, a set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided and their robustness assessed using statistical cross-validation. We demonstrate the utility of these approaches and the reported scaling parameters on applications to 9-tert-butyl anthracene, several histidine co-crystals, benzoic acid and the C-nitrosoarene SnCl2(CH3)2(NODMA)2.

Active control of methanol carbonylation selectivity over Au/carbon anode by electrochemical potential.

Science.gov (United States)

Funakawa, Akiyasu; Yamanaka, Ichiro; Otsuka, Kiyoshi

2005-05-12

Electrochemical oxidative carbonylation of methanol was studied over Au supported carbon anode in CO. The major carbonylation products were dimethyl oxalate (DMO) and dimethyl carbonate (DMC). The minor oxidation products were dimethoxy methane (DMM) and methyl formate (MF) from methanol and CO(2). Influences of various reaction conditions were studied on carbonylation activities and selectivities. The selectivities to DMO and DMC can be controlled by the electrochemical potential. Electrocatalysis of Au/carbon anode was studied by cyclic voltammetry (CV), stoichiometric reactions among Au(3+), methanol, and CO, and UV-vis spectra. The Au/carbon anode was characterized by XRD, SEM, and BE images before and after the carbonylation. These experimental facts strongly suggest that transition of oxidation states of Au affects changing of the carbonylation selectivities to DMO and DMC. Au(0) is the active species for the selective DMO formation by direct electrochemical carbonylation at low potentials (selective DMC formation by indirect electrochemical carbonylation through Au(3+)/Au(+) redox at high potentials (>+1.3 V).

Spatiotemporal distribution of carbonyl compounds in China.

Science.gov (United States)

Ho, K F; Ho, Steven Sai Hang; Huang, R-J; Dai, W T; Cao, J J; Tian, Linwei; Deng, W J

2015-02-01

A sampling campaign was carried out at nine Chinese cities in 2010/2011. Fifteen monocarbonyls (C# = 1-9) were quantified. Temperature is the rate-determining factor of the summertime carbonyl levels. The carbonyl emissions in winter are mainly driven by the primary anthropogenic sources like automobile. A molar ratio of propionaldehyde to nonaldehyde is a barometer of the impact of atmospheric vegetation emission which suggesting that strong vegetation emissions exist in summer and high propionaldehyde abundance is caused by fossil fuel combustion in winter. Potential health risk assessment of formaldehyde and acetaldehyde was conducted and the highest cumulative risks were observed at Chengdu in summer and Wuhan in winter. Because of the strong photochemical reaction and large amount of anthropogenic emissions, high concentrations of carbonyl compounds were observed in Chengdu. The use of ethanol-blended gasoline in Wuhan is the key reason of acetaldehyde emission and action should be taken to avoid potential health risks. Copyright © 2014 Elsevier Ltd. All rights reserved.

Comparison of carbonyl compounds emissions from diesel engine fueled with biodiesel and diesel

Science.gov (United States)

He, Chao; Ge, Yunshan; Tan, Jianwei; You, Kewei; Han, Xunkun; Wang, Junfang; You, Qiuwen; Shah, Asad Naeem

The characteristics of carbonyl compounds emissions were investigated on a direct injection, turbocharged diesel engine fueled with pure biodiesel derived from soybean oil. The gas-phase carbonyls were collected by 2,4-dinitrophenylhydrazine (DNPH)-coated silica cartridges from diluted exhaust and analyzed by HPLC with UV detector. A commercial standard mixture including 14 carbonyl compounds was used for quantitative analysis. The experimental results indicate that biodiesel-fueled engine almost has triple carbonyls emissions of diesel-fueled engine. The weighted carbonyls emission of 8-mode test cycle of biodiesel is 90.8 mg (kW h) -1 and that of diesel is 30.7 mg (kW h) -1. The formaldehyde is the most abundant compound of carbonyls for both biodiesel and diesel, taking part for 46.2% and 62.7% respectively. The next most significant compounds are acetaldehyde, acrolein and acetone for both fuels. The engine fueled with biodiesel emits a comparatively high content of propionaldehyde and methacrolein. Biodiesel, as an alternative fuel, has lower specific reactivity (SR) caused by carbonyls compared with diesel. When fueled with biodiesel, carbonyl compounds make more contribution to total hydrocarbon emission.

16th Carbonyl Metabolism Meeting: from enzymology to genomics

Directory of Open Access Journals (Sweden)

Maser Edmund

2012-12-01

Full Text Available Abstract The 16th International Meeting on the Enzymology and Molecular Biology of Carbonyl Metabolism, Castle of Ploen (Schleswig-Holstein, Germany, July 10–15, 2012, covered all aspects of NAD(P-dependent oxido-reductases that are involved in the general metabolism of xenobiotic and physiological carbonyl compounds. Starting 30 years ago with enzyme purification, structure elucidation and enzyme kinetics, the Carbonyl Society members have meanwhile established internationally recognized enzyme nomenclature systems and now consider aspects of enzyme genomics and enzyme evolution along with their roles in diseases. The 16th international meeting included lectures from international speakers from all over the world.

Advanced zirconia-coated carbonyl-iron particles for acidic magnetorheological finishing of chemical-vapor-deposited ZnS and other IR materials

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Salzman, S.; Giannechini, L. J.; Romanofsky, H. J.; Golini, N.; Taylor, B.; Jacobs, S. D.; Lambropoulos, J. C.

2015-10-01

We present a modified version of zirconia-coated carbonyl-iron (CI) particles that were invented at the University of Rochester in 2008. The amount of zirconia on the coating is increased to further protect the iron particles from corrosion when introduced to an acidic environment. Five low-pH, magnetorheological (MR) fluids were made with five acids: acetic, hydrochloric, nitric, phosphoric, and hydrofluoric. All fluids were based on the modified zirconia-coated CI particles. Off-line viscosity and pH stability were measured for all acidic MR fluids to determine the ideal fluid composition for acidic MR finishing of chemical-vapor-deposited (CVD) zinc sulfide (ZnS) and other infrared (IR) optical materials, such as hot-isostatic-pressed (HIP) ZnS, CVD zinc selenide (ZnSe), and magnesium fluoride (MgF2). Results show significant reduction in surface artifacts (millimeter-size, pebble-like structures on the finished surface) for several standard-grade CVD ZnS substrates and good surface roughness for the non-CVD MgF2 substrate when MR finished with our advanced acidic MR fluid.

Measurements of carbonyls in a 13-story building.

Science.gov (United States)

Báez, Armando P; Padilla, Hugo G; García, Rocío M; Belmont, Raúl D; Torres, Maria del Carmen B

2004-01-01

Formaldehyde and acetaldehyde are emitted by many mobile and stationary sources and secondary aldehydes are intermediates in the photo-oxidation of organic compounds in the atmosphere. These aldehydes are emitted indoors by many materials such as furniture, carpets, heating and cooling systems, an by smoking. Carbonyls, mainly formaldehyde and acetaldehyde, have been studied because of their adverse health effects. In addition, formaldehyde is a suspected carcinogen. Therefore, the concentrations of formaldehyde and acetaldehyde were determined to assess the inhalation exposure doses to carbonyls for people who work in a 13-story building and in order to evaluate the cancer hazard. Carbonyl compounds in indoor and outdoor air were measured at a 13-story building located in Mexico City. The mezzanine, fifth and tenth floors, and the third level-parking garage were selected for sampling. Samples were collected in two sampling periods, the first from April 20 to 29, 1998 and the second from December 1 to 20, 1998. Carbonyls were sampled by means of DNHP-coated cartridges at a flow rate of 1 l min(-1) from 9:00 to 19:00 hours, during 2-hour time intervals and analyzed by HPLC with hours, during 2-hour time intervals and analyzed by HPLC with UV/VIS detection. Mean carbonyl concentrations were highest in the 3rd level-parking garage, with the formaldehyde concentration being the highest ranging from 108 to 418 microg m(-3). In working areas, the highest carbonyl arithmetic mean concentrations (AM) were observed on the 5th floor. Acetone and formaldehyde concentrations were highest in April ranging from 161 to 348 microg m(-3) (AM = 226) and from 157 to 270 microg m(-3) (AM = 221), respectively. Propionaldehyde and butyraldehyde were present in smaller concentrations ranging from 2 to 25 and 1 to 28 microg m(-3), respectively, considering all the samples. Mean indoor/outdoor ratios of carbonyls ranged from 1.8 to 9.6. A reduction of inhalation exposure doses of 41% and

Orientation-dependent surface core-level shifts and chemical shifts on clean and H 2S-covered GaAs

Science.gov (United States)

Ranke, W.; Finster, J.; Kuhr, H. J.

1987-08-01

Photoelectron spectra of the As 3d and Ga 3d core levels were studied in situ on a cylindrically shaped GaAs single crystal for the six inequivalent orientations (001), (113), (111), (110), (11¯1) and (11¯3). On the clean surface, prepared by molecular beam epitaxy (MBE), surface core levels are shifted by 0.25 to 0.55 eV towards smaller binding energy (BE) for As 3d and -0.25 to -0.35 eV towards higher BE for Ga, depending on orientation. Additional As causes As 3d contributions shifted between -0.45 and -0.7 eV towards higher BE. The position and intensity of them is influenced by H 2S adsorption. At 150 K, H 2S adsorbs preferentially on As sites. As chemical shifts appear at -0.6 to -0.9 eV towards higher BE. Simultaneously, As accumulation occurs on all orientations with the exception of (110). High temperature adsorption (550 K, 720 K) influences mainly the Ga 3d peaks. Two peaks shifted by about -0.45 and -0.8 eV towards higher Be were found which are attributed to Ga atoms with one or two sulfur ligands, respectively. At 720 K, also As depletion is observed. The compatibility of surface core-level positions and intensities with recent structural models for the (111) and (11¯1) surfaces is discussed.

Criteria to average out the chemical shift anisotropy in solid-state NMR when irradiated with BABA I, BABA II, and C7 radiofrequency pulse sequences.

Science.gov (United States)

Stephane Mananga, Eugene

2013-01-01

Floquet-Magnus expansion is used to study the effect of chemical shift anisotropy in solid-state NMR of rotating solids. The chemical shift interaction is irradiated with two types of radiofrequency pulse sequences: BABA and C7. The criteria for the chemical shift anisotropy to be averaged out in each rotor period are obtained. Copyright © 2013 Elsevier Inc. All rights reserved.

TEN DAY EXPOSURES TO CARBONYL SULFIDE PRODUCE BRAINSTEM LESIONS AND CHANGES IN BRAINSTEM AUDITORY EVOKED RESPONSES IN FISCHER 344N RATS.

Science.gov (United States)

Carbonyl sulfide (COS) is a chemical intermediate in the production of pesticides and herbicides, a metabolite of carbon disulfide, a byproduct of the combustion of organic material, and a naturally occurring compound. COS was included in a Toxic Substances Control Act request fo...

Bifunctional dendrons for multiple carbohydrate presentation via carbonyl chemistry

Directory of Open Access Journals (Sweden)

Davide Bini

2014-07-01

Full Text Available The synthesis of new dendrons of the generations 0, 1 and 2 with a double bond at the focal point and a carbonyl group at the termini has been carried out. The carbonyl group has been exploited for the multivalent conjugation to a sample saccharide by reductive amination and alkoxyamine conjugation.

Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

DEFF Research Database (Denmark)

Christensen, Anders Steen; Linnet, Troels Emtekær; Borg, Mikael

2013-01-01

We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level...

Differentiation of osteoporotic and neoplastic vertebral fractures by chemical shift {in-phase and out-of phase} MR imaging

International Nuclear Information System (INIS)

Ragab, Yasser; Emad, Yasser; Gheita, Tamer; Mansour, Maged; Abou-Zeid, A.; Ferrari, Serge; Rasker, Johannes J.

2009-01-01

Objective: The objective of this study was to establish the cut-off value of the signal intensity drop on chemical shift magnetic resonance imaging (MRI) with appropriate sensitivity and specificity to differentiate osteoporotic from neoplastic wedging of the spine. Patients and methods: All patients with wedging of vertebral bodies were included consecutively between February 2006 and January 2007. A chemical shift MRI was performed and signal intensity after (in-phase and out-phase) images were obtained. A DXA was performed in all. Results: A total of 40 patients were included, 20 with osteoporotic wedging (group 1) and 20 neoplastic (group 2). They were 21 males and 19 females. Acute vertebral collapse was observed in 15 patients in group 1 and subacute collapse in another 5 patients, while in group 2, 11 patients showed acute collapse and 9 patients (45%) showed subacute vertebral collapse. On the chemical shift MRI a substantial reduction in signal intensity was found in all lesions in both groups. The proportional changes observed in signal intensity of bone marrow lesions on in-phase compared with out-of-phase images showed significant differences in both groups (P < 0.05). At a cut-off value of 35%, the observed sensitivity of out-of-phase images was 95%, specificity was 100%, positive predictive value was 100% and negative predictive value was 95.2%. Conclusion: A chemical shift MRI is useful in order to differentiate patients with vertebral collapse due to underlying osteoporosis or neoplastic process.

Measuring 13Cβ chemical shifts of invisible excited states in proteins by relaxation dispersion NMR spectroscopy

International Nuclear Information System (INIS)

Lundstroem, Patrik; Lin Hong; Kay, Lewis E.

2009-01-01

A labeling scheme is introduced that facilitates the measurement of accurate 13 C β chemical shifts of invisible, excited states of proteins by relaxation dispersion NMR spectroscopy. The approach makes use of protein over-expression in a strain of E. coli in which the TCA cycle enzyme succinate dehydrogenase is knocked out, leading to the production of samples with high levels of 13 C enrichment (30-40%) at C β side-chain carbon positions for 15 of the amino acids with little 13 C label at positions one bond removed (∼5%). A pair of samples are produced using [1- 13 C]-glucose/NaH 12 CO 3 or [2- 13 C]-glucose as carbon sources with isolated and enriched (>30%) 13 C β positions for 11 and 4 residues, respectively. The efficacy of the labeling procedure is established by NMR spectroscopy. The utility of such samples for measurement of 13 C β chemical shifts of invisible, excited states in exchange with visible, ground conformations is confirmed by relaxation dispersion studies of a protein-ligand binding exchange reaction in which the extracted chemical shift differences from dispersion profiles compare favorably with those obtained directly from measurements on ligand free and fully bound protein samples

Empirical isotropic chemical shift surfaces

International Nuclear Information System (INIS)

Czinki, Eszter; Csaszar, Attila G.

2007-01-01

A list of proteins is given for which spatial structures, with a resolution better than 2.5 A, are known from entries in the Protein Data Bank (PDB) and isotropic chemical shift (ICS) values are known from the RefDB database related to the Biological Magnetic Resonance Bank (BMRB) database. The structures chosen provide, with unknown uncertainties, dihedral angles φ and ψ characterizing the backbone structure of the residues. The joint use of experimental ICSs of the same residues within the proteins, again with mostly unknown uncertainties, and ab initio ICS(φ,ψ) surfaces obtained for the model peptides For-(l-Ala) n -NH 2 , with n = 1, 3, and 5, resulted in so-called empirical ICS(φ,ψ) surfaces for all major nuclei of the 20 naturally occurring α-amino acids. Out of the many empirical surfaces determined, it is the 13C α ICS(φ,ψ) surface which seems to be most promising for identifying major secondary structure types, α-helix, β-strand, left-handed helix (α D ), and polyproline-II. Detailed tests suggest that Ala is a good model for many naturally occurring α-amino acids. Two-dimensional empirical 13C α - 1 H α ICS(φ,ψ) correlation plots, obtained so far only from computations on small peptide models, suggest the utility of the experimental information contained therein and thus they should provide useful constraints for structure determinations of proteins

Propheromones that release pheromonal carbonyl compounds in light.

Science.gov (United States)

Liu, X; Macaulay, E D; Pickett, J A

1984-05-01

Pheromonal carbonyl compounds; (Z)-11-hexadecanal, (E)-citral, and 2-heptanone were treated with six alcohols to give acetals or ketals, some of which acted as propheromones by releasing the pheromonal carbonyl compounds in ultraviolet or simulated sunlight. Highest yields of pheromone were obtained from adducts prepared witho-nitrobenzyl alcohol ando-nitrophenylethane-1,2-diol. Adducts from (Z)-11-hexadecenal and these two alcohols were employed in lures to catch diamondback moths,Plutella xylostella (L.).

Lanthanide shift reagents, binding, shift mechanisms and exchange

International Nuclear Information System (INIS)

Boer, J.W.M. de

1977-01-01

Paramagnetic lanthanide shift reagents, when added to a solution of a substrate, induce shifts in the nuclear magnetic resonance (NMR) spectrum of the substrate molecules. The induced shifts contain information about the structure of the shift reagent substrate complex. The structural information, however, may be difficult to extract because of the following effects: (1) different complexes between shift reagent and substrate may be present in solution, e.g. 1:1 and 1:2 complexes, and the shift observed is a weighed average of the shifts of the substrate nuclei in the different complexes; (2) the Fermi contact interaction, arising from the spin density at the nucleus, contributes to the induced shift; (3) chemical exchange effects may complicate the NMR spectrum. In this thesis, the results of an investigation into the influence of these effects on the NMR spectra of solutions containing a substrate and LSR are presented. The equations describing the pseudo contact and the Fermi contact shift are derived. In addition, it is shown how the modified Bloch equations describing the effect of the chemical exchange processes occurring in the systems studied can be reduced to the familiar equations for a two-site exchange case. The binding of mono- and bifunctional ethers to the shift reagent are reported. An analysis of the induced shifts is given. Finally, the results of the experiments performed to study the exchange behavior of dimethoxyethane and heptafluorodimethyloctanedionato ligands are presented

Pressure dependence of side chain 13C chemical shifts in model peptides Ac-Gly-Gly-Xxx-Ala-NH2.

Science.gov (United States)

Beck Erlach, Markus; Koehler, Joerg; Crusca, Edson; Munte, Claudia E; Kainosho, Masatsune; Kremer, Werner; Kalbitzer, Hans Robert

2017-10-01

For evaluating the pressure responses of folded as well as intrinsically unfolded proteins detectable by NMR spectroscopy the availability of data from well-defined model systems is indispensable. In this work we report the pressure dependence of 13 C chemical shifts of the side chain atoms in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH 2 (Xxx, one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of a number of nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The size of the polynomial pressure coefficients B 1 and B 2 is dependent on the type of atom and amino acid studied. For H N , N and C α the first order pressure coefficient B 1 is also correlated to the chemical shift at atmospheric pressure. The first and second order pressure coefficients of a given type of carbon atom show significant linear correlations suggesting that the NMR observable pressure effects in the different amino acids have at least partly the same physical cause. In line with this observation the magnitude of the second order coefficients of nuclei being direct neighbors in the chemical structure also are weakly correlated. The downfield shifts of the methyl resonances suggest that gauche conformers of the side chains are not preferred with pressure. The valine and leucine methyl groups in the model peptides were assigned using stereospecifically 13 C enriched amino acids with the pro-R carbons downfield shifted relative to the pro-S carbons.

Reassigning the Structures of Natural Products Using NMR Chemical Shifts Computed with Quantum Mechanics: A Laboratory Exercise

Science.gov (United States)

Palazzo, Teresa A.; Truong, Tiana T.; Wong, Shirley M. T.; Mack, Emma T.; Lodewyk, Michael W.; Harrison, Jason G.; Gamage, R. Alan; Siegel, Justin B.; Kurth, Mark J.; Tantillo, Dean J.

2015-01-01

An applied computational chemistry laboratory exercise is described in which students use modern quantum chemical calculations of chemical shifts to assign the structure of a recently isolated natural product. A pre/post assessment was used to measure student learning gains and verify that students demonstrated proficiency of key learning…

Identifying Stereoisomers by ab-initio Calculation of Secondary Isotope Shifts on NMR Chemical Shieldings

Directory of Open Access Journals (Sweden)

Karl-Heinz Böhm

2014-04-01

Full Text Available We present ab-initio calculations of secondary isotope effects on NMR chemical shieldings. The change of the NMR chemical shift of a certain nucleus that is observed if another nucleus is replaced by a different isotope can be calculated by computing vibrational corrections on the NMR parameters using electronic structure methods. We demonstrate that the accuracy of the computational results is sufficient to even distinguish different conformers. For this purpose, benchmark calculations for fluoro(2-2Hethane in gauche and antiperiplanar conformation are carried out at the HF, MP2 and CCSD(T level of theory using basis sets ranging from double- to quadruple-zeta quality. The methodology is applied to the secondary isotope shifts for 2-fluoronorbornane in order to resolve an ambiguity in the literature on the assignment of endo- and exo-2-fluoronorbornanes with deuterium substituents in endo-3 and exo-3 positions, also yielding insight into mechanistic details of the corresponding synthesis.

Identifying stereoisomers by ab-initio calculation of secondary isotope shifts on NMR chemical shieldings.

Science.gov (United States)

Böhm, Karl-Heinz; Banert, Klaus; Auer, Alexander A

2014-04-23

We present ab-initio calculations of secondary isotope effects on NMR chemical shieldings. The change of the NMR chemical shift of a certain nucleus that is observed if another nucleus is replaced by a different isotope can be calculated by computing vibrational corrections on the NMR parameters using electronic structure methods. We demonstrate that the accuracy of the computational results is sufficient to even distinguish different conformers. For this purpose, benchmark calculations for fluoro(2-2H)ethane in gauche and antiperiplanar conformation are carried out at the HF, MP2 and CCSD(T) level of theory using basis sets ranging from double- to quadruple-zeta quality. The methodology is applied to the secondary isotope shifts for 2-fluoronorbornane in order to resolve an ambiguity in the literature on the assignment of endo- and exo-2-fluoronorbornanes with deuterium substituents in endo-3 and exo-3 positions, also yielding insight into mechanistic details of the corresponding synthesis.

Catalytic reactions of synthesis gas. Part 2. Methanol carbonylation and homologation

Energy Technology Data Exchange (ETDEWEB)

Niemelae, M.

1993-01-01

The aim of the review is to evaluate the applicability of methanol hydrocarbonylation as a second test reaction to study the nondissociative activation of CO by heterogeneous rhodium and cobalt catalysts. The main emphasis in methanol (hydro)carbonylation chemistry has been on homogeneous reactions. These systems have been seen advantageous in selectivity, activity and ease of modification. The heterogenization attempts have been carried out to obtain easier separation of the catalyst and the product. The activity of cobalt, rhodium and other metals supported on different materials have been studied in heterogeneous methanol (hydro)carbonylation. The observed activities have been considerably influenced by the support. The most effective catalyst support has been activated carbon. Good carbonylation activities and selectivities have also been observed in conjunction with zeolite supports. The literature study indicates that the typical experimental conditions of methanol (hydro)carbonylation do not exceed the constructional and operational limits of the available reactor system, i.e. 500 C and 50 bar. The reaction is suitable for testing Co and Rh precursors, since both cobalt and rhodium compounds have shown carbonylation activity.

Toward Green Acylation of (Heteroarenes: Palladium-Catalyzed Carbonylation of Olefins to Ketones

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Jie Liu

2017-11-01

Full Text Available Green Friedel–Crafts acylation reactions belong to the most desired transformations in organic chemistry. The resulting ketones constitute important intermediates, building blocks, and functional molecules in organic synthesis as well as for the chemical industry. Over the past 60 years, advances in this topic have focused on how to make this reaction more economically and environmentally friendly by using green acylating conditions, such as stoichiometric acylations and catalytic homogeneous and heterogeneous acylations. However, currently well-established methodologies for their synthesis either produce significant amounts of waste or proceed under harsh conditions, limiting applications. Here, we present a new protocol for the straightforward and selective introduction of acyl groups into (hetero­arenes without directing groups by using available olefins with inexpensive CO. In the presence of commercial palladium catalysts, inter- and intramolecular carbonylative C–H functionalizations take place with good regio- and chemoselectivity. Compared to classical Friedel–Crafts chemistry, this novel methodology proceeds under mild reaction conditions. The general applicability of this methodology is demonstrated by the direct carbonylation of industrial feedstocks (ethylene and diisobutene as well as of natural products (eugenol and safrole. Furthermore, synthetic applications to drug molecules are showcased.

Calculation of the NMR chemical shift for a 4d1 system in a strong crystal field environment of trigonal symmetry with a threefold axis of quantization

International Nuclear Information System (INIS)

Ahn, Sang Woon; Oh, Se Woung; Ro, Seung Woo

1986-01-01

The NMR chemical shift arising from 4d electron angular momentum and 4d electron angular momentum and 4d electron spin dipolar-nuclear spin angular momentum interactions for a 4d 1 system in a strong crystal field environment of trigonal symmetry, where the threefold axis is chosen to be the axis of quantization axis, has been examined. A general expression using the nonmultipole expansion method (exact method) is derived for the NMR chemical shift. From this expression all the multipolar terms are determined. we observe that along the (100), (010), (110), and (111) axes the NMR chemical shifts are positive while along the (001) axis, it is negative. We observe that the dipolar term (1/R 3 ) is the dominant contribution to the NMR chemical shift except for along the (111) axis. A comparison of the multipolar terms with the exact values shows also that the multipolar results are exactly in agreement with the exact values around R≥0.2 nm. The temperature dependence analysis on the NMR chemical shifts may imply that along the (111) axis the contribution to the NMR chemical shift is dominantly pseudo contact interaction. Separation of the contributions of the Fermi and the pseudo contact interactions would correctly imply that the dipolar interaction is the dominant contribution to the NMR chemical shifts along the (100), (010), (001), and (110) axes, but along the (111) axis the Fermi contact interaction is incorrectly the dominant contribution to the NMR chemical shift. (Author)

Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks

Energy Technology Data Exchange (ETDEWEB)

Shen Yang; Bax, Ad, E-mail: bax@nih.gov [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

2013-07-15

A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, {>=}90 % fraction of the residues, with an error rate smaller than ca 3.5 %, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed ({phi}, {psi}) torsion angles of ca 12 Masculine-Ordinal-Indicator . TALOS-N also reports sidechain {chi}{sup 1} rotameric states for about 50 % of the residues, and a consistency with reference structures of 89 %. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts.

Accuracy of chemical shift MR imaging in diagnosing indeterminate bone marrow lesions in the pelvis: review of a single institution's experience

International Nuclear Information System (INIS)

Kohl, Chad A.; Chivers, F.S.; Lorans, Roxanne; Roberts, Catherine C.; Kransdorf, Mark J.

2014-01-01

To re-assess the accuracy of chemical shift imaging in diagnosing indeterminate bone marrow lesions as benign or malignant. We retrospectively reviewed our experience with MR imaging of the pelvis to assess the accuracy of chemical shift imaging in distinguishing benign from malignant bone lesions. Two musculoskeletal radiologists retrospectively reviewed all osseous lesions biopsied since 2006, when chemical shift imaging was added to our routine pelvic imaging protocol. Study inclusion criteria required (1) MR imaging of an indeterminate bone marrow lesion about the pelvis and (2) subsequent histologic confirmation. The study group included 50 patients (29 male, 21 female) with an average age of 67 years (range, 41-89 years). MR imaging results were evaluated using biopsy results as the ''gold standard.'' There were 27 malignant and 23 benign lesions. Chemical shift imaging using an opposed-phase signal loss criteria of less than 20 % to indicate a malignant lesion, correctly diagnosed 27/27 malignant lesions and 14/23 benign lesions, yielding a 100 % sensitivity, 61 % specificity, 75 % PPV, 100 % NPV, and 82 % accuracy. The area under the receiver operator characteristic (ROC) curve was 0.88. The inter-rater and intra-rater agreement K values were both 1.0. Chemical shift imaging is a useful adjunct MR technique to characterize focal and diffuse marrow abnormalities on routine non-contrast pelvic imaging. It is highly sensitive in identifying malignant disease. Despite its lower specificity, the need for biopsy could be eliminated in more than 60 % of patients with benign disease. (orig.)

Deuterium enrichment by selective photo-induced dissociation of an organic carbonyl compound

International Nuclear Information System (INIS)

Marling, J.B.

1981-01-01

A deuterium-enriched material is produced by selective photoinduced dissociation of a gas phase organic carbonyl compound containing at least one hydrogen atom bonded to an atom adjacent to a carbonyl group. Alkyl carbonyl compounds such as acetone, acetaldehyde, trifluoroacetic acid, cyclobutanone, cyclopentanone, methyl acetate, 3,3-dimethyl-2-butanone, 2,4-pentanedione, and 4-methyl-2-pentanone are preferred. The carbonyl compound is subjected to intense infrared radiation from one laser, or two lasers operating at different frequencies, to selectively dissociate the deuterated molecules into stable products. The undissociated compound may be redeuterated by direct aqueous liquid phase H/D exchange, or by indirect liquid phase exchange using an alkanol in an intermediate step

Comparison of experimental and DFT-calculated NMR chemical shifts of 2-amino and 2-hydroxyl substituted phenyl benzimidazoles, benzoxazoles and benzothiazoles in four solvents using the IEF-PCM solvation model.

Science.gov (United States)

Pierens, Gregory K; Venkatachalam, T K; Reutens, David C

2016-04-01

A comparative study of experimental and calculated NMR chemical shifts of six compounds comprising 2-amino and 2-hydroxy phenyl benzoxazoles/benzothiazoles/benzimidazoles in four solvents is reported. The benzimidazoles showed interesting spectral characteristics, which are discussed. The proton and carbon chemical shifts were similar for all solvents. The largest chemical shift deviations were observed in benzene. The chemical shifts were calculated with density functional theory using a suite of four functionals and basis set combinations. The calculated chemical shifts revealed a good match to the experimentally observed values in most of the solvents. The mean absolute error was used as the primary metric. The use of an additional metric is suggested, which is based on the order of chemical shifts. The DP4 probability measures were also used to compare the experimental and calculated chemical shifts for each compound in the four solvents. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Predicting personal exposure to airborne carbonyls using residential measurements and time/activity data

Science.gov (United States)

Liu, Weili; Zhang, Junfeng (Jim); Korn, Leo R.; Zhang, Lin; Weisel, Clifford P.; Turpin, Barbara; Morandi, Maria; Stock, Tom; Colome, Steve

As a part of the Relationships of Indoor, Outdoor, and Personal Air (RIOPA) study, 48 h integrated residential indoor, outdoor, and personal exposure concentrations of 10 carbonyls were simultaneously measured in 234 homes selected from three US cities using the Passive Aldehydes and Ketones Samplers (PAKS). In this paper, we examine the feasibility of using residential indoor concentrations to predict personal exposures to carbonyls. Based on paired t-tests, the means of indoor concentrations were not different from those of personal exposure concentrations for eight out of the 10 measured carbonyls, indicating indoor carbonyls concentrations, in general, well predicted the central tendency of personal exposure concentrations. In a linear regression model, indoor concentrations explained 47%, 55%, and 65% of personal exposure variance for formaldehyde, acetaldehyde, and hexaldehyde, respectively. The predictability of indoor concentrations on cross-individual variability in personal exposure for the other carbonyls was poorer, explainingexposure concentrations. It was found that activities related to driving a vehicle and performing yard work had significant impacts on personal exposures to a few carbonyls.

Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements

Energy Technology Data Exchange (ETDEWEB)

Eghbalnia, Hamid R.; Wang Liya; Bahrami, Arash [National Magnetic Resonance Facility at Madison, Biochemistry Department (United States); Assadi, Amir [University of Wisconsin-Madison, Mathematics Department (United States); Markley, John L. [National Magnetic Resonance Facility at Madison, Biochemistry Department (United States)], E-mail: eghbalni@nmrfam.wisc.edu

2005-05-15

We present an energy model that combines information from the amino acid sequence of a protein and available NMR chemical shifts for the purposes of identifying low energy conformations and determining elements of secondary structure. The model ('PECAN', Protein Energetic Conformational Analysis from NMR chemical shifts) optimizes a combination of sequence information and residue-specific statistical energy function to yield energetic descriptions most favorable to predicting secondary structure. Compared to prior methods for secondary structure determination, PECAN provides increased accuracy and range, particularly in regions of extended structure. Moreover, PECAN uses the energetics to identify residues located at the boundaries between regions of predicted secondary structure that may not fit the stringent secondary structure class definitions. The energy model offers insights into the local energetic patterns that underlie conformational preferences. For example, it shows that the information content for defining secondary structure is localized about a residue and reaches a maximum when two residues on either side are considered. The current release of the PECAN software determines the well-defined regions of secondary structure in novel proteins with assigned chemical shifts with an overall accuracy of 90%, which is close to the practical limit of achievable accuracy in classifying the states.

Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements

International Nuclear Information System (INIS)

Eghbalnia, Hamid R.; Wang Liya; Bahrami, Arash; Assadi, Amir; Markley, John L.

2005-01-01

We present an energy model that combines information from the amino acid sequence of a protein and available NMR chemical shifts for the purposes of identifying low energy conformations and determining elements of secondary structure. The model ('PECAN', Protein Energetic Conformational Analysis from NMR chemical shifts) optimizes a combination of sequence information and residue-specific statistical energy function to yield energetic descriptions most favorable to predicting secondary structure. Compared to prior methods for secondary structure determination, PECAN provides increased accuracy and range, particularly in regions of extended structure. Moreover, PECAN uses the energetics to identify residues located at the boundaries between regions of predicted secondary structure that may not fit the stringent secondary structure class definitions. The energy model offers insights into the local energetic patterns that underlie conformational preferences. For example, it shows that the information content for defining secondary structure is localized about a residue and reaches a maximum when two residues on either side are considered. The current release of the PECAN software determines the well-defined regions of secondary structure in novel proteins with assigned chemical shifts with an overall accuracy of 90%, which is close to the practical limit of achievable accuracy in classifying the states

Fluoride-Mediated Dephosphonylation of α-Diazo-β-carbonyl Phosphonates.

Science.gov (United States)

Phatake, Ravindra S; Mullapudi, Venkannababu; Wakchaure, Vivek C; Ramana, Chepuri V

2017-01-20

The possibility of fluoride-mediated selective dephosphonylation of α-diazo-β-carbonyl phosphonates such as the Ohira-Bestmann reagent has been proposed and executed. The resulting α-diazocarbonyl intermediates undergo a (3 + 2)-cycloaddition at room temperature with conjugated olefins and benzynes. Interestingly, under the current conditions, the resulting cycloaddition products underwent either N-acylation (with excess α-diazo-β-carbonyl phosphonates) or Michael addition (with conjugated olefins).

Millimeter wave spectra of carbonyl cyanide

Science.gov (United States)

Bteich, S. B.; Tercero, B.; Cernicharo, J.; Motiyenko, R. A.; Margulès, L.; Guillemin, J.-C.

2016-07-01

Context. More than 30 cyanide derivatives of simple organic molecules have been detected in the interstellar medium, but only one dicarbonitrile has been found and that very recently. There is still a lack of high-resolution spectroscopic data particularly for dinitriles derivatives. The carbonyl cyanide molecule is a new and interesting candidate for astrophysical detection. It could be formed by the reaction of CO and CN radicals, or by substitution of the hydrogen atom by a cyano group in cyanoformaldehyde, HC(=O)CN, that has already been detected in the interstellar medium. Aims: The available data on the rotational spectrum of carbonyl cyanide is limited in terms of quantum number values and frequency range, and does not allow accurate extrapolation of the spectrum into the millimeter-wave range. To provide a firm basis for astrophysical detection of carbonyl cyanide we studied its millimeter-wave spectrum. Methods: The rotational spectrum of carbonyl cyanide was measured in the frequency range 152-308 GHz and analyzed using Watson's A- and S-reduction Hamiltonians. Results: The ground and first excited state of v5 vibrational mode were assigned and analyzed. More than 1100 distinct frequency lines of the ground state were fitted to produce an accurate set of rotational and centrifugal distortion constants up to the eighth order. The frequency predictions based on these constants should be accurate enough for astrophysical searches in the frequency range up to 500 GHz and for transition involving energy levels with J ≤ 100 and Ka ≤ 42. Based on the results we searched for interstellar carbonyl cyanide in available observational data without success. Thus, we derived upper limits to its column density in different sources. This paper makes use of the following ALMA data: ADS/JAO.ALMA#2011.0.00009.SV. ALMA is a partnership of ESO (representing its member states), NSF (USA), and NINS (Japan) with NRC (Canada), NSC, and ASIAA (Taiwan), and KASI (Republic of

Interactions of triglycerides with phospholipids: Incorporation into the bilayer structure and formation of emulsions

International Nuclear Information System (INIS)

Hamilton, J.A.

1989-01-01

Interactions of carbonyl 13 C-enriched triacylglycerols (TG) with phospholipid bilayers were studied by 13 C NMR spectroscopy. In spectra of DPPC vesicles with TG at 40-50 degree C, both triolein (TO) and tripalmitin (TP) had narrow carbonyl resonances, indicative of rapid motions, and chemical shifts indicative of H bonding of the TG carbonyls with solvent (H 2 O) at the aqueous interfaces of the vesicle bilayer. Below the phase transition temperature of the DPPC/TG vesicles, most phospholipid peaks broadened markedly. In DPPC vesicles with TP, the TP carbonyl peaks broadened beyond detection below the transition, whereas in vesicles with TO, the TO carbonyl peaks showed little change in line width or chemical shift and no change in the integrated intensity. These properties (extent of solubility in the PC surface, conformation, solvent accessibility, and molecular mobility) may be important for enzymatic hydrolysis and protein-mediated transfer of TG. In gel-phase DPPC, the molecular mobility of the TG depends on the nature of the TG acyl chains. In the DPPC/TG mixtures studied, attempts to incorporate TG in excess of the bilayer solubility resulted in production of emulsion particles. The significance of these results for TG metabolism is discussed

pH-Dependent spin state population and 19F NMR chemical shift via remote ligand protonation in an iron(ii) complex.

Science.gov (United States)

Gaudette, Alexandra I; Thorarinsdottir, Agnes E; Harris, T David

2017-11-30

An Fe II complex that features a pH-dependent spin state population, by virtue of a variable ligand protonation state, is described. This behavior leads to a highly pH-dependent 19 F NMR chemical shift with a sensitivity of 13.9(5) ppm per pH unit at 37 °C, thereby demonstrating the potential utility of the complex as a 19 F chemical shift-based pH sensor.

Determination of carbonyl compounds (acetaldehyde and formaldehyde in polyethylene terephthalate containers designated for water conservation

Directory of Open Access Journals (Sweden)

Redžepović Azra S.

2012-01-01

Full Text Available Polyethylene terephthalate (PET has in the last several years become the main packaging material for many food products, particularly carbonated beverages and bottled water, as well as for products of chemical industry (packaging of various hygiene maintenance agents, pesticides, solvents, etc.. The strength and permeability properties of PET are very good for packaging of beverages, its resistance to chemicals is high and it has a high degree of transparency. Acetaldehyde and formaldehyde are formed during the thermoforming of PET containers. After cooling, acetaldehyde and formaldehyde remain trapped in the walls of a PET bottle and may migrate into the water after filling and storage. Since there are no migration tests in Serbia prescribed for the determination of acetaldehyde and formaldehyde, the purpose of the paper is to test the quantitative contents of carbonyl compounds (acetaldehyde and formaldehyde in PET containers of different volumes, made by various manufacturers of bottled mineral carbonated and noncarbonated water, and exposed to different temperatures. In this study, the migration of acetaldehyde and formaldehyde from PET bottles into mineral carbonated and noncarbonated water was determined by high performance liquid chromatography. Taking into consideration that formaldehyde and acetaldehyde have no UV active or fluorescent group, the chromatography shall be preceded by derivatization in a closed system (due to a low boiling point of acetaldehyde and formaldehyde, which shall transform carbonyl compounds into UV active compounds.

Role of protein-bound carbonyl groups in the formation of advanced glycation endproducts.

Science.gov (United States)

Liggins, J; Furth, A J

1997-08-22

Several mechanisms have been postulated for the formation of advanced glycation endproducts (AGEs) from glycated proteins; they all feature protein-bound carbonyl intermediates. Using 2,4-dinitrophenylhydrazine (DNPH), we have detected these intermediates on bovine serum albumin, lysozyme and beta-lactoglobulin after in vitro glycation by glucose or fructose. Carbonyls were formed in parallel with AGE-fluorophores, via oxidative Maillard reactions. Neither Amadori nor Heyns products contributed to the DNPH reaction. Fluorophore and carbonyl yields were much enhanced in lipid-associated proteins, but both groups could also be detected in lipid-free proteins. When pre-glycated proteins were incubated in the absence of free sugar, carbonyl groups were rapidly lost in a first-order reaction, while fluorescence continued to develop beyond the 21 days of incubation. Another unexpected finding was that not all carbonyl groups were blocked by aminoguanidine, although there was complete inhibition of reactions leading to AGE-fluorescence. It is suggested that carbonyls acting as fluorophore precursors react readily with aminoguanidine, while others are resistant to this hydrazine, possibly because they are involved in ring closure. Factors influencing the relative rates of acyclisation and hydrazone formation are discussed, together with possible implications for antiglycation therapy.

A biotin enrichment strategy identifies novel carbonylated amino acids in proteins from human plasma

DEFF Research Database (Denmark)

Havelund, Jesper F; Wojdyla, Katarzyna; Davies, Michael J

2017-01-01

Protein carbonylation is an irreversible protein oxidation correlated with oxidative stress, various diseases and ageing. Here we describe a peptide-centric approach for identification and characterisation of up to 14 different types of carbonylated amino acids in proteins. The modified residues...... in vitro metal ion-catalysed oxidation. Furthermore, we assigned 133 carbonylated sites in 36 proteins in native human plasma protein samples. The optimised workflow enabled detection of 10 hitherto undetected types of carbonylated amino acids in proteins: aldehyde and ketone modifications of leucine...

Formation of neutral and charged gold carbonyls on highly facetted gold nanostructures

Science.gov (United States)

Chau, Thoi-Dai; Visart de Bocarmé, Thierry; Kruse, Norbert; Wang, Richard L. C.; Kreuzer, Hans Jürgen

2003-12-01

We show that gold mono- and di-carbonyls are formed on gold field emitter tips during interaction with carbon monoxide gas at room temperature and in the presence of high electrostatic fields. The experiments are done in a time-of-flight atom probe to obtain mass spectra. The yield of monocarbonyl cations is about twice that of di-carbonyl ions. Density functional theory calculations are reported that explain the field stabilization of adsorbed carbonyls and the desorption yield of their cations.

NMR chemical shift and J coupling parameterization and quantum mechanical reference spectrum simulation for selected nerve agent degradation products in aqueous conditions.

Science.gov (United States)

Koskela, Harri; Anđelković, Boban

2017-10-01

The spectral parameters of selected nerve agent degradation products relevant to the Chemical Weapons Convention, namely, ethyl methylphosphonate, isopropyl methylphosphonate, pinacolyl methylphosphonate and methylphosphonic acid, were studied in wide range of pH conditions and selected temperatures. The pH and temperature dependence of chemical shifts and J couplings was parameterized using Henderson-Hasselbalch-based functions. The obtained parameters allowed calculation of precise chemical shifts and J coupling constants in arbitrary pH conditions and typical measurement temperatures, thus facilitating quantum mechanical simulation of reference spectra in the chosen magnetic field strength for chemical verification. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

A green synthesis of α,β-unsaturated carbonyl compounds from glyceraldehyde acetonide

Directory of Open Access Journals (Sweden)

Cláudia O. Veloso

2011-01-01

Full Text Available The catalytic behavior of Cs-exchanged and Cs-impregnated zeolites (X and Y was studied using the Knoevenagel condensation between glyceraldehyde acetonide and ethyl acetoacetate in order to produce the corresponding α,β-unsaturated carbonyl compound that is an important intermediate for fine chemicals. The influence of reaction temperature, type of zeolite, and basicity of the sites on the catalytic behavior of the samples was evaluated. All zeolites were active for the studied reaction. The formation of the main condensation product was favored at lower reaction temperatures. Products of further condensations were also observed especially for samples that were only dried before catalytic test.

Emissions of Toxic Carbonyls in an Electronic Cigarette

Directory of Open Access Journals (Sweden)

Guthery William

2016-01-01

Full Text Available Electronic cigarettes (e-cigs provide a smoke-free alternative for inhalation of nicotine without the vast array of toxic and carcinogenic combustion products produced by tobacco smoke. Elevated levels of toxic carbonyls may be generated during vaporisation; however, it is unclear whether that is indicative of a fault with the device or is due to the applied conditions of the test. A device, designed and built at this facility, was tested to determine the levels of selected toxic carbonyls. The reservoir was filled with approximately 960 mg of an e-liquid formulation containing 1.8% (w/v nicotine. Devices were puffed 200 times in blocks of 40 using a standardised regime consisting of a 55 mL puff volume; 3 s puff duration; 30 s puff interval; square wave puff profile. Confirmatory testing for nicotine and total aerosol delivery resulted in mean (n = 8 values of 10 mg (RSD 12.3% and 716 mg (RSD 11.2%, respectively. Emissions of toxic carbonyls were highly variable yet were between < 0.1% and 22.9% of expected levels from a Kentucky Reference Cigarette (K3R4F puffed 200 times under Health Canada Intense smoking conditions. It has been shown that a device built to a high specification with relatively consistent nicotine and aerosol delivery emits inconsistent levels of carbonyls. The exposure is greatly reduced when compared with lit tobacco products. However, it was observed that as the reservoirs neared depletion then emission levels were significantly higher

Penicitroamide, an Antimicrobial Metabolite with High Carbonylization from the Endophytic Fungus Penicillium sp. (NO. 24).

Science.gov (United States)

Feng, Zi-Wei; Lv, Meng-Meng; Li, Xue-Shuang; Zhang, Liang; Liu, Cheng-Xiong; Guo, Zhi-Yong; Deng, Zhang-Shuang; Zou, Kun; Proksch, Peter

2016-10-28

Penicitroamide ( 1 ), a new metabolite with a new framework, was isolated from the ethyl acetate extract of the PDB (Potato Dextrose Broth) medium of Penicillium sp. (NO. 24). The endophytic fungus Penicillium sp. (NO. 24) was obtained from the healthy leaves of Tapiscia sinensis Oliv. The structure of penicitroamide ( 1 ) features a bicyclo[3.2.1]octane core unit with a high degree of carbonylization (four carbonyl groups and one enol group). The chemical structure of penicitroamide ( 1 ) was elucidated by analysis of 1D-, 2D-NMR and MS data. In bioassays, penicitroamide ( 1 ) displayed antibacterial potency against two plant pathogens, Erwinia carotovora subsp. Carotovora (Jones) Bersey, et al. and Sclerotium rolfsii Sacc. with MIC 50 at 45 and 50 μg/mL. Compound 1 also showed 60% lethality against brine shrimp at 10 μg/mL. Penicitroamide ( 1 ) exhibited no significant activity against A549, Caski, HepG2 and MCF-7 cells with IC 50 > 50 μg/mL. Finally, the possible biosynthetic pathway of penicitroamide ( 1 ) was discussed.

Carbonyl Emissions in E-cigarette Aerosol: A Systematic Review and Methodological Considerations

Directory of Open Access Journals (Sweden)

Konstantinos E. Farsalinos

2018-01-01

Full Text Available Carbonyl emissions from tobacco cigarettes represent a substantial health risk contributing to smoking-related morbidity and mortality. As expected, this is an important research topic for tobacco harm reduction products, in an attempt to compare the relative risk of these products compared to tobacco cigarettes. In this study, a systematic review of the literature available on PubMed was performed analyzing the studies evaluating carbonyl emissions from e-cigarettes. A total of 32 studies were identified and presented. We identified a large diversity of methodologies, with substantial discrepancies in puffing patterns, aerosol collection and analytical methods as well as reported units of measurements. Such discrepancies make comparisons difficult, and in some cases the accuracy of the findings cannot be determined. Importantly, control for the generation of dry puffs was not performed in the vast majority of studies, particularly in studies using variable power devices, which could result in testing conditions and reported carbonyl levels that have no clinical relevance or context. Some studies have been replicated, verifying the presence of dry puff conditions. Whenever realistic use conditions were ensured, carbonyl emissions from e-cigarettes were substantially lower than tobacco cigarette smoke, while newer generation (bottom-coil, cotton wick atomizers appeared to emit minimal levels of carbonyls with questionable clinical significance in terms of health risk. However, extremely high levels of carbonyl emissions were reported in some studies, and all these studies need to be replicated because of potentially important health implications.

Protein carbonylation associated to high-fat, high-sucrose diet and its metabolic effects.

Science.gov (United States)

Méndez, Lucía; Pazos, Manuel; Molinar-Toribio, Eunice; Sánchez-Martos, Vanesa; Gallardo, José M; Rosa Nogués, M; Torres, Josep L; Medina, Isabel

2014-12-01

The present research draws a map of the characteristic carbonylation of proteins in rats fed high-caloric diets with the aim of providing a new insight of the pathogenesis of metabolic diseases derived from the high consumption of fat and refined carbohydrates. Protein carbonylation was analyzed in plasma, liver and skeletal muscle of Sprague-Dawley rats fed a high-fat, high-sucrose (HFHS) diet by a proteomics approach based on carbonyl-specific fluorescence-labeling, gel electrophoresis and mass spectrometry. Oxidized proteins along with specific sites of oxidative damage were identified and discussed to illustrate the consequences of protein oxidation. The results indicated that long-term HFHS consumption increased protein oxidation in plasma and liver; meanwhile, protein carbonyls from skeletal muscle did not change. The increment of carbonylation by HFHS diet was singularly selective on specific target proteins: albumin from plasma and liver, and hepatic proteins such as mitochondrial carbamoyl-phosphate synthase (ammonia), mitochondrial aldehyde dehydrogenase, argininosuccinate synthetase, regucalcin, mitochondrial adenosine triphosphate synthase subunit beta, actin cytoplasmic 1 and mitochondrial glutamate dehydrogenase 1. The possible consequences that these specific protein carbonylations have on the excessive weight gain, insulin resistance and nonalcoholic fatty liver disease resulting from HFHS diet consumption are discussed. Copyright © 2014 Elsevier Inc. All rights reserved.

Design and fabrication of microfluidic mixer from carbonyl iron–PDMS composite membrane

KAUST Repository

Li, Jiaxing; Zhang, Mengying; Wang, Limu; Li, Weihua; Sheng, Ping; Wen, Weijia

2010-01-01

This paper introduces a carbonyl iron-PDMS (CI-PDMS) composite magnetic elastomer in which carbonyl iron (CI) particles are uniformly distributed in a PDMS matrix. The CI particles and the PDMS were mixed at different weight ratios and tested

Protein carbonylation, protein aggregation and neuronal cell death in a murine model of multiple sclerosis

Science.gov (United States)

Dasgupta, Anushka

Many studies have suggested that oxidative stress plays an important role in the pathophysiology of both multiple sclerosis (MS) and its animal model experimental autoimmune encephalomyelitis (EAE). Yet, the mechanism by which oxidative stress leads to tissue damage in these disorders is unclear. Recent work from our laboratory has revealed that protein carbonylation, a major oxidative modification caused by severe and/or chronic oxidative stress conditions, is elevated in MS and EAE. Furthermore, protein carbonylation has been shown to alter protein structure leading to misfolding/aggregation. These findings prompted me to hypothesize that carbonylated proteins, formed as a consequence of oxidative stress and/or decreased proteasomal activity, promote protein aggregation to mediate neuronal apoptosis in vitro and in EAE. To test this novel hypothesis, I first characterized protein carbonylation, protein aggregation and apoptosis along the spinal cord during the course of myelin-oligodendrocyte glycoprotein (MOG)35-55 peptide-induced EAE in C57BL/6 mice [Chapter 2]. The results show that carbonylated proteins accumulate throughout the course of the disease, albeit by different mechanisms: increased oxidative stress in acute EAE and decreased proteasomal activity in chronic EAE. I discovered not only that there is a temporal correlation between protein carbonylation and apoptosis but also that carbonyl levels are significantly higher in apoptotic cells. A high number of juxta-nuclear and cytoplasmic protein aggregates containing the majority of the oxidized proteins are also present during the course of EAE, which seems to be due to reduced autophagy. In chapter 3, I show that when gluthathione levels are reduced to those in EAE spinal cord, both neuron-like PC12 (nPC12) cells and primary neuronal cultures accumulate carbonylated proteins and undergo cell death (both by necrosis and apoptosis). Immunocytochemical and biochemical studies also revealed a temporal

Pressure dependence of backbone chemical shifts in the model peptides Ac-Gly-Gly-Xxx-Ala-NH2.

Science.gov (United States)

Erlach, Markus Beck; Koehler, Joerg; Crusca, Edson; Kremer, Werner; Munte, Claudia E; Kalbitzer, Hans Robert

2016-06-01

For a better understanding of nuclear magnetic resonance (NMR) detected pressure responses of folded as well as unstructured proteins the availability of data from well-defined model systems are indispensable. In this work we report the pressure dependence of chemical shifts of the backbone atoms (1)H(α), (13)C(α) and (13)C' in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH2 (Xxx one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of these nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The polynomial pressure coefficients B 1 and B 2 are dependent on the type of amino acid studied. The coefficients of a given nucleus show significant linear correlations suggesting that the NMR observable pressure effects in the different amino acids have at least partly the same physical cause. In line with this observation the magnitude of the second order coefficients of nuclei being direct neighbors in the chemical structure are also weakly correlated.

Substitution effect in nuclear magnetic resonance of C-13: α methoxicyclohexanones

International Nuclear Information System (INIS)

Lopez Holland, M.A.G.

1984-01-01

Eletronic and steric interactions between the carbonyl and methoxyl groups in α-methoxicyclohexanones by H-1 and C-13 nuclear magnetic resonance spectroscopy (n.m.r) is studied. Interpretation of H-1 n.m.r measurements based on the carbonyl group anisotropy is made. The asigment of spectral lines to specific nuclear by Lanthanide Shift Reagent Experiments is confirmed. Interpretation of C-13 n.m.r. spectra with respect to molecular effects and emphirical relationships associated with the substituent was analysed. The C-13 chemical shift asignment by comparison with results of partially (SFORD) and fully decompled spectra and also by relating the measured chemical shift with values cited in the literature for similar compounds are made. A qualitative study using I.R. spectroscopy in attempt to evaluate the predominance of one the conformers of the studied compounds in solutions of n-hexan and chloroform is made. (M.J.C.) [pt

Benchmarking Hydrogen and Carbon NMR Chemical Shifts at HF, DFT, and MP2 Levels.

Science.gov (United States)

Flaig, Denis; Maurer, Marina; Hanni, Matti; Braunger, Katharina; Kick, Leonhard; Thubauville, Matthias; Ochsenfeld, Christian

2014-02-11

An extensive study of error distributions for calculating hydrogen and carbon NMR chemical shifts at Hartree-Fock (HF), density functional theory (DFT), and Møller-Plesset second-order perturbation theory (MP2) levels is presented. Our investigation employs accurate CCSD(T)/cc-pVQZ calculations for providing reference data for 48 hydrogen and 40 carbon nuclei within an extended set of chemical compounds covering a broad range of the NMR scale with high relevance to chemical applications, especially in organic chemistry. Besides the approximations of HF, a variety of DFT functionals, and conventional MP2, we also present results with respect to a spin component-scaled MP2 (GIAO-SCS-MP2) approach. For each method, the accuracy is analyzed in detail for various basis sets, allowing identification of efficient combinations of method and basis set approximations.

Low pressure carbonylation of benzyl chloride = Die carbonylierung von benzylchlorid bei niedrigen drücken

NARCIS (Netherlands)

Luggenhorst, H.J.; Westerterp, K.R.

1986-01-01

For carbonylations, metal carbonyls, particularly cobalt and iron carbonyls, are often used as catalysts. These reactions take place under rather drastic reaction conditions, e.g. 200–300 °C and 60–100 MPa. In some patents it is stated that similar reactions using the same catalysts can also be

12 WEEK EXPOSURE TO CARBONYL SULFIDE PRODUCES BRAIN LESIONS AND CHANGES IN BRAINSTEM AUDITORY (BAER) AND SOMATOSENAORY (SEP) EVOKED POTENTIALS IN FISCHER 344N RATS

Science.gov (United States)

Carbonyl sulfide (COS) is a chemical intermediate in the production of pesticides and herbicides, is a metabolite of carbon disulfide, is produced by the combustion of organic material, and is found occurring in nature. COS was included in a Toxic Substances Control Act request f...

Protein carbonyl content: a novel biomarker for aging in HIV/AIDS patients

Directory of Open Access Journals (Sweden)

Vaishali Kolgiri

2017-01-01

Conclusions: Carbonyl content may has a role as a biomarker for detecting oxidative DNA damage induced ART toxicity and/or accelerated aging in HIV/AIDS patients. Larger studies are warranted to elucidate the role of carbonyl content as a biomarker for premature aging in HIV/AIDS patients.

Studies of coupled chemical and catalytic coal conversion methods

Energy Technology Data Exchange (ETDEWEB)

Stock, L.M.

1990-01-01

This report concerns our research on base-catalyzed coal solubilization and a new approach for hydrogen addition. The work on base-catalyzed, chemical solubilization is continuing. this report is focused on the hydrogenation research. Specifically it deals with the use of arene chromium carbonyl complexes as reagents for the addition of dideuterium to coal molecules. In one phase of the work, he has established that the aromatic hydrocarbons in a representative coal liquid can be converted in very good yield to arene chromium carbonyl compounds. In a second phase of the work directly related to our objective of improved methods for catalytic hydrogenation, he has established that the aromatic constituents of the same coal liquid add dideuterium in the presence of added napththalene chromium carbonyl.

Optimal voxel size for measuring global gray and white matter proton metabolite concentrations using chemical shift imaging

DEFF Research Database (Denmark)

Hanson, Lars Peter Grüner; Adalsteinsson, E; Pfefferbaum, A

2000-01-01

Quantification of gray and white matter levels of spectroscopically visible metabolites can provide important insights into brain development and pathological conditions. Chemical shift imaging offers a gain in efficiency for estimation of global gray and white matter metabolite concentrations co...

Study of chemical shifts of the chloroform complexes with cyclic donors of electrons

International Nuclear Information System (INIS)

Blaszkiewicz, B.; Pajak, Z.

1973-01-01

Chemical shifts of chloroform complexes with the heterocyclic electron donors: pyridine, piperidine, alpha-picoline and gamma-picoline have been studied using the high resolution (5.10 -9 ) spectrometer operating at 80 MHz. An attempt has also been made to study the three - component solutions of : chloroform, a heterocyclic donor of electrons and carbon tetrachloride. The results, which have been obtained, indicate that the complex-forming power of pyridine and other electron donors is greater in carbon tetrachloride than in other solvents. (S.B.)

Coronary artery atherosclerosis associated with shift work in chemical plant workers by using coronary CT angiography.

Science.gov (United States)

Kang, WonYang; Park, Won-Ju; Jang, Keun-Ho; Kim, Soo-Hyeon; Gwon, Do-Hyeong; Lim, Hyeong-Min; Ahn, Ji-Sung; Moon, Jai-Dong

2016-08-01

The aim of this study was to investigate whether shift work is related to elevated risk of coronary artery disease (CAD) by determining the coronary artery calcium (CAC) score and the presence of coronary artery stenosis by using coronary artery CT angiography (CCTA). In this study, 110 male workers participated and underwent a CCTA examination for CAC scoring, which represents coronary artery plaque, and were evaluated for luminal stenosis. All of the participants were working in the same chemical plant, of whom 70 worked day shifts and 40 worked rotating shifts. In a multivariate logistic regression analysis, including age, smoking status, alcohol consumption, regular exercise and waist circumference, shift work was associated with a 2.89-fold increase in the odds of developing coronary plaque compared with day work (OR, 2.89; 95% CI 1.07 to 7.82). The association between shift work and coronary plaque was strong after adjustment for age, low-density lipoprotein cholesterol, hypertension and diabetes mellitus (OR, 2.92; 95% CI 1.02 to 8.33). In addition, the number of years of shift work employment was associated with coronary plaque. However, no association was found between shift work and coronary artery stenosis. Shift work could induce CAD onset via the atherosclerotic process, and shift work employment duration was associated with an increased risk of atherosclerosis in male workers. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Using 1H and 13C NMR chemical shifts to determine cyclic peptide conformations: a combined molecular dynamics and quantum mechanics approach.

Science.gov (United States)

Nguyen, Q Nhu N; Schwochert, Joshua; Tantillo, Dean J; Lokey, R Scott

2018-05-10

Solving conformations of cyclic peptides can provide insight into structure-activity and structure-property relationships, which can help in the design of compounds with improved bioactivity and/or ADME characteristics. The most common approaches for determining the structures of cyclic peptides are based on NMR-derived distance restraints obtained from NOESY or ROESY cross-peak intensities, and 3J-based dihedral restraints using the Karplus relationship. Unfortunately, these observables are often too weak, sparse, or degenerate to provide unequivocal, high-confidence solution structures, prompting us to investigate an alternative approach that relies only on 1H and 13C chemical shifts as experimental observables. This method, which we call conformational analysis from NMR and density-functional prediction of low-energy ensembles (CANDLE), uses molecular dynamics (MD) simulations to generate conformer families and density functional theory (DFT) calculations to predict their 1H and 13C chemical shifts. Iterative conformer searches and DFT energy calculations on a cyclic peptide-peptoid hybrid yielded Boltzmann ensembles whose predicted chemical shifts matched the experimental values better than any single conformer. For these compounds, CANDLE outperformed the classic NOE- and 3J-coupling-based approach by disambiguating similar β-turn types and also enabled the structural elucidation of the minor conformer. Through the use of chemical shifts, in conjunction with DFT and MD calculations, CANDLE can help illuminate conformational ensembles of cyclic peptides in solution.

Is the Lamb shift chemically significant?

Science.gov (United States)

Dyall, Kenneth G.; Bauschlicher, Charles W., Jr.; Schwenke, David W.; Pyykko, Pekka; Arnold, James (Technical Monitor)

2001-01-01

The contribution of the Lamb shift to the atomization energies of some prototype molecules, BF3, AlF3, and GaF3, is estimated by a perturbation procedure. It is found to be in the range of 3-5% of the one-electron scalar relativistic contribution to the atomization energy. The maximum absolute value is 0.2 kcal/mol for GaF3. These sample calculations indicate that the Lamb shift is probably small enough to be neglected for energetics of molecules containing light atoms if the target accuracy is 1 kcal/mol, but for higher accuracy calculations and for molecules containing heavy elements it must be considered.

Impact of HVAC filter on indoor air quality in terms of ozone removal and carbonyls generation

Science.gov (United States)

Lin, Chi-Chi; Chen, Hsuan-Yu

2014-06-01

This study aims at detecting ozone removal rates and corresponding carbonyls generated by ozone reaction with HVAC filters from various building, i.e., shopping mall, school, and office building. Studies were conducted in a small-scale environmental chamber. By examining dust properties including organic carbon proportion and specific surface area of dusts adsorbed on filters along with ozone removal rates and carbonyls generation rate, the relationship among dust properties, ozone removal rates, and carbonyls generation was identified. The results indicate a well-defined positive correlation between ozone removal efficiency and carbonyls generation on filters, as well as a positive correlation among the mass of organic carbon on filters, ozone removal efficiency and carbonyls generations.

Degradation of carbonyl hydroperoxides in the atmosphere and in combustion

KAUST Repository

Xing, Lili

2017-10-12

Oxygenates with carbonyl and hydroperoxy functional groups are important intermediates that are generated during the autooxidation of organic compounds in the atmosphere and during the autoignition of transport fuels. In the troposphere, the degradation of carbonyl hydroperoxides leads to low-vapor-pressure polyfunctional species that be taken into in cloud and fog droplets or to the formation of secondary organic aerosols (SOAs). In combustion, the fate of carbonyl hydroperoxides is important for the performance of advanced combustion engines, especially for autoignition. A key fate of the carbonyl hydroperoxides is reac-tion with OH radicals, for which kinetics data are experimentally unavailable. Here, we study 4-hydroperoxy-2-pentanone (CH3C(=O)CH2CH(OOH)CH3) as a model compound to clarify the kinetics of OH reactions with carbonyl hydroperoxides, in par-ticular H-atom abstraction and OH addition reactions. With a combination of electronic structure calculations, we determine previ-ously missing thermochemical data, and with multipath variational transition state theory (MP-VTST), a multidimensional tunnel-ing (MT) approximation, multiple-structure anharmonicity, and torsional potential anharmonicity we obtained much more accurate rate constants than the ones that can computed by conventional single-structure harmonic transition state theory (TST) and than the empirically estimated rate constants that are currently used in atmospheric and combustion modeling. The roles of various factors in determining the rates are elucidated. The pressure-dependent rate constants for the addition reaction are computed using system-specific quantum RRK theory. The calculated temperature range is 298-2400 K, and the pressure range is 0.01–100 atm. The accu-rate thermodynamic and kinetics data determined in this work are indispensable in the global modeling of SOAs in atmospheric science and in the detailed understanding and prediction of ignition properties of hydrocarbons

Diffusion-weighted imaging of the liver at 3 T using section-selection gradient reversal: emphasis on chemical shift artefacts and lesion conspicuity

International Nuclear Information System (INIS)

Lee, J.S.; Kim, Y.K.; Jeong, W.K.; Choi, D.; Lee, W.J.

2015-01-01

Aim: To assess the value of section-selection gradient reversal (SSGR) in liver diffusion-weighted imaging (DWI) by comparing it to conventional DWI with an emphasis on chemical shift artefacts and lesion conspicuity. Materials and methods: Forty-eight patients (29 men and 19 women; age range 33–80 years) with 48 liver lesions underwent two DWI examinations using spectral presaturation with inversion recovery fat suppression with and without SSGR at 3 T. Two reviewers evaluated each DWI (b = 100 and b = 800 image) with respect to chemical shift artefacts and liver lesion conspicuity using five-point scales and performed pairwise comparisons between the two DWIs. The signal-to-noise ratio (SNR) of the liver and the lesion and the lesion–liver contrast-to-noise ratio (CNR) were also calculated. Results: SSGR-DWI was significantly better than conventional DWI with respect to chemical shift artefacts and lesion conspicuity in both separate reviews and pairwise comparisons (p < 0.05). There were significant differences in the SNR of the liver (b = 100 and b = 800 images) and lesion (b = 800) between SSGR-DWI and conventional DWI (p < 0.05). Conclusion: Applying the SSGR method to DWI using SPIR fat suppression at 3 T could significantly reduce chemical shift artefacts without incurring additional acquisition time or SNR penalties, which leads to increased conspicuity of focal liver lesions. - Highlights: • Chemical shift artefact in liver DWI is markedly decreased by applying SSGR. • Liver lesion conspicuity is improved by applying SSGR to DWI. • In SNR of the liver, SSGR-DWI is better than conventional DWI

Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction

International Nuclear Information System (INIS)

Lehtivarjo, Juuso; Tuppurainen, Kari; Hassinen, Tommi; Laatikainen, Reino; Peräkylä, Mikael

2012-01-01

While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein 1 H chemical shifts in which molecular motions, the 4th dimension, were modeled using molecular dynamics (MD) simulations. Although the approach clearly improved the prediction, the X-ray structures and single NMR conformers used in the model cannot be considered fully realistic models of protein in solution. In this work, NMR ensembles (NMRE) were used to expand the conformational space of proteins (e.g. side chains, flexible loops, termini), followed by MD simulations for each conformer to map the local fluctuations. Compared with the non-dynamic model, the NMRE+MD model gave 6–17% lower root-mean-square (RMS) errors for different backbone nuclei. The improved prediction indicates that NMR ensembles with MD simulations can be used to obtain a more realistic picture of protein structures in solutions and moreover underlines the importance of short and long time-scale dynamics for the prediction. The RMS errors of the NMRE+MD model were 0.24, 0.43, 0.98, 1.03, 1.16 and 2.39 ppm for 1 Hα, 1 HN, 13 Cα, 13 Cβ, 13 CO and backbone 15 N chemical shifts, respectively. The model is implemented in the prediction program 4DSPOT, available at http://www.uef.fi/4dspothttp://www.uef.fi/4dspot.

Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction

Energy Technology Data Exchange (ETDEWEB)

Lehtivarjo, Juuso, E-mail: juuso.lehtivarjo@uef.fi; Tuppurainen, Kari; Hassinen, Tommi; Laatikainen, Reino [University of Eastern Finland, School of Pharmacy (Finland); Peraekylae, Mikael [University of Eastern Finland, Institute of Biomedicine (Finland)

2012-03-15

While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein {sup 1}H chemical shifts in which molecular motions, the 4th dimension, were modeled using molecular dynamics (MD) simulations. Although the approach clearly improved the prediction, the X-ray structures and single NMR conformers used in the model cannot be considered fully realistic models of protein in solution. In this work, NMR ensembles (NMRE) were used to expand the conformational space of proteins (e.g. side chains, flexible loops, termini), followed by MD simulations for each conformer to map the local fluctuations. Compared with the non-dynamic model, the NMRE+MD model gave 6-17% lower root-mean-square (RMS) errors for different backbone nuclei. The improved prediction indicates that NMR ensembles with MD simulations can be used to obtain a more realistic picture of protein structures in solutions and moreover underlines the importance of short and long time-scale dynamics for the prediction. The RMS errors of the NMRE+MD model were 0.24, 0.43, 0.98, 1.03, 1.16 and 2.39 ppm for {sup 1}H{alpha}, {sup 1}HN, {sup 13}C{alpha}, {sup 13}C{beta}, {sup 13}CO and backbone {sup 15}N chemical shifts, respectively. The model is implemented in the prediction program 4DSPOT, available at http://www.uef.fi/4dspothttp://www.uef.fi/4dspot.

A three-membered ring approach to carbonyl olefination.

Science.gov (United States)

Niyomchon, Supaporn; Oppedisano, Alberto; Aillard, Paul; Maulide, Nuno

2017-10-23

The carbon-carbon double bond, with its diverse and multifaceted reactivity, occupies a prominent position in organic synthesis. Although a variety of simple alkenes are readily available, the mild and chemoselective introduction of a unit of unsaturation into a functionalized organic molecule remains an ongoing area of research, and the olefination of carbonyl compounds is a cornerstone of such approaches. Here we show the direct olefination of hydrazones via the intermediacy of three-membered ring species generated by addition of sulfoxonium ylides, departing from the general dogma of alkenes synthesis from carbonyls. Moreover, the mild reaction conditions and operational simplicity of the transformation render the methodology appealing from a practical point of view.

Carbonylation of 1-hexene in the presence of palladium-anion-exchange resin catalysts

Energy Technology Data Exchange (ETDEWEB)

Lapidus, A.L.; Pirozhkov, S.D.; Buiya, M.A.; Lunin, A.F.; Karapetyan, L.P.; Saldadze, K.M.

1986-06-20

Activated charcoal, silica gel, and zeolites containing palladium are active in the carbonylation of lower olefins by carbon monoxide. In the present work, they studied the carbonylation of 1-hexene in the presence of a series of palladium catalysts containing An-221, An-251, and AN-511 anion-exchange catalysts produced in the USSR as the supports. A catalyst obtained by the deposition of palladium(II) on weakly basic anion-exchange resins displays high efficiency in the carbonylation of 1-hexene with the formation of a nixture of enanthoic and 2-methylcaproic acids.

Convenient Reduction of Carbonyl Compounds to their ...

African Journals Online (AJOL)

NICO

Alcohols and their derivatives occupy an important position in organic synthesis. ... review also reveals that the reduction of carbonyl compounds ..... 1 H.B. Ji and Y.B. She, Green Oxidation and Reduction, China Petrochemi- cal Press, Beijing ...

Chemical shift of U L3 edges in different uranium compounds obtained by X-ray absorption spectroscopy with synchrotron radiation

International Nuclear Information System (INIS)

Joseph, D.; Jha, S.N.; Nayak, C.; Bhattacharyya, D.; Babu, P. Venu

2014-01-01

Uranium L 3 X-ray absorption edge was measured in various compounds containing uranium in U 4+ , U 5+ and U 5+ oxidation states. The measurements have been carried out at the Energy Dispersive EXAFS beamline (BL-08) at INDUS-2 synchrotron radiation source at RRCAT, Indore. Energy shifts of ∼ 2-3 eV were observed for U L 3 edge in the U-compounds compared to their value in elemental U. The different chemical shifts observed for the compounds having the same oxidation state of the cation but different anions or ligands show the effect of different chemical environments surrounding the cations in determining their X-ray absorption edges in the above compounds. The above chemical effect has been quantitatively described by determining the effective charges on U cation in the above compounds. (author)

COMPARATIVE STUDY OF EFFICACY OF FERROUS SULPHATE AND CARBONYL IRON IN ANEMIA OF ANTENATAL WOMEN

Directory of Open Access Journals (Sweden)

Radhika

2015-03-01

Full Text Available Iron deficiency anemia is the most common and important public health problem all over the world in the risk group of antenatal women. Research is going on to improve the iron status of the pregnant women with different forms of iron available. In this regard, Carbonyl Iron is showing promising results in improving the red cell mass with better compliance. 120 antenatal women were recruited in this study. The study comprised of 6weeks for each patient. They were given Carbonyl Iron 100 mg/day and FeS04 100gm/day . Before and after treatment all the baseline and specific investigations were one. Results were tabulated, comparison and significance were tested by unpaired student ’s’ test and their 'p' value was calculated. Results were shown graphically also. Carbonyl Iron showed improvement in hemoglobin, PCV and better than ferrous Sulphate (P <0.001. Incidence of side effects were less with Carbonyl Iron than Ferrous Sulphate, better compliance was seen with Carbonyl Iron. In conclusion, the present study s howed that Carbonyl Iron had better efficacy and safety in the management of Iron deficiency anemia in antenatal women than ferrous Sulphate

Pressure dependence of backbone chemical shifts in the model peptides Ac-Gly-Gly-Xxx-Ala-NH{sub 2}

Energy Technology Data Exchange (ETDEWEB)

Erlach, Markus Beck; Koehler, Joerg [University of Regensburg, Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine (Germany); Crusca, Edson [University of São Paulo, Physics Institute of São Carlos (Brazil); Kremer, Werner [University of Regensburg, Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine (Germany); Munte, Claudia E. [University of São Paulo, Physics Institute of São Carlos (Brazil); Kalbitzer, Hans Robert, E-mail: hans-robert.kalbitzer@biologie.uni-regensburg.de [University of Regensburg, Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine (Germany)

2016-06-15

For a better understanding of nuclear magnetic resonance (NMR) detected pressure responses of folded as well as unstructured proteins the availability of data from well-defined model systems are indispensable. In this work we report the pressure dependence of chemical shifts of the backbone atoms {sup 1}H{sup α}, {sup 13}C{sup α} and {sup 13}C′ in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH{sub 2} (Xxx one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of these nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The polynomial pressure coefficients B{sub 1} and B{sub 2} are dependent on the type of amino acid studied. The coefficients of a given nucleus show significant linear correlations suggesting that the NMR observable pressure effects in the different amino acids have at least partly the same physical cause. In line with this observation the magnitude of the second order coefficients of nuclei being direct neighbors in the chemical structure are also weakly correlated.Graphical Abstract.

Application of the Fenske-Hall molecular orbital method to the calculation of 11B NMR chemical shifts. Antipodal substituent effects in deltahedral clusters

International Nuclear Information System (INIS)

Fehlner, T.P.; Czech, P.T.; Fenske, R.F.

1990-01-01

Utilizing Fenske-Hall wave functions and eigenvalues combined with the Ramsey sum over states (SOS) approximation, it is demonstrated that the sign and magnitude of the paramagnetic contribution to the shielding correlates well with the observed 11 B chemical shifts of a substantial variety of boron- and metal-containing compounds. Analysis of the molecular orbital (MO) contributions in the SOS approximation leads to an explanation of the large downfield shifts associated with metal-rich metallaboranes. A similar analysis demonstrates the importance of selected cluster occupied and unoccupied MO's in explaining both exo-cage substituent effects in which the antipodal boron resonance is shifted upfield and endo-cage substituent effects (interchange of isolobal fragments within the cage framework) in which the antipodal boron resonance is shifted downfield. Exo- and endo-cage substitution perturbs these MO's in an understandable fashion, leading to an internally consistent explanation of the observed chemical shift changes. 36 refs., 8 figs., 4 tabs

Unusually large chemical potential shift in a degenerate semiconductor: Angle-resolved photoemission study of SnSe and Na-doped SnSe

Science.gov (United States)

Maeda, M.; Yamamoto, K.; Mizokawa, T.; Saini, N. L.; Arita, M.; Namatame, H.; Taniguchi, M.; Tan, G.; Zhao, L. D.; Kanatzidis, M. G.

2018-03-01

We have studied the electronic structure of SnSe and Na-doped SnSe by means of angle-resolved photoemission spectroscopy. The valence-band top reaches the Fermi level by the Na doping, indicating that Na-doped SnSe can be viewed as a degenerate semiconductor. However, in the Na-doped system, the chemical potential shift with temperature is unexpectedly large and is apparently inconsistent with the degenerate semiconductor picture. The large chemical potential shift and anomalous spectral shape are key ingredients for an understanding of the novel metallic state with the large thermoelectric performance in Na-doped SnSe.

Impaired cardiac SIRT1 activity by carbonyl stress contributes to aging-related ischemic intolerance.

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Chunhu Gu

Full Text Available Reactive aldehydes can initiate protein oxidative damage which may contribute to heart senescence. Sirtuin 1 (SIRT1 is considered to be a potential interventional target for I/R injury management in the elderly. We hypothesized that aldehyde mediated carbonyl stress increases susceptibility of aged hearts to ischemia/reperfusion (I/R injury, and elucidate the underlying mechanisms with a focus on SIRT1. Male C57BL/6 young (4-6 mo and aged (22-24 mo mice were subjected to myocardial I/R. Cardiac aldehyde dehydrogenase (ALDH2, SIRT1 activity and protein carbonyls were assessed. Our data revealed that aged heart exhibited increased endogenous aldehyde/carbonyl stress due to impaired ALDH2 activity concomitant with blunted SIRT1 activity (P<0.05. Exogenous toxic aldehydes (4-HNE exposure in isolated cardiomyocyte verified that aldehyde-induced carbonyl modification on SIRT1 impaired SIRT1 activity leading to worse hypoxia/reoxygenation (H/R injury, which could all be rescued by Alda-1 (ALDH2 activator (all P<0.05. However, SIRT1 inhibitor blocked the protective effect of Alda-1 on H/R cardiomyocyte. Interestingly, myocardial I/R leads to higher carbonylation but lower activity of SIRT1 in aged hearts than that seen in young hearts (P<0.05. The application of Alda-1 significantly reduced the carbonylation on SIRT1 and markedly improved the tolerance to in vivo I/R injury in aged hearts, but failed to protect Sirt1(+/- knockout mice against myocardial I/R injury. This was verified by Alda-1 treatment improved postischemic contractile function recovery in ex vivo perfused aged but not in Sirt1(+/- hearts. Thus, aldehyde/carbonyl stress is accelerated in aging heart. These results provide a new insight that impaired cardiac SIRT1 activity by carbonyl stress plays a critical role in the increased susceptibility of aged heart to I/R injury. ALDH2 activation can restore this aging-related myocardial ischemic intolerance.

Molecular Engineering with Organic Carbonyl Electrode Materials for Advanced Stationary and Redox Flow Rechargeable Batteries.

Science.gov (United States)

Zhao, Qing; Zhu, Zhiqiang; Chen, Jun

2017-12-01

Organic carbonyl electrode materials that have the advantages of high capacity, low cost and being environmentally friendly, are regarded as powerful candidates for next-generation stationary and redox flow rechargeable batteries (RFBs). However, low carbonyl utilization, poor electronic conductivity and undesired dissolution in electrolyte are urgent issues to be solved. Here, we summarize a molecular engineering approach for tuning the capacity, working potential, concentration of active species, kinetics, and stability of stationary and redox flow batteries, which well resolves the problems of organic carbonyl electrode materials. As an example, in stationary batteries, 9,10-anthraquinone (AQ) with two carbonyls delivers a capacity of 257 mAh g -1 (2.27 V vs Li + /Li), while increasing the number of carbonyls to four with the formation of 5,7,12,14-pentacenetetrone results in a higher capacity of 317 mAh g -1 (2.60 V vs Li + /Li). In RFBs, AQ, which is less soluble in aqueous electrolyte, reaches 1 M by grafting -SO 3 H with the formation of 9,10-anthraquinone-2,7-disulphonic acid, resulting in a power density exceeding 0.6 W cm -2 with long cycling life. Therefore, through regulating substituent groups, conjugated structures, Coulomb interactions, and the molecular weight, the electrochemical performance of carbonyl electrode materials can be rationally optimized. This review offers fundamental principles and insight into designing advanced carbonyl materials for the electrodes of next-generation rechargeable batteries. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Differentiation of osteoporotic and neoplastic vertebral fractures by chemical shift {l_brace}in-phase and out-of phase{r_brace} MR imaging

Energy Technology Data Exchange (ETDEWEB)

Ragab, Yasser [Radiology Department, Faculty of Medicine, Cairo University (Egypt); Radiology Department, Dr Erfan and Bagedo General Hospital (Saudi Arabia)], E-mail: yragab61@hotmail.com; Emad, Yasser [Rheumatology and Rehabilitation Department, Faculty of Medicine, Cairo University (Egypt); Rheumatology and Rehabilitation Department, Dr Erfan and Bagedo General Hospital (Saudi Arabia)], E-mail: yasseremad68@yahoo.com; Gheita, Tamer [Rheumatology and Rehabilitation Department, Faculty of Medicine, Cairo University (Egypt)], E-mail: gheitamer@yahoo.com; Mansour, Maged [Oncology Department, Faculty of Medicine, Cairo University (Egypt); Oncology Department, Dr Erfan and Bagedo General Hospital (Saudi Arabia)], E-mail: magedmansour@yahoo.com; Abou-Zeid, A. [Public Health Department, Faculty of Medicine, Cairo University, Cairo (Egypt)], E-mail: alaabouzeid@yahoo.com; Ferrari, Serge [Division of Bone Diseases, Department of Rehabilitation and Geriatrics, and WHO, Collaborating Center for Osteoporosis Prevention, Geneva University Hospital (Switzerland)], E-mail: serge.ferrari@medecine.unige.ch; Rasker, Johannes J. [Rheumatologist University of Twente, Enschede (Netherlands)], E-mail: j.j.rasker@utwente.nl

2009-10-15

Objective: The objective of this study was to establish the cut-off value of the signal intensity drop on chemical shift magnetic resonance imaging (MRI) with appropriate sensitivity and specificity to differentiate osteoporotic from neoplastic wedging of the spine. Patients and methods: All patients with wedging of vertebral bodies were included consecutively between February 2006 and January 2007. A chemical shift MRI was performed and signal intensity after (in-phase and out-phase) images were obtained. A DXA was performed in all. Results: A total of 40 patients were included, 20 with osteoporotic wedging (group 1) and 20 neoplastic (group 2). They were 21 males and 19 females. Acute vertebral collapse was observed in 15 patients in group 1 and subacute collapse in another 5 patients, while in group 2, 11 patients showed acute collapse and 9 patients (45%) showed subacute vertebral collapse. On the chemical shift MRI a substantial reduction in signal intensity was found in all lesions in both groups. The proportional changes observed in signal intensity of bone marrow lesions on in-phase compared with out-of-phase images showed significant differences in both groups (P < 0.05). At a cut-off value of 35%, the observed sensitivity of out-of-phase images was 95%, specificity was 100%, positive predictive value was 100% and negative predictive value was 95.2%. Conclusion: A chemical shift MRI is useful in order to differentiate patients with vertebral collapse due to underlying osteoporosis or neoplastic process.

Protein Carbonylation in Patients with Myelodysplastic Syndromes

Czech Academy of Sciences Publication Activity Database

Hlaváčková, A.; Štikarová, J.; Kotlín, R.; Chrastinová, L.; Šácha, Pavel; Májek, P.; Čermák, J.; Suttnar, J.; Dyr, J. E.

2015-01-01

Roč. 126, č. 23 (2015), s. 5232 ISSN 0006-4971. [Annual Meeting and Exposition of the American Society of Hematology /55./. 07.12.2013-10.12.2013, New Orleans] Institutional support: RVO:61388963 Keywords : protein carbonylation * myelodysplastic syndromes Subject RIV: CE - Biochemistry

Correlations of the chemical shift on fasly rotating biological solids by means of NMR spectroscopy

International Nuclear Information System (INIS)

Herbst, Christian

2010-01-01

The basic aim of the thesis was the development and improvement of homo- and heteronuclear feedback sequences for the generation of correlation spectra of the chemical shift. In a first step the possibility of the acquisition of 13 C- 13 correlation spectra of the chemical shift by means of inversion pulses with low RF power factor was studied. Furthermore it was shown that broad-band phase-modulated inversion and universal rotational pulses can be constructed by means of global optimization procedures like the genetic algorithms under regardment of the available RF field strength. By inversion, universal rotational, and 360 pulses as starting values of the optimization efficient homonuclear CN n ν and RN n ν mixing sequences as well as heteronuclear RN n ν s ,ν k feedback sequences were generated. The satisfactory power of the numerically optimized sequences was shown by means of the simulation as well by means of correlation experiments of the chemical shift of L-histidine, L-arginine, and the (CUG) 97 -RNA. This thesis deals furthermore with the possibility to acquire simultaneously different signals with several receivers. By means of numerically optimized RN n ν s ,ν k pulse sequences both 15 N- 13 C and 13 C- 15 N correlation spectra were simultaneously generated. Furthermore it could be shown that the simultaneous acquisition of 3D- 15 N- 13 C- 13 C and 13 C- 15 N-( 1 H)- 1 H correlation spectra is possible. By this in only one measurement process resonance assignments can be met and studies of the global folding performed. A further application of several receivers is the simultaneous acquisition of CHHC, NHHN, NHHC, as well as CHHN spectra. By such experiments it is possible to characterize the hydrogen-bonding pattern and the glycosidic torsion angle χ in RNA. This was demonstrated by means of the (CUG) 97 -RNA. The simultaneous acquisition of all relevant crossing signals of the correlation spectra leads not only to an essential time saving, but

Determination of hydration numbers of electrolytes from temperature dependence of PMR chemical shifts

International Nuclear Information System (INIS)

Subramanian, N.

1979-01-01

The method proposed by Malinowski et al. for the determination of effective hydration numbers (h) of electrolytes leads to a consistent incrrease in the observed values of 'h' with increase in solution concentration. An attempt is made to rationalize the experimental results by cosidering the simultaneous effects of temperature and concentration on the proton chemical shift. It is suggested that Malinowski's technique might yeld 'h' values very close to the true value for those ions for which there is a fortuitous cancellation of structure-making and structure-breaking properties. (Author) [pt

Organocatalyzed α-Sulfenylation of carbonyl compounds using N-formly/Acyl Sulfenmides

International Nuclear Information System (INIS)

Noh, Hyeon Wan; Lee, Chan; Jang, Hye Young

2017-01-01

α-Sulfenylation of aldehydes and ketones using N-formyl and N-acyl sulfenamides, prepared by Cu-catalyzed aerobic coupling of amides and thiols, was achieved in the presence of cyclic secondary amine⋅HCl catalysts. To obtain various sulfur-functionalized carbonyl compounds, sulfenamides containing aromatic and aliphatic organosulfur were investigated. As carbonyl compounds, cyclic and acyclic ketones, 1,3-dicarbonyl compounds, and aldehydes were investigated, affording the desired α-sulfenylation products in good yields

Organocatalyzed α-Sulfenylation of carbonyl compounds using N-formly/Acyl Sulfenmides

Energy Technology Data Exchange (ETDEWEB)

Noh, Hyeon Wan; Lee, Chan; Jang, Hye Young [Dept. of Energy Systems Research, Ajou University, Suwon (Korea, Republic of)

2017-03-15

α-Sulfenylation of aldehydes and ketones using N-formyl and N-acyl sulfenamides, prepared by Cu-catalyzed aerobic coupling of amides and thiols, was achieved in the presence of cyclic secondary amine⋅HCl catalysts. To obtain various sulfur-functionalized carbonyl compounds, sulfenamides containing aromatic and aliphatic organosulfur were investigated. As carbonyl compounds, cyclic and acyclic ketones, 1,3-dicarbonyl compounds, and aldehydes were investigated, affording the desired α-sulfenylation products in good yields.

Simultaneous detection of low and high molecular weight carbonylated compounds derived from lipid peroxidation by electrospray ionization-tandem mass spectrometry.

Science.gov (United States)

Milic, Ivana; Hoffmann, Ralf; Fedorova, Maria

2013-01-02

Reactive oxygen species (ROS) and other oxidative agents such as free radicals can oxidize polyunsaturated fatty acids (PUFA) as well as PUFA in lipids. The oxidation products can undergo consecutive reactions including oxidative cleavages to yield a chemically diverse group of products, such as lipid peroxidation products (LPP). Among them are aldehydes and ketones ("reactive carbonyls") that are strong electrophiles and thus can readily react with nucleophilic side chains of proteins, which can alter the protein structure, function, cellular distribution, and antigenicity. Here, we report a novel technique to specifically derivatize both low molecular and high molecular weight carbonylated LPP with 7-(diethylamino)coumarin-3-carbohydrazide (CHH) and analyze all compounds by electrospray ionization-mass spectrometry (ESI-MS) in positive ion mode. CHH-derivatized compounds were identified by specific neutral losses or fragment ions. The fragment ion spectra displayed additional signals that allowed unambiguous identification of the lipid, fatty acids, cleavage sites, and oxidative modifications. Oxidation of docosahexaenoic (DHA, 22:6), arachidonic (AA, 20:4), linoleic (LA, 18:2), and oleic acids (OA, 18:1) yielded 69 aliphatic carbonyls, whose structures were all deduced from the tandem mass spectra. When four phosphatidylcholine (PC) vesicles containing the aforementioned unsaturated fatty acids were oxidized, we were able to deduce the structures of 122 carbonylated compounds from the tandem mass spectra of a single shotgun analysis acquired within 15 min. The high sensitivity (LOD ∼ 1 nmol/L for 4-hydroxy-2-nonenal, HNE) and a linear range of more than 3 orders of magnitude (10 nmol/L to 10 μmol/L for HNE) will allow further studies on complex biological samples including plasma.

Proteomic identification of carbonylated proteins in F344 rat hippocampus after 1-bromopropane exposure

Energy Technology Data Exchange (ETDEWEB)

Huang, Zhenlie [Department of Occupational and Environmental Health, Nagoya University Graduate School of Medicine, Nagoya 466‐8550 (Japan); Department of Toxicology, Guangdong Prevention and Treatment Center for Occupational Diseases, Guangzhou 510‐300 (China); Ichihara, Sahoko [Graduate School of Regional Innovation Studies, Mie University, Tsu 514‐8507 (Japan); Oikawa, Shinji [Department of Environmental and Molecular Medicine, Mie University Graduate School of Medicine, Mie 514‐8507 (Japan); Chang, Jie; Zhang, Lingyi; Subramanian, Kaviarasan; Mohideen, Sahabudeen Sheik [Department of Occupational and Environmental Health, Nagoya University Graduate School of Medicine, Nagoya 466‐8550 (Japan); Ichihara, Gaku, E-mail: gak@med.nagoya-u.ac.jp [Department of Occupational and Environmental Health, Nagoya University Graduate School of Medicine, Nagoya 466‐8550 (Japan)

2012-08-15

1-Bromopropane (1-BP) is neurotoxic in both experimental animals and humans. Previous proteomic analysis of rat hippocampus implicated alteration of protein expression in oxidative stress, suggesting that oxidative stress plays a role in 1-BP-induced neurotoxicity. To understand this role at the protein level, we exposed male F344 rats to 1-BP at 0, 400, or 1000 ppm for 8 h/day for 1 week or 4 weeks by inhalation and quantitated changes in hippocampal protein carbonyl using a protein carbonyl assay, two-dimensional gel electrophoresis (2-DE), immunoblotting, and matrix-assisted laser-desorption ionization time-of-flight mass spectrometry (MALDI-TOF-TOF/MS). Hippocampal reactive oxygen species and protein carbonyl were significantly increased, demonstrating 1-BP-associated induction of oxidative stress and protein damage. MALDI-TOF-TOF/MS identified 10 individual proteins with increased carbonyl modification (p < 0.05; fold-change ≥ 1.5). The identified proteins were involved in diverse biological processes including glycolysis, ATP production, tyrosine catabolism, GTP binding, guanine degradation, and neuronal metabolism of dopamine. Hippocampal triosephosphate isomerase (TPI) activity was significantly reduced and negatively correlated with TPI carbonylation (p < 0.001; r = 0.83). Advanced glycation end-product (AGE) levels were significantly elevated both in the hippocampus and plasma, and hippocampal AGEs correlated negatively with TPI activity (p < 0.001; r = 0.71). In conclusion, 1-BP-induced neurotoxicity in the rat hippocampus seems to involve oxidative damage of cellular proteins, decreased TPI activity, and elevated AGEs. -- Highlights: ► 1-BP increases hippocampal ROS levels and hippocampal and plasma protein carbonyls. ► 1-BP increases TPI carbonylation and decreases TPI activity in the hippocampus. ► 1-BP increases hippocampal and plasma AGE levels.

Ammonia synthesis in the presence of rhodium-ruthenium-iridium carbonyl clusters

International Nuclear Information System (INIS)

Fedoseev, I.V.; Solov'ev, N.V.

2007-01-01

Researches in the field of platinum metal coordination compounds, where nitrogen enters as a ligand in coordination sphere of metal, are discussed. Results of experiments on the ammonia synthesis during the CO+N 2 mixture passing through alkali solution containing mixture of carbonyl clusters of rhodium, ruthenium and iridium at atmospheric pressure are given. Technique of the experiment and steps of assumed reactions of nitrogen fixation by Rh, Ir and Ru carbonyl clusters are demonstrated [ru

Protein carbonyl content: a novel biomarker for aging in HIV/AIDS patients.

Science.gov (United States)

Kolgiri, Vaishali; Patil, Vinayak Wamanrao

The major complications of "treated" Human Immunodeficiency Virus (HIV) infection are cardiovascular disease, malignancy, renal disease, liver disease, bone disease, and perhaps neurological complications, which are phenomena of the normal aging process occurring at an earlier age in the HIV-infected population. The present study is aimed to explore protein carbonyl content as a biomarker for detecting oxidative DNA damage induced ART toxicity and/or accelerated aging in HIV/AIDS patients. To investigate the potential of carbonyl content as a biomarker for detecting oxidative Deoxyribonucleic acid (DNA) damage induced Antiretroviral Theraphy (ART) toxicity and/or accelerated aging in HIV/AIDS patients. In this case-control study a total 600 subjects were included. All subjects were randomly selected and grouped as HIV-negative (control group) (n=300), HIV-infected ART naive (n=100), HIV-infected on first line ART (n=100), and HIV-infected on second line ART (n=100). Seronegative control subjects were age- and sex-matched with the ART naive patients and the two other groups. Carbonyl protein was determined by the method described in Levine et al. DNA damage marker 8-OH-dG was determined using 8-hydroxy-2-deoxy Guanosine StressXpress ELA Kit by StressMarq Biosciences. Protein carbonyl content levels and oxidative DNA damage were significantly higher (paging in HIV/AIDS patients. Larger studies are warranted to elucidate the role of carbonyl content as a biomarker for premature aging in HIV/AIDS patients. Copyright © 2016 Sociedade Brasileira de Infectologia. Published by Elsevier Editora Ltda. All rights reserved.

Metal-atom fluorescence from the quenching of metastable rare gases by metal carbonyls

International Nuclear Information System (INIS)

Hollingsworth, W.E.

1982-11-01

A flowing afterglow apparatus was used to study the metal fluorescence resulting from the quenching of metastable rare-gas states by metal carbonyls. The data from the quenching or argon, neon, and helium by iron and nickel carbonyl agreed well with a restricted degree of freedom model indicating a concerted bond-breaking dissociation

Chemical constituents of Ottonia corcovadensis Miq. from Amazon forest: 1H and 13C chemical shift assignments

International Nuclear Information System (INIS)

Facundo, Valdir A.; Morais, Selene M.; Braz Filho, Raimundo

2004-01-01

In an ethanolic extract of leaves of Ottonia corcovadensis (Piperaceae) were identified sixteen terpenoids of essential oil and the three flavonoids 3',4',5,5',7-penta methoxyflavone (1), 3',4',5,7-tetra methoxyflavone (2) and 5-hydroxy-3',4',5',7-tetra methoxyflavone (3) and cafeic acid (4). Two amides (5 and 6) were isolated from an ethanolic extract of the roots. The structures were established by spectral analysis, meanly NMR (1D and 2D) and mass spectra. Extensive NMR analysis was also used to complete 1 H and 13 C chemical shift assignments of the flavonoids and amides. The components of the essential oil were identified by computer library search, retention indices and visual interpretation of mass spectra. (author)

Thalassiosira spp. community composition shifts in response to chemical and physical forcing in the northeast Pacific Ocean.

Directory of Open Access Journals (Sweden)

Phoebe Dreux Chappell

2013-09-01

Full Text Available Diatoms are genetically diverse unicellular photosynthetic eukaryotes that are key primary producers in the ocean. Many of the over 100 extant diatom species in the cosmopolitan genus Thalassiosira are difficult to distinguish in mixed populations using light microscopy. Here we examine shifts in Thalassiosira spp. composition along a coastal to open ocean transect that encountered a three-month-old Haida eddy in the northeast Pacific Ocean. To quantify shifts in Thalassiosira species composition, we developed a targeted automated ribosomal intergenic spacer analysis (ARISA method to identify Thalassiosira spp. in environmental samples. As many specific fragment lengths are indicative of individual Thalassiosira spp., the ARISA method is a useful screening tool to identify changes in the relative abundance and distribution of specific species. The method also enabled us to assess changes in Thalassiosira community composition in response to chemical and physical forcing. Thalassiosira spp. community composition in the core of a three-month-old Haida eddy remained largely (>80% similar over a two-week period, despite moving 24 km southwestward. Shifts in Thalassiosira species correlated with changes in dissolved iron (Fe and temperature throughout the sampling period. Simultaneously tracking community composition and relative abundance of Thalassiosira species within the physical and chemical context they occurred allowed us to identify quantitative linkages between environmental conditions and community response.

Characteristics of carbonyl compounds in public vehicles of Beijing city: Concentrations, sources, and personal exposures

Science.gov (United States)

Pang, Xiaobing; Mu, Yujing

The characteristics of carbonyl compounds (carbonyls) including concentrations, major sources, and personal exposure were investigated for 29 vehicles including taxi, bus and subway in Beijing. It was found that the taxis (Xiali, TA) and buses (Huanghe, BA) fueled by gasoline with longer service years had the higher indoor carbonyl levels (178±42.7 and 188±31.6 μg m -3) while subways energized by electricity without exhaust and the jingwa buses (BB) driven in the suburb had the lower levels with total concentrations of 98.5±26.3 and 92.1±20.3 μg m -3, respectively. Outdoor carbonyls of taxi cars and buses were nearly at the same level with their total concentrations varying from 80 to 110 μg m -3. The level of outdoor subways carbonyls was equal with the ambient air levels. Exhaust leakage, indoor material emissions, photochemical formation, and infiltration of outdoor air were considered to be the major sources to in-vehicle carbonyls. Personal exposures and cancer risk to formaldehyde and acetaldehyde were calculated for professional bus and taxi drivers, respectively. Taxi drivers had the highest cancer risk with personal exposure to formaldehyde and acetaldehyde of 212 and 243 μg day -1, respectively. The public concern should pay considerable attention to professional drivers' health.

Applications of Chemical Shift Imaging to Marine Sciences

Directory of Open Access Journals (Sweden)

Haakil Lee

2010-08-01

Full Text Available The successful applications of magnetic resonance imaging (MRI in medicine are mostly due to the non-invasive and non-destructive nature of MRI techniques. Longitudinal studies of humans and animals are easily accomplished, taking advantage of the fact that MRI does not use harmful radiation that would be needed for plain film radiographic, computerized tomography (CT or positron emission (PET scans. Routine anatomic and functional studies using the strong signal from the most abundant magnetic nucleus, the proton, can also provide metabolic information when combined with in vivo magnetic resonance spectroscopy (MRS. MRS can be performed using either protons or hetero-nuclei (meaning any magnetic nuclei other than protons or 1H including carbon (13C or phosphorus (31P. In vivo MR spectra can be obtained from single region ofinterest (ROI or voxel or multiple ROIs simultaneously using the technique typically called chemical shift imaging (CSI. Here we report applications of CSI to marine samples and describe a technique to study in vivo glycine metabolism in oysters using 13C MRS 12 h after immersion in a sea water chamber dosed with [2-13C]-glycine. This is the first report of 13C CSI in a marine organism.

Reactions of ruthenium and osmium cluster carbonyls with heteroatom-substituted and functionalized alkynes

International Nuclear Information System (INIS)

Koridze, A.A.

2000-01-01

The results of studies of the reactions of ruthenium and osmium cluster carbonyls with metal (M = Re, Mn, Fe) alkynes, silylalkynes, propargyl alcohols and their derivatives, diynes, enynes, and ferrocenylacetylene are summarized. Intramolecular rearrangements in the cluster complexes including migrations of carbonyl, hydride, and hydrocarbon ligands and the metal core reorganization are considered [ru

Improvement of chemical shift selective saturation (CHESS) pulse for MR angiography

International Nuclear Information System (INIS)

Ishimori, Yoshiyuki; Sashie, Hiroyuki; Hiraga, Akira; Matsuda, Tsuyoshi

2000-01-01

We improved the fat suppression technique based on chemical shift selective saturation (CHESS). To do this, we shortened the duration of the CHESS pulse to achieve a short repetition time (TR) for MR angiography (MRA). A short-duration CHESS pulse causes broad frequency band saturation, creating extensive offset from the resonance frequency of water. In our phantom experiment, the best parameters of the short-duration CHESS pulse were 3.84 ms in duration, -650 Hz in offset frequency from water resonance, and had a 130-degree flip angle. With this technique, MRA will be able to be carried out without a significant increase in TR. Thus, better vessel contrast will be maintained in time-of-flight (TOF) MRA or contrast-enhanced MRA when using the maximum intensity projection (MIP) method. (author)

Isomer shifts and chemical bonding in crystalline Sn(II) and Sn(IV) compounds

International Nuclear Information System (INIS)

Terra, J.; Guenzburger, D.

1991-01-01

First-principles self-consistent Local Density calculations of the electronic structure of clusters representing Sn(II) (SnO, SnF 2 , SnS, SnSe) and Sn(IV) (SnO 2 , SnF 4 ) crystalline compounds were performed. Values of the electron density at the Sn nucleus were obtained and related to measured values of the Moessbauer Isomer Shifts reported in the literature. The nuclear parameter of 119 Sn derived was ΔR/R=(1.58±0.14)x10 -4 . The chemical bonding in the solids was analysed and related to the electron densities obtained. (author)

Stereoselective Carbonyl Olefination with Fluorosulfoximines: Facile Access to Z or E Terminal Monofluoroalkenes.

Science.gov (United States)

Liu, Qinghe; Shen, Xiao; Ni, Chuanfa; Hu, Jinbo

2017-01-09

Terminal monofluoroalkenes are important structural motifs in the design of bioactive compounds, such as homeostasis regulators and mechanism-based enzyme inhibitors. However, it is difficult to control the stereoselectivity of known carbonyl olefination reactions, and olefin metathesis is limited to disubstituted terminal monofluoroalkenes. Although sulfoximines have been used extensively in organic synthesis, reports on their use in carbonyl olefination reactions have not appeared to date. Herein, we report highly stereoselective carbonyl monofluoroolefination with a fluorosulfoximine reagent. The potential of this method is demonstrated by the synthesis of MDL 72161 and by the late-stage monofluoromethylenation of complex molecules, such as haloperidol and steroid derivatives. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Predicting Heats of Explosion of Nitroaromatic Compounds through NBO Charges and 15N NMR Chemical Shifts of Nitro Groups

Directory of Open Access Journals (Sweden)

Ricardo Infante-Castillo

2012-01-01

Full Text Available This work presents a new quantitative model to predict the heat of explosion of nitroaromatic compounds using the natural bond orbital (NBO charge and 15N NMR chemical shifts of the nitro groups (15NNitro as structural parameters. The values of the heat of explosion predicted for 21 nitroaromatic compounds using the model described here were compared with experimental data. The prediction ability of the model was assessed by the leave-one-out cross-validation method. The cross-validation results show that the model is significant and stable and that the predicted accuracy is within 0.146 MJ kg−1, with an overall root mean squared error of prediction (RMSEP below 0.183 MJ kg−1. Strong correlations were observed between the heat of explosion and the charges (R2 = 0.9533 and 15N NMR chemical shifts (R2 = 0.9531 of the studied compounds. In addition, the dependence of the heat of explosion on the presence of activating or deactivating groups of nitroaromatic explosives was analyzed. All calculations, including optimizations, NBO charges, and 15NNitro NMR chemical shifts analyses, were performed using density functional theory (DFT and a 6-311+G(2d,p basis set. Based on these results, this practical quantitative model can be used as a tool in the design and development of highly energetic materials (HEM based on nitroaromatic compounds.

CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts.

Science.gov (United States)

Hafsa, Noor E; Arndt, David; Wishart, David S

2015-07-01

The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I', II' and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Enhanced microwave absorption in ZnO/carbonyl iron nano-composites by coating dielectric material

Energy Technology Data Exchange (ETDEWEB)

Zhou Chang [School of Physics and Material Science, Anhui University, Hefei 230036 (China); Key Laboratory of Opto-electronic Information Acquisition and Manipulation Ministry of Education, Anhui University, Hefei 230039 (China); Fang Qingqing, E-mail: physfangqq@126.com [School of Physics and Material Science, Anhui University, Hefei 230036 (China) and Key Laboratory of Opto-electronic Information Acquisition and Manipulation Ministry of Education, Anhui University, Hefei 230039 (China); Yan Fangliang; Wang Weina; Wu Keyue; Liu Yanmei; Lv Qingrong; Zhang Hanming; Zhang Qiping; Li Jinguang; Ding Qiongqiong [School of Physics and Material Science, Anhui University, Hefei 230036 (China); Key Laboratory of Opto-electronic Information Acquisition and Manipulation Ministry of Education, Anhui University, Hefei 230039 (China)

2012-05-15

The microwave absorption properties of zinc oxide/carbonyl iron composite nanoparticles fabricated by high energy ball milling were studied at 0-20 GHz. Experiments showed that ZnO as a kind of dielectric material coating carbonyl iron particles made the bandwidth of reflection loss (RL)<-5 dB expanding to the low frequency, and enhanced absorption effect obviously. For a 3 mm thickness absorber of ZnO/carbonyl iron after 30 h milling, the values of RL<-5 dB and RL<-8 dB were obtained in the frequency range from 7.0 GHz to 17.8 GHz and from 9.8 dB to 14.9 dB, respectively, and its strongest RL peak was -29.34 dB at 13.59 GHz. The magnetic loss of carbonyl iron particles and the dielectric loss of ZnO particles were the main mechanisms of microwave absorption for the composites. - Highlights: Black-Right-Pointing-Pointer We fabricated zinc oxide/carbonyl iron composites by high energy ball milling. Black-Right-Pointing-Pointer ZnO dielectric property increased absorption effect and absorption bandwidth. Black-Right-Pointing-Pointer Absorbing frequence of composites is expanding to low frequency direction. Black-Right-Pointing-Pointer The craft of high energy ball milling is easy to realize commerce production.

Enhanced microwave absorption in ZnO/carbonyl iron nano-composites by coating dielectric material

International Nuclear Information System (INIS)

Zhou Chang; Fang Qingqing; Yan Fangliang; Wang Weina; Wu Keyue; Liu Yanmei; Lv Qingrong; Zhang Hanming; Zhang Qiping; Li Jinguang; Ding Qiongqiong

2012-01-01

The microwave absorption properties of zinc oxide/carbonyl iron composite nanoparticles fabricated by high energy ball milling were studied at 0–20 GHz. Experiments showed that ZnO as a kind of dielectric material coating carbonyl iron particles made the bandwidth of reflection loss (RL)<−5 dB expanding to the low frequency, and enhanced absorption effect obviously. For a 3 mm thickness absorber of ZnO/carbonyl iron after 30 h milling, the values of RL<−5 dB and RL<−8 dB were obtained in the frequency range from 7.0 GHz to 17.8 GHz and from 9.8 dB to 14.9 dB, respectively, and its strongest RL peak was −29.34 dB at 13.59 GHz. The magnetic loss of carbonyl iron particles and the dielectric loss of ZnO particles were the main mechanisms of microwave absorption for the composites. - Highlights: ► We fabricated zinc oxide/carbonyl iron composites by high energy ball milling. ► ZnO dielectric property increased absorption effect and absorption bandwidth. ► Absorbing frequence of composites is expanding to low frequency direction. ► The craft of high energy ball milling is easy to realize commerce production.

Parameter-free calculation of K alpha chemical shifts for Al, Si, and Ge oxides

DEFF Research Database (Denmark)

Lægsgaard, Jesper

2001-01-01

The chemical shifts of the K alpha radiation line from Al, Si, and Ge ions between their elemental and oxide forms are calculated within the framework of density functional theory using ultrasoft pseudopotentials. It is demonstrated that this theoretical approach yields quantitatively accurate...... results fur the systems investigated, provided that relaxations of the valence electrons upon the core-hole transition are properly accounted for. Therefore, such calculations provide a powerful tool for identification of impurity states based on x-ray fluorescence data. Results for an Al impurity...

Determination of Carbonyl Compounds in Cigarette Mainstream Smoke. The CORESTA 2010 Collaborative Study and Recommended Method

Directory of Open Access Journals (Sweden)

Intorp M

2014-12-01

Full Text Available A recommended method has been developed and published by CORESTA, applicable to the quantification of selected carbonyl compounds (acetaldehyde, formaldehyde, acetone, acrolein, methyl ethyl ketone, crotonaldehyde, propionaldehyde and butyraldehyde in cigarette mainstream smoke. The method involved smoke collection in impinger traps, derivatisation of carbonyls with 2,4-dinitrophenylhydrazine (DNPH, separation of carbonyl hydrazones by reversed phase high performance liquid chromatography and detection by ultra violet or diode array.

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Journals; Journal of Chemical Sciences; Volume 123; Issue 5 ... to study the decay of the excited states and the fast reactions of photo produced ... Ruthenium(II) carbonyl complexes containing chalconates and triphenylphosphine/arsine ..... Diversity in electrochemical oxidation of dihydroxybenzenes in the presence ...

A Bayesian-probability-based method for assigning protein backbone dihedral angles based on chemical shifts and local sequences

Energy Technology Data Exchange (ETDEWEB)

Wang Jun; Liu Haiyan [University of Science and Technology of China, Hefei National Laboratory for Physical Sciences at the Microscale, and Key Laboratory of Structural Biology, School of Life Sciences (China)], E-mail: hyliu@ustc.edu.cn

2007-01-15

Chemical shifts contain substantial information about protein local conformations. We present a method to assign individual protein backbone dihedral angles into specific regions on the Ramachandran map based on the amino acid sequences and the chemical shifts of backbone atoms of tripeptide segments. The method uses a scoring function derived from the Bayesian probability for the central residue of a query tripeptide segment to have a particular conformation. The Ramachandran map is partitioned into representative regions at two levels of resolution. The lower resolution partitioning is equivalent to the conventional definitions of different secondary structure regions on the map. At the higher resolution level, the {alpha} and {beta} regions are further divided into subregions. Predictions are attempted at both levels of resolution. We compared our method with TALOS using the original TALOS database, and obtained comparable results. Although TALOS may produce the best results with currently available databases which are much enlarged, the Bayesian-probability-based approach can provide a quantitative measure for the reliability of predictions.

Instrument for Airborne Measurement of Carbonyl Sulfide, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — Southwest Sciences proposes to develop small, low power instrumentation for the real-time direct measurement of carbonyl sulfide (OCS) in the atmosphere, especially...

Solubilization and localization of weakly polar lipids in unsonicated egg phosphatidylcholine: A 13C MAS NMR study

International Nuclear Information System (INIS)

Hamilton, J.A.; Fujito, D.T.; Hammer, C.F.

1991-01-01

The weakly polar lipids cholesteryl ester, triacylglycerol, and diacylglycerol incorporate to a limited extent into the lamellar structure of small unilamellar vesicles. The localization of the carbonyl group(s) at the aqueous interface was detected by [ 13 C]carbonyl chemical shift changes relative to the neat unhydrated lipid. This study uses 13 C NMR to investigate the interactions of thes lipids with unsonicated (multilamellar) phosphatidylcholine, a model system for cellular membranes and surfaces of emulsion particles with low curvature. Magic angle spinning reduced the broad lines of the unsonicated dispersions to narrow lines comparable to those from sonicated dispersions. [ 13 C]Carbonyl chemical shifts revealed incorporation of the three lipids into the lamellar structure of the unsonicated phospholipids and a partial hydration of the carbonyl groups similar to that observed in small vesicles. Other properties of interfacial weakly polar lipids in multilayers were similar to those in small unilamellar bilayers. There is thus a general tendency of weakly polar lipids to incorparate at least to a small extent into the lamellar structure of phospholipids and take on interfacial properties that are distinct from their bulk-phase properties. This pool of surface-located lipid is likely to be directly involved in enzymatyic transformations and protein-mediated transport. The 13 C magic angle spinning NMR method may be generally useful for determining the orientation of molecules in model membranes

Instrument for Airborne Measurement of Carbonyl Sulfide, Phase II

Data.gov (United States)

National Aeronautics and Space Administration — In this Phase II SBIR program, Southwest Sciences will continue the development of small, low power instrumentation for real-time direct measurement of carbonyl...

Anchoring selenido-carbonyl ruthenium clusters to functionalized silica xerogels

International Nuclear Information System (INIS)

Cauzzi, Daniele; Graiff, Claudia; Pattacini, Roberto; Predieri, Giovanni; Tiripicchio, Antonio

2003-01-01

Silica Xerogels containing carbonyl Ru 3 Se 2 nido clusters were prepared in three different ways. The simple dispersion of [Ru 3 (μ 3 -Se) 2 (CO) 7 (PPh 3 ) 2 ] via sol gel process produces an inhomogeneous material; by contrast, homogeneous xerogels were obtained by reaction of [Ru 3 (μ 3 -Se) 2 (CO) 8 (PPh 3 )] with functionalized xerogels containing grafted diphenylphosphine moieties and by reaction of [Ru 3 (CO) 12 ] with a xerogel containing grafted phosphine-selenide groups. The reaction between [Ru 3 (CO) 12 ] and dodecyl diphenylphosphine selenide led to the formation of four selenido carbonyl clusters, which are soluble in hydrocarbon solvents and can be deposited as thin films from their solution by slow evaporation. (author)

Low pressure carbonylation of benzyl chloride = Die carbonylierung von benzylchlorid bei niedrigen drücken

OpenAIRE

Luggenhorst, H.J.; Westerterp, K.R.

1986-01-01

For carbonylations, metal carbonyls, particularly cobalt and iron carbonyls, are often used as catalysts. These reactions take place under rather drastic reaction conditions, e.g. 200–300 °C and 60–100 MPa. In some patents it is stated that similar reactions using the same catalysts can also be carried out under rather mild reaction conditions, such as 0–100 °C and 0–2.5 MPa. We studied the conversion of benzyl chloride to phenyl acetic methyl ester in a semi-batch reactor in which one of the...

Carbonyl compounds and PAH emissions from CNG heavy-duty engine

International Nuclear Information System (INIS)

Gambino, M.; Cericola, R.; Corbo, P.; Iannaccone, S.

1993-01-01

Previous works carried out in Istituto Motori laboratories have shown that natural gas is a suitable fuel for general means of transportation. This is because of its favorable effects on engine performance and pollutant emissions. The natural gas fueled engine provided the same performance as the diesel engine, met R49 emission standards, and showed very low smoke levels. On the other hand, it is well known that internal combustion engines emit some components that are harmful for human health, such as carbonyl compounds and polycyclic aromatic hydrocarbons (PAH). This paper shows the results of carbonyl compounds and PAH emissions analysis for a heavy-duty Otto cycle engine fueled with natural gas. The engine was tested using the R49 cycle that is used to measure the regulated emissions. The test analysis has been compared with an analysis of a diesel engine, tested under the same conditions. Total PAH emissions from the CNG engine were about three orders of magnitude lower than from the diesel engine. Formaldehyde emission from the CNG engine was about ten times as much as from the diesel engine, while emissions of other carbonyl compounds were comparable

Selective transformation of carbonyl ligands to organic molecules

Energy Technology Data Exchange (ETDEWEB)

Cutler, A.R.

1992-05-12

Studies on the carbonylation of ({eta}{sup 5}-indenyl)(L)(CO)Ru-R complexes (L = CO, PPh{sub 3}; R = CH{sub 2}OMe, CH{sub 3}) have been completed. Particularly noteworthy is that the methoxymethyl complexes readily transform to their acyl derivatives under mild conditions that leave their iron congeners inert towards CO. Surprisingly, even ({eta}{sup 5}-indenyl)(PPh{sub 3}){sub 2}Ru-CH{sub 3} carbonylates and gives ({eta}{sup 5}-indenyl)(PPh{sub 3})(CO)Ru-C(O)CH{sub 3}. Mechanistic studies on the non catalyzed'' hydrosilation of the manganese acyls (CO){sub 5}Mn-C(O)CH{sub 2}R (R = H, OCH{sub 3}, CH{sub 3}) with Et{sub 3}SiH and of cobalt acetyls (CO){sub 3}(PR{sub 3})CoC(O)CH{sub 3} with several monohydrosilanes have been completed. The cobalt acetyls cleanly give ethoxysilanes (not acetaldehyde), and the manganese acyls provide {alpha}-siloxyvinyl complexes Z-(CO){sub 5}Mn-C(OSiEt{sub 3})=CHR (R = H, CH{sub 3}, OCH{sub 3}). Carbonylation and protolytic cleavage of the latter generate pyruvoyl complexes (CO){sub 5}Mn-COCOR (R = CH{sub 3}, CH{sub 2}CH{sub 3}), formally the products of net double carbonylation'' sequences. Studies in progress are concerned with how manganese complexes as diverse as (CO){sub 5}Mn-Y (Y = C(O)R, R, BR - but not SiMe{sub 3} or Mn(CO){sub 5}) and ({eta}{sup 3}-C{sub 3}H{sub 5})Mn(CO){sub 2}L (but not CpMn(CO){sub 3} or CpMn(CO){sub 2}({eta}{sup 2}HSiR{sub 3})) function as efficient hydrosilation catalysts towards Cp(CO){sub 2}FeC(O)CH{sub 3}, for example. These reactions cleanly afford fully characterized {alpha}-siloxyethyl complexes Fp-CH(OSiR{sub 3})CH{sub 3} under conditions where typically Rh(1) hydrosilation catalysts are inactive. Several of these manganese complexes also catalytically hydrosilate organic esters, including lactones, to their ethers R-CH{sub 2}OR; these novel ester reductions occur quantitatively at room temperature and appear to be general in scope.

Comparison of sampling methods for radiocarbon dating of carbonyls in air samples via accelerator mass spectrometry

Energy Technology Data Exchange (ETDEWEB)

Schindler, Matthias, E-mail: matthias.schindler@physik.uni-erlangen.de; Kretschmer, Wolfgang; Scharf, Andreas; Tschekalinskij, Alexander

2016-05-15

Three new methods to sample and prepare various carbonyl compounds for radiocarbon measurements were developed and tested. Two of these procedures utilized the Strecker synthetic method to form amino acids from carbonyl compounds with either sodium cyanide or trimethylsilyl cyanide. The third procedure used semicarbazide to form crystalline carbazones with the carbonyl compounds. The resulting amino acids and semicarbazones were then separated and purified using thin layer chromatography. The separated compounds were then combusted to CO{sub 2} and reduced to graphite to determine {sup 14}C content by accelerator mass spectrometry (AMS). All of these methods were also compared with the standard carbonyl compound sampling method wherein a compound is derivatized with 2,4-dinitrophenylhydrazine and then separated by high-performance liquid chromatography (HPLC).

Comparison of sampling methods for radiocarbon dating of carbonyls in air samples via accelerator mass spectrometry

Science.gov (United States)

Schindler, Matthias; Kretschmer, Wolfgang; Scharf, Andreas; Tschekalinskij, Alexander

2016-05-01

Three new methods to sample and prepare various carbonyl compounds for radiocarbon measurements were developed and tested. Two of these procedures utilized the Strecker synthetic method to form amino acids from carbonyl compounds with either sodium cyanide or trimethylsilyl cyanide. The third procedure used semicarbazide to form crystalline carbazones with the carbonyl compounds. The resulting amino acids and semicarbazones were then separated and purified using thin layer chromatography. The separated compounds were then combusted to CO2 and reduced to graphite to determine 14C content by accelerator mass spectrometry (AMS). All of these methods were also compared with the standard carbonyl compound sampling method wherein a compound is derivatized with 2,4-dinitrophenylhydrazine and then separated by high-performance liquid chromatography (HPLC).

Enzyme-like specificity in zeolites: a unique site position in mordenite for selective carbonylation of methanol and dimethyl ether with CO.

Science.gov (United States)

Boronat, Mercedes; Martínez-Sánchez, Cristina; Law, David; Corma, Avelino

2008-12-03

The mechanism of methanol carbonylation at different positions of zeolite MOR is investigated by quantum-chemical methods in order to discover which are the active sites that can selectively catalyze the desired reaction. It is shown that when methanol carbonylation competes with hydrocarbon formation, the first reaction occurs preferentially within 8MR channels. However, the unique selectivity for the carbonylation of methanol and dimethyl ether in mordenite is not only due to the size of the 8MR channel: neither process occurs equally at the two T3-O31 and T3-O33 positions. We show that only the T3-O33 positions are selective and that this selectivity is due to the unusual orientation of the methoxy group in relation to the 8MR channel (parallel to the cylinder axis). Only in this situation does the transition state for the attack of CO fit perfectly in the 8MR channel, while the reaction with methanol or DME is sterically impeded. This result explains why T3-O31, while also located in the 8MR channel of mordenite, is not as selective as the T3-O33 position and why ferrierite, although it contains 8MR channels, is less selective than mordenite. The competing effect of water is explained at the molecular level, and the molecular microkinetic reaction model has been established.

Plasma protein carbonyl levels and breast cancer risk

Czech Academy of Sciences Publication Activity Database

Rössner ml., Pavel; Terry, M. B.; Gammon, M. D.; Agrawal, M.; Zhang, F. F.; Ferris, J.S.; Teitelbaum, S. L.; Eng, S. M.; Gaudet, M. M.; Neugut, A. I.; Santella, R. M.

2007-01-01

Roč. 11, č. 5 (2007), s. 1138-1148 ISSN 1582-1838 Institutional research plan: CEZ:AV0Z50390512 Keywords : oxidative stress * protein carbonyl * breast cancer Subject RIV: DN - Health Impact of the Environment Quality Impact factor: 6.807, year: 2007

Nonsuppressing normal thymus on chemical-shift MR imaging and anterior mediastinal lymphoma. Differentiation with diffusion-weighted MR imaging by using the apparent diffusion coefficient

International Nuclear Information System (INIS)

Priola, Adriano Massimiliano; Priola, Sandro Massimo; Gned, Dario; Veltri, Andrea; Giraudo, Maria Teresa

2018-01-01

To prospectively evaluate usefulness of the apparent diffusion coefficient (ADC) in differentiating anterior mediastinal lymphoma from nonsuppressing normal thymus on chemical-shift MR, and to look at the relationship between patient age and ADC. Seventy-three young subjects (25 men, 48 women; age range, 9-29 years), who underwent chemical-shift MR and diffusion-weighted MR were divided into a normal thymus group (group A, 40 subjects), and a lymphoma group (group B, 33 patients). For group A, all subjects had normal thymus with no suppression on opposed-phase chemical-shift MR. Two readers measured the signal intensity index (SII) and ADC. Differences in SII and ADC between groups were tested using t-test. ADC was correlated with age using Pearson correlation coefficient. Mean SII±standard deviation was 2.7±1.8% for group A and 2.2±2.4% for group B, with no significant difference between groups (P=.270). Mean ADC was 2.48±0.38 x 10 -3 mm 2 /s for group A and 1.24±0.23 x 10 -3 mm 2 /s for group B. A significant difference between groups was found (P<.001), with no overlap in range. Lastly, significant correlation was found between age and ADC (r=0.935, P<.001) in group A. ADC of diffusion-weighted MR is a noninvasive and accurate parameter for differentiating lymphoma from nonsuppressing thymus on chemical-shift MR in young subjects. (orig.)

Proteomic evaluation of myofibrillar carbonylation in chilled fish mince and its inhibition by catechin.

Science.gov (United States)

Pazos, Manuel; Maestre, Rodrigo; Gallardo, José M; Medina, Isabel

2013-01-01

The present study investigates the susceptibility of individual myofibrillar proteins from mackerel (Scomber scombrus) mince to undergo carbonylation reactions during chilled storage, and the antioxidant capacity of (+)-catechin to prevent oxidative processes of proteins. The carbonylation of each particular protein was quantified by combining the labelling of protein carbonyls by fluorescein-5-thiosemicarbazide (FTSC) with 1-D or 2-D gel electrophoresis. Alpha skeletal actin, glycogen phosphorylase, unnamed protein product (UNP) similar to enolase, pyruvate kinase, isoforms of creatine kinase, aldolase A and an isoform of glyceraldehyde 3-phosphate dehydrogenase (G3PDH) showed elevated oxidation in chilled non-supplemented mince. Myosin heavy chain (MHC) was not carbonylated in chilled muscle, but an extensive MHC degradation was observed in those samples. The supplementation of catechin reduced protein oxidation and lipid oxidation in a concentration-dependent manner: control>25>100≈200ppm. Therefore, the highest catechin concentrations (100 and 200ppm) exhibited the strongest antioxidant activity. Catechin (200ppm) reduced significantly carbonylation of protein spots identified as glycogen phosphorylase, pyruvate kinase muscle isozyme, isoforms of creatine kinase. Conversely, catechin was ineffective to inhibit the oxidation of actin and UNP similar to enolase. These results draw attention to the inefficiency of catechin to prevent actin oxidation, in contrast to the extremely high efficiency of catechin in inhibiting oxidation of lipids and other proteins. Copyright © 2012 Elsevier Ltd. All rights reserved.

MR chemical shift imaging and spectroscopy of atherosclerotic plaque

International Nuclear Information System (INIS)

Vinitski, S.; Consigny, P.M.; Shapiro, M.J.; Janes, N.; Smullens, S.N.; Rifkin, M.D.

1989-01-01

The purpose of this study was to develop a technique for in vivo imaging and characterization of atherosclerotic plaque. The authors used a spin-echo technique with a short echo time (TE) of 11 msec. Lipid/water suppression was achieved by means of hybrid chemical shift imaging. Lesions were induced in three rabbits by a combination of balloon denudation of the abdominal aorta and a high-cholesterol diet. Following in vivo imaging of these rabbit aortas and human carotid arteries (1.5 T), the animals were killed or carotid endarterectomy was performed so that the plaques could be excised. The plaques were then analyzed in vitro both histologically and with high-resolution spectroscopy (8.5 T). Use of the short TE improved lesion visualization. The fat/water suppression showed only a small amount of mobile lipids in plaque. Both MR spectroscopic and histologic analysis corroborated these images. The composition of atherosclerotic plaques in both humans and rabbits was demonstrated to be heterogeneous, with predominantly nonmobile lipids. These results suggest that the combination of short TE MR imaging and fat/water suppression can identify plaque and delineate areas containing mobile lipids

Study of α-monosubstituted methyl acetates by C-13 and H-1 Nuclear Magnetic resonance

International Nuclear Information System (INIS)

Silva, E.L.

1987-01-01

The substituents effects on the methylene and carbonyl carbons chemical shifts of some α-monosubstituted methyl acetates Z-CH 2 -COOMe(Z=H,Cl,Br,I,OME,SMe,NMe 2 and Me) is studied. Some data of Carbon 13 NMr in the light of the substituents empirical and electronic effects are shown. Solvent and concentration effects on the hydrogen-1 chemical shifts of methyl acetate, bromoacetate and Iodoacetate were interpreted in the light of the Cα-C(O)-bond rotational isomerism. (M.J.C.) [pt

Nicotine and Carbonyl Emissions From Popular Electronic Cigarette Products: Correlation to Liquid Composition and Design Characteristics.

Science.gov (United States)

El-Hellani, Ahmad; Salman, Rola; El-Hage, Rachel; Talih, Soha; Malek, Nathalie; Baalbaki, Rima; Karaoghlanian, Nareg; Nakkash, Rima; Shihadeh, Alan; Saliba, Najat A

2018-01-05

Available in hundreds of device designs and thousands of flavors, electronic cigarette (ECIG) may have differing toxicant emission characteristics. This study assesses nicotine and carbonyl yields in the most popular brands in the U.S. market. These products included disposable, prefilled cartridge, and tank-based ECIGs. Twenty-seven ECIG products of 10 brands were procured and their power outputs were measured. The e-liquids were characterized for pH, nicotine concentration, propylene glycol/vegetable glycerin (PG/VG) ratio, and water content. Aerosols were generated using a puffing machine and nicotine and carbonyls were, respectively, quantified using gas chromatograph and high-performance liquid chromatography. A multiregression model was used to interpret the data. Nicotine yields varied from 0.27 to 2.91 mg/15 puffs, a range corresponding to the nicotine yield of less than 1 to more than 3 combustible cigarettes. Nicotine yield was highly correlated with ECIG type and brand, liquid nicotine concentration, and PG/VG ratio, and to a lower significance with electrical power, but not with pH and water content. Carbonyls, including the carcinogen formaldehyde, were detected in all ECIG aerosols, with total carbonyl concentrations ranging from 3.72 to 48.85 µg/15 puffs. Unlike nicotine, carbonyl concentrations were mainly correlated with power. In 15 puffs, some ECIG devices emit nicotine quantities that exceed those of tobacco cigarettes. Nicotine emissions vary widely across products but carbonyl emissions showed little variations. In spite of that ECIG users are exposed to toxicologically significant levels of carbonyl compounds, especially formaldehyde. Regression analysis showed the importance of design and e-liquid characteristics as determinants of nicotine and carbonyl emissions. Periodic surveying of characteristics of ECIG products available in the marketplace is valuable for understanding population-wide changes in ECIG use patterns over time. © The

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

Science.gov (United States)

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.

Solid state NMR of proteins at high MAS frequencies: symmetry-based mixing and simultaneous acquisition of chemical shift correlation spectra

International Nuclear Information System (INIS)

Bellstedt, Peter; Herbst, Christian; Häfner, Sabine; Leppert, Jörg; Görlach, Matthias; Ramachandran, Ramadurai

2012-01-01

We have carried out chemical shift correlation experiments with symmetry-based mixing sequences at high MAS frequencies and examined different strategies to simultaneously acquire 3D correlation spectra that are commonly required in the structural studies of proteins. The potential of numerically optimised symmetry-based mixing sequences and the simultaneous recording of chemical shift correlation spectra such as: 3D NCAC and 3D NHH with dual receivers, 3D NC′C and 3D C′NCA with sequential 13 C acquisitions, 3D NHH and 3D NC′H with sequential 1 H acquisitions and 3D CANH and 3D C’NH with broadband 13 C– 15 N mixing are demonstrated using microcrystalline samples of the β1 immunoglobulin binding domain of protein G (GB1) and the chicken α-spectrin SH3 domain.

Calculation of 125Te NMR Chemical Shifts at the Full Four-Component Relativistic Level with Taking into Account Solvent and Vibrational Corrections: A Gateway to Better Agreement with Experiment.

Science.gov (United States)

Rusakova, Irina L; Rusakov, Yuriy Yu; Krivdin, Leonid B

2017-06-29

Four-component relativistic calculations of 125 Te NMR chemical shifts were performed in the series of 13 organotellurium compounds, potential precursors of the biologically active species, at the density functional theory level under the nonrelativistic and four-component fully relativistic conditions using locally dense basis set scheme derived from relativistic Dyall's basis sets. The relativistic effects in tellurium chemical shifts were found to be of as much as 20-25% of the total calculated values. The vibrational and solvent corrections to 125 Te NMR chemical shifts are about, accordingly, 6 and 8% of their total values. The PBE0 exchange-correlation functional turned out to give the best agreement of calculated tellurium shifts with their experimental values giving the mean absolute percentage error of 4% in the range of ∼1000 ppm, provided all corrections are taken into account.

The use of biodiesel blends on a non-road generator and its impacts on ozone formation potentials based on carbonyl emissions

International Nuclear Information System (INIS)

Chai, Ming; Lu, Mingming; Liang, Fuyan; Tzillah, Aisha; Dendramis, Nancy; Watson, Libya

2013-01-01

In this study, emissions of carbonyl compounds from the use B50 and B100 were measured with a non-road diesel generator. A total of 25 carbonyl compounds were identified in the exhaust, including 10 with laboratory-synthesized standards. Formaldehyde, acetaldehyde, and acrolein were found as the most abundant carbonyl compounds emitted for both diesel and biodiesel. The sulphur content of diesel fuels and the source of biodiesel fuels were not found to have a significant impact on the emission of carbonyl compounds. The overall maximum incremental reactivity (MIR) was the highest at 0 kW and slightly increased from 25 to 75 kW. The MIR of B100 was the highest, followed by diesel and B50, which is consistent with the emission rates of total carbonyl compounds. This suggests that the use of biodiesel blends may be more beneficial to the environment than using pure biodiesel. -- Highlights: •Carbonyl compound emission from biodiesel blends combustion on a non-road generator. •25 compounds were identified, including 10 by laboratory-synthesized standards. •Sources of biodiesel have insignificant impacts on carbonyl compounds emission. •Sulphur contents have insignificant impacts on carbonyl compounds emission. •MIR of emitted carbonyls decreases in the following order: B100, diesel, B50. -- The study found that B50 resulted in lower total carbonyl emission rates and ozone formation potential resultant from these compounds, whereas both increased with B100

Frustrated Lewis pairs-assisted reduction of carbonyl compounds

DEFF Research Database (Denmark)

Marek, Ales; Pedersen, Martin Holst Friborg

2015-01-01

An alternative and robust method for the reduction of carbonyl groups by frustrated Lewis pairs (FLPs) is reported in this paper. With its very mild reaction conditions, good to excellent yields, absolute regioselectivity and the non-metallic character of the reagent, it provides an excellent too...

A New Paradigm for Chemical Engineering?

DEFF Research Database (Denmark)

Gani, Rafiqul

evidence of this change comes from the jobs taken by graduating chemical engineering professionals in North America, Europe, and some of the Asian countries. In terms of where the graduating chemical engineers are going to work, a clear shift from the commodity chemical industry to the product oriented...... businesses has been observed. There is an increasing trend within the chemical industry to focus on products and the sustainable processes that can make them. Do these changes point to a paradigm shift in chemical engineering as a discipline? Historically, two previous paradigm shifts in chemical engineering...... corresponded to major shifts in chemical engineering as a discipline, which affected not only the education of chemical engineers, but also the development of chemical engineering as a discipline. Has the time come for a new paradigm shift that will prepare the current and future chemical engineering graduates...

Deoxygenative gem-difluoroolefination of carbonyl compounds with (chlorodifluoromethyltrimethylsilane and triphenylphosphine

Directory of Open Access Journals (Sweden)

Fei Wang

2014-02-01

Full Text Available Background: 1,1-Difluoroalkenes cannot only be used as valuable precursors for organic synthesis, but also act as bioisosteres for enzyme inhibitors. Among various methods for their preparation, the carbonyl olefination with difluoromethylene phosphonium ylide represents one of the most straightforward methods.Results: The combination of (chlorodifluoromethyltrimethylsilane (TMSCF2Cl and triphenylphosphine (PPh3 can be used for the synthesis of gem-difluoroolefins from carbonyl compounds. Comparative experiments demonstrate that TMSCF2Cl is superior to (bromodifluoromethyltrimethylsilane (TMSCF2Br and (trifluoromethyltrimethylsilane (TMSCF3 in this reaction.Conclusion: Similar to many other Wittig-type gem-difluoroolefination reactions in the presence of PPh3, the reaction of TMSCF2Cl with aldehydes and activated ketones is effective.

Reaction of acid esters of methylenebis(phosphonous acid) with carbonyl compounds

International Nuclear Information System (INIS)

Novikova, Z.S.; Odinets, I.L.; Lutsenko, I.F.

1987-01-01

The reaction of methylenebis(phosphonites) containing two hydrophosphoryl groupings with aliphatic and aromatic aldehydes and ketones in the presence of alkali metal fluorides leads to methylenebis(α-hydroxyalkylphosphinates). The reaction of methylenebis(phosphonites) containing one hydrophosphoryl groupings with carbonyl compounds in the presence of alkali metal fluorides proceeds with the formation of a new type of heterocyclic phosphorus compound, viz., 1,2λ 3 ,4λ 5 -oxadiphospholanes. The reaction of acid esters of methylenebis(phosphonous) acid with carbonyl compounds in the presence of alkali metal alkoxides or a tertiary amine is accompanied by phosphinate-phosphonate rearrangement of the intermediately formed α-hydroxylalkylphosphinates

Unsuitability of using the DNPH-coated solid sorbent cartridge for determination of airborne unsaturated carbonyls

Science.gov (United States)

Ho, Steven Sai Hang; Ho, K. F.; Liu, W. D.; Lee, S. C.; Dai, W. T.; Cao, J. J.; Ip, H. S. S.

2011-01-01

Measurements of aldehydes and ketones are typically conducted by derivatization using sorbent cartridges coated with 2,4-dinitrophenylhydrazine (DNPH). The collected samples are eluted with acetonitrile and analyzed by high-pressure liquid chromatography coupled with an ultra-violet detector (HPLC/UV). This paper intends to examine artifacts about its suitability in identification of unsaturated carbonyls. Kinetic tests for acrolein, crotonaldehyde, methacrolein and methyl vinyl ketone (MVK) showed formations of carbonyl-DNP-hydrazone during sampling, which could further react with DNPH, resulting in undesired UV absorption products [e.g., carbonyl-DNP-hydrazone-DNPH (dimer) and 2(carbonyl-DNP-hydrazone)-DNPH (trimer)]. The dimerization and trimerization occurred for acrolein and MVK whereas only dimerization for crotonaldehyde and methacrolein. The polymerization products undoubtedly affect the integrity of the chromatogram, leading to misidentification and inaccurate quantification. Whether precautions taken during sampling and/or sample treatment could avoid or minimize this artifact has not been thoughtfully investigated. More often, such artifacts are usually overlooked by scientists when the data are reported.

Cross-talk between lipid and protein carbonylation in a dynamic cardiomyocyte model of mild nitroxidative stress

Directory of Open Access Journals (Sweden)

Eva Griesser

2017-04-01

Full Text Available Reactive oxygen and nitrogen species (ROS/RNS play an important role in the regulation of cardiac function. Increase in ROS/RNS concentration results in lipid and protein oxidation and is often associated with onset and/or progression of many cardiovascular disorders. However, interplay between lipid and protein modifications has not been simultaneously studied in detail so far. Biomolecule carbonylation is one of the most common biomarkers of oxidative stress. Using a dynamic model of nitroxidative stress we demonstrated rapid changes in biomolecule carbonylation in rat cardiomyocytes. Levels of carbonylated species increased as early as 15 min upon treatment with the peroxynitrite donor, 3-morpholinosydnonimine (SIN-1, and decreased to values close to control after 16 h. Total (lipids+proteins vs. protein-specific carbonylation showed different dynamics, with a significant increase in protein-bound carbonyls at later time points. Treatment with SIN-1 in combination with inhibitors of proteasomal and autophagy/lysosomal degradation pathways allowed confirmation of a significant role of the proteasome in the degradation of carbonylated proteins, whereas lipid carbonylation increased in the presence of autophagy/lysosomal inhibitors. Electrophilic aldehydes and ketones formed by lipid peroxidation were identified and relatively quantified using LC-MS/MS. Molecular identity of reactive species was used for data-driven analysis of their protein targets. Combination of different enrichment strategies with LC-MS/MS analysis allowed identification of more than 167 unique proteins with 332 sites modified by electrophilic lipid peroxidation products. Gene ontology analysis of modified proteins demonstrated enrichment of several functional categories including proteins involved in cytoskeleton, extracellular matrix, ion channels and their regulation. Using calcium mobilization assays, the effect of nitroxidative stress on the activity of several ion

Hydrogen exchange rate of tyrosine hydroxyl groups in proteins as studied by the deuterium isotope effect on C(zeta) chemical shifts.

Science.gov (United States)

Takeda, Mitsuhiro; Jee, Jungoo; Ono, Akira Mei; Terauchi, Tsutomu; Kainosho, Masatsune

2009-12-30

We describe a new NMR method for monitoring the individual hydrogen exchange rates of the hydroxyl groups of tyrosine (Tyr) residues in proteins. The method utilizes (2S,3R)-[beta(2),epsilon(1,2)-(2)H(3);0,alpha,beta,zeta-(13)C(4);(15)N]-Tyr, zeta-SAIL Tyr, to detect and assign the (13)C(zeta) signals of Tyr rings efficiently, either by indirect (1)H-detection through 7-8 Hz (1)H(delta)-(13)C(zeta) spin couplings or by direct (13)C(zeta) observation. A comparison of the (13)C(zeta) chemical shifts of three Tyr residues of an 18.2 kDa protein, EPPIb, dissolved in H(2)O and D(2)O, revealed that all three (13)C(zeta) signals in D(2)O appeared at approximately 0.13 ppm ( approximately 20 Hz at 150.9 MHz) higher than those in H(2)O. In a H(2)O/D(2)O (1:1) mixture, however, one of the three signals for (13)C(zeta) appeared as a single peak at the averaged chemical shifts, and the other two appeared as double peaks at exactly the same chemical shifts in H(2)O and D(2)O, in 50 mM phosphate buffer (pH 6.6) at 40 degrees C. These three peaks were assigned to Tyr-36, Tyr-120, and Tyr-30, from the lower to higher chemical shifts, respectively. The results indicate that the hydroxyl proton of Tyr-120 exchanges faster than a few milliseconds, whereas those of Tyr-30 and Tyr-36 exchange more slowly. The exchange rate of the Tyr-30 hydroxyl proton, k(ex), under these conditions was determined by (13)C NMR exchange spectroscopy (EXSY) to be 9.2 +/- 1.1 s(-1). The Tyr-36 hydroxyl proton, however, exchanges too slowly to be determined by EXSY. These profound differences among the hydroxyl proton exchange rates are closely related to their relative solvent accessibility and the hydrogen bonds associated with the Tyr hydroxyl groups in proteins.

Performance test of multicomponent quantum mechanical calculation with polarizable continuum model for proton chemical shift.

Science.gov (United States)

Kanematsu, Yusuke; Tachikawa, Masanori

2015-05-21

Multicomponent quantum mechanical (MC_QM) calculations with polarizable continuum model (PCM) have been tested against liquid (1)H NMR chemical shifts for a test set of 80 molecules. Improvement from conventional quantum mechanical calculations was achieved for MC_QM calculations. The advantage of the multicomponent scheme could be attributed to the geometrical change from the equilibrium geometry by the incorporation of the hydrogen nuclear quantum effect, while that of PCM can be attributed to the change of the electronic structure according to the polarization by solvent effects.

Clinical application of 1H-chemical-shift imaging (CSI) to brain diseases

International Nuclear Information System (INIS)

Naruse, Shoji; Furuya, Seiichi; Ide, Mariko

1992-01-01

An H-1 chemical shift imaging (CSI) was developed as part of the clinical MRI system, by which magnetic resonance spectra (MRS) can be obtained from multiple small voxels and metabolite distribution in the brain can be visualized. The present study was to determine the feasibility and clinical potential of using an H-1 CSI. The device used was a Magnetom H 15 apparatus. The study population was comprised of 25 healthy subjects, 20 patients with brain tumor, 4 with ischemic disease, and 6 with miscellaneous degenerative disease. The H-1 CSI was obtained by the 3-dimensional Fourier transformation. After suppressing the lipid signal by the inversion-recovery method and the water signal by the chemical-shift selective pulse with a following dephasing gradient, 2-directional 16 x 16 phase encodings were applied to the 16 x 16∼18 x 18 cm field of view, in which a 8 x 8 x 2∼10 x 10 x 2 cm area was selected by the stimulated echo or spin-echo method. The metabolite mapping and its contour mapping were created by using the curve-fitted area, with interpolation to the 256 x 256 matrix. In the healthy group, high resolution spectra for N-acetyl aspartate (NAA), creatine, choline (Cho), and glutamine/glutamate were obtained from each voxel; and metabolite mapping and contour mapping also clearly showed metabolite distribution in the brain. In the group of brain tumor, an increased Cho and lactate and loss of NAA were observed, along with heterogeneity within the tumor and changes in the surrounding tissue; and there was a good correlation between lactate peak and tumor malignancy. The group of ischemic and degenerative disease had a decreased NAA and increased lactate on both spectra and metabolite mapping, depending on disease stage. These findings indicated that H-1 CSI is helpful for detecting spectra over the whole brain, as well as for determining metabolite distribution. (N.K.)

Expression, purification, crystallization and preliminary X-ray diffraction analysis of carbonyl reductase from Candida parapsilosis ATCC 7330

International Nuclear Information System (INIS)

Aggarwal, Nidhi; Mandal, P. K.; Gautham, Namasivayam; Chadha, Anju

2013-01-01

The expression, purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies on C. parapsilosis carbonyl reductase are reported. The NAD(P)H-dependent carbonyl reductase from Candida parapsilosis ATCC 7330 catalyses the asymmetric reduction of ethyl 4-phenyl-2-oxobutanoate to ethyl (R)-4-phenyl-2-hydroxybutanoate, a precursor of angiotensin-converting enzyme inhibitors such as Cilazapril and Benazepril. The carbonyl reductase was expressed in Escherichia coli and purified by GST-affinity and size-exclusion chromatography. Crystals were obtained by the hanging-drop vapour-diffusion method and diffracted to 1.86 Å resolution. The asymmetric unit contained two molecules of carbonyl reductase, with a solvent content of 48%. The structure was solved by molecular replacement using cinnamyl alcohol dehydrogenase from Saccharomyces cerevisiae as a search model

On the Confounding Effect of Temperature on Chemical Shift-Encoded Fat Quantification

Science.gov (United States)

Hernando, Diego; Sharma, Samir D.; Kramer, Harald; Reeder, Scott B.

2014-01-01

Purpose To characterize the confounding effect of temperature on chemical shift-encoded (CSE) fat quantification. Methods The proton resonance frequency of water, unlike triglycerides, depends on temperature. This leads to a temperature dependence of the spectral models of fat (relative to water) that are commonly used by CSE-MRI methods. Simulation analysis was performed for 1.5 Tesla CSE fat–water signals at various temperatures and echo time combinations. Oil–water phantoms were constructed and scanned at temperatures between 0 and 40°C using spectroscopy and CSE imaging at three echo time combinations. An explanted human liver, rejected for transplantation due to steatosis, was scanned using spectroscopy and CSE imaging. Fat–water reconstructions were performed using four different techniques: magnitude and complex fitting, with standard or temperature-corrected signal modeling. Results In all experiments, magnitude fitting with standard signal modeling resulted in large fat quantification errors. Errors were largest for echo time combinations near TEinit ≈ 1.3 ms, ΔTE ≈ 2.2 ms. Errors in fat quantification caused by temperature-related frequency shifts were smaller with complex fitting, and were avoided using a temperature-corrected signal model. Conclusion Temperature is a confounding factor for fat quantification. If not accounted for, it can result in large errors in fat quantifications in phantom and ex vivo acquisitions. PMID:24123362

Synthetic and mechanistic aspects of titanium-mediated carbonyl olefinations

Energy Technology Data Exchange (ETDEWEB)

Petasis, N.A.; Staszewski, J.P.; Hu, Yong-Han; Lu, Shao-Po [Univ. of Southern California, Los Angeles, CA (United States)

1995-12-31

A new method for the olefination of carbonyl compounds with dimethyl titanocene, and other related bishydrocarbyl titanocene derivatives has been recently developed in the author`s laboratories. This process is experimentally convenient and works with various types of carbonyl compounds, including aldehydes, ketones, esters, lactones, carbonates, anhydrides, amides, imides, lactams, thioesters, selenoesters, and acylsilanes. More recent studies have focused on the scope and utility of this reaction, including mechanistic studies and synthetic applications. In addition to varying the reaction conditions, the authors have examined several mixed titanocene derivatives and have found ways for carrying out this type of olefination at room temperature, such as the use of tris(trimethylsilyl) titanacyclobutene. The authors have also employed this reaction in the modification of carbohydrates and cyclobutenediones. This olefination was also followed-up with subsequent transformations to produce carbocycles and heterocycles, including tetrahydrofurans and tetrahydropyrans.

Characterization of hydrocarbons, halocarbons and carbonyls in the atmosphere of Hong Kong.

Science.gov (United States)

Guo, H; Lee, S C; Louie, P K K; Ho, K F

2004-12-01

Ambient air quality measurements of 156 species including 39 alkanes, 32 alkenes, 2 alkynes, 24 aromatic hydrocarbons, 43 halocarbons and 16 carbonyls, were carried out for 120 air samples collected at two sampling stations (CW and TW) in 2001 throughout Hong Kong. Spatial variations of volatile organic compounds (VOCs) in the atmosphere were investigated. Levels of most alkanes and alkenes at TW site were higher than that at the CW site, while the BTEX concentrations at the two sites were close. The BTEX ratios at CW and TW were 1.6:10.1:1.0:1.6 and 2.1:10.8:1.0:2.0, respectively. For major halogenated hydrocarbons, the mean concentrations of chloromethane, CFCs 12 and 22 did not show spatial variations at the two sites. However, site-specific differences were observed for trichloroethene and tetrachloroethene. Furthermore, there were no significant differences for carbonyls such as formaldehyde, acetaldehyde and acetone between the two sites. The levels of selected hydrocarbons in winter were 1-5 times that in summer. There were no common seasonal trends for carbonyls in Hong Kong. The ambient level of formaldehyde, the most abundant carbonyl, was higher in summer. However, levels of acetaldehyde, acetone and benzaldehyde in winter were 1.6-3.8 times that in summer. The levels of CFCs 11 and 12, and chloromethane in summer were higher than that in winter. Strong correlation of most hydrocarbons with propene and n-butane suggested that the primary contributors of hydrocarbons were vehicular emissions in Hong Kong. In addition, gasoline evaporation, use of solvents, leakage of liquefied petroleum gas (LPG), natural gas leakage and other industrial emissions, and even biogenic emissions affected the ambient levels of hydrocarbons. The sources of halocarbons were mainly materials used in industrial processes and as solvents. Correlation analysis suggested that photochemical reactions made significant contributions to the ambient levels of carbonyls in summer whereas

Solid state NMR of proteins at high MAS frequencies: symmetry-based mixing and simultaneous acquisition of chemical shift correlation spectra

Energy Technology Data Exchange (ETDEWEB)

Bellstedt, Peter [Fritz Lipmann Institute, Biomolecular NMR spectroscopy, Leibniz Institute for Age Research (Germany); Herbst, Christian [Ubon Ratchathani University, Department of Physics, Faculty of Science (Thailand); Haefner, Sabine; Leppert, Joerg; Goerlach, Matthias; Ramachandran, Ramadurai, E-mail: raman@fli-leibniz.de [Fritz Lipmann Institute, Biomolecular NMR spectroscopy, Leibniz Institute for Age Research (Germany)

2012-12-15

We have carried out chemical shift correlation experiments with symmetry-based mixing sequences at high MAS frequencies and examined different strategies to simultaneously acquire 3D correlation spectra that are commonly required in the structural studies of proteins. The potential of numerically optimised symmetry-based mixing sequences and the simultaneous recording of chemical shift correlation spectra such as: 3D NCAC and 3D NHH with dual receivers, 3D NC Prime C and 3D C Prime NCA with sequential {sup 13}C acquisitions, 3D NHH and 3D NC Prime H with sequential {sup 1}H acquisitions and 3D CANH and 3D C'NH with broadband {sup 13}C-{sup 15}N mixing are demonstrated using microcrystalline samples of the {beta}1 immunoglobulin binding domain of protein G (GB1) and the chicken {alpha}-spectrin SH3 domain.

Characterization of mu s-ms dynamics of proteins using a combined analysis of N-15 NMR relaxation and chemical shift: Conformational exchange in plastocyanin induced by histidine protonations

DEFF Research Database (Denmark)

Hass, M. A. S.; Thuesen, Marianne Hallberg; Christensen, Hans Erik Mølager

2004-01-01

of the exchanging species can be determined independently of the relaxation rates. The applicability of the approach is demonstrated by a detailed analysis of the conformational exchange processes previously observed in the reduced form of the blue copper protein, plastocyanin from the cyanobacteria Anabaena......An approach is presented that allows a detailed, quantitative characterization of conformational exchange processes in proteins on the mus-ms time scale. The approach relies on a combined analysis of NMR relaxation rates and chemical shift changes and requires that the chemical shift...... quantitatively by the correlation between the R-ex terms and the corresponding chemical shift differences of the exchanging species. By this approach, the R-ex terms of N-15 nuclei belonging to contiguous regions in the protein could be assigned to the same exchange process. Furthermore, the analysis...

Dormancy alleviation by NO or HCN leading to decline of protein carbonylation levels in apple (Malus domestica Borkh.) embryos.

Science.gov (United States)

Krasuska, Urszula; Ciacka, Katarzyna; Dębska, Karolina; Bogatek, Renata; Gniazdowska, Agnieszka

2014-08-15

Deep dormancy of apple (Malus domestica Borkh.) embryos can be overcome by short-term pre-treatment with nitric oxide (NO) or hydrogen cyanide (HCN). Dormancy alleviation of embryos modulated by NO or HCN and the first step of germination depend on temporary increased production of reactive oxygen species (ROS). Direct oxidative attack on some amino acid residues or secondary reactions via reactive carbohydrates and lipids can lead to the formation of protein carbonyl derivatives. Protein carbonylation is a widely accepted covalent and irreversible modification resulting in inhibition or alteration of enzyme/protein activities. It also increases the susceptibility of proteins to proteolytic degradation. The aim of this work was to investigate protein carbonylation in germinating apple embryos, the dormancy of which was removed by pre-treatment with NO or HCN donors. It was performed using a quantitative spectrophotometric method, while patterns of carbonylated protein in embryo axes were analyzed by immunochemical techniques. The highest concentration of protein carbonyl groups was observed in dormant embryos. It declined in germinating embryos pre-treated with NO or HCN, suggesting elevated degradation of modified proteins during seedling formation. A decrease in the concentration of carbonylated proteins was accompanied by modification in proteolytic activity in germinating apple embryos. A strict correlation between the level of protein carbonyl groups and cotyledon growth and greening was detected. Moreover, direct in vitro carbonylation of BSA treated with NO or HCN donors was analyzed, showing action of both signaling molecules as protein oxidation agents. Copyright © 2014 Elsevier GmbH. All rights reserved.

CSSI-PRO: a method for secondary structure type editing, assignment and estimation in proteins using linear combination of backbone chemical shifts

International Nuclear Information System (INIS)

Swain, Monalisa; Atreya, Hanudatta S.

2009-01-01

Estimation of secondary structure in polypeptides is important for studying their structure, folding and dynamics. In NMR spectroscopy, such information is generally obtained after sequence specific resonance assignments are completed. We present here a new methodology for assignment of secondary structure type to spin systems in proteins directly from NMR spectra, without prior knowledge of resonance assignments. The methodology, named Combination of Shifts for Secondary Structure Identification in Proteins (CSSI-PRO), involves detection of specific linear combination of backbone 1 H α and 13 C' chemical shifts in a two-dimensional (2D) NMR experiment based on G-matrix Fourier transform (GFT) NMR spectroscopy. Such linear combinations of shifts facilitate editing of residues belonging to α-helical/β-strand regions into distinct spectral regions nearly independent of the amino acid type, thereby allowing the estimation of overall secondary structure content of the protein. Comparison of the predicted secondary structure content with those estimated based on their respective 3D structures and/or the method of Chemical Shift Index for 237 proteins gives a correlation of more than 90% and an overall rmsd of 7.0%, which is comparable to other biophysical techniques used for structural characterization of proteins. Taken together, this methodology has a wide range of applications in NMR spectroscopy such as rapid protein structure determination, monitoring conformational changes in protein-folding/ligand-binding studies and automated resonance assignment

On the Reaction of Carbonyl Diphosphonic Acid with Hydroxylamine and O-alkylhydroxylamines: Unexpected Degradation of P-C-P Bridge.

Science.gov (United States)

Khomich, Olga A; Yanvarev, Dmitry V; Novikov, Roman A; Kornev, Alexey B; Puljulla, Elina; Vepsäläinen, Jouko; Khomutov, Alex R; Kochetkov, Sergey N

2017-06-23

Derivatives of methylenediphosphonic acid possess wide spectra of biological activities and are used in enzymology as research tools as well as in practical medicine. Carbonyl diphosphonic acid is a promising starting building block for synthesis of functionally substituted methylenediphosphonates. Investigation of the interaction of carbonyl diphosphonic acid with hydroxylamine clearly demonstrates that it is impossible to isolate oxime within the pH range 2-12, while only cyanophosphonic and phosphoric acids are the products of the fast proceeding Beckmann-like fragmentation. In the case of O -alkylhydroxylamines, corresponding alcohols are found in the reaction mixtures in addition to cyanophosphonic and phosphoric acids. Therefore, two residues of phosphonic acid being attached to a carbonyl group provide new properties to this carbonyl group, making its oximes very unstable. This principally differs carbonyl diphosphonic acid from structurally related phosphonoglyoxalic acid and other α-ketophosphonates.

Development of 19F-NMR chemical shift detection of DNA B-Z equilibrium using 19F-NMR.

Science.gov (United States)

Nakamura, S; Yang, H; Hirata, C; Kersaudy, F; Fujimoto, K

2017-06-28

Various DNA conformational changes are in correlation with biological events. In particular, DNA B-Z equilibrium showed a high correlation with translation and transcription. In this study, we developed a DNA probe containing 5-trifluoromethylcytidine or 5-trifluoromethylthymidine to detect DNA B-Z equilibrium using 19 F-NMR. Its probe enabled the quantitative detection of B-, Z-, and ss-DNA based on 19 F-NMR chemical shift change.

Olefination of carbonyl compounds: modern and classical methods

Energy Technology Data Exchange (ETDEWEB)

Korotchenko, V N; Nenajdenko, Valentine G; Balenkova, Elizabeth S [Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow (Russian Federation); Shastin, Aleksey V [Institute of Problems of Chemical Physics, Russian Academy of Sciences, Chernogolovka, Moscow Region (Russian Federation)

2004-10-31

The published data on the methods for alkene synthesis by olefination of carbonyl compounds are generalised and systematised. The main attention is given to the use of transition metals and organoelement compounds. The review covers the data on both classical and newly developed methods that are little known to chemists at large.

Olefination of carbonyl compounds: modern and classical methods

Science.gov (United States)

Korotchenko, V. N.; Nenajdenko, Valentine G.; Balenkova, Elizabeth S.; Shastin, Aleksey V.

2004-10-01

The published data on the methods for alkene synthesis by olefination of carbonyl compounds are generalised and systematised. The main attention is given to the use of transition metals and organoelement compounds. The review covers the data on both classical and newly developed methods that are little known to chemists at large.

Adsorption/desorption of low concentration of carbonyl sulfide by impregnated activated carbon under micro-oxygen conditions

International Nuclear Information System (INIS)

Wang, Xueqian; Qiu, Juan; Ning, Ping; Ren, Xiaoguang; Li, Ziyan; Yin, Zaifei; Chen, Wei; Liu, Wei

2012-01-01

Highlights: ► Carbonyl sulfide can be catalytic oxidized by micro-oxygen in the off-gas. ► How to use the trace oxygen for the oxidation of carbonyl sulfide was a challenge. ► The SO 4 2− species in the adsorbent sample were generated by a catalytic oxidation process. - Abstract: Activated carbon modified with different impregnants has been studied for COS removal efficiency under micro-oxygen conditions. Activated carbon modified with Cu(NO 3 ) 2 –CoPcS–KOH (denoted as Cu–Co–KW) is found to have markedly enhanced adsorption purification ability. In the adsorption purification process, the reaction temperature, oxygen concentration, and relative humidity of the gas are determined to be three crucial factors. A breakthrough of 43.34 mg COS/g adsorbent at 60 °S and 30% relative humidity with 1.0% oxygen is shown in Cu–Co–KW for removing COS. The structures of the activated carbon samples are characterized using nitrogen adsorption, and their surface chemical structures are analyzed with X-ray photoelectron spectroscopy (XPS). Modification of Cu(NO 3 ) 2 –CoPcS–KOH appears to improve the COS removal capacity significantly, during which, SO 4 2− is presumably formed, strongly adsorbed, and present in the micropores ranging from 0.7 to 1.5 nm. TPD is used to identify the products containing sulfur species on the carbon surface, where SO 2 and COS are detected in the effluent gas generated from exhausted Cu–Co–KW (denoted Cu–Co–KWE). According to the current study results, the activated carbon impregnated with Cu(NO 3 ) 2 –CoPcS–KOH promises a good candidate for COS adsorbent, with the purified gas meeting requirements for desirable chemical feed stocks.

Adsorption/desorption of low concentration of carbonyl sulfide by impregnated activated carbon under micro-oxygen conditions

Energy Technology Data Exchange (ETDEWEB)

Wang, Xueqian, E-mail: wxqian3000@yahoo.com.cn [Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650093 (China); Qiu, Juan; Ning, Ping; Ren, Xiaoguang; Li, Ziyan; Yin, Zaifei; Chen, Wei; Liu, Wei [Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650093 (China)

2012-08-30

Highlights: Black-Right-Pointing-Pointer Carbonyl sulfide can be catalytic oxidized by micro-oxygen in the off-gas. Black-Right-Pointing-Pointer How to use the trace oxygen for the oxidation of carbonyl sulfide was a challenge. Black-Right-Pointing-Pointer The SO{sub 4}{sup 2-} species in the adsorbent sample were generated by a catalytic oxidation process. - Abstract: Activated carbon modified with different impregnants has been studied for COS removal efficiency under micro-oxygen conditions. Activated carbon modified with Cu(NO{sub 3}){sub 2}-CoPcS-KOH (denoted as Cu-Co-KW) is found to have markedly enhanced adsorption purification ability. In the adsorption purification process, the reaction temperature, oxygen concentration, and relative humidity of the gas are determined to be three crucial factors. A breakthrough of 43.34 mg COS/g adsorbent at 60 Degree-Sign S and 30% relative humidity with 1.0% oxygen is shown in Cu-Co-KW for removing COS. The structures of the activated carbon samples are characterized using nitrogen adsorption, and their surface chemical structures are analyzed with X-ray photoelectron spectroscopy (XPS). Modification of Cu(NO{sub 3}){sub 2}-CoPcS-KOH appears to improve the COS removal capacity significantly, during which, SO{sub 4}{sup 2-} is presumably formed, strongly adsorbed, and present in the micropores ranging from 0.7 to 1.5 nm. TPD is used to identify the products containing sulfur species on the carbon surface, where SO{sub 2} and COS are detected in the effluent gas generated from exhausted Cu-Co-KW (denoted Cu-Co-KWE). According to the current study results, the activated carbon impregnated with Cu(NO{sub 3}){sub 2}-CoPcS-KOH promises a good candidate for COS adsorbent, with the purified gas meeting requirements for desirable chemical feed stocks.

Efficient Conversion of Oximes to the Corresponding Carbonyl Compounds with Tetrabutylammonium Chromate under Aprotic Conditions

International Nuclear Information System (INIS)

Pourali, Ali Reza; Goli, Arezou

2006-01-01

The solubility in several solvents, mildness, simple work-up and absence of side reactions provide advantages of using TBAC in deoximation reactions. This is an efficient and selective method for homogeneous deoximation of structurally different compounds under the moderately acidic and aprotic conditions in high yields. Regeneration of ketones and aldehydes from their oximes has assumed added importance since the discovery of the Barton reaction in which oximes are produced at non-activated hydrocarbon sites. Also, their synthesis from non-carbonyl compounds, such as by nitrosation of an active methylene group, nitrosation of an α-halo carbonyl compound and condensation of a nitro-alkene with an aldehyde provides a valid alternative pathway to carbonyl compounds. Therefore, there has been a continued interest in the effective regeneration of carbonyl compounds from the corresponding oximes especially under mild conditions. Oxidative and reductive methods have been found to show advantages over the classical hydrolytic methods. Although many oxidizing agents have been used, only a limited number of methods are efficient because of the low solubility of these metallic reagents in most organic solvents

Degradation of carbonyl hydroperoxides in the atmosphere and in combustion

KAUST Repository

Xing, Lili; Bao, Junwei Lucas; Wang, Zhandong; Zhang, Feng; Truhlar, Donald G.

2017-01-01

Oxygenates with carbonyl and hydroperoxy functional groups are important intermediates that are generated during the autooxidation of organic compounds in the atmosphere and during the autoignition of transport fuels. In the troposphere

Studies of coupled chemical and catalytic coal conversion methods. Tenth quarterly report, January--March 1990

Energy Technology Data Exchange (ETDEWEB)

Stock, L.M.

1990-12-31

This report concerns our research on base-catalyzed coal solubilization and a new approach for hydrogen addition. The work on base-catalyzed, chemical solubilization is continuing. this report is focused on the hydrogenation research. Specifically it deals with the use of arene chromium carbonyl complexes as reagents for the addition of dideuterium to coal molecules. In one phase of the work, he has established that the aromatic hydrocarbons in a representative coal liquid can be converted in very good yield to arene chromium carbonyl compounds. In a second phase of the work directly related to our objective of improved methods for catalytic hydrogenation, he has established that the aromatic constituents of the same coal liquid add dideuterium in the presence of added napththalene chromium carbonyl.

Proteomic and carbonylation profile analysis of rat skeletal muscles following acute swimming exercise.

Directory of Open Access Journals (Sweden)

Francesca Magherini

Full Text Available Previous studies by us and other groups characterized protein expression variation following long-term moderate training, whereas the effects of single bursts of exercise are less known. Making use of a proteomic approach, we investigated the effects of acute swimming exercise (ASE on protein expression and carbonylation patterns in two hind limb muscles: the Extensor Digitorum Longus (EDL and the Soleus, mostly composed of fast-twitch and slow-twitch fibres, respectively. Carbonylation is one of the most common oxidative modifications of proteins and a marker of oxidative stress. In fact, several studies suggest that physical activity and the consequent increase in oxygen consumption can lead to increase in reactive oxygen and nitrogen species (RONS production, hence the interest in examining the impact of RONS on skeletal muscle proteins following ASE. Results indicate that protein expression is unaffected by ASE in both muscle types. Unexpectedly, the protein carbonylation level was reduced following ASE. In particular, the analysis found 31 and 5 spots, in Soleus and EDL muscles respectively, whose carbonylation is reduced after ASE. Lipid peroxidation levels in Soleus were markedly reduced as well. Most of the decarbonylated proteins are involved either in the regulation of muscle contractions or in the regulation of energy metabolism. A number of hypotheses may be advanced to account for such results, which will be addressed in future studies.

Hexa pyranoside homologation: use of spectral width narrowing, and the chemical shift homonuclear correlation for characterization of the 4,6-0-benzylidene-2,3-di des oxy-3-C-hydroxymethyl-{alpha}-D-methyl ribopyranoside; Homologacao de hexopiranosideos: utilizacao de reducao da largura espectral e de correlacao homonuclear de deslocamentos quimicos para a caracterizacao do 4,6-O-benzilideno-2,3-didesoxi-3-C-hidroximetil-{alpha}-D- ribopiranosideo de metila (7)

Energy Technology Data Exchange (ETDEWEB)

Souza Filho, J D; Silva, L.G. Fonseca e; Oliveira, A Braga de; Alves, R Jose [Minas Gerais Univ., Belo Horizonte, MG (Brazil); Lukacs, G [Centre National de la Recherche Scientifique (CNRS), 91 - Gif-sur-Yvette (France). Inst. de Chimie des Substances Naturelles

1992-12-31

The discovery of ramified sugars as various antibiotics constituents, leads to the development of various preparation technologies. In the framework of hexapiranose analogues synthesis, the alcohol-7 was the intermediary on which functional group interconversion reactions were performed. The carbonyl group reduction with Na B H{sub 4} in MeOH{sup 5} was performed, for obtaining the ethyl alcohol-6 a (99%). Later on, the reaction of stereoselective reduction of the double binding between C-2 and C-3 was conducted in presence of Ni-Ra in Ac O Et, allowing to obtain the two epimer 7 and 7 a alcohols, with 86.9 and 7.5% yield respectively. The 7 {sup 1} H NMR signals were easily assigned by analysing the extended spectrum obtained by narrowing the spectral line. In accordance with predictable multiplicity and H-6{alpha} (Triplet at 3.7 ppm) patterns, the triple doublet H-5, at 4.1 ppm has been assigned. The assignments were confirmed by a chemical shift homonuclear correlation experiment (COSY H-H). H-7, H-7{sup `} and H-4 have been assigned through the H-3. The use of hydroxyl proton as reference (d d, 2.72 ppm) allowed the confirmation of the chemical shift assigned to H-7 and H-7{sup `} 5 refs., 6 figs.

Spin-orbit ZORA and four-component Dirac-Coulomb estimation of relativistic corrections to isotropic nuclear shieldings and chemical shifts of noble gas dimers.

Science.gov (United States)

Jankowska, Marzena; Kupka, Teobald; Stobiński, Leszek; Faber, Rasmus; Lacerda, Evanildo G; Sauer, Stephan P A

2016-02-05

Hartree-Fock and density functional theory with the hybrid B3LYP and general gradient KT2 exchange-correlation functionals were used for nonrelativistic and relativistic nuclear magnetic shielding calculations of helium, neon, argon, krypton, and xenon dimers and free atoms. Relativistic corrections were calculated with the scalar and spin-orbit zeroth-order regular approximation Hamiltonian in combination with the large Slater-type basis set QZ4P as well as with the four-component Dirac-Coulomb Hamiltonian using Dyall's acv4z basis sets. The relativistic corrections to the nuclear magnetic shieldings and chemical shifts are combined with nonrelativistic coupled cluster singles and doubles with noniterative triple excitations [CCSD(T)] calculations using the very large polarization-consistent basis sets aug-pcSseg-4 for He, Ne and Ar, aug-pcSseg-3 for Kr, and the AQZP basis set for Xe. For the dimers also, zero-point vibrational (ZPV) corrections are obtained at the CCSD(T) level with the same basis sets were added. Best estimates of the dimer chemical shifts are generated from these nuclear magnetic shieldings and the relative importance of electron correlation, ZPV, and relativistic corrections for the shieldings and chemical shifts is analyzed. © 2015 Wiley Periodicals, Inc.

Furan- and Thiophene-2-Carbonyl Amino Acid Derivatives Activate Hypoxia-Inducible Factor via Inhibition of Factor Inhibiting Hypoxia-Inducible Factor-1

Directory of Open Access Journals (Sweden)

Shin-ichi Kawaguchi

2018-04-01

Full Text Available Induction of a series of anti-hypoxic proteins protects cells during exposure to hypoxic conditions. Hypoxia-inducible factor-α (HIF-α is a major transcription factor that orchestrates this protective effect. To activate HIF exogenously, without exposing cells to hypoxic conditions, many small-molecule inhibitors targeting prolyl hydroxylase domain-containing protein have been developed. In addition, suppression of factor inhibiting HIF-1 (FIH-1 has also been shown to have the potential to activate HIF-α. However, few small-molecule inhibitors of FIH-1 have been developed. In this study, we synthesized a series of furan- and thiophene-2-carbonyl amino acid derivatives having the potential to inhibit FIH-1. The inhibitory activities of these compounds were evaluated in SK-N-BE(2c cells by measuring HIF response element (HRE promoter activity. Several furan- and thiophene-2-carbonyl amino acid derivatives inhibited FIH-1 based on correlations among the docking score of the FIH-1 active site, the chemical structure of the compounds, and biological HIF-α/HRE transcriptional activity.

First application of supported ionic liquid phase (SILP) catalysis for continuous methanol carbonylation

DEFF Research Database (Denmark)

Riisager, Anders; Jørgensen, Betina; Wasserscheid, Peter

2006-01-01

A solid, silica-supported ionic liquid phase (SILP) rhodium iodide Monsanto-type catalyst system, [BMIM][Rh(CO)(2)I-2]-[BMIM]I -SiO2, exhibits excellent activity and selectivity towards acetyl products in fixed-bed, continuous gas-phase methanol carbonylation.......A solid, silica-supported ionic liquid phase (SILP) rhodium iodide Monsanto-type catalyst system, [BMIM][Rh(CO)(2)I-2]-[BMIM]I -SiO2, exhibits excellent activity and selectivity towards acetyl products in fixed-bed, continuous gas-phase methanol carbonylation....

Solid-state NMR chemical-shift perturbations indicate domain reorientation of the DnaG primase in the primosome of Helicobacter pylori

Energy Technology Data Exchange (ETDEWEB)

Gardiennet, Carole [Université de Lorraine, CNRS, CRM2, UMR 7036 (France); Wiegand, Thomas [ETH Zurich, Physical Chemistry (Switzerland); Bazin, Alexandre [Université de Lyon 1, Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS (France); Cadalbert, Riccardo [ETH Zurich, Physical Chemistry (Switzerland); Kunert, Britta; Lacabanne, Denis [Université de Lyon 1, Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS (France); Gutsche, Irina [Université Grenoble Alpes, Institut de Biologie Structurale (IBS), CNRS, IBS, CEA, IBS (France); Terradot, Laurent, E-mail: l.terradot@ibcp.fr [Université de Lyon 1, Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS (France); Meier, Beat H., E-mail: beme@ethz.ch [ETH Zurich, Physical Chemistry (Switzerland); Böckmann, Anja, E-mail: a.bockmann@ibcp.fr [Université de Lyon 1, Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS (France)

2016-03-15

We here investigate the interactions between the DnaB helicase and the C-terminal domain of the corresponding DnaG primase of Helicobacter pylori using solid-state NMR. The difficult crystallization of this 387 kDa complex, where the two proteins interact in a six to three ratio, is circumvented by simple co-sedimentation of the two proteins directly into the MAS-NMR rotor. While the amount of information that can be extracted from such a large protein is still limited, we can assign a number of amino-acid residues experiencing significant chemical-shift perturbations upon helicase-primase complex formation. The location of these residues is used as a guide to model the interaction interface between the two proteins in the complex. Chemical-shift perturbations also reveal changes at the interaction interfaces of the hexameric HpDnaB assembly on HpDnaG binding. A structural model of the complex that explains the experimental findings is obtained.

Chemical shift assignments of the partially deuterated Fyn SH2-SH3 domain.

Science.gov (United States)

Kieken, Fabien; Loth, Karine; van Nuland, Nico; Tompa, Peter; Lenaerts, Tom

2018-04-01

Src Homology 2 and 3 (SH2 and SH3) are two key protein interaction modules involved in regulating the activity of many proteins such as tyrosine kinases and phosphatases by respective recognition of phosphotyrosine and proline-rich regions. In the Src family kinases, the inactive state of the protein is the direct result of the interaction of the SH2 and the SH3 domain with intra-molecular regions, leading to a closed structure incompetent with substrate modification. Here, we report the 1 H, 15 N and 13 C backbone- and side-chain chemical shift assignments of the partially deuterated Fyn SH3-SH2 domain and structural differences between tandem and single domains. The BMRB accession number is 27165.

Rapid protein fold determination using secondary chemical shifts and cross-hydrogen bond 15N-13C’ scalar couplings (3hbJNC’)

NARCIS (Netherlands)

Bonvin, A.M.J.J.; Houben, K.; Guenneugues, M.N.L.; Kaptein, R.; Boelens, R.

2001-01-01

The possibility of generating protein folds at the stage of backbone assignment using structural restraints derived from experimentally measured cross-hydrogen bond scalar couplings and secondary chemical shift information is investigated using as a test case the small alpha/beta protein

SHIFTING WEED COMPOSITIONS AND BIOMASS PRODUCTION IN SWEET CORN FIELD TREATED WITH ORGANIC COMPOSTS AND CHEMICAL WEED CONTROLS

Directory of Open Access Journals (Sweden)

Marulak Simarmata

2015-10-01

Full Text Available The objectives of the research were to study the shift of weed compositions in sweet corn field treated with organic compost and chemical weed controls and to compare the effect of treatment combinations on weed growth, weed biomass and sweet corn biomass. The research was conducted in Bengkulu, Indonesia, from April to July 2014. Results showed that the number of weed species decreased after the trials from 14 to 13. There was a shift in weed compositions because 5 species of weeds did not emerge after the trials, but 4 new species were found. Chemical weed control used a herbiside mixture of atrazine and mesotrione applied during postemergence was the most effective method to control weeds, which was observed on decreased weed emergence and weed biomass down to 22.33 and 25.00 percent of control, respectively. Subsequently, biomass production of sweet corn increased up to 195.64 percent at the same trials. Biomass of weeds and sweet corn were also affected by the organic composts. Weed biomass was inhibited by treatment of composted empty fruith bunches of oil palm, whereas significantly increased of sweet corn biomass were observed in the plots of organic manure.

Bidirectional shifts of TRPM8 channel gating by temperature and chemical agents modulate the cold sensitivity of mammalian thermoreceptors.

Science.gov (United States)

Mälkiä, Annika; Madrid, Rodolfo; Meseguer, Victor; de la Peña, Elvira; Valero, María; Belmonte, Carlos; Viana, Félix

2007-05-15

TRPM8, a member of the melastatin subfamily of transient receptor potential (TRP) cation channels, is activated by voltage, low temperatures and cooling compounds. These properties and its restricted expression to small sensory neurons have made it the ion channel with the most advocated role in cold transduction. Recent work suggests that activation of TRPM8 by cold and menthol takes place through shifts in its voltage-activation curve, which cause the channel to open at physiological membrane potentials. By contrast, little is known about the actions of inhibitors on the function of TRPM8. We investigated the chemical and thermal modulation of TRPM8 in transfected HEK293 cells and in cold-sensitive primary sensory neurons. We show that cold-evoked TRPM8 responses are effectively suppressed by inhibitor compounds SKF96365, 4-(3-chloro-pyridin-2-yl)-piperazine-1-carboxylic acid (4-tert-butyl-phenyl)-amide (BCTC) and 1,10-phenanthroline. These antagonists exert their effect by shifting the voltage dependence of TRPM8 activation towards more positive potentials. An opposite shift towards more negative potentials is achieved by the agonist menthol. Functionally, the bidirectional shift in channel gating translates into a change in the apparent temperature threshold of TRPM8-expressing cells. Accordingly, in the presence of the antagonist compounds, the apparent response-threshold temperature of TRPM8 is displaced towards colder temperatures, whereas menthol sensitizes the response, shifting the threshold in the opposite direction. Co-application of agonists and antagonists produces predictable cancellation of these effects, suggesting the convergence on a common molecular process. The potential for half maximal activation of TRPM8 activation by cold was approximately 140 mV more negative in native channels compared to recombinant channels, with a much higher open probability at negative membrane potentials in the former. In functional terms, this difference translates

The contribution of chemical shift imaging with digital subtracting images to the diagnosis of steatohepatitis

International Nuclear Information System (INIS)

Guo Xinghua; Wang Juanping; Zhang Chongjie; Zheng Guofang; Fan Ruiqiang; Zhu Sumei; Liu Qiwang

2006-01-01

Objective: To investigate the diagnosis value of chemical shift imaging with digital subtracting in steatohepatitis. Methods: The in-phase images were subtracted by the out-phase ones in 34 cases of steatohepatitis, and the CNR were measured on these subtracted images to estimate the steatosis of the liver. The relationship of CT grade of steatohepatitis and CNR from the subtracted images was analyzed to evaluate the relationship between CNR and the degree of hepatic steatosis. The sensitivity and specificity of the subtracting and eyeballing methods were compared with chi-square test. Results: On the subtracted images, the liver and spleen were seen nearly the same aspects as low signals, CNR=0.98±0.06, meanwhile the spongy vertebra and the subcutaneous or abdominal lipid were seen as obvious higher signals in 52 normal cases. On the 34 steatohepatitis, scattered high signals were seen in the liver, which made the signal of liver higher than that of spleen, CNR=3.25±0.91--14.35±6.10. There was positive correlation between CNR and CT grade in the 34 cases of steatohepatitis, r=0.893, P<0.01. The sensitivity and specificity of the subtracting method were 88.24% and 94. 23%, significantly higher than that of the eyeballing results, 32.35% and 80.77%, P<0.01 and P<0.05. Conclusion: Chemical shift imaging with digital subtracting is a sensitive, specific, objective method to diagnose steatohepatitis and it is of potential ability for quantitative diagnosis. (authors)

cyclo-addition reaction of triplet carbonyl compounds to substituted ...

Indian Academy of Sciences (India)

Unknown

cited state energy of the olefin must be higher than that of the ketone so that ... the first singlet and triplet1,3 (n, π*) excited state of the carbonyl compounds.3,4 ... of the oxetane via carbon–carbon and carbon–oxygen attacks. They found the ...

Microwave absorption properties of a wave-absorbing coating employing carbonyl-iron powder and carbon black

International Nuclear Information System (INIS)

Liu Lidong; Duan Yuping; Ma Lixin; Liu Shunhua; Yu Zhen

2010-01-01

To prevent serious electromagnetic interference, a single-layer wave-absorbing coating employing complex absorbents composed of carbonyl-iron powder (CIP) and carbon black (CB) with epoxy resin as matrix was prepared. The morphologies of CIP and CB were characterized by scanning electron microscope (SEM) and transmission electron microscope (TEM), respectively. The electromagnetic parameters of CIP and CB were measured in the frequency range of 2-18 GHz by transmission/reflection technology, and the electromagnetic loss mechanisms of the two particles were discussed, respectively. The microwave absorption properties of the coatings were investigated by measuring reflection loss (RL) using arch method. The effects of CIP ratio, CB content and thickness on the microwave absorption properties were discussed, respectively. The results showed that the higher thickness, CIP or CB content could make the absorption band shift towards the lower frequency range. Significantly, the wave-absorbing coating could be applied in different frequency ranges according to actual demand by controlling the content of CIP or CB in composites.

Microwave absorption properties of a wave-absorbing coating employing carbonyl-iron powder and carbon black

Science.gov (United States)

Liu, Lidong; Duan, Yuping; Ma, Lixin; Liu, Shunhua; Yu, Zhen

2010-11-01

To prevent serious electromagnetic interference, a single-layer wave-absorbing coating employing complex absorbents composed of carbonyl-iron powder (CIP) and carbon black (CB) with epoxy resin as matrix was prepared. The morphologies of CIP and CB were characterized by scanning electron microscope (SEM) and transmission electron microscope (TEM), respectively. The electromagnetic parameters of CIP and CB were measured in the frequency range of 2-18 GHz by transmission/reflection technology, and the electromagnetic loss mechanisms of the two particles were discussed, respectively. The microwave absorption properties of the coatings were investigated by measuring reflection loss (RL) using arch method. The effects of CIP ratio, CB content and thickness on the microwave absorption properties were discussed, respectively. The results showed that the higher thickness, CIP or CB content could make the absorption band shift towards the lower frequency range. Significantly, the wave-absorbing coating could be applied in different frequency ranges according to actual demand by controlling the content of CIP or CB in composites.

Spatial distributions of and diurnal variations in low molecular weight carbonyl compounds in coastal seawater, and the controlling factors

Energy Technology Data Exchange (ETDEWEB)

Takeda, Kazuhiko, E-mail: takedaq@hiroshima-u.ac.jp [Graduate School of Biosphere Science, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521 (Japan); Katoh, Shinya; Mitsui, Yumi; Nakano, Shinichi [Graduate School of Biosphere Science, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521 (Japan); Nakatani, Nobutake [Graduate School of Biosphere Science, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521 (Japan); Department of Environmental and Symbiotic Sciences, Rakuno Gakuen University, 582 Bunkyodai-Midorimachi, Ebetsu, Hokkaido 069-8501 (Japan); Sakugawa, Hiroshi [Graduate School of Biosphere Science, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521 (Japan)

2014-09-15

We studied the spatial distributions of and the diurnal variations in four low molecular weight (LMW) carbonyl compounds, formaldehyde, acetaldehyde, propionaldehyde, and glyoxal, in coastal seawater. The samples were taken from the coastal areas of Hiroshima Bay, the Iyo Nada, and the Bungo Channel, western Japan. The formaldehyde, acetaldehyde, and glyoxal concentrations were higher in the northern part of Hiroshima Bay than at offshore sampling points in the Iyo Nada and the Bungo Channel. These three compounds were found at much higher concentrations in the surface water than in deeper water layers in Hiroshima Bay. It is noteworthy that propionaldehyde was not detected in any of the seawater samples, the concentrations present being lower than the detection limit (1 nanomole per liter (nM)) of the high performance liquid chromatography (HPLC) system we used. Photochemical and biological experiments were performed in the laboratory to help understand the characteristic distributions and fates of the LMW carbonyl compounds. The primary process controlling their fate in the coastal environment appears to be their biological consumption. The direct photo degradation of propionaldehyde, initiated by ultraviolet (UV) absorption, was observed, although formaldehyde and acetaldehyde were not degraded by UV irradiation. Our results suggest that the degradation of the LMW carbonyl compounds by photochemically formed hydroxyl radicals is relatively insignificant in the study area. Atmospheric deposition is a possible source of soluble carbonyl compounds in coastal surface seawater, but it may not influence the carbonyl concentrations in offshore waters. - Highlights: • Low molecular weight (LMW) carbonyl compounds in coastal seawater were determined. • Photochemical productions of LMW carbonyl compounds in seawater were observed. • LMW carbonyl compounds were largely consumed biologically. • Photochemical degradation was relatively insignificant in the study area.

Spatial distributions of and diurnal variations in low molecular weight carbonyl compounds in coastal seawater, and the controlling factors

International Nuclear Information System (INIS)

Takeda, Kazuhiko; Katoh, Shinya; Mitsui, Yumi; Nakano, Shinichi; Nakatani, Nobutake; Sakugawa, Hiroshi

2014-01-01

We studied the spatial distributions of and the diurnal variations in four low molecular weight (LMW) carbonyl compounds, formaldehyde, acetaldehyde, propionaldehyde, and glyoxal, in coastal seawater. The samples were taken from the coastal areas of Hiroshima Bay, the Iyo Nada, and the Bungo Channel, western Japan. The formaldehyde, acetaldehyde, and glyoxal concentrations were higher in the northern part of Hiroshima Bay than at offshore sampling points in the Iyo Nada and the Bungo Channel. These three compounds were found at much higher concentrations in the surface water than in deeper water layers in Hiroshima Bay. It is noteworthy that propionaldehyde was not detected in any of the seawater samples, the concentrations present being lower than the detection limit (1 nanomole per liter (nM)) of the high performance liquid chromatography (HPLC) system we used. Photochemical and biological experiments were performed in the laboratory to help understand the characteristic distributions and fates of the LMW carbonyl compounds. The primary process controlling their fate in the coastal environment appears to be their biological consumption. The direct photo degradation of propionaldehyde, initiated by ultraviolet (UV) absorption, was observed, although formaldehyde and acetaldehyde were not degraded by UV irradiation. Our results suggest that the degradation of the LMW carbonyl compounds by photochemically formed hydroxyl radicals is relatively insignificant in the study area. Atmospheric deposition is a possible source of soluble carbonyl compounds in coastal surface seawater, but it may not influence the carbonyl concentrations in offshore waters. - Highlights: • Low molecular weight (LMW) carbonyl compounds in coastal seawater were determined. • Photochemical productions of LMW carbonyl compounds in seawater were observed. • LMW carbonyl compounds were largely consumed biologically. • Photochemical degradation was relatively insignificant in the study area

Combined echo offset (Dixon) and line volume chemical shift imaging as a clinical imaging protocol

International Nuclear Information System (INIS)

Listerud, J.; Chan, T.; Lenkinski, R.E.; Kressel, H.Y.; Chao, P.W.

1989-01-01

The authors have studied the sensitivity and specificity of the line-volume chemical-shift imaging (CSI) method as compared with the Dixon method they have recently implemented on a Signa, which supports a variety of options. Potential sources or error for the Dixon method include line broadening due to susceptibility, field inhomogeneity, and errors form olefinic resonances associated with fat, which behave like water in the Dixon regime. The authors investigate whether a combined Dixon/line-volume CSI method could be used to improve the placement of the line volume and to provide higher sensitivity and specificity than does the Dixon method alone

Increased precision for analysis of protein-ligand dissociation constants determined from chemical shift titrations

Energy Technology Data Exchange (ETDEWEB)

Markin, Craig J.; Spyracopoulos, Leo, E-mail: leo.spyracopoulos@ualberta.ca [University of Alberta, Department of Biochemistry (Canada)

2012-06-15

NMR is ideally suited for the analysis of protein-protein and protein ligand interactions with dissociation constants ranging from {approx}2 {mu}M to {approx}1 mM, and with kinetics in the fast exchange regime on the NMR timescale. For the determination of dissociation constants (K{sub D}) of 1:1 protein-protein or protein-ligand interactions using NMR, the protein and ligand concentrations must necessarily be similar in magnitude to the K{sub D}, and nonlinear least squares analysis of chemical shift changes as a function of ligand concentration is employed to determine estimates for the parameters K{sub D} and the maximum chemical shift change ({Delta}{delta}{sub max}). During a typical NMR titration, the initial protein concentration, [P{sub 0}], is held nearly constant. For this condition, to determine the most accurate parameters for K{sub D} and {Delta}{delta}{sub max} from nonlinear least squares analyses requires initial protein concentrations that are {approx}0.5 Multiplication-Sign K{sub D}, and a maximum concentration for the ligand, or titrant, of {approx}10 Multiplication-Sign [P{sub 0}]. From a practical standpoint, these requirements are often difficult to achieve. Using Monte Carlo simulations, we demonstrate that co-variation of the ligand and protein concentrations during a titration leads to an increase in the precision of the fitted K{sub D} and {Delta}{delta}{sub max} values when [P{sub 0}] > K{sub D}. Importantly, judicious choice of protein and ligand concentrations for a given NMR titration, combined with nonlinear least squares analyses using two independent variables (ligand and protein concentrations) and two parameters (K{sub D} and {Delta}{delta}{sub max}) is a straightforward approach to increasing the accuracy of measured dissociation constants for 1:1 protein-ligand interactions.

Acute inhalation toxicity of carbonyl sulfide

Energy Technology Data Exchange (ETDEWEB)

Benson, J.M.; Hahn, F.F.; Barr, E.B. [and others

1995-12-01

Carbonyl sulfide (COS), a colorless gas, is a side product of industrial procedures sure as coal hydrogenation and gasification. It is structurally related to and is a metabolite of carbon disulfide. COS is metabolized in the body by carbonic anhydrase to hydrogen sulfide (H{sub 2}S), which is thought to be responsible for COS toxicity. No threshold limit value for COS has been established. Results of these studies indicate COS (with an LC{sub 50} of 590 ppm) is slightly less acutely toxic than H{sub 2}S (LC{sub 50} of 440 ppm).

Characterization of selected volatile organic compounds, polycyclic aromatic hydrocarbons and carbonyl compounds at a roadside monitoring station

Science.gov (United States)

Ho, K. F.; Lee, S. C.; Chiu, Gloria M. Y.

Volatile organic compounds (VOCs), PAHs and carbonyl compounds are the major toxic components in Hong Kong. Emissions from motor vehicles have been one of the primary pollution sources in the metropolitan areas throughout Hong Kong for a long time. A 1-yr monitoring program for VOCs, PAHs and carbonyl compounds had been performed at a roadside urban station at Hong Kong Polytechnic University in order to determine the variations and correlations of each selected species (VOCs, PAHs and carbonyl compounds). This study is aimed to analyze toxic volatile organic compounds (benzene, toluene, ethylbenzene and xylene), two carbonyl compounds (formaldehyde, acetaldehyde), and selective polycyclic aromatic hydrocarbons. The monitoring program started from 16 April 1999 to 30 March 2000. Ambient VOC concentrations, many of which originate from the same sources as particulate PAHs and carbonyls compounds, show significant quantities of benzene, toluene and xylenes. Correlations and multivariate analysis of selected gaseous and particulate phase organic pollutants were performed. Source identification by principle component analysis and hierarchical cluster analysis allowed the identification of four sources (factors) for the roadside monitoring station. Factor 1 represents the effect of diesel vehicle exhaust. Factor 2 shows the contribution of aromatic compounds. Factor 3 explains photochemical products—formaldehyde and acetaldehyde. Factor 4 explains the effect of gasoline vehicle exhaust.

MR imaging of osteonecrosis using frequency selective chemical shift sequences; Neue Aspekte in der MR-Diagnostik der Osteonekrose: Selektive Fett/Wasser-Bildgebung

Energy Technology Data Exchange (ETDEWEB)

Duda, S H [Abt. fuer Radiologische Diagnostik, Tuebingen Univ. (Germany); Laniado, M [Abt. fuer Radiologische Diagnostik, Tuebingen Univ. (Germany); Schick, F [Inst. fuer Physik, Tuebingen Univ. (Germany)

1994-12-31

The MR appearance of osteonecrosis was assessed on selective fat- and water images to further evaluate the nature of double-line sign. Conventional T1- and T2-weighted SE and frequency selective chemical shift images of eight patients with avascular necrosis of the femoral head and three patients with bone infarcts were retrospectively reviewed. Eight of 11 patients showed a double-line sign on T2-weighted SE images. In these cases, correlation with selective water images revealed that a chemical shift artifact contributed to appearance and location of the hyperintense line. The authors conclude that chemical shift imaging improves our understanding of the nature of the double-line sign. (orig.) [Deutsch] Das MR-tomographische Erscheinungsbild der Osteonekrose auf selektiven Fett- und Wasserbildern wurde analysiert, um das in der Literatur beschriebene Doppellinienzeichen naeher zu untersuchen. Hierfuer wurden sowohl die herkoemmlichen T1- und T2-gewichteten Spin-Echo-Sequenzen herangezogen, als auch frequenzselektive Bilder, die aufgrund chemischer Verschiebung gewonnen wurden (1,5 T). Es wurden die Untersuchungen von acht Patienten mit avaskulaerer Hueftkopfnekrose und von drei Patienten mit Knocheninfarkten retrospektiv ausgewertet. Acht von 11 Patienten zeigten ein Doppellinienzeichen auf den T2-gewichteten Bildern. Die Korrelation mit den selektiven Wasserbildern ergab, dass durch chemische Verschiebung bedingte Artefakte das Erscheinungsbild und den Ort der hyperintensen Linie beeinflussten. Die Bildgebung mit Hilfe der chemischen Verschiebung verbessert unser Verstaendnis der MRT-Charakteristika der Osteonekrose. (orig.)

Nucleophilic tetrafluoroethylation of carbonyl compounds with fluorinated sulfones

Czech Academy of Sciences Publication Activity Database

Václavík, Jiří; Chernykh, Yana; Jurásek, Bronislav; Beier, Petr

2015-01-01

Roč. 169, Jan (2015), s. 24-31 ISSN 0022-1139 R&D Projects: GA ČR GAP207/11/0421 Grant - others:GA MŠk(CZ) ED3.2.00/08.0144; GA MŠk(CZ) LM2010005 Institutional support: RVO:61388963 Keywords : fluorine * tetrafluoroethylation * sulfones * nucleophilic addition * carbonyl compounds Subject RIV: CC - Organic Chemistry Impact factor: 2.213, year: 2015

Characterisation and optimisation of a method for the detection and quantification of atmospherically relevant carbonyl compounds in aqueous medium

Science.gov (United States)

Rodigast, M.; Mutzel, A.; Iinuma, Y.; Haferkorn, S.; Herrmann, H.

2015-01-01

Carbonyl compounds are ubiquitous in the atmosphere and either emitted primarily from anthropogenic and biogenic sources or they are produced secondarily from the oxidation of volatile organic compounds (VOC). Despite a number of studies about the quantification of carbonyl compounds a comprehensive description of optimised methods is scarce for the quantification of atmospherically relevant carbonyl compounds. Thus a method was systematically characterised and improved to quantify carbonyl compounds. Quantification with the present method can be carried out for each carbonyl compound sampled in the aqueous phase regardless of their source. The method optimisation was conducted for seven atmospherically relevant carbonyl compounds including acrolein, benzaldehyde, glyoxal, methyl glyoxal, methacrolein, methyl vinyl ketone and 2,3-butanedione. O-(2,3,4,5,6-pentafluorobenzyl)hydroxylamine hydrochloride (PFBHA) was used as derivatisation reagent and the formed oximes were detected by gas chromatography/mass spectrometry (GC/MS). The main advantage of the improved method presented in this study is the low detection limit in the range of 0.01 and 0.17 μmol L-1 depending on carbonyl compounds. Furthermore best results were found for extraction with dichloromethane for 30 min followed by derivatisation with PFBHA for 24 h with 0.43 mg mL-1 PFBHA at a pH value of 3. The optimised method was evaluated in the present study by the OH radical initiated oxidation of 3-methylbutanone in the aqueous phase. Methyl glyoxal and 2,3-butanedione were found to be oxidation products in the samples with a yield of 2% for methyl glyoxal and 14% for 2,3-butanedione.

Selectivity of a heterogeneous rhodium catalyst for the carbonylation of monohydric alcohols

Energy Technology Data Exchange (ETDEWEB)

Christensen, B; Scurrell, M S

1977-01-01

Selectivity of a heterogeneous rhodium catalyst for the carbonylation of monohydric alcohols with carbon monoxide in the presence of the corresponding alkyl iodides as promotors was studied in a glass reactor at approx. 0.05:1 alcohol/carbon monoxide ratio. The 1% by wt rhodium-zeolite catalyst was prepared by immersing a Linde molecular sieve zeolite Type 13X in rhodium trichloride at 80/sup 0/C for 15 hr. Methanol was converted to methyl acetate at 433/sup 0/-513/sup 0/K with selectivites > 90% even at the highest temperatures, and dimethyl ether was by-produced. In the absence of methyl iodide, the carbonylation rate decreased drastically but the dehydration was virtually unaffected. The selectivity for ethanol carbonylation decreased from 99% at 383/sup 0/K to 6% at 523/sup 0/K due to the formation of ethylene (predominant at > 470/sup 0/K) and diethyl ether. The only product of the reaction with propan-2-ol studied at 433/sup 0/ or 473/sup 0/K was propene with 100% conversion at 473/sup 0/K. These results are consistent with the relative ease of reactant dehydration on polar catalysts. Table and 13 references.

Ruthenium(II) carbonyl compounds with the 4'-chloro-2,2':6',2''-terpyridine ligand.

Science.gov (United States)

Tatikonda, Rajendhraprasad; Haukka, Matti

2017-04-01

Two ruthenium carbonyl complexes with the 4'-chloro-2,2':6',2''-terpyridine ligand (tpy-Cl, C 15 H 10 ClN 3 ), i.e. [RuCl(tpy-Cl)(CO) 2 ][RuCl 3 (CO) 3 ] (I) [systematic name: cis -di-carbonyl-chlorido(4'-chloro-2,2':6',2''-terpyridine-κ 3 N )ruthenium(II) fac -tricarbonyltri-chlorido-ruthenate(II)], and [RuCl 2 (tpy-Cl)(CO) 2 ] (II) [ cis -dicarbonyl- trans -di-chlorido(4'-chloro-2,2':6',2''-terpyridine-κ 2 N 1 , N 1' )ruthenium(II)], were synthesized and characterized by single-crystal X-ray diffraction. The Ru II atoms in both centrosymmetric structures (I) and (II) display similar, slightly distorted octa-hedral coordination spheres. The coordination sphere in the complex cation in compound (I) is defined by three N atoms of the tridentate tpy-Cl ligand, two carbonyl carbon atoms and one chlorido ligand; the charge is balanced by an octa-hedral [Ru(CO) 3 Cl 3 ] - counter-anion. In the neutral compound (II), the tpy-Cl ligand coordinates to the metal only through two of its N atoms. The coordination sphere of the Ru II atom is completed by two carbonyl and two chlorido ligands. In the crystal structures of both (I) and (II), weak C-H⋯Cl inter-actions are observed.

Ruthenium and osmium carbonyl nitrosyl complexes: Matrix infrared spectra and density functional calculations for M(CO){sub 2}(NO){sub 2} and M(CO)(NO) (M = Ru, Os)

Energy Technology Data Exchange (ETDEWEB)

Song, Zhenjun [Department of Chemistry, Tongji University, Shanghai 200092 (China); Wang, Xuefeng, E-mail: xfwang@tongji.edu.cn [Department of Chemistry, Tongji University, Shanghai 200092 (China); Key Laboratory of Yangtze River Water Environment, Ministry of Education, Tongji University (China)

2012-10-15

Highlights: Black-Right-Pointing-Pointer Laser-ablated ruthenium or osmium atom reactions with CO and NO mixtures in solid argon. Black-Right-Pointing-Pointer Metal carbonyl nitrosyls including M(CO)(NO) and 18-electron configuration M(CO){sub 2}(NO){sub 2} molecules (M = Ru, Os). Black-Right-Pointing-Pointer The observed absorption bands of reaction products are identified by isotopic substitution and DFT calculations. Black-Right-Pointing-Pointer The bonding and reaction mechanism are discussed in detail. -- Abstract: Laser-ablated ruthenium or osmium atom reactions with CO and NO mixtures in solid argon produce unsaturated metal carbonyl nitrosyls including M(CO)(NO) and 18-electron configuration M(CO){sub 2}(NO){sub 2} molecules (M = Ru, Os). The observed absorption bands of reaction products are identified by isotopic substitution, isotopic ratios and isotopic distributions ({sup 13}CO, {sup 15}NO, and mixtures). DFT (B3LYP and BP86) vibrational fundamental calculations reproduce observed frequencies and isotopic shifts very well. The bonding and reaction mechanism are discussed.

Gas chromatographic analysis of reactive carbonyl compounds formed from lipids upon UV-irradiation

International Nuclear Information System (INIS)

Dennis, K.J.; Shibamoto, T.

1990-01-01

Peroxidation of lipids produces carbonyl compounds; some of these, e.g., malonaldehyde and 4-hydroxynonenal, are genotoxic because of their reactivity with biological nucleophiles. Analysis of the reactive carbonyl compounds is often difficult. The methylhydrazine method developed for malonaldehyde analysis was applied to simultaneously measure the products formed from linoleic acid, linolenic acid, arachidonic acid, and squalene upon ultraviolet-irradiation (UV-irradiation). The photoreaction products, saturated monocarbonyl, alpha,beta-unsaturated carbonyls, and beta-dicarbonyls, were derivatized with methylhydrazine to give hydrazones, pyrazolines, and pyrazoles, respectively. The derivatives were analyzed by gas chromatography and gas chromatography-mass spectrometry. Lipid peroxidation products identified included formaldehyde, acetaldehyde, acrolein, malonaldehyde, n-hexanal, and 4-hydroxy-2-nonenal. Malonaldehyde levels formed upon 4 hr of irradiation were 0.06 micrograms/mg from squalene, 2.4 micrograms/mg from linolenic acid, and 5.7 micrograms/mg from arachidonic acid. Significant levels of acrolein (2.5 micrograms/mg) and 4-hydroxy-2-nonenal (0.17 micrograms/mg) were also produced from arachidonic acid upon 4 hr irradiation

Investigation of carbonyl compound sources at a rural site in the Yangtze River Delta region of China.

Science.gov (United States)

Wang, Ming; Chen, Wentai; Shao, Min; Lu, Sihua; Zeng, Limin; Hu, Min

2015-02-01

Carbonyl compounds are important intermediates in atmospheric photochemistry, but their primary sources are still not understood well. In this work, carbonyls, hydrocarbons, and alkyl nitrates were continuously measured during November 2011 at a rural site in the Yangtze River Delta region of China. Mixing ratios of carbonyls and hydrocarbons showed large fluctuations during the entire measurement. The average level for total measured volatile organic compounds during the pollution episode from 25th to 27th November, 2011 was 91.6 ppb, about 7 times the value for the clean period of 7th-8th, November, 2011. To preliminarily identify toluene sources at this site, the emission ratio of toluene to benzene (T/B) during the pollution episode was determined based on photochemical ages derived from the relationship of alkyl nitrates to their parent alkanes. The calculated T/B was 5.8 ppb/ppb, significantly higher than the values of 0.2-1.7 ppb/ppb for vehicular exhaust and other combustion sources, indicating the dominant influence of industrial emissions on ambient toluene. The contributions of industrial sources to ambient carbonyls were then calculated using a multiple linear regression fit model that used toluene and alkyl nitrates as respective tracers for industrial emission and secondary production. During the pollution episode, 18.5%, 69.0%, and 52.9% of measured formaldehyde, acetaldehyde, and acetone were considered to be attributable to industrial emissions. The emission ratios relative to toluene for formaldehyde, acetaldehyde, and acetone were determined to be 0.10, 0.20 and 0.40 ppb/ppb, respectively. More research on industrial carbonyl emission characteristics is needed to understand carbonyl sources better. Copyright © 2014. Published by Elsevier B.V.

Selective Oxidative Carbonylation of Aniline to Diphenylurea with Ionic Liquids

DEFF Research Database (Denmark)

Zahrtmann, Nanette; Claver, Carmen; Godard, Cyril

2018-01-01

A catalytic system for the selective oxidative carbonylation of aniline to diphenylurea based on Pd complexes in combination with imidazolium ionic liquids is presented. Both oxidants, Pd complexes and ionic liquids affect the activity of the reaction while the choice of oxidant determines...

Determination of gaseous and particulate carbonyls (glycolaldehyde, hydroxyacetone, glyoxal, methylglyoxal, nonanal and decanal in the atmosphere at Mt. Tai

Directory of Open Access Journals (Sweden)

K. Kawamura

2013-05-01

Full Text Available Gaseous and particulate semi-volatile carbonyl compounds were determined every three hours in the atmosphere of Mount Tai (elevation, 1534 m in the North China Plain during 2–5, 23–24 and 25 June 2006 under clear sky conditions. Using a two-step filter cartridge in a series, particulate carbonyls were first collected on a quartz filter and then gaseous carbonyls were collected on a quartz filter impregnated with O-benzylhydroxylamine (BHA. After the two-step derivatization with BHA and N,O-Bis(trimethylsilyltrifluoroacetamide (BSTFA, carbonyl derivatives were measured using a gas chromatography. The gaseous concentrations were obtained as follow: glycolaldehyde (range 0–826 ng m−3, average 303 ng m−3, hydroxyacetone (0–579 ng m−3, 126 ng m−3, glyoxal (46–1200 ng m−3, 487 ng m−3, methylglyoxal (88–2690 ng m−3, 967 ng m−3, n-nonanal (0–500 ng m−3, 89 ng m−3, and n-decanal (0–230 ng m−3, 39 ng m−3. These concentrations are among the highest ever reported in the urban and forest atmosphere. We found that gaseous α-dicarbonyls (glyoxal and methylglyoxal are more than 20 times more abundant than particulate carbonyls and that glycolaldehyde is one order of magnitude more abundant than in aerosol phase. In contrast, hydroxyacetone and normal aldehydes (nonanal and decanal are equally present in both phases. Time-resolved variations of carbonyls did not show any a clear diurnal pattern, except for hydroxyacetone. We found that glyoxal, methylglyoxal and glycolaldehyde positively correlated with levoglucosan (a tracer of biomass burning, suggesting that a contribution from field burning of agricultural wastes (wheat crops is significant for the bifunctional carbonyls in the atmosphere of Mt. Tai. Upward transport of the pollutants to the mountaintop from the low lands in the North China Plain is a major process to control the distributions of carbonyls in the upper atmosphere over Mt. Tai.

Reactions of rhodium(I) carbonyl chloride with olefins

International Nuclear Information System (INIS)

Varshavskii, Yu.S.; Kiseleva, N.V.; Cherkasova, T.G.; Buzina, N.A.; Bresler, L.S.

1987-01-01

The reactions of [Rh(CO) 2 Cl] 2 (Y 0 ) with cyclooctene and several other olefins (1-heptene, 1-hexene, ethylene, and cyclohexene) have been studied by IR and 13 C NMR spectroscopy. The main reaction products are the binuclear complexes Rh 2 L(CO) 3 Cl 2 (Y 1 ) and [RhL(CO)Cl] 2 (Y 2 ), where L denotes the olefin. The extent of replacement of the carbonyl groups depends on the nature of the olefin and the conditions under which the reaction is carried out (the L:Rh ratio and the removal of CO from the reaction sphere). The liquid olefins form the following series according to their ability to replace the carbonyl groups: C 8 H 14 > C 7 H 14 , C 6 H 12 > C 6 H 10 . In the presence of an excess of C 8 H 14 , Y 2 disproportionates with the formation of a dicarbonyl product, which presumably corresponds to the formula Rh(C 8 H 14 ) 2 (CO) 2 Cl (a pentacoordinate complex with a trigonal-bipyramidal structure). The 13 C signal in the NMR spectrum of a solution of Y 2 in C 8 H 14 is a singlet with σ( 13 C) 180.3 ppm, which is an indication of the rapid exchange of the carbonyl groups. Rapid exchange of the CO ligands is also observed in solutions of Y 0 in the olefins (with the exception of C 6 H 10 ). For example, the 13 C signal in the spectrum of a solution of Y 0 in C 8 H 14 is a singlet with σ( 13 C) 179.8 ppm. The spectrum of Y 0 in C 6 H 10 is a doublet with σ( 13 C) = 178.5 ppm and 1 J(CRh) = 76.3 Hz. A scheme for the interaction of Y 0 with olefins based on the conception of the trans antagonism of π-acceptor ligands has been proposed

Multiparametric fat-water separation method for fast chemical-shift imaging guidance of thermal therapies.

Science.gov (United States)

Lin, Jonathan S; Hwang, Ken-Pin; Jackson, Edward F; Hazle, John D; Stafford, R Jason; Taylor, Brian A

2013-10-01

A k-means-based classification algorithm is investigated to assess suitability for rapidly separating and classifying fat/water spectral peaks from a fast chemical shift imaging technique for magnetic resonance temperature imaging. Algorithm testing is performed in simulated mathematical phantoms and agar gel phantoms containing mixed fat/water regions. Proton resonance frequencies (PRFs), apparent spin-spin relaxation (T2*) times, and T1-weighted (T1-W) amplitude values were calculated for each voxel using a single-peak autoregressive moving average (ARMA) signal model. These parameters were then used as criteria for k-means sorting, with the results used to determine PRF ranges of each chemical species cluster for further classification. To detect the presence of secondary chemical species, spectral parameters were recalculated when needed using a two-peak ARMA signal model during the subsequent classification steps. Mathematical phantom simulations involved the modulation of signal-to-noise ratios (SNR), maximum PRF shift (MPS) values, analysis window sizes, and frequency expansion factor sizes in order to characterize the algorithm performance across a variety of conditions. In agar, images were collected on a 1.5T clinical MR scanner using acquisition parameters close to simulation, and algorithm performance was assessed by comparing classification results to manually segmented maps of the fat/water regions. Performance was characterized quantitatively using the Dice Similarity Coefficient (DSC), sensitivity, and specificity. The simulated mathematical phantom experiments demonstrated good fat/water separation depending on conditions, specifically high SNR, moderate MPS value, small analysis window size, and low but nonzero frequency expansion factor size. Physical phantom results demonstrated good identification for both water (0.997 ± 0.001, 0.999 ± 0.001, and 0.986 ± 0.001 for DSC, sensitivity, and specificity, respectively) and fat (0.763 ± 0.006, 0

Diagnostic value of chemical shift artifact in distinguishing benign lymphadenopathy

Energy Technology Data Exchange (ETDEWEB)

Farshchian, Nazanin, E-mail: farshchian.n@gmail.com [Department of Radiology, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Tamari, Saghar; Farshchian, Negin [Department of Radiology, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Madani, Hamid [Department of Pathology, Imam-Reza Hospital, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Rezaie, Mansour [Department of Biostatistics, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Mohammadi-Motlagh, Hamid-Reza, E-mail: mohammadimotlagh@gmail.com [Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of)

2011-11-15

Purpose: Today, distinguishing metastatic lymph nodes from secondary benign inflammatory ones via using non-invasive methods is increasingly favorable. In this study, the diagnostic value of chemical shift artifact (CSA) in magnetic resonance imaging (MRI) was evaluated to distinguish benign lymphadenopathy. Subjects and methods: A prospective intraindividual internal review board-approved study was carried out on 15 men and 15 women having lymphadenopathic lesions in different locations of the body who underwent contrast-enhanced dynamic MR imaging at 1.5 T. Then, the imaging findings were compared with pathology reports, using the statistics analyses. Results: Due to the findings of the CSA existence in MRI, a total of 56.7% of the studied lesions (17 of 30) were identified as benign lesions and the rest were malignant, whereas the pathology reports distinguished twelve malignant and eighteen benign cases. Furthermore, the CSA findings comparing the pathology reports indicated that CSA, with confidence of 79.5%, has a significant diagnostic value to differentiate benign lesions from malignant ones. Conclusion: Our study demonstrated that CSA in MR imaging has a suitable diagnostic potential nearing readiness for clinical trials. Furthermore, CSA seems to be a feasible tool to differentiate benign lymph nodes from malignant ones; however, further studies including larger numbers of patients are required to confirm our results.

Evidence of chemical-potential shift with hole doping in Bi2Sr2CaCu2O8+δ

International Nuclear Information System (INIS)

Shen, Z.; Dessau, D.S.; Wells, B.O.; Olson, C.G.; Mitzi, D.B.; Lombado, L.; List, R.S.; Arko, A.J.

1991-01-01

We have performed photoemission studies on high-quality Bi 2 Sr 2 CaCu 2 O 8+δ samples with various δ. Our results show a clear chemical-potential shift (0.15--0.2 eV) as a function of doping. This result and the existing angle-resolved-photoemission data give a rather standard doping behavior of this compound in its highly doped regime

Dithioacetals as an Entry to Titanium-Alkylidene Chemistry: A New and Efficient Carbonyl Olefination.

Science.gov (United States)

Breit, Bernhard

1998-03-02

Wittig, Horner-Wadsworth-Emmons, Julia-Lythgoe, Tebbe, Grubbs, and Petasis-when it comes to carbonyl olefinations, these names are familiar to all chemistry students. In the future, the name Takeda will probably have to be added to this list. His recent work on the formation of titanium-alkylidene species from dithioacetals has provided organic chemists with a remarkable method for carbonyl olefination that is generally applicable under neutral to Lewis acidic conditions. © 1998 WILEY-VCH Verlag GmbH, Weinheim, Fed. Rep. of Germany.

Spectral fitting for signal assignment and structural analysis of uniformly {sup 13}C-labeled solid proteins by simulated annealing based on chemical shifts and spin dynamics

Energy Technology Data Exchange (ETDEWEB)

Matsuki, Yoh; Akutsu, Hideo; Fujiwara, Toshimichi [Osaka University, Institute for Protein Research (Japan)], E-mail: tfjwr@protein.osaka-u.ac.jp

2007-08-15

We describe an approach for the signal assignment and structural analysis with a suite of two-dimensional {sup 13}C-{sup 13}C magic-angle-spinning solid-state NMR spectra of uniformly {sup 13}C-labeled peptides and proteins. We directly fit the calculated spectra to experimental ones by simulated annealing in restrained molecular dynamics program CNS as a function of atomic coordinates. The spectra are calculated from the conformation dependent chemical shift obtained with SHIFTX and the cross-peak intensities computed for recoupled dipolar interactions. This method was applied to a membrane-bound 14-residue peptide, mastoparan-X. The obtained C', C{sup {alpha}} and C{sup {beta}} chemical shifts agreed with those reported previously at the precisions of 0.2, 0.7 and 0.4 ppm, respectively. This spectral fitting program also provides backbone dihedral angles with a precision of about 50 deg. from the spectra even with resonance overlaps. The restraints on the angles were improved by applying protein database program TALOS to the obtained chemical shifts. The peptide structure provided by these restraints was consistent with the reported structure at the backbone RMSD of about 1 A.

Carbonyl Compounds Produced by Vaporizing Cannabis Oil Thinning Agents.

Science.gov (United States)

Troutt, William D; DiDonato, Matthew D

2017-11-01

Cannabis use has increased in the United States, particularly the use of vaporized cannabis oil, which is often mixed with thinning agents for use in vaporizing devices. E-cigarette research shows that heated thinning agents produce potentially harmful carbonyls; however, similar studies have not been conducted (1) with agents that are commonly used in the cannabis industry and (2) at temperatures that are appropriate for cannabis oil vaporization. The goal of this study was to determine whether thinning agents used in the cannabis industry produce potentially harmful carbonyls when heated to a temperature that is appropriate for cannabis oil vaporization. Four thinning agents (propylene glycol [PG], vegetable glycerin [VG], polyethylene glycol 400 [PEG 400], and medium chain triglycerides [MCT]) were heated to 230°C and the resulting vapors were tested for acetaldehyde, acrolein, and formaldehyde. Each agent was tested three times. Testing was conducted in a smoking laboratory. Carbonyl levels were measured in micrograms per puff block. Analyses showed that PEG 400 produced significantly higher levels of acetaldehyde and formaldehyde than PG, MCT, and VG. Formaldehyde production was also significantly greater in PG compared with MCT and VG. Acrolein production did not differ significantly across the agents. PG and PEG 400 produced high levels of acetaldehyde and formaldehyde when heated to 230°C. Formaldehyde production from PEG 400 isolate was particularly high, with one inhalation accounting for 1.12% of the daily exposure limit, nearly the same exposure as smoking one cigarette. Because PG and PEG 400 are often mixed with cannabis oil, individuals who vaporize cannabis oil products may risk exposure to harmful formaldehyde levels. Although more research is needed, consumers and policy makers should consider these potential health effects before use and when drafting cannabis-related legislation.

{sup 31}P-MR spectroscopy of all regions of the human heart at 1.5 T with acquisition-weighted chemical shift imaging; P-MR-Spektroskopie aller Wandabschnitte des menschlichen Herzens bei 1,5 T mit akquisitionsgewichteter Chemical-shift-Bildgebung

Energy Technology Data Exchange (ETDEWEB)

Koestler, H.; Beer, M.; Buchner, S.; Sandstede, J.; Pabst, T.; Kenn, W.; Hahn, D. [Wuerzburg Univ. (Germany). Abt. fuer Roentgendiagnostik; Landschuetz, W.; Kienlin, M. von [Wuerzburg Univ. (Germany). Physikalisches Inst.; Neubauer, S. [Dept. of Cardiovascular Medicine, John Radcliffe Hospital, Oxford (United Kingdom)

2001-12-01

Aim: Aim of this study was to show whether or not acquisition-weighted chemical shift imaging (AW-CSI) allows the determination of PCr and ATP in the lateral and posterior wall of the human heart at 1.5 T. Methods: 12 healthy volunteers were examined using a conventional chemical shift imaging (CSI) and an AW-CSI. The sequences differed only in the number of repetitions for each point in k space. A hanning function was used as filter function leading to 7 repetitions in the center of the k space and 0 in the corners. Thus, AW-CSI had the same resolution as the CSI sequence. The results for both sequences were analyzed using identically positioned voxels in the septal, anterior, lateral and posterior wall. Results: The determined averaged AW-CSI signal to noise ratios were higher for PCr by a factor of 1.3 and for ATP by 1.4 than those of CSI. The PCr/ATP ratios were higher by a factor of 1.2 - 1.3 and showed a smaller standard deviation in all locations for AW-CSI. The mean PCr/ATP ratios determined by AW-CSI of septal, lateral and posterior wall were almost identical (1.72 - 1.76), while it was higher in the anterior wall (1.9). Conclusions: The reduced contamination in AW-CSI improves the signal to noise ratio and the determination of the PCr/ATP ratio in cardiac {sup 31}P spectroscopy compared to CSI with the same resolution. The results in volunteers indicate that AW-CSI renders {sup 31}P spectroscopy of the lateral and posterior wall of the human heart feasible for patient studies at 1.5 T. (orig.) [German] Ziel: Ziel der Arbeit war es zu untersuchen, ob die akquisitionsgewichtete Chemical-shift-Bildgebung (AW-CSI) die Bestimmung von PCr und ATP in der Seiten- und Hinterwand des menschlichen Herzens an einem klinischen 1,5 T MR-Tomographen erlaubt. Methoden: 12 gesunde Probanden wurden jeweils mit einer chemical shift imaging (CSI) und einer AW-CSI-Sequenz untersucht. Die Sequenzen unterschieden sich lediglich in der Anzahl der Wiederholungen der einzelnen

Ionization of oriented carbonyl sulfide molecules by intense circularly polarized laser pulses

DEFF Research Database (Denmark)

Dimitrovski, Darko; Abu-Samha, Mahmoud; Madsen, Lars Bojer

2011-01-01

We present combined experimental and theoretical results on strong-field ionization of oriented carbonyl sulfide molecules by circularly polarized laser pulses. The obtained molecular frame photoelectron angular distributions show pronounced asymmetries perpendicular to the direction of the molec......We present combined experimental and theoretical results on strong-field ionization of oriented carbonyl sulfide molecules by circularly polarized laser pulses. The obtained molecular frame photoelectron angular distributions show pronounced asymmetries perpendicular to the direction......-dimensionally-oriented polar molecules, in particular asymmetries in the emission direction of the photoelectrons. In the following article [Phys. Rev. A 83, 023406 (2011)] the focus is to understand strong-field ionization from three-dimensionally-oriented asymmetric top molecules, in particular the suppression of electron...

A Simple Catalytic Mechanism for the Direct Coupling of α-Carbonyls with Functionalized Amines: A One-Step Synthesis of Plavix

OpenAIRE

Evans, Ryan W.; Zbieg, Jason R.; Zhu, Shaolin; Li, Wei; MacMillan, David W. C.

2013-01-01

The direct α-amination of ketones, esters, and aldehydes has been accomplished via copper catalysis. In the presence of catalytic copper(II) bromide, a diverse range of carbonyl and amine substrates undergo fragment coupling to produce synthetically useful α-amino substituted motifs. The transformation is proposed to proceed via a catalytically generated α-bromo carbonyl species; nucleophilic displacement of the bromide by the amine then delivers the α-amino carbonyl adduct while the catalyst...

Synthesis of dimethyl carbonate by oxidative carbonylation of methanol

Energy Technology Data Exchange (ETDEWEB)

Lee, B.G.; Han, M.S.; Kim, H.S.; Ahn, B.S.; Park, K.Y.

1999-07-01

Dimethyl carbonate (DMC) synthesis reaction by oxidative carbonylation of methanol has been studied using vapor phase flow reaction system in the presence of Cu-based catalysts. A series of Cu-based catalysts were prepared by the conventional impregnation method using activated carbon (AC) as support. The effect of various promoters and reaction conditions on the catalytic reactivities was intensively evaluated in terms of methanol conversion and DMC selectivity. The morphological change of catalysts during the reaction was also compared by X-ray diffraction and SEM analysis. Regardless of catalyst compositions, the optimal reaction temperature for oxidative carbonylation of methanol was found to be around 120--130 C. The reaction rate was too slow below 100 C, while too many by-products were produced above 150 C. Among the various catalysts employed, CuCl{sub 2}/NaOH/AC catalyst with the mole ratio of OH/Cu = 0.5--1.0 has shown the best catalytic performance, which appears to have a strong relationship with the formation of intermediate species, Cu{sub 2}(OH){sub 3}Cl.

Protein conjugated with aldehydes derived from lipid peroxidation as an independent parameter of the carbonyl stress in the kidney damage

Directory of Open Access Journals (Sweden)

Medina-Navarro Rafael

2011-11-01

Full Text Available Abstract Background One of the well-defined and characterized protein modifications usually produced by oxidation is carbonylation, an irreversible non-enzymatic modification of proteins. However, carbonyl groups can be introduced into proteins by non-oxidative mechanisms. Reactive carbonyl compounds have been observed to have increased in patients with renal failure. In the present work we have described a procedure designed as aldehyde capture to calculate the protein carbonyl stress derived solely from lipid peroxidation. Methods Acrolein-albumin adduct was prepared as standard at alkaline pH. Rat liver microsomal membranes and serum samples from patients with diabetic nephropathy were subjected to the aldehyde capture procedure and aldol-protein formation. Before alkalinization and incubation, samples were precipitated and redisolved in 6M guanidine. The absorbances of the samples were read with a spectrophotometer at 266 nm against a blank of guanidine. Results Evidence showed abundance of unsaturated aldehydes derived from lipid peroxidation in rat liver microsomal membranes and in the serum of diabetic patients with advanced chronic kidney disease. Carbonyl protein and aldol-proteins resulted higher in the diabetic nephropathy patients (p Conclusion The aldehyde-protein adduct represents a non oxidative component of carbonyl stress, independent of the direct amino acid oxidation and could constitute a practical and novelty strategy to measure the carbonyl stress derived solely from lipid peroxidation and particularly in diabetic nephropathy patients. In addition, we are in a position to propose an alternative explanation of why alkalinization of urine attenuates rhabdomyolysis-induced renal dysfunction.

Engineered Trx2p industrial yeast strain protects glycolysis and fermentation proteins from oxidative carbonylation during biomass propagation

Directory of Open Access Journals (Sweden)

Gómez-Pastor Rocío

2012-01-01

Full Text Available Abstract Background In the yeast biomass production process, protein carbonylation has severe adverse effects since it diminishes biomass yield and profitability of industrial production plants. However, this significant detriment of yeast performance can be alleviated by increasing thioredoxins levels. Thioredoxins are important antioxidant defenses implicated in many functions in cells, and their primordial functions include scavenging of reactive oxygen species that produce dramatic and irreversible alterations such as protein carbonylation. Results In this work we have found several proteins specifically protected by yeast Thioredoxin 2 (Trx2p. Bidimensional electrophoresis and carbonylated protein identification from TRX-deficient and TRX-overexpressing cells revealed that glycolysis and fermentation-related proteins are specific targets of Trx2p protection. Indeed, the TRX2 overexpressing strain presented increased activity of the central carbon metabolism enzymes. Interestingly, Trx2p specifically preserved alcohol dehydrogenase I (Adh1p from carbonylation, decreased oligomer aggregates and increased its enzymatic activity. Conclusions The identified proteins suggest that the fermentative capacity detriment observed under industrial conditions in T73 wine commercial strain results from the oxidative carbonylation of specific glycolytic and fermentation enzymes. Indeed, increased thioredoxin levels enhance the performance of key fermentation enzymes such as Adh1p, which consequently increases fermentative capacity.

H-1 chemical shift imaging of the brain in guanidino methyltransferase deficiency, a creatine deficiency syndrome; guanidinoacetate accumulation in the gray matter

NARCIS (Netherlands)

Sijens, PE; Verbruggen, KT; Meiners, LC; Soorani-Lunsing, RJ; Rake, JP; Oudkerk, M

MR spectroscopy results in a mild case of guanidinoacetate methyltransferase (GAMT) deficiency are presented. The approach differs from previous MRS studies in the acquisition of a chemical shift imaging spectral map showing gray and white matter with the corresponding spectra in one overview. MR

Saturated amine oxides: Part 8. Hydroacridines: Part 27. Effects of N-oxidation and of N-quaternization on the 15N NMR chemical shifts of N-methylpiperidine-derived mono-, bi-, and tricycloaliphatic tertiary amines.

Science.gov (United States)

Potmischil, Francisc; Duddeck, Helmut; Nicolescu, Alina; Deleanu, Calin

2007-03-01

The (15)N chemical shifts of 13 N-methylpiperidine-derived mono-, bi- and tricycloaliphatic tertiary amines, their methiodides and their N-epimeric pairs of N-oxides were measured, and the contributions of specific structural parameters to the chemical shifts were determined by multilinear regression analysis. Within the examined compounds, the effects of N-oxidation upon the (15)N chemical shifts of the amines vary from +56 ppm to +90 ppm (deshielding), of which approx. +67.7 ppm is due to the inductive effect of the incoming N(+)--O(-) oxygen atom, whereas the rest is due to the additive shift effects of the various C-alkyl substituents of the piperidine ring. The effects of quaternization vary from -3.1 ppm to +29.3 ppm, of which approx. +8.9 ppm is due to the inductive effect of the incoming N(+)--CH(3) methyl group, and the rest is due to the additive shift effects of the various C-alkyl substituents of the piperidine ring. The shift effects of the C-alkyl substituents in the amines, the N-oxides and the methiodides are discussed. Copyright (c) 2007 John Wiley & Sons, Ltd.

Correlates to sleepiness on night shift among male workers engaged in three-shift work in a chemical plant: its association with sleep practice and job stress.

Science.gov (United States)

Kageyama, Takayuki; Kobayashi, Toshio; Abe-Gotoh, Ayano

2011-01-01

The purpose of this study was to examine the correlation of sleepiness during night shift (SNS) in male shiftworkers with nonpharmacological self-management (nPSM) practices to facilitate good day sleep, and also with job stress. Sleepiness on the job and possible correlates to SNS among 157 male shiftworkers in a rotating three-shift schedule at a chemical plant were cross-sectionally investigated using a self-administered questionnaire. Multivariate analyses revealed that SNS was positively associated with drinking alcoholic beverages before day sleep, but inversely associated with subjective health status, being of the evening type, abstaining from caffeine before day sleep, having a bath before day sleep, job control, reward from work, feeling suited to the job, and support from colleagues. SNS correlated with certain nPSM practices and also with possible modifiers of job stress. These findings provide clues to developing countermeasures against SNS among shiftworkers. The effects of nPSM practices and job stress management on their day sleep and SNS should be examined in detail.

Synthesis and preclinical evaluation of [11C-carbonyl]PF-04457845 for neuroimaging of fatty acid amide hydrolase

International Nuclear Information System (INIS)

Hicks, Justin W.; Parkes, Jun; Sadovski, Oleg; Tong, Junchao; Houle, Sylvain; Vasdev, Neil; Wilson, Alan A.

2013-01-01

Introduction: Fatty acid amide hydrolase (FAAH) has a significant role in regulating endocannabinoid signaling in the central nervous system. As such, FAAH inhibitors are being actively sought for pain, addiction, and other indications. This has led to the recent pursuit of positron emission tomography (PET) radiotracers targeting FAAH. We report herein the preparation and preclinical evaluation of [ 11 C-carbonyl]PF-04457845, an isotopologue of the potent irreversible FAAH inhibitor. Methods: PF-04457845 was radiolabeled at the carbonyl position via automated [ 11 C]CO 2 -fixation. Ex vivo brain biodistribution of [ 11 C-carbonyl]PF-04457845 was carried out in conscious rats. Specificity was determined by pre-administration of PF-04457845 or URB597 prior to [ 11 C-carbonyl]PF-04457845. In a separate experiment, rats injected with the title radiotracer had whole brains excised, homogenized and extracted to examine irreversible binding to brain parenchyma. Results: The title compound was prepared in 5 ± 1% (n = 4) isolated radiochemical yield based on starting [ 11 C]CO 2 (decay uncorrected) within 25 min from end-of-bombardment in > 98% radiochemical purity and a specific activity of 73.5 ± 8.2 GBq/μmol at end-of-synthesis. Uptake of [ 11 C-carbonyl]PF-04457845 into the rat brain was high (range of 1.2–4.4 SUV), heterogeneous, and in accordance with reported FAAH distribution. Saturable binding was demonstrated by a dose-dependent reduction in brain radioactivity uptake following pre-treatment with PF-04457845. Pre-treatment with the prototypical FAAH inhibitor, URB597, reduced the brain radiotracer uptake in all regions by 71–81%, demonstrating specificity for FAAH. The binding of [ 11 C-carbonyl]PF-04457845 to FAAH at 40 min post injection was irreversible as 98% of the radioactivity in the brain could not be extracted. Conclusions: [ 11 C-carbonyl]PF-04457845 was rapidly synthesized via an automated radiosynthesis. Ex vivo biodistribution studies in

Alkylselenite-catalyzed Oxidative Carbonylation of Amines: Density Functional Theory Study

Energy Technology Data Exchange (ETDEWEB)

Hwang, Sun; Kim, Hoon Sik; Cheong, Minserk [Kyung Hee Univ., Seoul (Korea, Republic of)

2012-11-15

Ureas and carbamates have been conventionally produced by the reaction of amines with phosgene. However, phosgenation processes raise severe environmental concerns, which are attributed to the toxicity of phosgene and the formation of corrosive hydrogen chloride as a co-product. The considerable industrial interest in replacing current phosgene-based processes prompted several methods using non-phosgene routes including carbonylation of amines or nitro compounds and carbomethoxylation of amines with dialkylcarbonates. Among these, catalytic oxidative carbonylation of an amine in the presence of alcohol has been studied most extensively. Catalytic systems based on precious metals such as Rh and Pd are commonly used for this purpose, but most of these catalytic systems suffer from either low reactivity or severe reaction conditions such as high temperature and pressures. In conclusion, the facile change of selenium oxidation state by CO and O{sub 2} might be the main reason for the activity of the selenium catalyst for this reaction.

Alkylselenite-catalyzed Oxidative Carbonylation of Amines: Density Functional Theory Study

International Nuclear Information System (INIS)

Hwang, Sun; Kim, Hoon Sik; Cheong, Minserk

2012-01-01

Ureas and carbamates have been conventionally produced by the reaction of amines with phosgene. However, phosgenation processes raise severe environmental concerns, which are attributed to the toxicity of phosgene and the formation of corrosive hydrogen chloride as a co-product. The considerable industrial interest in replacing current phosgene-based processes prompted several methods using non-phosgene routes including carbonylation of amines or nitro compounds and carbomethoxylation of amines with dialkylcarbonates. Among these, catalytic oxidative carbonylation of an amine in the presence of alcohol has been studied most extensively. Catalytic systems based on precious metals such as Rh and Pd are commonly used for this purpose, but most of these catalytic systems suffer from either low reactivity or severe reaction conditions such as high temperature and pressures. In conclusion, the facile change of selenium oxidation state by CO and O 2 might be the main reason for the activity of the selenium catalyst for this reaction

Backbone dynamics of a model membrane protein: measurement of individual amide hydrogen-exchange rates in detergent-solubilized M13 coat protein using 13C NMR hydrogen/deuterium isotope shifts

International Nuclear Information System (INIS)

Henry, G.D.; Weiner, J.H.; Sykes, B.D.

1987-01-01

Hydrogen-exchange rates have been measured for individual assigned amide protons in M13 coat protein, a 50-residue integral membrane protein, using a 13 C nuclear magnetic resonance (NMR) equilibrium isotope shift technique. The locations of the more rapidly exchanging amides have been determined. In D 2 O solutions, a peptide carbonyl resonance undergoes a small upfield isotope shift (0.08-0.09 ppm) from its position in H 2 O solutions; in 1:1 H 2 O/D 2 O mixtures, the carbonyl line shape is determined by the exchange rate at the adjacent nitrogen atom. M13 coat protein was labeled biosynthetically with 13 C at the peptide carbonyls of alanine, glycine, phenylalanine, proline, and lysine, and the exchange rates of 12 assigned amide protons in the hydrophilic regions were measured as a function of pH by using the isotope shift method. This equilibrium technique is sensitive to the more rapidly exchanging protons which are difficult to measure by classical exchange-out experiments. In proteins, structural factors, notably H bonding, can decrease the exchange rate of an amide proton by many orders of magnitude from that observed in the freely exposed amides of model peptides such as poly(DL-alanine). With corrections for sequence-related inductive effects, the retardation of amide exchange in sodium dodecyl sulfate solubilized coat protein has been calculated with respect to poly(DL-alanine). The most rapidly exchanging protons, which are retarded very little or not at all, are shown to occur at the N- and C-termini of the molecule. A model of the detergent-solubilized coat protein is constructed from these H-exchange data which is consistent with circular dichroism and other NMR results

Radiation-chemical destruction of cellulose and other polysaccharides

International Nuclear Information System (INIS)

Ershov, B.G.

1998-01-01

The studies concerning the radiation-chemical destruction of cellulose, its ethers and some polysaccharides (xylan, starch, decstrans, chitin, chitosan and geparin) are discussed. Ionising irradiation causes the destruction of these compounds with the decay of pyranose ring, accompanied by the formation of compounds containing carbonyl or carboxyl groups, as well as hydrogen, carbon dioxide, and carbon oxide. The efficiency of radiation degradation increases with increasing the temperature and depends on the structure of polysaccharides and the nature of substituents. The mechanism of radiation-chemical transformations of cellulose and others polysaccharides is proposed. Prospects of the application of radiation-chemical methods of treatment of cellulose and other polysaccharides in industry and agriculture considered [ru

Carbonyl Activation by Borane Lewis Acid Complexation: Transition States of H2 Splitting at the Activated Carbonyl Carbon Atom in a Lewis Basic Solvent and the Proton-Transfer Dynamics of the Boroalkoxide Intermediate.

Science.gov (United States)

Heshmat, Mojgan; Privalov, Timofei

2017-07-06

By using transition-state (TS) calculations, we examined how Lewis acid (LA) complexation activates carbonyl compounds in the context of hydrogenation of carbonyl compounds by H 2 in Lewis basic (ethereal) solvents containing borane LAs of the type (C 6 F 5 ) 3 B. According to our calculations, LA complexation does not activate a ketone sufficiently enough for the direct addition of H 2 to the O=C unsaturated bond; but, calculations indicate a possibly facile heterolytic cleavage of H 2 at the activated and thus sufficiently Lewis acidic carbonyl carbon atom with the assistance of the Lewis basic solvent (i.e., 1,4-dioxane or THF). For the solvent-assisted H 2 splitting at the carbonyl carbon atom of (C 6 F 5 ) 3 B adducts with different ketones, a number of TSs are computed and the obtained results are related to insights from experiment. By using the Born-Oppenheimer molecular dynamics with the DFT for electronic structure calculations, the evolution of the (C 6 F 5 ) 3 B-alkoxide ionic intermediate and the proton transfer to the alkoxide oxygen atom were investigated. The results indicate a plausible hydrogenation mechanism with a LA, that is, (C 6 F 5 ) 3 B, as a catalyst, namely, 1) the step of H 2 cleavage that involves a Lewis basic solvent molecule plus the carbonyl carbon atom of thermodynamically stable and experimentally identifiable (C 6 F 5 ) 3 B-ketone adducts in which (C 6 F 5 ) 3 B is the "Lewis acid promoter", 2) the transfer of the solvent-bound proton to the oxygen atom of the (C 6 F 5 ) 3 B-alkoxide intermediate giving the (C 6 F 5 ) 3 B-alcohol adduct, and 3) the S N 2-style displacement of the alcohol by a ketone or a Lewis basic solvent molecule. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Analysis of protein carbonylation - pitfalls and promise in commonly used methods

DEFF Research Database (Denmark)

Rogowska-Wrzesinska, A.; Wojdyla, K.; Nedic, O.

2014-01-01

that research scientists are becoming more eager to be able to measure accurately the level of oxidized protein in biological materials, and to determine the precise site of the oxidative attack on the protein, in order to get insights into the molecular mechanisms involved in the progression of diseases....... Several methods for measuring protein carbonylation have been implemented in different laboratories around the world. However, to date no methods prevail as the most accurate, reliable, and robust. The present paper aims at giving an overview of the common methods used to determine protein carbonylation...... in biological material as well as to highlight the limitations and the potential. The ultimate goal is to give quick tips for a rapid decision making when a method has to be selected and taking into consideration the advantage and drawback of the methods....

Analysis of protein carbonylation-pitfalls and promise in commonly used methods

DEFF Research Database (Denmark)

Rogowska-Wrzesinska, Adelina; Wojdyla, K; Nedić, O

2014-01-01

that research scientists are becoming more eager to be able to measure accurately the level of oxidized protein in biological materials, and to determine the precise site of the oxidative attack on the protein, in order to get insights into the molecular mechanisms involved in the progression of diseases....... Several methods for measuring protein carbonylation have been implemented in different laboratories around the world. However, to date no methods prevail as the most accurate, reliable, and robust. The present paper aims at giving an overview of the common methods used to determine protein carbonylation...... in biological material as well as to highlight the limitations and the potential. The ultimate goal is to give quick tips for a rapid decision making when a method has to be selected and taking into consideration the advantage and drawback of the methods....

Heat Integration of the Water-Gas Shift Reaction System for Carbon Sequestration Ready IGCC Process with Chemical Looping

Energy Technology Data Exchange (ETDEWEB)

Juan M. Salazara; Stephen E. Zitney; Urmila M. Diwekara

2010-01-01

Integrated gasification combined cycle (IGCC) technology has been considered as an important alternative for efficient power systems that can reduce fuel consumption and CO2 emissions. One of the technological schemes combines water-gas shift reaction and chemical-looping combustion as post gasification techniques in order to produce sequestration-ready CO2 and potentially reduce the size of the gas turbine. However, these schemes have not been energetically integrated and process synthesis techniques can be applied to obtain an optimal flowsheet. This work studies the heat exchange network synthesis (HENS) for the water-gas shift reaction train employing a set of alternative designs provided by Aspen energy analyzer (AEA) and combined in a process superstructure that was simulated in Aspen Plus (AP). This approach allows a rigorous evaluation of the alternative designs and their combinations avoiding all the AEA simplifications (linearized models of heat exchangers). A CAPE-OPEN compliant capability which makes use of a MINLP algorithm for sequential modular simulators was employed to obtain a heat exchange network that provided a cost of energy that was 27% lower than the base case. Highly influential parameters for the pos gasification technologies (i.e. CO/steam ratio, gasifier temperature and pressure) were calculated to obtain the minimum cost of energy while chemical looping parameters (oxidation and reduction temperature) were ensured to be satisfied.

Excited state characterization of carbonyl containing carotenoids: a comparison between single and multireference descriptions

Science.gov (United States)

Spezia, Riccardo; Knecht, Stefan; Mennucci, Benedetta

Carotenoids can play multiple roles in biological photoreceptors thanks to their rich photophysics. In the present work, we have investigated six of the most common carbonyl containing carotenoids: Echinenone, Canthaxanthin, Astaxanthin, Fucoxanthin, Capsanthin and Capsorubin. Their excitation properties are investigated by means of a hybrid density functional theory (DFT) and multireference configuration interaction (MRCI) approach to elucidate the role of the carbonyl group: the bright transition is of {\\pi}{\\pi}* character, as expected, but the presence of a C=O moiety reduces the energy of n{\\pi}* transitions which may become closer to the {\\pi}{\\pi}* transition, in particular as the conjugation chain decreases. This can be related to the presence of a low-lying charge transfer state typical of short carbonyl- containing carotenoids. The DFT/MRCI results are finally used to benchmark single- reference time-dependent DFT-based methods: among the investigated functionals, the meta- GGA (and in particular M11L and MN12L) functionals show to perform the best for all six investigated systems.

Nuclear spin relaxation due to chemical shift anisotropy of gas-phase 129Xe.

Science.gov (United States)

Hanni, Matti; Lantto, Perttu; Vaara, Juha

2011-08-14

Nuclear spin relaxation provides detailed dynamical information on molecular systems and materials. Here, first-principles modeling of the chemical shift anisotropy (CSA) relaxation time for the prototypic monoatomic (129)Xe gas is carried out, both complementing and predicting the results of NMR measurements. Our approach is based on molecular dynamics simulations combined with pre-parametrized ab initio binary nuclear shielding tensors, an "NMR force field". By using the Redfield relaxation formalism, the simulated CSA time correlation functions lead to spectral density functions that, for the first time, quantitatively determine the experimental spin-lattice relaxation times T(1). The quality requirements on both the Xe-Xe interaction potential and binary shielding tensor are investigated in the context of CSA T(1). Persistent dimers Xe(2) are found to be responsible for the CSA relaxation mechanism in the low-density limit of the gas, completely in line with the earlier experimental findings.

Ring current shifts in {sup 19}F-NMR of membrane proteins

Energy Technology Data Exchange (ETDEWEB)

Liu, Dongsheng, E-mail: liudsh@shanghaitech.edu.cn; Wüthrich, Kurt, E-mail: kwuthrich@shanghaitech.edu.cn [ShanghaiTech University, iHuman Institute (China)

2016-05-15

Fluorine-19 NMR markers are attractive reporter groups for use in studies of complex biomacromolecular systems, in particular also for studies of function-related conformational equilibria and rate processes in membrane proteins. Advantages of {sup 19}F-NMR probes include high sensitivity of the {sup 19}F chemical shifts to variations in the non-covalent environment. Nonetheless, in studies of G protein-coupled receptors (GPCR) we encountered situations where {sup 19}F chemical shifts were not responsive to conformational changes that had been implicated by other methods. This prompted us to examine possible effects of aromatic ring current fields on the chemical shifts of {sup 19}F-NMR probes used in GPCRs. Analysis of previously reported {sup 19}F-NMR data on the β{sub 2}-adrenergic receptor and mammalian rhodopsin showed that all {sup 19}F-labeling sites which manifested conformational changes are located near aromatic residues. Although ring current effects are small when compared to other known non-covalent effects on {sup 19}F chemical shifts, there is thus an indication that their contributions are significant when studying activation processes in GPCRs, since the observed activation-related {sup 19}F-NMR chemical shifts are comparable in size to the calculated ring current shifts. Considering the impact of ring current shifts may thus be helpful in identifying promising indigenous or engineered labeling sites for future {sup 19}F-NMR studies of GPCR activation, and novel information may be obtained on the nature of conformational rearrangements near the {sup 19}F-labels. It will then also be interesting to see if the presently indicated role of ring current shifts in membrane protein studies with {sup 19}F-NMR markers can be substantiated by a more extensive data base resulting from future studies.

NMR spectroscopic studies of a TAT-derived model peptide in imidazolium-based ILs: influence on chemical shifts and the cis/trans equilibrium state.

Science.gov (United States)

Wiedemann, Christoph; Ohlenschläger, Oliver; Mrestani-Klaus, Carmen; Bordusa, Frank

2017-09-13

NMR spectroscopy was used to study systematically the impact of imidazolium-based ionic liquid (IL) solutions on a TAT-derived model peptide containing Xaa-Pro peptide bonds. The selected IL anions cover a wide range of the Hofmeister series of ions. Based on highly resolved one- and two-dimensional NMR spectra individual 1 H and 13 C peptide chemical shift differences were analysed and a classification of IL anions according to the Hofmeister series was derived. The observed chemical shift changes indicate significant interactions between the peptide and the ILs. In addition, we examined the impact of different ILs towards the cis/trans equilibrium state of the Xaa-Pro peptide bonds. In this context, the IL cations appear to be of exceptional importance for inducing an alteration of the native cis/trans equilibrium state of Xaa-Pro bonds in favour of the trans-isomers.

NMR spectroscopy of organic compounds of selenium and tellurium. Communication 9. Chemical shifts of /sup 13/C in isological series of unsaturated ethers, sulfides, selenides and tellurides

Energy Technology Data Exchange (ETDEWEB)

Kalabin, G.A.; Bzhezovskii, V.M.; Kushnarev, D.F.; Proidakov, A.G. (Irkutskii Gosudarstvennyj Univ. (USSR))

1981-06-01

The effects of heteroatoms Eh(Eh=O, S, Se, Te) on /sup 13/C chemical shifts in eleven isological series of R/sup 1/-Eh-R/sup 2/ unsaturated compounds are compared. A linear relation between /sup 13/C nuclei screening and tEh electronegativity is observed. An assumption is suggested that both likeness of the effects of 6A and 7A group elements on /sup 13/C chemical shifts of R/sup 1/ and R/sup 2/ substituents and their difference for elements of the 4A group are caused by unbonded interactions of the substituents with unshared electron pairs of heteroatoms.