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Khare R, Weindl R, Jentys A, Reuter K, Shi H, Lercher JA. Di- and Tetrameric Molybdenum Sulfide Clusters Activate and Stabilize Dihydrogen as Hydrides. JACS Au 2022; 2:613-622. [PMID: 35373212 PMCID: PMC8965828 DOI: 10.1021/jacsau.1c00507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Indexed: 06/14/2023]
Abstract
NaY zeolite-encapsulated dimeric (Mo2S4) and tetrameric (Mo4S4) molybdenum sulfide clusters stabilize hydrogen as hydride binding to Mo atoms. Density functional theory (DFT) calculations and adsorption measurements suggest that stabilization of hydrogen as sulfhydryl (SH) groups, as typical for layered MoS2, is thermodynamically disfavored. Competitive adsorption of H2 and ethene on Mo was probed by quantifying adsorbed CO on partly hydrogen and/or ethene covered samples with IR spectroscopy. During hydrogenation, experiment and theory suggest that Mo is covered predominately with ethene and sparsely with hydride. DFT calculations further predict that, under reaction conditions, each Mo x S y cluster can activate only one H2, suggesting that the entire cluster (irrespective of its nuclearity) acts as one active site for hydrogenation. The nearly identical turnover frequencies (24.7 ± 3.3 molethane·h-1·molcluster -1), apparent activation energies (31-32 kJ·mol-1), and reaction orders (∼0.5 in ethene and ∼1.0 in H2) show that the active sites in both clusters are catalytically indistinguishable.
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Affiliation(s)
- Rachit Khare
- Department
of Chemistry and Catalysis Research Center, Technical University of Munich, 85747 Garching, Germany
| | - Roland Weindl
- Department
of Chemistry and Catalysis Research Center, Technical University of Munich, 85747 Garching, Germany
| | - Andreas Jentys
- Department
of Chemistry and Catalysis Research Center, Technical University of Munich, 85747 Garching, Germany
| | - Karsten Reuter
- Department
of Chemistry and Catalysis Research Center, Technical University of Munich, 85747 Garching, Germany
- Fritz
Haber Institute of the Max Planck Society, 14195 Berlin, Germany
| | - Hui Shi
- School
of Chemistry and Chemical Engineering, Yangzhou
University, Yangzhou, 225009 Jiangsu China
| | - Johannes A. Lercher
- Department
of Chemistry and Catalysis Research Center, Technical University of Munich, 85747 Garching, Germany
- Institute
for Integrated Catalysis, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
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2
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Zapata F, López-Fernández A, Ortega-Ojeda F, Quintanilla G, García-Ruiz C, Montalvo G. Introducing ATR-FT IR Spectroscopy through Analysis of Acetaminophen Drugs: Practical Lessons for Interdisciplinary and Progressive Learning for Undergraduate Students. J Chem Educ 2021; 98:2675-2686. [PMID: 35281766 PMCID: PMC8908246 DOI: 10.1021/acs.jchemed.0c01231] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 05/19/2021] [Indexed: 05/10/2023]
Abstract
Infrared (IR) spectroscopy is a vibrational spectroscopic technique useful in chemical, pharmaceutical, and forensic sciences. It is essential to identify chemicals for reasons spanning from scientific research and academic practices to quality control in companies. However, in some university degrees, graduate students do not get the proficiency to optimize the experimental parameters to obtain the best IR spectra; to correlate the IR spectral bands with the molecular vibrations (chemical elucidation); to have some criteria for any substance identification (especially relevant in quality control to recognize counterfeit); and to apply chemometrics for comparing, visualizing, and classifying the IR spectra. This work presents an experimental laboratory practice for an introductory teaching of the IR instrumental conditions in the identification of substances based on visual spectra comparison and statistical analysis and matching. Then, the selected IR conditions are applied to different commercial drugs, in the solid state or in solution, mostly composed of acetaminophen. Finally, the students apply chemometrics analysis to the IR data. This practice was designed for the training in a chemistry subject for undergraduate students of the chemistry, pharmacy, or forensics degrees, among others related to science, medical, food, or technological sciences.
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Affiliation(s)
- Félix Zapata
- Department
of Analytical Chemistry, Physical Chemistry, and Chemical
Engineering, Department of Physics and Mathematics, University Institute of Research
in Police Sciences (IUICP), and Department of Organic Chemistry and Inorganic
Chemistry, University of Alcalá, Ctra. Madrid-Barcelona km 33.6, 28871 Alcalá de Henares, Madrid, Spain
| | - Adrián López-Fernández
- Department
of Analytical Chemistry, Physical Chemistry, and Chemical
Engineering, Department of Physics and Mathematics, University Institute of Research
in Police Sciences (IUICP), and Department of Organic Chemistry and Inorganic
Chemistry, University of Alcalá, Ctra. Madrid-Barcelona km 33.6, 28871 Alcalá de Henares, Madrid, Spain
| | - Fernando Ortega-Ojeda
- Department
of Analytical Chemistry, Physical Chemistry, and Chemical
Engineering, Department of Physics and Mathematics, University Institute of Research
in Police Sciences (IUICP), and Department of Organic Chemistry and Inorganic
Chemistry, University of Alcalá, Ctra. Madrid-Barcelona km 33.6, 28871 Alcalá de Henares, Madrid, Spain
| | - Gloria Quintanilla
- Department
of Analytical Chemistry, Physical Chemistry, and Chemical
Engineering, Department of Physics and Mathematics, University Institute of Research
in Police Sciences (IUICP), and Department of Organic Chemistry and Inorganic
Chemistry, University of Alcalá, Ctra. Madrid-Barcelona km 33.6, 28871 Alcalá de Henares, Madrid, Spain
| | - Carmen García-Ruiz
- Department
of Analytical Chemistry, Physical Chemistry, and Chemical
Engineering, Department of Physics and Mathematics, University Institute of Research
in Police Sciences (IUICP), and Department of Organic Chemistry and Inorganic
Chemistry, University of Alcalá, Ctra. Madrid-Barcelona km 33.6, 28871 Alcalá de Henares, Madrid, Spain
| | - Gemma Montalvo
- Department
of Analytical Chemistry, Physical Chemistry, and Chemical
Engineering, Department of Physics and Mathematics, University Institute of Research
in Police Sciences (IUICP), and Department of Organic Chemistry and Inorganic
Chemistry, University of Alcalá, Ctra. Madrid-Barcelona km 33.6, 28871 Alcalá de Henares, Madrid, Spain
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3
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Potter ME, Cho KM, Lee JJ, Jones CW. Role of Alumina Basicity in CO 2 Uptake in 3-Aminopropylsilyl-Grafted Alumina Adsorbents. ChemSusChem 2017; 10:2192-2201. [PMID: 28388018 DOI: 10.1002/cssc.201700115] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Revised: 04/02/2017] [Indexed: 06/07/2023]
Abstract
Oxide-supported amine materials are widely known to be effective CO2 sorbents under simulated flue-gas and direct-air-capture conditions. Most work has focused on amine species loaded onto porous silica supports, though potential stability advantages may be offered through the use of porous alumina supports. Unlike silica materials, which are comparably inert, porous alumina materials can be tuned to have substantial acidity and/or basicity. Owing to their amphoteric nature, alumina supports play a more active role in CO2 sorption than silica supports, potentially directly participating in the adsorption process. In this work, primary amines associated with 3-aminopropyltriethoxysilane are grafted onto two different mesoporous alumina materials having different levels of basicity. Adsorbent materials with different amine loadings are prepared, and the CO2 -adsorption behavior of similar amines on the two alumina supports is demonstrated to be different. At low amine loadings, the inherent properties of the support surface play a significant role, whereas at high amine loadings, when the alumina surface is effectively blocked, the sorbents prepared on the two supports behave similarly. At high amine loadings, amine-CO2 -amine interactions are shown to dominate, leading to adsorbed species that appear similar to the species formed over silica-supported amine materials. The sorbent properties are comprehensively characterized using N2 physisorption analysis, in situ FTIR spectroscopy, and adsorption microcalorimetry.
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Affiliation(s)
- Matthew E Potter
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive, NW, Atlanta, GA, 30332, USA
| | - Kyeong Min Cho
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive, NW, Atlanta, GA, 30332, USA
- Department of Chemical and Biomolecular Engineering (BK-21 plus), Korea Advanced Institute of Science and Technology, Daejeon, 305-701, Republic of Korea
| | - Jason J Lee
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive, NW, Atlanta, GA, 30332, USA
| | - Christopher W Jones
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive, NW, Atlanta, GA, 30332, USA
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4
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Abstract
Disulfide cleavage is one of the major causes underlying ultraviolet (UV) light-induced protein damage. While previous studies have provided strong evidence to support the notion that this process is mediated by photo-induced electron transfer from the excited state of an aromatic residue (e.g., tryptophan) to the disulfide bond, many mechanistic details are still lacking. For example, we do not know how quickly this process occurs in a protein environment. Herein, we design an experiment, which uses the unfolding kinetics of a protein as an observable, to directly assess the kinetics and mechanism of photo-induced disulfide cleavage. Our results show that this disulfide bond cleavage event takes place in ∼2 μs via a mechanism involving electron transfer from the triplet state of a tryptophan (Trp) residue to the disulfide bond. Furthermore, we find that one of the photoproducts of this reaction, a Trp-SR adduct, is formed locally, thus preventing the protein from re-cross-linking. Taken together, these findings suggest that a Trp-disulfide pair could be used as a photo-trigger to initiate protein folding dynamics and control the biological activities of disulfide-containing peptides.
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Affiliation(s)
- Rachel M Abaskharon
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
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5
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Pleissner D, Lau KY, Zhang C, Lin CSK. Plasticizer and surfactant formation from food-waste- and algal biomass-derived lipids. ChemSusChem 2015; 8:1686-1691. [PMID: 25425530 DOI: 10.1002/cssc.201402888] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Revised: 10/09/2014] [Indexed: 06/04/2023]
Abstract
The potential of lipids derived from food-waste and algal biomass (produced from food-waste hydrolysate) for the formation of plasticizers and surfactants is investigated herein. Plasticizers were formed by epoxidation of double bonds of methylated unsaturated fatty acids with in situ generated peroxoformic acid. Assuming that all unsaturated fatty acids are convertible, 0.35 and 0.40 g of plasticizer can be obtained from 1 g of crude algae- or food-waste-derived lipids, respectively. Surfactants were formed by transesterification of saturated and epoxidized fatty acid methyl esters (FAMEs) with polyglycerol. The addition of polyglycerol would result in a complete conversion of saturated and epoxidized FAMEs to fatty acid polyglycerol esters. This study successfully demonstrates the conversion of food-waste into value-added chemicals using simple and conventional chemical reactions.
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Affiliation(s)
- Daniel Pleissner
- School of Energy and Environment, City University of Hong, Tat Chee Avenue, Kowloon, Hong Kong (PR China)
| | - Kin Yan Lau
- School of Energy and Environment, City University of Hong, Tat Chee Avenue, Kowloon, Hong Kong (PR China)
| | - Chengwu Zhang
- Laboratory of Microalgal Bioenergy and Biotechnology, Jinan University, No. 601, Huangpu Boulevard, Tianhe District, Guangzhou City, 510630 (PR China)
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong, Tat Chee Avenue, Kowloon, Hong Kong (PR China).
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6
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McMullin D, Mizaikoff B, Krska R. Advancements in IR spectroscopic approaches for the determination of fungal derived contaminations in food crops. Anal Bioanal Chem 2015; 407:653-60. [PMID: 25258282 PMCID: PMC4305099 DOI: 10.1007/s00216-014-8145-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 08/25/2014] [Accepted: 08/28/2014] [Indexed: 11/19/2022]
Abstract
Infrared spectroscopy is a rapid, nondestructive analytical technique that can be applied to the authentication and characterization of food samples in high throughput. In particular, near infrared spectroscopy is commonly utilized in the food quality control industry to monitor the physical attributes of numerous cereal grains for protein, carbohydrate, and lipid content. IR-based methods require little sample preparation, labor, or technical competence if multivariate data mining techniques are implemented; however, they do require extensive calibration. Economically important crops are infected by fungi that can severely reduce crop yields and quality and, in addition, produce mycotoxins. Owing to the health risks associated with mycotoxins in the food chain, regulatory limits have been set by both national and international institutions for specific mycotoxins and mycotoxin classes. This article discusses the progress and potential of IR-based methods as an alternative to existing chemical methods for the determination of fungal contamination in crops, as well as emerging spectroscopic methods.
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Affiliation(s)
- David McMullin
- Center for Analytical Chemistry, Department for Agrobiotechnology, University of Natural Resources and Applied Life Sciences Vienna, Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
| | - Boris Mizaikoff
- Institute of Analytical and Bioanalytical Chemistry, University of Ulm, Albert-Einstein-Allee 11, 89075 Ulm, Germany
| | - Rudolf Krska
- Center for Analytical Chemistry, Department for Agrobiotechnology, University of Natural Resources and Applied Life Sciences Vienna, Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
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7
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Zencirci N, Griesser UJ, Gelbrich T, Apperley D, Harris RK. Crystal polymorphs of barbital: news about a classic polymorphic system. Mol Pharm 2014; 11:338-50. [PMID: 24283960 PMCID: PMC4066893 DOI: 10.1021/mp400515f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 11/25/2013] [Accepted: 11/27/2013] [Indexed: 11/28/2022]
Abstract
Barbital is a hypnotic agent that has been intensely studied for many decades. The aim of this work was to establish a clear and comprehensible picture of its polymorphic system. Four of the six known solid forms of barbital (denoted I(0), III, IV, and V) were characterized by various analytical techniques, and the thermodynamic relationships between the polymorph phases were established. The obtained data permitted the construction of the first semischematic energy/temperature diagram for the barbital system. The modifications I(0), III, and V are enantiotropically related to one another. Polymorph IV is enantiotropically related to V and monotropically related to the other two forms. The transition points for the pairs I(0)/III, I(0)/V, and III/IV lie below 20 °C, and the transition point for IV/V is above 20 °C. At room temperature, the order of thermodynamic stability is I(0) > III > V > IV. The metastable modification III is present in commercial samples and has a high kinetic stability. The solid-state NMR spectra provide information on aspects of crystallography (viz., the asymmetric units and the nature of hydrogen bonding). The known correlation between specific N-H···O═C hydrogen bonding motifs of barbiturates and certain IR characteristics was used to predict the H-bonded pattern of polymorph IV.
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Affiliation(s)
- Neslihan Zencirci
- Institute
of Pharmacy, University of Innsbruck, Innrain 52, 6020 Innsbruck, Austria
| | - Ulrich J. Griesser
- Institute
of Pharmacy, University of Innsbruck, Innrain 52, 6020 Innsbruck, Austria
| | - Thomas Gelbrich
- Institute
of Pharmacy, University of Innsbruck, Innrain 52, 6020 Innsbruck, Austria
| | - David
C. Apperley
- Department
of Chemistry, University of Durham, South Road, Durham DH1 3LE, United
Kingdom
| | - Robin K. Harris
- Department
of Chemistry, University of Durham, South Road, Durham DH1 3LE, United
Kingdom
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8
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Bazzo A, Urakawa A. Origin of photocatalytic activity in continuous gas phase CO(2) reduction over Pt/TiO(2). ChemSusChem 2013; 6:2095-2102. [PMID: 24039144 DOI: 10.1002/cssc.201300307] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 06/11/2013] [Indexed: 06/02/2023]
Abstract
The dynamic nature of continuous photocatalytic reduction of gaseous CO2 in the presence of water vapor was studied by using Pt/TiO2 as catalyst under UV irradiation at 353 and 423 K in the absence of sacrificial electron donors. The reaction was studied with a good time resolution (order of seconds), to monitor product concentrations by means of mass spectrometry. Two distinct photocatalytic activities, namely steady-state and transient, were identified. The former is active at the lower temperature and only for H2 production, whereas the latter dominates for CH4 production. The transient activity was recovered during dark time (i.e., the light is off) in the reaction mixture, with the magnitude of recovery proportionally increasing with the duration of the dark time. Higher temperature was found to be more effective for the recovery. Furthermore, insights into deactivation and reactivation mechanisms are explained by in situ diffuse reflectance infrared Fourier transform spectroscopy study.
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Affiliation(s)
- Antonio Bazzo
- Institute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans 16, 43007 Tarragona (Spain), Fax: (+34) 977-920-224
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9
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Surmacki J, Musial J, Kordek R, Abramczyk H. Raman imaging at biological interfaces: applications in breast cancer diagnosis. Mol Cancer 2013; 12:48. [PMID: 23705882 PMCID: PMC3681552 DOI: 10.1186/1476-4598-12-48] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 05/22/2013] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND One of the most important areas of Raman medical diagnostics is identification and characterization of cancerous and noncancerous tissues. The methods based on Raman scattering has shown significant potential for probing human breast tissue to provide valuable information for early diagnosis of breast cancer. A vibrational fingerprint from the biological tissue provides information which can be used to identify, characterize and discriminate structures in breast tissue, both in the normal and cancerous environment. RESULTS The paper reviews recent progress in understanding structure and interactions at biological interfaces of the human tissue by using confocal Raman imaging and IR spectroscopy. The important differences between the noncancerous and cancerous human breast tissues were found in regions characteristic for vibrations of carotenoids, fatty acids, proteins, and interfacial water. Particular attention was paid to the role played by unsaturated fatty acids and their derivatives as well as carotenoids and interfacial water. CONCLUSIONS We demonstrate that Raman imaging has reached a clinically relevant level in regard to breast cancer diagnosis applications. The results presented in the paper may have serious implications on understanding mechanisms of interactions in living cells under realistically crowded conditions of biological tissue.
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Affiliation(s)
- Jakub Surmacki
- Laboratory of Laser Molecular Spectroscopy, Institute of Applied Radiation Chemistry, Lodz University of Technology, Wroblewskiego 15, Lodz 93-590, Poland
| | - Jacek Musial
- Department of Pathology, Chair of Oncology, Medical University of Lodz, Paderewskiego 4, Lodz 93-509, Poland
| | - Radzislaw Kordek
- Department of Pathology, Chair of Oncology, Medical University of Lodz, Paderewskiego 4, Lodz 93-509, Poland
| | - Halina Abramczyk
- Laboratory of Laser Molecular Spectroscopy, Institute of Applied Radiation Chemistry, Lodz University of Technology, Wroblewskiego 15, Lodz 93-590, Poland
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10
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Serényi M, Frigeri C, Szekrényes Z, Kamarás K, Nasi L, Csik A, Khánh NQ. On the formation of blisters in annealed hydrogenated a-Si layers. Nanoscale Res Lett 2013; 8:84. [PMID: 23413996 PMCID: PMC3599494 DOI: 10.1186/1556-276x-8-84] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 01/10/2013] [Indexed: 06/01/2023]
Abstract
Differently hydrogenated radio frequency-sputtered a-Si layers have been studied by infrared (IR) spectroscopy as a function of the annealing time at 350°C with the aim to get a deeper understanding of the origin of blisters previously observed by us in a-Si/a-Ge multilayers prepared under the same conditions as the ones applied to the present a-Si layers. The H content varied between 10.8 and 17.6 at.% as measured by elastic recoil detection analysis. IR spectroscopy showed that the concentration of the clustered (Si-H)n groups and of the (Si-H2)n (n ≥ 1) polymers increased at the expense of the Si-H mono-hydrides with increasing annealing time, suggesting that there is a corresponding increase of the volume of micro-voids whose walls are assumed from literature to be decorated by the clustered mono-hydride groups and polymers. At the same time, an increase in the size of surface blisters was observed. Also, with increasing annealing time, the total concentration of bonded H of any type decreases, indicating that H is partially released from its bonds to Si. It is argued that the H released from the (Si-H)n complexes and polymers at the microvoid surfaces form molecular H2 inside the voids, whose size increases upon annealing because of the thermal expansion of the H2 gas, eventually producing plastic surface deformation in the shape of blisters.
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Affiliation(s)
- Miklós Serényi
- Institute of Technical Physics and Materials Science, Research Centre for Natural Sciences, Hungarian Academy of Sciences, P.O. Box 49, Budapest H-1525, Hungary
| | - Cesare Frigeri
- CNR-IMEM Institute, Parco Area delle Scienze 37/A, Parma 43100, Italy
| | - Zsolt Szekrényes
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, P.O. Box 49, Budapest H-1525, Hungary
| | - Katalin Kamarás
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, P.O. Box 49, Budapest H-1525, Hungary
| | - Lucia Nasi
- CNR-IMEM Institute, Parco Area delle Scienze 37/A, Parma 43100, Italy
| | - Attila Csik
- Institute of Nuclear Research of the Hungarian Academy of Sciences, P.O. Box 51, Debrecen H-4001, Hungary
| | - Nguyen Quoc Khánh
- Institute of Technical Physics and Materials Science, Research Centre for Natural Sciences, Hungarian Academy of Sciences, P.O. Box 49, Budapest H-1525, Hungary
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11
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Abstract
A universal label-free method for the spectroscopic investigation of polyhistidine-tagged proteins is presented. A solid supported lipid bilayer (SSLB, picture) containing nitrilotriacetic-acid-modified lipids is attached on top of a germanium attenuated total reflection crystal by hydrophilic interactions. Any His tag-modified protein can be immobilized and investigated by FTIR spectroscopy.
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Affiliation(s)
| | - Jörn Güldenhaupt
- Lehrstuhl für Biophysik, Ruhr-Universität Bochum44780 Bochum (Germany)
| | - Klaus Gerwert
- Lehrstuhl für Biophysik, Ruhr-Universität Bochum44780 Bochum (Germany)
| | - Carsten Kötting
- Lehrstuhl für Biophysik, Ruhr-Universität Bochum44780 Bochum (Germany)
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12
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Abstract
Structures of enzymes invariably reveal the proximity of acidic and basic residues to reactive sites on the substrate, so it is natural and common to suggest that enzymes employ concerted mechanisms to catalyze their difficult reactions. Ketosteroid isomerase (KSI) has served as a paradigm of enzymatic proton transfer chemistry, and its catalytic effect has previously been attributed to concerted proton transfer. We employ a specific inhibitor that contains an IR probe that reports directly and quantitatively on the ionization state of the ligand when bound in the active site of KSI. Measurement of the fractional ionization provides a missing link in a thermodynamic cycle that can discriminate the free energy advantage of a concerted versus nonconcerted mechanism. It is found that the maximum thermodynamic advantage that KSI could capture from a concerted mechanism (ΔΔG° = 0.5 kcal mol(-1)) is quite small.
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Affiliation(s)
- Stephen D. Fried
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080
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13
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Batoo KM. Microstructural and Mössbauer properties of low temperature synthesized Ni-Cd-Al ferrite nanoparticles. Nanoscale Res Lett 2011; 6:499. [PMID: 21851597 PMCID: PMC3224598 DOI: 10.1186/1556-276x-6-499] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 08/18/2011] [Indexed: 05/27/2023]
Abstract
We report the influence of Al3+ doping on the microstructural and Mössbauer properties of ferrite nanoparticles of basic composition Ni0.2Cd0.3Fe2.5 - xAlxO4 (0.0 ≤ x ≤ 0.5) prepared through simple sol-gel method. X-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive X-ray, transmission electron microscopy (TEM), Fourier transformation infrared (FTIR), and Mössbauer spectroscopy techniques were used to investigate the structural, chemical, and Mössbauer properties of the grown nanoparticles. XRD results confirm that all the samples are single-phase cubic spinel in structure excluding the presence of any secondary phase corresponding to any structure. SEM micrographs show the synthesized nanoparticles are agglomerated but spherical in shape. The average crystallite size of the grown nanoparticles was calculated through Scherrer formula and confirmed by TEM and was found between 2 and 8 nm (± 1). FTIR results show the presence of two vibrational bands corresponding to tetrahedral and octahedral sites. Mössbauer spectroscopy shows that all the samples exhibit superparamagnetism, and the quadrupole interaction increases with the substitution of Al3+ ions.
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Affiliation(s)
- Khalid Mujasam Batoo
- King Abdullah Institute for Nanotechnology, King Saud University, Riyadh, 11451, Saudi Arabia.
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14
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Abstract
Vibrational reporters have shown significant promise as sensitive probes of local environments in proteins and nucleic acids. The utility of two potential vibrational probes, the cyanate and azide groups in phenyl cyanate and 3-azidopyridine, respectively, has been hindered by accidental Fermi resonance. Anharmonic coupling, between the fundamental -OCN or -N(3) asymmetric stretch vibration with a near resonant combination band, results in an extremely broad and complex absorption profile for each of these probes. A total of eight phenyl cyanate and six 3-azidopyridine isotopomers were synthesized and studied. Isotopic editing effectively modulated the accidental Fermi resonance - the absorption profiles of several isotopomers were greatly simplified while others remained complex. The origins of the observed profiles are discussed. Addition of a single neutron to the middle atom of the oscillator converted the absorption profile to essentially a single band resulting from either the cyanate or azide asymmetric stretch vibration.
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Affiliation(s)
| | | | - Edward E. Fenlon
- Corresponding authors. , Phone: (717) 291-4201, Fax: (717) 291-4343; , Phone: (717) 358-4766, Fax: (717) 291-4343
| | - Scott H. Brewer
- Corresponding authors. , Phone: (717) 291-4201, Fax: (717) 291-4343; , Phone: (717) 358-4766, Fax: (717) 291-4343
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15
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Galinato MGI, Whaley CM, Roberts D, Wang P, Lehnert N. Favorable Protonation of the (μ-edt)[Fe(2)(PMe(3))(4)(CO)(2)(H-terminal)](+) Hydrogenase Model Complex Over Its Bridging μ-H Counterpart: A Spectroscopic and DFT Study. Eur J Inorg Chem 2011; 2011:1147-1154. [PMID: 23162378 PMCID: PMC3498055 DOI: 10.1002/ejic.201001037] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Indexed: 11/11/2022]
Abstract
The mechanism of hydrogen production in [FeFe] hydrogenase remains elusive. However, a species featuring a terminal hydride bound to the distal Fe is thought to be the key intermediate leading to hydrogen production. In this study, density functional theory (DFT) calculations on the terminal (H-term) and bridging (μ-H) hydride isomers of (μ-edt)-[Fe(2)(PMe(3))(4)(CO)(2)H](+) are presented in order to understand the factors affecting their propensity for protonation. Relative to H-term, μ-H is 12.7 kcal/mol more stable, which contributes to its decreased reactivity towards an acid. Potential energy surface (PES) calculations for the reaction of the H-term isomer with 4-nitropyridinium, a proton source, further reveal a lower activation energy barrier (14.5 kcal/mol) for H-term than for μ-H (29 kcal/mol). Besides these energetic considerations, the H-term isomer displays a key molecular orbital (MO <139>) that has a relatively strong hydride (1s) contribution (23%), which is not present in the μ-H isomer. This indicates a potential orbital control of the reaction of the hydride complexes with acid. The lower activation energy barrier and this key MO together control the overall catalytic activity of (μ-edt)[Fe(2)(PMe(3))(4)(CO)(2)(H-term)](+). Lastly, Raman and IR spectroscopy were performed in order to probe the ν(Fe-H) stretching mode of the two isomers and their deuterated counterparts. A ν(Fe-H) stretching mode was observed for the μ-H complex at 1220 cm(-1). However, the corresponding mode is not observed for the less stable H-term isomer.
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Affiliation(s)
| | - C. Matthew Whaley
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Dean Roberts
- Bruker Optics Inc. 19 Fortune Drive, Manning Park, Billerica, MA 01821, USA
| | - Peng Wang
- Bruker Optics Inc. 19 Fortune Drive, Manning Park, Billerica, MA 01821, USA
| | - Nicolai Lehnert
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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16
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Abstract
Stainless steel 316L is widely used as a biomedical implant material; however, there is concern about the corrosion of metallic implants in the physiological environment. The corrosion process can cause mechanical failure due to resulting cracks and cavities in the implant. Alkyl phosphonic acid forms a thin film by self-assembly on the stainless steel surface and this report conclusively shows that thermal treatment of the octadecylphosphonic acid (ODPA) film greatly enhances the stability of the ODPA molecules on the substrate surface. AFM images taken from the modified substrates revealed that thermally treated films remain intact after methanol, THF, and water flushes, whereas untreated films suffer substantial loss. Water contact angles also show that the hydrophobicity of thermally treated films does not diminish after being incubated in a dynamic flow of water for a 3-hour period, whereas the untreated film becomes increasingly hydrophilic due to loss of ODPA. IR spectra taken of both treated and untreated films after water and THF flushes show that the remaining film retains its initial crystallinity. A model is suggested to explain the stability of ODPA film enhanced by thermal treatment. An ODPA molecule is physisorbed to the surface weakly by hydrogen bonding. Heating drives away water molecules leading to the formation of strong monodentate or mixed mono/bi-dentate bonds of ODPA molecule to the surface.
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Affiliation(s)
- Min Soo Lim
- Department of Chemistry, Slippery Rock University, Slippery Rock, PA 16057, USA.
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17
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Abstract
Acid remarks: The anhydrous diprotic boron acids H(2)(B(12)X(12)) (X = Cl, Br; see picture, B orange, X green) are the first examples of diprotic superacids and may be the strongest acids yet isolated. Both protons protonate benzene to give benzenium ion salts that are stable at room temperature. These acids owe their existence to the stability of the icosahedral B(12) cluster with its dinegative charge buried beneath a layer of halide substituents.
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Affiliation(s)
- Amy Avelar
- Center for S and P Block Chemistry, Department of Chemistry University of California, Riverside, CA 92521-0403 (USA)
| | - Fook S. Tham
- Center for S and P Block Chemistry, Department of Chemistry University of California, Riverside, CA 92521-0403 (USA)
| | - Christopher A. Reed
- Center for S and P Block Chemistry, Department of Chemistry University of California, Riverside, CA 92521-0403 (USA)
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18
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Stoyanov ES, Stoyanova IV, Reed CA. The basicity of unsaturated hydrocarbons as probed by hydrogen-bond-acceptor ability: bifurcated N-H+ ...pi hydrogen bonding. Chemistry 2008; 14:7880-91. [PMID: 18637650 PMCID: PMC2730148 DOI: 10.1002/chem.200800337] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The competitive substitution of the anion (A(-)) in contact ion pairs of the type [Oct3NH+]B(C6F5)4 (-) by unsaturated hydrocarbons (L) in accordance with the equilibrium Oct3NH+...A(-) + nL right arrow over left arrow [Oct3NH+...Ln]A(-) has been studied in CCl4. On the basis of equilibrium constants, K, and shifts of nuNH to low frequency, it has been established that complexed Oct3NH...+Ln cations with n=1 and 2 are formed and have unidentate and bifurcated N--H+...pi hydrogen bonds, respectively. Bifurcated hydrogen bonds to unsaturated hydrocarbons have not been observed previously. The unsaturated hydrocarbons studied include benzene and methylbenzenes, fused-ring aromatics, alkenes, conjugated dienes, and alkynes. From the magnitude of the redshifts in the N--H stretching frequencies, Delta nuNH, a new scale for ranking the pi basicity of unsaturated hydrocarbons is proposed: fused-ring aromatics
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Affiliation(s)
- Evgenii S. Stoyanov
- Department of Chemistry University of California, Riverside Riverside, California 92521, USA
| | - Irina V. Stoyanova
- Department of Chemistry University of California, Riverside Riverside, California 92521, USA
| | - Christopher A. Reed
- Department of Chemistry University of California, Riverside Riverside, California 92521, USA
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19
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Arslan H, Demircan A. The Molecular Structure and Vibrational Spectrum of 6-bromo-8-thia-1,4-epoxybicyclo[4.3.0]non-2-ene. Int J Mol Sci 2007. [PMCID: PMC3871846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Geometric parameters and FT-IR spectrum of 6-bromo-8-thia-1,4-epoxybicyclo[4.3.0]non-2-ene were computed by the HF, B3LYP, B3PW91 and mPW1PW91 methods in conjunction with the 6-31G(d,p) basis set. The calculated IR spectra are in a good agreement with the observed FT-IR spectrum. A general better performance of B3LYP, B3PW91 and mPW1PW91 versus HF was quantitatively characterized by using PAVF 1.0 program. Optimal uniform scaling factors calculated for the title compound are 0.8952, 0.9552, 0.9520 and 0.9456 for HF, B3LYP, B3PW91 and MPW1PW91 methods, respectively.
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Affiliation(s)
- Hakan Arslan
- Department of Chemistry, Faculty of Arts and Science, Mersin University, 33343-Mersin, Turkey; E-mail: ,Author to whom correspondence should be addressed; E-mail: ; Tel: +90.532.7073122
| | - Aydın Demircan
- Department of Chemistry, Faculty of Arts and Science, Niğde University, 51100-Niğde, Turkey; E-mail:
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20
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Abstract
Water autoionization reaction 2H2O --> H3O- + OH- is a textbook process of basic importance, resulting in pH = 7 for pure water. However, pH of pure water surface is shown to be significantly lower, the reduction being caused by proton stabilization at the surface. The evidence presented here includes ab initio and classical molecular dynamics simulations of water slabs with solvated H3O+ and OH- ions, density functional studies of (H2O)(48)H+ clusters, and spectroscopic isotopic-exchange data for D2O substitutional impurities at the surface and in the interior of ice nanocrystals. Because H3O+ does, but OH- does not, display preference for surface sites, the H2O surface is predicted to be acidic with pH < 4.8. For similar reasons, the strength of some weak acids, such as carbonic acid, is expected to increase at the surface. Enhanced surface acidity can have a significant impact on aqueous surface chemistry, e.g., in the atmosphere.
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Affiliation(s)
- Victoria Buch
- *Fritz Haber Institute for Molecular Dynamics, Hebrew University, Jerusalem 91904, Israel
| | - Anne Milet
- Département de Chimie Moléculaire, Unité Mixte de Recherche 5250, Centre National de la Recherche Scientifique, Université Joseph Fourier, BP53, 38041 Grenoble, France
| | - Robert Vácha
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, 16610 6 Prague, Czech Republic; and
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, 16610 6 Prague, Czech Republic; and
| | - J. Paul Devlin
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078
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21
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Abstract
Networks of internal water molecules are thought to provide proton transfer pathways in many enzymatic and photosynthetic reactions. Extremely broad absorption continua observed in recent IR spectroscopic measurements on the photodriven proton pump bacteriorhodopsin (BR) suggest such networks may also serve as proton storage and release sites for these reactions. By combining electronic structure calculations with molecular mechanical force fields, we examine the dynamics and the resulting IR spectra of two protonated water networks, H+.(H2O)3 and H+.(H2O)4, in the release pocket of the initial state of BR, which possibly serve as proton donors to the extracellular surface. For both network sizes, topologically similar structures are found, which are anchored at residues E194 and E204 and stabilized by additional hydrogen bonds from neighboring protein side chains. These protonated water networks assume neither the classic Zundel nor Eigen motives but prefer wire-like topologies. Upon gauging calculated IR spectra of finite clusters with experimental gas-phase data, it is possible to link spectral features computed for these chain-like structures in the initial state of the BR photocycle to the measured absorption continua, in particular for the larger H+.(H2O)4 network. Furthermore, the free energy of proton dislocation along these chains is found to be within the range that is easily accessible at room temperature because of fluctuations.
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Affiliation(s)
- Gerald Mathias
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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22
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Paschek D, Gnanakaran S, Garcia AE. Simulations of the pressure and temperature unfolding of an alpha-helical peptide. Proc Natl Acad Sci U S A 2005; 102:6765-70. [PMID: 15800045 PMCID: PMC1100754 DOI: 10.1073/pnas.0408527102] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2004] [Indexed: 11/18/2022] Open
Abstract
We study by molecular simulations the reversible folding/unfolding equilibrium as a function of density and temperature of a solvated alpha-helical peptide. We use an extension of the replica exchange molecular dynamics method that allows for density and temperature Monte Carlo exchange moves. We studied 360 thermodynamic states, covering a density range from 0.96 to 1.14 g.cm(-3) and a temperature range from 300 to 547.6 K. We simulated 10 ns per replica for a total simulation time of 3.6 micros. We characterize the structural, thermodynamic, and hydration changes as a function of temperature and pressure. We also calculate the compressibility and expansivity of unfolding. We find that pressure does not affect the helix-coil equilibrium significantly and that the volume change upon pressure unfolding is small and negative (-2.3 ml/mol). However, we find significant changes in the coordination of water molecules to the backbone carbonyls. This finding predicts that changes in the chemical shifts and IR spectra with pressure can be due to changes in coordination and not only changes in the helical content. A simulation of the IR spectrum shows that water coordination effects on frequency shifts are larger than changes due to elastic structural changes in the peptide.
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Affiliation(s)
- Dietmar Paschek
- Department of Physical Chemistry, Otto-Hahn Strasse 6, University of Dortmund, D-44221 Dortmund, Germany
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23
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Raussens V, Drury J, Forte T, Choy N, Goormaghtigh E, Ruysschaert JM, Narayanaswami V. Orientation and mode of lipid-binding interaction of human apolipoprotein E C-terminal domain. Biochem J 2005; 387:747-54. [PMID: 15588256 PMCID: PMC1135005 DOI: 10.1042/bj20041536] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2004] [Revised: 12/02/2004] [Accepted: 12/10/2004] [Indexed: 11/17/2022]
Abstract
ApoE (apolipoprotein E) is an anti-atherogenic lipid transport protein that plays an integral role in lipoprotein metabolism and cholesterol homoeostasis. Lipid association educes critical functional features of apoE, mediating reduction in plasma and cellular cholesterol levels. The 10-kDa CT (C-terminal) domain of apoE facilitates helix-helix interactions in lipid-free state to promote apoE self-association and helix-lipid interactions during binding with lipoproteins, although the mode of lipid-binding interaction is not well understood. We investigated the mode of lipid-binding interaction and orientation of apoE CT domain on reconstituted lipoproteins. Isolated recombinant human apoE CT domain (residues 201-299) possesses a strong ability to interact with phospholipid vesicles, yielding lipoprotein particles with an apparent molecular mass of approximately 600 kDa, while retaining the overall alpha-helical content. Electron microscopy and non-denaturing PAGE analysis of DMPC (dimyristoylphosphatidylcholine)--apoE CT domain lipoprotein complexes revealed discoidal complexes with a diameter of approx. 17 nm. Cross-linking apoE CT domain on discoidal particles yielded dimeric species as the major product. Attenuated total reflectance Fourier transform IR spectroscopy of phospholipid-apoE CT domain complexes reveals that the helical axis is oriented perpendicular to fatty acyl chains of the phospholipid. Fluorescence quenching analysis of DMPC-apoE CT domain discoidal complexes by spin-labelled stearic acid indicated a relatively superficial location of the native tryptophan residues with respect to the plane of the phospholipid bilayer. Taken together, we propose that apoE CT domain interacts with phospholipid vesicles, forming a long extended helix that circumscribes the discoidal bilayer lipoprotein complex.
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Key Words
- apolipoprotein e
- cross-linking
- electron microscopy
- ir spectroscopy
- lipid-bound conformation
- lipoprotein-binding surface
- apoa-i, apolipoprotein a-i
- apoe, apolipoprotein e
- atr-ftir, attenuated total reflectance fourier transform ir
- ct, c-terminal
- dmpc, dimyristoylphosphatidylcholine
- dmpg, dimyristoylphosphatidylglycerol
- 5-dsa, 5-doxyl stearic acid
- 12-dsa, 12-doxyl stearic acid
- dss, disuccinimidyl suberate
- hdl, high-density lipoprotein
- ldl, low-density lipoprotein
- nt, n-terminal
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Affiliation(s)
- Vincent Raussens
- *Structure and Function of Biological Membranes, Université Libre de Bruxelles, CP-206/2, bd. Du Triomphe, B-1050 Brussels, Belgium
| | - Jessica Drury
- †Lipid Biology in Health and Disease Research Group, Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, CA 94609, U.S.A
| | - Trudy M. Forte
- †Lipid Biology in Health and Disease Research Group, Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, CA 94609, U.S.A
| | - Nicole Choy
- †Lipid Biology in Health and Disease Research Group, Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, CA 94609, U.S.A
| | - Erik Goormaghtigh
- *Structure and Function of Biological Membranes, Université Libre de Bruxelles, CP-206/2, bd. Du Triomphe, B-1050 Brussels, Belgium
| | - Jean-Marie Ruysschaert
- *Structure and Function of Biological Membranes, Université Libre de Bruxelles, CP-206/2, bd. Du Triomphe, B-1050 Brussels, Belgium
| | - Vasanthy Narayanaswami
- †Lipid Biology in Health and Disease Research Group, Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, CA 94609, U.S.A
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