1
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Iritani Y, Ishikawa H, Mizuno M, Mizutani Y. Heme Pocket Structure and Its Functional Implications in an Ancestral Globin Protein. Biochemistry 2023; 62:2727-2737. [PMID: 37647623 DOI: 10.1021/acs.biochem.3c00203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Proteins have undergone evolutionary processes to achieve optimal stability, increased functionality, and novel functions. Comparative analysis of existent and ancestral proteins provides insights into the factors that influence protein stability and function. Ancestral sequence reconstruction allows us to deduce the amino acid sequences of ancestral proteins. Here, we present the structural and functional characteristics of an ancestral protein, AncMH, reconstructed to be the last common ancestor of hemoglobins and myoglobins. Our findings reveal that AncMH harbors heme and that the heme binds oxygen. Furthermore, we demonstrate that the ferrous heme in AncMH is pentacoordinated, similar to that of human adult hemoglobin and horse myoglobin. A detailed comparison of the heme pocket structure indicates that the heme pocket in AncMH is more similar to that of hemoglobin than that of myoglobin. However, the autoxidation of AncMH is faster than that of both hemoglobin and myoglobin. Collectively, our results suggest that ancestral proteins of hemoglobins and myoglobins evolved in steps, including the hexa- to pentacoordination transition, followed by stabilization of the oxygen-bound form.
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Affiliation(s)
- Yu Iritani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Haruto Ishikawa
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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2
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Valle-Altamirano RG, Baratto MC, Badillo-Ramírez I, Gasteazoro F, Pogni R, Saniger JM, Valderrama B. Identification of Fe( iii)–OH species as a catalytic intermediate in plant peroxidases at high H 2O 2 concentration. NEW J CHEM 2022. [DOI: 10.1039/d1nj04837f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The structure for compound III formed after exposure of plant heme peroxidases to excess H2O2 seems to be a hydroxylated form, providing new evidence for understanding the structural basis of the substrate-induced suicidal behavior of these enzymes.
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Affiliation(s)
- Rodolfo G. Valle-Altamirano
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad, 62210 Morelos, Mexico
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 Ciudad de México, Mexico
| | - Maria Camilla Baratto
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro, 53100 Siena, Italy
| | - Isidro Badillo-Ramírez
- Instituto de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, 04510, Ciudad de México, Mexico
| | - Francisco Gasteazoro
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad, 62210 Morelos, Mexico
| | - Rebecca Pogni
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro, 53100 Siena, Italy
| | - José M. Saniger
- Instituto de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, 04510, Ciudad de México, Mexico
| | - Brenda Valderrama
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad, 62210 Morelos, Mexico
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3
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Li J, Du Q, Peng H, Wei D, Liu Q, Bi Y, Liu T, Lin J, Qin C. Spectroscopic investigation of the interaction between extracellular polymeric substances and tetracycline during sorption onto anaerobic ammonium-oxidising sludge. ENVIRONMENTAL TECHNOLOGY 2021; 42:1787-1797. [PMID: 31622177 DOI: 10.1080/09593330.2019.1680743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 10/01/2019] [Indexed: 06/10/2023]
Abstract
In this study, the interaction between extracellular polymeric substances (EPS) and tetracycline during sorption onto anaerobic ammonium-oxidising (anammox) sludge was investigated. The results showed that EPS significantly enhanced the adsorption efficiency of tetracycline by sludge, and the adsorption data were better fitted with the pseudo-second-order kinetics model. Further, the concentration of proteins in the EPS decreased from 12.31 ± 0.42 to 6.82 ± 0.46 mg/gVSS for various tetracycline dosages (0-20 mg/L), whereas the concentration of polysaccharides did not change. Multiple spectroscopic methods were used to analyze the interaction between EPS and tetracycline. A three-dimensional excitation-emission matrix revealed that the fluorescence intensity of protein-like substances obviously decreased with the increasing addition of tetracycline. According to synchronous fluorescence spectra analysis, static quenching was the major quenching process and there was one type of binding site in the protein-like substances. Additionally, two-dimensional correlation spectroscopy showed that tryptophan-like aromatic protein was more susceptible to tetracycline binding than tyrosine-like aromatic protein. Moreover, the main functional groups involved in complexation of tetracycline and EPS were C-O, C-C and C-N (stretching vibration) and the pyrrole ring of the tryptophan side chain. This study provides useful information on the interaction between EPS and tetracycline and demonstrates the role of EPS in protecting microorganism from tetracycline in the anammox process.
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Affiliation(s)
- Jiayi Li
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, People's Republic of China
| | - Qingping Du
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, People's Republic of China
| | - Huangqiang Peng
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, People's Republic of China
| | - Dongyang Wei
- South China Institute of Environmental Sciences, Ministry of Environmental Protection, Guangzhou, People's Republic of China
| | - Qian Liu
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, People's Republic of China
| | - Yunqian Bi
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, People's Republic of China
| | - Tao Liu
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, People's Republic of China
| | - Junxi Lin
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, People's Republic of China
| | - Chunyi Qin
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, People's Republic of China
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4
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Mehta M, Liu Y, Waterland M, Holmes G. Characterization of the Degradation of Sheepskin by Monitoring Cytochrome c of Bacteria by Raman Spectroscopy. ANAL LETT 2020. [DOI: 10.1080/00032719.2020.1792476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Megha Mehta
- New Zealand Leather and Shoe Research Association (LASRA®), Palmerston North, New Zealand
| | - Yang Liu
- New Zealand Leather and Shoe Research Association (LASRA®), Palmerston North, New Zealand
| | - Mark Waterland
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Geoff Holmes
- New Zealand Leather and Shoe Research Association (LASRA®), Palmerston North, New Zealand
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5
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Buhrke D, Hildebrandt P. Probing Structure and Reaction Dynamics of Proteins Using Time-Resolved Resonance Raman Spectroscopy. Chem Rev 2019; 120:3577-3630. [PMID: 31814387 DOI: 10.1021/acs.chemrev.9b00429] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The mechanistic understanding of protein functions requires insight into the structural and reaction dynamics. To elucidate these processes, a variety of experimental approaches are employed. Among them, time-resolved (TR) resonance Raman (RR) is a particularly versatile tool to probe processes of proteins harboring cofactors with electronic transitions in the visible range, such as retinal or heme proteins. TR RR spectroscopy offers the advantage of simultaneously providing molecular structure and kinetic information. The various TR RR spectroscopic methods can cover a wide dynamic range down to the femtosecond time regime and have been employed in monitoring photoinduced reaction cascades, ligand binding and dissociation, electron transfer, enzymatic reactions, and protein un- and refolding. In this account, we review the achievements of TR RR spectroscopy of nearly 50 years of research in this field, which also illustrates how the role of TR RR spectroscopy in molecular life science has changed from the beginning until now. We outline the various methodological approaches and developments and point out current limitations and potential perspectives.
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Affiliation(s)
- David Buhrke
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
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6
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Yasuda M, Takeshita N, Shigeto S. Inhomogeneous Molecular Distributions and Cytochrome Types and Redox States in Fungal Cells Revealed by Raman Hyperspectral Imaging Using Multivariate Curve Resolution–Alternating Least Squares. Anal Chem 2019; 91:12501-12508. [DOI: 10.1021/acs.analchem.9b03261] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Mitsuru Yasuda
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan
| | - Norio Takeshita
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Shinsuke Shigeto
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan
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7
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Mak PJ, Denisov IG. Spectroscopic studies of the cytochrome P450 reaction mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2018; 1866:178-204. [PMID: 28668640 PMCID: PMC5709052 DOI: 10.1016/j.bbapap.2017.06.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/22/2017] [Indexed: 10/19/2022]
Abstract
The cytochrome P450 monooxygenases (P450s) are thiolate heme proteins that can, often under physiological conditions, catalyze many distinct oxidative transformations on a wide variety of molecules, including relatively simple alkanes or fatty acids, as well as more complex compounds such as steroids and exogenous pollutants. They perform such impressive chemistry utilizing a sophisticated catalytic cycle that involves a series of consecutive chemical transformations of heme prosthetic group. Each of these steps provides a unique spectral signature that reflects changes in oxidation or spin states, deformation of the porphyrin ring or alteration of dioxygen moieties. For a long time, the focus of cytochrome P450 research was to understand the underlying reaction mechanism of each enzymatic step, with the biggest challenge being identification and characterization of the powerful oxidizing intermediates. Spectroscopic methods, such as electronic absorption (UV-Vis), electron paramagnetic resonance (EPR), nuclear magnetic resonance (NMR), electron nuclear double resonance (ENDOR), Mössbauer, X-ray absorption (XAS), and resonance Raman (rR), have been useful tools in providing multifaceted and detailed mechanistic insights into the biophysics and biochemistry of these fascinating enzymes. The combination of spectroscopic techniques with novel approaches, such as cryoreduction and Nanodisc technology, allowed for generation, trapping and characterizing long sought transient intermediates, a task that has been difficult to achieve using other methods. Results obtained from the UV-Vis, rR and EPR spectroscopies are the main focus of this review, while the remaining spectroscopic techniques are briefly summarized. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.
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Affiliation(s)
- Piotr J Mak
- Department of Chemistry, Saint Louis University, St. Louis, MO, United States.
| | - Ilia G Denisov
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, United States.
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8
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Mizutani Y. Time-Resolved Resonance Raman Spectroscopy and Application to Studies on Ultrafast Protein Dynamics. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20170218] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043
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9
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Kucheryavy P, Lahanas N, Lockard JV. Spectroscopic interrogations of isostructural metalloporphyrin-based metal-organic frameworks with strongly and weakly coordinating guest molecules. J COORD CHEM 2016. [DOI: 10.1080/00958972.2016.1193598] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Pavel Kucheryavy
- Department of Chemistry, Rutgers University-Newark, Newark, NJ, USA
| | - Nicole Lahanas
- Department of Chemistry, Rutgers University-Newark, Newark, NJ, USA
| | - Jenny V. Lockard
- Department of Chemistry, Rutgers University-Newark, Newark, NJ, USA
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10
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Kozicki M, Czepiel J, Biesiada G, Nowak P, Garlicki A, Wesełucha-Birczyńska A. The ring-stage of Plasmodium falciparum observed in RBCs of hospitalized malaria patients. Analyst 2015; 140:8007-16. [PMID: 26524434 DOI: 10.1039/c5an01598g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Raman spectra of the blood samples obtained directly from hospitalized malaria patients with Plasmodium falciparum (P. falciparum) in the ring-stage were analyzed. Changes observed in the Raman band intensities of the infected patients compared to healthy volunteers are the result of parasite activity inside red blood cells. The obtained spectra were discussed by analyzing differences in particular spectral regions by evaluating changes in the band intensity ratios as well as using PCA analysis. The alterations of erythrocyte membranes caused by parasite penetration are visible by a reduced I1130/I1075 intensity ratio expressing the lowering of the amount of domains arranged in trans conformation. The I2930/I2850 ratio, which is a measure of modifications in structures of membrane proteins and lipids, in infected red blood cells increases, which is caused by malaria protein export to the erythrocyte membrane and expresses the membrane disarrangement. In the pyrrole ring vibration region, the ν4 band marker of the oxygenated-Hb shows at 1371 cm(-1) whereas the ν4 band at 1353 cm(-1) related to the deoxygenated-Hb is observed for malaria patients and is characterized by a higher intensity in infected erythrocytes. The amide I analysis shows the modifications in the secondary structure composition in the infected RBCs. We found that the P. falciparum infection leads to a decrease in the α-helical content and a concurrent increase in undefined (random-coil) structures. It was observed that the Raman spectra changes are also the result of the hemozoin formation process. In the pyrrole ring stretching vibration region, the increase of 1220 cm(-1) (deoxyHb) as against 1248 cm(-1) (oxyHb) may be considered as a signal of hemozoin formation in the RBCs. Relatively intense band patterns at 1560 cm(-1) and also at 1570 cm(-1) and 1552 cm(-1) may be due to the hemozoin that is formed according to parasite activity. The results of medical diagnostic tests had not presented changes in patient RBC parameters. A significant reduction in WBC count was noticed along with a decrease in neutrophil and platelet count when compared with the control group. Although no change is observed in the overall picture of the erythrocytes, pathological changes are evident in the Raman spectrum.
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Affiliation(s)
- Mateusz Kozicki
- Faculty of Chemistry, Jagiellonian University, Kraków, Poland.
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11
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Czepiel J, Kozicki M, Panasiuk P, Birczyńska M, Garlicki A, Wesełucha-Birczyńska A. Clostridium difficile the hospital plague. Analyst 2015; 140:2513-22. [PMID: 25627751 DOI: 10.1039/c4an01947d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Clostridium difficile infection (CDI) has become one of the major public health threats in the last two decades. An increase has been observed not only in the rate of CDI, but also in its severity and mortality. Symptoms caused by this pathogen are accompanied by intense local and systemic inflammation. We confirmed that Raman microspectroscopy can help us in understanding CDI pathogenesis. A single erythrocyte of patients with CDI shows a difference, approximately 10 times, in the intensity of the Raman spectra at the beginning of hospitalization and after one week of treatment. The intensity level is an indicator of the spread of the inflammation within the cell, confirmed by standard laboratory tests. Many of the observed bands with enormously enhanced intensity, e.g. 1587, 1344, 1253, 1118 and 664 cm(-1), come from the symmetric vibration of the pyrrole ring. Heme variation of recovered cells in the acute CDI state between the first and the seventh day of treatment seems to show increased levels of oxygenated hemoglobin. Intense inflammation alters the conformation of the protein which is reflected in the significant changes in the amide I, II and III bands. There is an observed shift and a significant intensity increase of 1253 and 970 cm(-1) amide III and skeletal protein backbone CC stretching vibration bands, respectively. Principal Component Analysis (PCA) was used to find the variance in the data collected on the first and seventh day. PC2 loading in the 1645-1500 cm(-1) range shows an increase of heme, Tyr, Trp, or Phe vibrations because of changes in the protein microenvironment due to their exposure. Positive maxima at 1621, 1563 and 1550 in the PC2 loading originated from the ring vibrations. These observations indicate that Clostridium difficile toxins induce cytopathogenicity by altering cellular proteins.
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Affiliation(s)
- J Czepiel
- Department of Infectious Diseases, Jagiellonian University, Medical College, Sniadeckich 5, Kraków, Poland.
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12
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Zheng RH, Wei WM, Zhu LL, Shi Q. Theoretical study of the resonance Raman spectra for meso-tetrakis(3,5-di-tertiarybutylphenyl)-porphyrin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 133:707-713. [PMID: 24996212 DOI: 10.1016/j.saa.2014.06.047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 05/26/2014] [Accepted: 06/03/2014] [Indexed: 06/03/2023]
Abstract
Applying time-dependent density functional theory (TDDFT), we study the resonance Raman spectra for the Q and B bands of the meso-tetrakis(3,5-di-tertiarybutylphenyl)-porphyrin (H2TBPP) molecule including both Raman A term (Franck-Condon term) and Raman B term (Herzberg-Teller term) contributions. It is found that Raman B term can be one order of magnitude larger than Raman A term and dominates resonance Raman for the Q band resonance. In comparison with the recent experimental Raman spectra of H2TBPP with incident light frequency 532nm, we predict the absence of 1580cm(-1) band in the resonance Raman spectra which agrees well with the experimental results, whereas the previous theoretical calculation using non-resonance strategy failed to do so.
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Affiliation(s)
- Ren-hui Zheng
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, People's Republic of China.
| | - Wen-mei Wei
- Department of Chemistry, College of Basic Medicine, Anhui Medical University, Hefei, Anhui 230032, People's Republic of China
| | - Li-li Zhu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, People's Republic of China
| | - Qiang Shi
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, People's Republic of China
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13
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Marzec KM, Perez-Guaita D, de Veij M, McNaughton D, Baranska M, Dixon MWA, Tilley L, Wood BR. Red blood cells polarize green laser light revealing hemoglobin's enhanced non-fundamental Raman modes. Chemphyschem 2014; 15:3963-8. [PMID: 25257821 PMCID: PMC4501318 DOI: 10.1002/cphc.201402598] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Indexed: 11/11/2022]
Abstract
In general, the first overtone modes produce weak bands that appear at approximately twice the wavenumber value of the fundamental transitions in vibrational spectra. Here, we report the existence of a series of enhanced non-fundamental bands in resonance Raman (RR) spectra recorded for hemoglobin (Hb) inside the highly concentrated heme environment of the red blood cell (RBC) by exciting with a 514.5 nm laser line. Such bands are most intense when detecting parallel-polarized light. The enhancement is explained through excitonic theory invoking a type C scattering mechanism and bands have been assigned to overtone and combination bands based on symmetry arguments and polarization measurements. By using malaria diagnosis as an example, we demonstrate that combining the non-fundamental and fundamental regions of the RR spectrum improves the sensitivity and diagnostic capability of the technique. The discovery will have considerable implications for the ongoing development of Raman spectroscopy for blood disease diagnoses and monitoring heme perturbation in response to environmental stimuli.
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Affiliation(s)
- Katarzyna M Marzec
- Centre for Biospectroscopy, School of Chemistry, Monash University, Clayton, VIC, 3800 (Australia); Jagiellonian Centre for Experimental Therapeutics, Jagiellonian University, Bobrzynskiego 14, 30-348 Krakow (Poland)
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15
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Tsivadze AY, Averin AA, Chernyad’ev AY. Unusual resonance raman spectra of nickel(II), palladium(II), and platinum(II) meso-tetra(benzo-15-crown-5)porphyrinates. DOKLADY PHYSICAL CHEMISTRY 2013. [DOI: 10.1134/s0012501613090054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Fościak M, Proniewicz E, Zborowski K, Kim Y, Proniewicz LM. Resonance Raman and absorption infrared with density functional theory studies of Fe(III)/Fe(II) and Ni(II) complexes of modified 21-oxaporphyrins. J PORPHYR PHTHALOCYA 2013. [DOI: 10.1142/s1088424613500053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
This work presents a complete vibrational analysis of iron [ Fe (II) and Fe (III)] and nickel [ Ni (II)] complexes with 5,10,15,20-tetraphenyl-21-oxaporphyrin [OTPPH] and 5,20-bis(p-tolyl)-10,15-diphenyl-21-oxaporphyrin [ODTDPPH]. In these porphyrins, a furan ring replaces one of the pyrrole rings. The six-coordinate (OTPP) FeIIICl2 and (ODTDPP) FeIIICl2 as well as the five-coordinate (OTPP) FeIICl and (OTPP) NiIICl complexes were investigated using experimental and theoretical methods. The experimental part of this work involved Fourier-transform absorption infrared (FT-IR), resonance Raman (RR), and electron absorption (UV-vis) measurements for all of the investigated complexes. In the theoretical section, optimized geometries and vibrational frequencies for model compounds are provided. The theoretical calculations were performed at the B3LYP level with the LANL2DZ basis set. Good agreement was achieved between the experimental and theoretical vibrational spectra. In addition, charge distributions (GAPT) and geometrical aromaticity indices (Bird's I5 and HOMA) were calculated and discussed.
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Affiliation(s)
- Mateusz Fościak
- Faculty of Chemistry, Jagiellonian University, 3 Ingardena Street, 30-060 Krakow, Poland
| | - Edyta Proniewicz
- Faculty of Chemistry, Jagiellonian University, 3 Ingardena Street, 30-060 Krakow, Poland
| | - Krzysztof Zborowski
- Faculty of Chemistry, Jagiellonian University, 3 Ingardena Street, 30-060 Krakow, Poland
| | - Younkyoo Kim
- Department of Chemistry, Hankuk University of Foreign Studies, Yongin, Kyunggi-Do 449-791, Korea
| | - Leonard M. Proniewicz
- Faculty of Chemistry, Jagiellonian University, 3 Ingardena Street, 30-060 Krakow, Poland
- The State Higher Vocational School, ul. Mickiewicza 8, 33-100 Tarnów, Poland
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17
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Merlino A, Fuchs MR, Pica A, Balsamo A, Dworkowski FSN, Pompidor G, Mazzarella L, Vergara A. Selective X-ray-induced NO photodissociation in haemoglobin crystals: evidence from a Raman-assisted crystallographic study. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 69:137-40. [DOI: 10.1107/s0907444912042229] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 10/09/2012] [Indexed: 11/10/2022]
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18
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Ohta T, Liu JG, Saito M, Kobayashi Y, Yoda Y, Seto M, Naruta Y. Axial Ligand Effects on Vibrational Dynamics of Iron in Heme Carbonyl Studied by Nuclear Resonance Vibrational Spectroscopy. J Phys Chem B 2012; 116:13831-8. [DOI: 10.1021/jp304398g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Takehiro Ohta
- Institute
for Materials Chemistry
and Engineering and International Institute for Carbon-Neutral Energy
Research (WPI-I2CNER), Kyushu University, Fukuoka 812-8581, Japan
- JST, ACT-C, Saitama 332-0012,
Japan
| | - Jin-Gang Liu
- Institute
for Materials Chemistry
and Engineering and International Institute for Carbon-Neutral Energy
Research (WPI-I2CNER), Kyushu University, Fukuoka 812-8581, Japan
- Department of Chemistry, East China University of Science and Technology, 130
Meilong Rd, 200237, Shanghai, P. R. China
| | - Makina Saito
- Research Reactor Institute, Kyoto University, Osaka 590-0494, Japan
| | - Yasuhiro Kobayashi
- Research Reactor Institute, Kyoto University, Osaka 590-0494, Japan
- CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research Institute, Hyogo 679-5198, Japan
- CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan
| | - Makoto Seto
- Research Reactor Institute, Kyoto University, Osaka 590-0494, Japan
- Japan Atomic Energy Agency, Hyogo 679-5148, Japan
- CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan
| | - Yoshinori Naruta
- Institute
for Materials Chemistry
and Engineering and International Institute for Carbon-Neutral Energy
Research (WPI-I2CNER), Kyushu University, Fukuoka 812-8581, Japan
- JST, ACT-C, Saitama 332-0012,
Japan
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Neugebauer U, März A, Henkel T, Schmitt M, Popp J. Spectroscopic detection and quantification of heme and heme degradation products. Anal Bioanal Chem 2012; 404:2819-29. [PMID: 22903430 DOI: 10.1007/s00216-012-6288-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 07/17/2012] [Accepted: 07/19/2012] [Indexed: 10/28/2022]
Abstract
Heme and heme degradation products play critical roles in numerous biological phenomena which until now have only been partially understood. One reason for this is the very low concentrations at which free heme, its complexes and the partly unstable degradation products occur in living cells. Therefore, powerful and specific detection methods are needed. In this contribution, the potential of nondestructive Raman spectroscopy for the detection, quantification and discrimination of heme and heme degradation products is investigated. Resonance Raman spectroscopy using different excitation wavelengths (413, 476, 532, and 752 nm) is employed to estimate the limit of detection for hemin, myoglobin, biliverdin, and bilirubin. Concentrations in the low micromolar range (down to 3 μmol/L) could be reliably detected when utilizing the resonance enhancement effect. Furthermore, a systematic study on the surface-enhanced Raman spectroscopy (SERS) detection of hemin in the presence of other cellular components, such as the highly similar cytochrome c, DNA, and the important antioxidant glutathione, is presented. A microfluidic device was used to reproducibly create a segmented flow of aqueous droplets and oil compartments. Those aqueous droplets acted as model chambers where the analytes have to compete for the colloid. With the help of statistical analysis, it was possible to detect and differentiate the pure substances as well as the binary mixtures and gain insights into their interaction.
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Affiliation(s)
- U Neugebauer
- Center for Sepsis Control and Care, Jena University Hospital, Erlanger Allee 101, 07747 Jena, Germany
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20
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Abstract
The main topics in resonance Raman spectroscopy presented at ICPP-2 in Kyoto are briefly discussed. These include: (i) coherent spectroscopy and low frequency vibrations of ligand-photodissociated heme proteins, (ii) vibrational relaxation revealed by time-resolved anti-Stokes Raman spectroscopy, (iii) electron transfer in porphyrin arrays, (iv) vibrational assignments of tetraazaporphyrins and (v) resonance Raman spectra of an NO storing protein, nitrophorin.
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Affiliation(s)
- Teizo Kitagawa
- Institute for Molecular Science, Okazaki National Research Institutes, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
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21
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Hersleth HP, Andersson KK. How different oxidation states of crystalline myoglobin are influenced by X-rays. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:785-96. [PMID: 20691815 DOI: 10.1016/j.bbapap.2010.07.019] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Revised: 07/14/2010] [Accepted: 07/20/2010] [Indexed: 10/19/2022]
Abstract
X-ray induced radiation damage of protein crystals is well known to occur even at cryogenic temperatures. Redox active sites like metal sites seem especially vulnerable for these radiation-induced reductions. It is essential to know correctly the oxidation state of metal sites in protein crystal structures to be able to interpret the structure-function relation. Through previous structural studies, we have tried to characterise and understand the reactions between myoglobin and peroxides. These reaction intermediates are relevant because myoglobin is proposed to take part as scavenger of reactive oxygen species during oxidative stress, and because these intermediates are similar among the haem peroxidases and oxygenases. We have in our previous studies shown that these different myoglobin states are influenced by the X-rays used. In this study, we have in detail investigated the impact that X-rays have on these different oxidation states of myoglobin. An underlying goal has been to find a way to be able to determine mostly unreduced states. We have by using single-crystal light absorption spectroscopy found that the different oxidation states of myoglobin are to a different extent influenced by the X-rays (e.g. ferric Fe(III) myoglobin is faster reduced than ferryl Fe(IV)═O myoglobin). We observe that the higher oxidation states are not reduced to normal ferrous Fe(II) or ferric Fe(III) states, but end up in some intermediate and possibly artificial states. For ferric myoglobin, it seems that annealing of the radiation-induced/reduced state can reversibly more or less give the starting point (ferric myoglobin). Both scavengers and different dose-rates might influence to which extent the different states are affected by the X-rays. Our study shows that it is essential to do a time/dose monitoring of the influence X-rays have on each specific redox-state with spectroscopic techniques like single-crystal light absorption spectroscopy. This will determine to which extent you can collect X-ray diffraction data on your crystal before it becomes too heavily influenced/reduced by X-rays. This article is part of a Special Issue entitled: Protein Structure and Function in the Crystalline State.
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Affiliation(s)
- Hans-Petter Hersleth
- Department of Molecular Biosciences, University of Oslo, P.O. Box 1041 Blindern, NO-0316 Oslo, Norway.
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22
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Rwere F, Mak PJ, Kincaid JR. Resonance Raman interrogation of the consequences of heme rotational disorder in myoglobin and its ligated derivatives. Biochemistry 2009; 47:12869-77. [PMID: 18986170 DOI: 10.1021/bi801779d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Resonance Raman spectroscopy is employed to characterize heme site structural changes arising from conformational heterogeneity in deoxyMb and ligated derivatives, i.e., the ferrous CO (MbCO) and ferric cyanide (MbCN) complexes. The spectra for the reversed forms of these derivatives have been extracted from the spectra of reconstituted samples. Dramatic changes in the low-frequency spectra are observed, where newly observed RR modes of the reversed forms are assigned using protohemes that are selectively deuterated at the four methyl groups or at the four methine carbons. Interestingly, while substantial changes in the disposition of the peripheral vinyl and propionate groups can be inferred from the dramatic spectral shifts, the bonds to the internal histidyl imidazole ligand and those of the Fe-CO and Fe-CN fragments are not significantly affected by the heme rotation, as judged by lack of significant shifts in the nu(Fe-N(His)), nu(Fe-C), and nu(C-O) modes. In fact, the apparent lack of an effect on these key vibrational parameters of the Fe-N(His), Fe-CO, and Fe-CN fragments is entirely consistent with previously reported equilibrium and kinetic studies that document virtually identical functional properties for the native and reversed forms.
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Affiliation(s)
- Freeborn Rwere
- Chemistry Department, Marquette University, Milwaukee, Wisconsin 53233, USA
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23
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Starovoitova V, Wyllie GRA, Scheidt WR, Sturhahn W, Alp EE, Durbin SM. Intermolecular dynamics in crystalline iron octaethylporphyrin (FeOEP). J Phys Chem B 2008; 112:12656-61. [PMID: 18793016 DOI: 10.1021/jp806215r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The new technique of nuclear resonance vibrational spectroscopy (NRVS) has increased the range and quality of dynamical data from Fe-containing molecules that when combined with Raman and infrared spectroscopies impose stricter constraints on normal mode simulations, especially at lower frequencies. Going beyond the usual single molecule approximation, a classical normal-mode analysis that includes intermolecular coupling and the full crystalline symmetry is found to produce a better fit with fewer free parameters for the heme compound iron octaethylporphyrin (FeOEP), using NRVS data from polycrystalline material. Off-diagonal force constants were completely unnecessary, indicating that their role in previous single molecule fits was just to emulate intermolecular coupling. Sound velocities deduced from the calculated phonon dispersion curves are compared to NRVS measurements to further constrain the intermolecular force constants. The NRVS data by themselves are insufficient to rigorously determine all unknown force constants for molecules of this size, but the improved crystal model fit indicates the necessity of including intermolecular interactions for normal-mode analyses.
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Kozlowski PM, Bingham JR, Jarzecki AA. Theoretical Analysis of Core Size Effect in Metalloporphyrins. J Phys Chem A 2008; 112:12781-8. [DOI: 10.1021/jp801696c] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pawel M. Kozlowski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, and Department of Chemistry, Brooklyn College and the Graduate School of the City University of New York, Brooklyn, New York 11210
| | - Jason R. Bingham
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, and Department of Chemistry, Brooklyn College and the Graduate School of the City University of New York, Brooklyn, New York 11210
| | - Andrzej A. Jarzecki
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, and Department of Chemistry, Brooklyn College and the Graduate School of the City University of New York, Brooklyn, New York 11210
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25
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Karumuri SR, Sarkar NK, Choudhury J, Bhattacharjee R. Vibrational spectroscopy of Cm–H, Cβ–Cβstretching vibrations of Nickel metalloporphyrins: An algebraic approach. Mol Phys 2008. [DOI: 10.1080/00268970802248998] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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26
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Pätzold R, Keuntje M, Theophile K, Müller J, Mielcarek E, Ngezahayo A, Anders-von Ahlften A. In situ mapping of nitrifiers and anammox bacteria in microbial aggregates by means of confocal resonance Raman microscopy. J Microbiol Methods 2008; 72:241-8. [DOI: 10.1016/j.mimet.2007.12.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2007] [Revised: 12/09/2007] [Accepted: 12/10/2007] [Indexed: 11/30/2022]
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27
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Mukamel S. Solvation Effects in Four-Wave Mixing and Spontaneous Raman and Fluorescence Lineshapes of Polyatomic Molecules. ADVANCES IN CHEMICAL PHYSICS 2007. [DOI: 10.1002/9780470141199.ch6] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Paulat F, Praneeth VKK, Näther C, Lehnert N. Quantum chemistry-based analysis of the vibrational spectra of five-coordinate metalloporphyrins [M(TPP)Cl]. Inorg Chem 2007; 45:2835-56. [PMID: 16562940 DOI: 10.1021/ic0510866] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Vibrational properties of the five-coordinate porphyrin complexes [M(TPP)(Cl)] (M = Fe, Mn, Co) are analyzed in detail. For [Fe(TPP)(Cl)] (1), a complete vibrational data set is obtained, including nonresonance (NR) Raman, and resonance Raman (RR) spectra at multiple excitation wavelengths as well as IR spectra. These data are completely assigned using density functional (DFT) calculations and polarization measurements. Compared to earlier works, a number of bands are reassigned in this one. These include the important, structure-sensitive band at 390 cm(-1), which is reassigned here to the totally symmetric nu(breathing)(Fe-N) vibration for complex 1. This is in agreement with the assignments for [Ni(TPP)]. In general, the assignments are on the basis of an idealized [M(TPP)]+ core with D(4h) symmetry. In this Work, small deviations from D(4h) are observed in the vibrational spectra and analyzed in detail. On the basis of the assignments of the vibrational spectra of 1, [Mn(TPP)(Cl)] (2), and diamagnetic [Co(TPP)(Cl)] (3), eight metal-sensitive bands are identified. Two of them correspond to the nu(M-N) stretching modes with B(1g) and Eu symmetries and are assigned here for the first time. The shifts of the metal sensitive modes are interpreted on the basis of differences in the porphyrin C-C, C-N, and M-N distances. Besides the porphyrin core vibrations, the M-Cl stretching modes also show strong metal sensitivity. The strength of the M-Cl bond in 1-3 is further investigated. From normal coordinate analysis (NCA), force constants of 1.796 (Fe), 0.932 (Mn), and 1.717 (Co) mdyn/A are obtained for 1-3, respectively. The weakness of the Mn-Cl bond is attributed to the fact that it only corresponds to half a sigma bond. Finally, RR spectroscopy is used to gain detailed insight into the nature of the electronically excited states. This relates to the mechanism of resonance enhancement and the actual nature of the enhanced vibrations. It is of importance that anomalous polarized bands (A(2g) vibrations), which are diagnostic for vibronic mixing, are especially useful for this purpose.
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Affiliation(s)
- Florian Paulat
- Institut für Anorganische Chemie, Christian-Albrechts-Universität Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany
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29
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Kitagawa T, Ozaki Y. Infrared and Raman spectra of metalloporphyrins. STRUCTURE AND BONDING 2006. [DOI: 10.1007/bfb0036790] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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30
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Krim L, Sorgues S, Soep B, Shafizadeh N. Infrared Spectra of RuTPP, RuCOTPP, and Ru(CO)2TPP Isolated in Solid Argon. J Phys Chem A 2005; 109:8268-74. [PMID: 16834214 DOI: 10.1021/jp0580930] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Infrared spectra of unstable species such as CO-free ruthenium tetraphenylporphyrin RuTPP and RuCOTPP (species with vacant coordination sites) isolated in solid argon at 8 K have been recorded. Selective deposition conditions allow the isolation of either RuTPP and RuCOTPP or RuCOTPP and Ru(CO)2TPP. This depends on the preparation conditions of the sample. A specific Ru-CO bending mode has been characterized at 590.1 cm(-1) for Ru(CO)2TPP. The behavior of each vibrational mode of RuTPP, RuCOTPP, and Ru(CO)2TPP has been analyzed. Modes such as gamma8 at 721.3 cm(-1) (out-of-plane stretching mode gamma(Cbeta-H)sym) and nu41 at 1342.8 cm(-1) (nuCalpha-N coupled with deltaCalpha-Cm) reflect the charge transfer in the porphyrin. Indeed, the addition of one or two CO ligands to RuTPP reduces the charge transfer between the metal center and the porphyrin, which appears as an increase in the frequency of the nu41 mode and in a decrease in that of the gamma8 mode.
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Affiliation(s)
- Lahouari Krim
- L.A.D.I.R./U.M.R. 7075 CNRS-Université Pierre et Marie Curie, Boîte 49, 4 Place Jussieu, 75252 Paris, Cedex 05, France.
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31
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Verdal N, Kozlowski PM, Hudson BS. Inelastic Neutron Scattering Spectra of Free Base and Zinc Porphines: A Comparison with DFT-Based Vibrational Analysis. J Phys Chem A 2005; 109:5724-33. [PMID: 16833905 DOI: 10.1021/jp0507795] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Inelastic neutron scattering (INS) spectra of free base (FBP) and zinc (ZnP) porphines are presented and compared with the results of density functional theory (DFT) calculations using the B3LYP functional with 6-31G(d) or 6-311G(d,p) basis sets. To obtain quantitative agreement between experiment and theory, two different scaling techniques have been applied: a scaled quantum mechanical (DFT-SQM) force field was developed for B3LYP/6-31G(d) calculations and the uniform frequency scaling technique (DFT-UFS) was applied to B3LYP/6-311G(d,p) results. The DFT-SQM calculations have been previously compared with IR and Raman spectra with good agreement, which allows for a nearly complete vibrational assignment. The results of the present study extend previous vibrational analysis to a higher level of reliability and complexity. The previous results are augmented by the comparison of calculated and observed INS intensities and the comparison of calculated modes with those observed in INS spectra but previously unobserved in optical spectra. Excellent agreement is acquired between the INS spectra and the results of both calculations, permitting a more detailed and reliable description of the vibrational properties of porphyrins.
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Affiliation(s)
- Nina Verdal
- Department of Chemistry, Syracuse University, Syracuse, New York 13244, USA
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32
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Ataka K, Heberle J. Functional Vibrational Spectroscopy of a CytochromecMonolayer: SEIDAS Probes the Interaction with Different Surface-Modified Electrodes. J Am Chem Soc 2004; 126:9445-57. [PMID: 15281838 DOI: 10.1021/ja048346n] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Electrochemically induced infrared difference spectra of cytochrome c on various chemically modified electrodes (CMEs) are recorded by exploiting the surface-enhancement exerted by a granular gold film. We have recently developed surface-enhanced infrared difference absorption spectroscopy (SEIDAS), which provides acute sensitivity to observe the minute enzymatic change of a protein on the level of a monolayer. By these means, we demonstrate that the relative band intensities in the potential-induced difference spectra of adsorbed cytochrome c are significantly dependent on the type of CME used (mercaptopropionic acid, mercaptoethanol, 4,4'-dithiodipyridine, or L-cysteine). These differences are attributed to the altered interaction of cytochrome c with the headgroup of the various CMEs leading to variations in surface orientation and relative distance from the surface. Nevertheless, the peak positions of the observed bands are identical among the CMEs employed. This implies that the internal conformational changes induced by the redox reaction of the adsorbed cytochrome c are not disturbed by the interaction with the CME and that full functionality of the protein is retained. Finally, we critically discuss our results within the framework of the different models for cytochrome c adsorption on CMEs.
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Affiliation(s)
- Kenichi Ataka
- Forschungszentrum Jülich, IBI-2: Structural Biology, 52425 Jülich, Germany
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33
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Tsai HH(G, Simpson MC. Isolated Impact of Ruffling on the Vibrational Spectrum of Ni Porphyrins. Diagnosing Out-of-Plane Distortions. J Phys Chem A 2004. [DOI: 10.1021/jp036880w] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hui-Hsu (Gavin) Tsai
- Center for Chemical Dynamics, Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106
| | - M. Cather Simpson
- Center for Chemical Dynamics, Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106
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34
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Egawa T, Suzuki N, Dokoh T, Higuchi T, Shimada H, Kitagawa T, Ishimura Y. Vibronic Coupling between Soret and Higher Energy Excited States in Iron(II) Porphyrins: Raman Excitation Profiles of A2g Modes in the Soret Region. J Phys Chem A 2003. [DOI: 10.1021/jp0355612] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tsuyoshi Egawa
- Department of Biochemistry, School of Medicine, Keio University, Shinjuku-ku, Tokyo 160-8582, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8654, and Institute for Molecular Science, Okazaki National Research Institutes, Myodaiji, Okazaki 444-8585, Japan
| | - Noriyuki Suzuki
- Department of Biochemistry, School of Medicine, Keio University, Shinjuku-ku, Tokyo 160-8582, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8654, and Institute for Molecular Science, Okazaki National Research Institutes, Myodaiji, Okazaki 444-8585, Japan
| | - Takashi Dokoh
- Department of Biochemistry, School of Medicine, Keio University, Shinjuku-ku, Tokyo 160-8582, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8654, and Institute for Molecular Science, Okazaki National Research Institutes, Myodaiji, Okazaki 444-8585, Japan
| | - Tsunehiko Higuchi
- Department of Biochemistry, School of Medicine, Keio University, Shinjuku-ku, Tokyo 160-8582, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8654, and Institute for Molecular Science, Okazaki National Research Institutes, Myodaiji, Okazaki 444-8585, Japan
| | - Hideo Shimada
- Department of Biochemistry, School of Medicine, Keio University, Shinjuku-ku, Tokyo 160-8582, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8654, and Institute for Molecular Science, Okazaki National Research Institutes, Myodaiji, Okazaki 444-8585, Japan
| | - Teizo Kitagawa
- Department of Biochemistry, School of Medicine, Keio University, Shinjuku-ku, Tokyo 160-8582, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8654, and Institute for Molecular Science, Okazaki National Research Institutes, Myodaiji, Okazaki 444-8585, Japan
| | - Yuzuru Ishimura
- Department of Biochemistry, School of Medicine, Keio University, Shinjuku-ku, Tokyo 160-8582, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8654, and Institute for Molecular Science, Okazaki National Research Institutes, Myodaiji, Okazaki 444-8585, Japan
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35
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Jeong DH, Jang SM, Hwang IW, Kim D, Matsuzaki Y, Tanaka K, Tsuda A, Nakamura T, Osuka A. Resonance Raman spectroscopic study of fused multiporphyrin linear arrays. J Chem Phys 2003. [DOI: 10.1063/1.1596854] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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36
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Stoll LK, Zgierski MZ, Kozlowski PM. Infrared Spectra of Nickel Octaethylporphyrin and Its Isotopomers Computed via Density Functional Theory−Scaled Quantum Mechanical (DFT−SQM) Method. J Phys Chem A 2003. [DOI: 10.1021/jp022398m] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lindy K. Stoll
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, and Steacie Institute for Molecular Science, National Research Council of Canada, Ottawa, Ontario K1A OR6, Canada
| | - Marek Z. Zgierski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, and Steacie Institute for Molecular Science, National Research Council of Canada, Ottawa, Ontario K1A OR6, Canada
| | - Pawel M. Kozlowski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, and Steacie Institute for Molecular Science, National Research Council of Canada, Ottawa, Ontario K1A OR6, Canada
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37
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Tsai HH(G, Simpson MC. HBFF-SVD Force Field Treatment of Ni(II) Porphine: Important Long Range Cross Terms. J Phys Chem A 2003. [DOI: 10.1021/jp0218037] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - M. Cather Simpson
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106
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38
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Nagatomo S, Nagai M, Shibayama N, Kitagawa T. Differences in changes of the alpha1-beta2 subunit contacts between ligand binding to the alpha and beta subunits of hemoglobin A: UV resonance raman analysis using Ni-Fe hybrid hemoglobin. Biochemistry 2002; 41:10010-20. [PMID: 12146965 DOI: 10.1021/bi0200460] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The alpha1-beta2 subunit contacts in the half-ligated hemoglobin A (Hb A) have been explored with ultraviolet resonance Raman (UVRR) spectroscopy using the Ni-Fe hybrid Hb under various solution conditions. Our previous studies demonstrated that Trpbeta37, Tyralpha42, and Tyralpha140 are mainly responsible for UVRR spectral differences between the complete T (deoxyHb A) and R (COHb A) structures [Nagai, M., Wajcman, H., Lahary, A., Nakatsukasa, T., Nagatomo, S., and Kitagawa, T. (1999) Biochemistry, 38, 1243-1251]. On the basis of it, the UVRR spectra observed for the half-ligated alpha(Ni)beta(CO) and alpha(CO)beta(Ni) at pH 6.7 in the presence of IHP indicated the adoption of the complete T structure similar to alpha(Ni)beta(deoxy) and alpha(deoxy)beta(Ni). The extent of the quaternary structural changes upon ligand binding depends on pH and IHP, but their characters are qualitatively the same. For alpha(Ni)beta(Fe), it is not until pH 8.7 in the absence of IHP that the Tyr bands are changed by ligand binding. The change of Tyr residues is induced by binding of CO, but not of NO, to the alpha heme, while it was similarly induced by binding of CO and NO to the beta heme. The Trp bands are changed toward R-like similarly for alpha(Ni)beta(CO) and alpha(CO)beta(Ni), indicating that the structural changes of Trp residues are scarcely different between CO binding to either the alpha or beta heme. The ligand induced quaternary structural changes of Tyr and Trp residues did not take place in a concerted way and were different between alpha(Ni)beta(CO) and alpha(CO)beta(Ni). These observations directly indicate that the phenomenon occurring at the alpha1-beta2 interface is different between the ligand binding to the alpha and beta hemes and is greatly influenced by IHP. A plausible mechanism of the intersubunit communication upon binding of a ligand to the alpha or beta subunit to the other subunit and its difference between NO and CO as a ligand are discussed.
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Affiliation(s)
- Shigenori Nagatomo
- Center for Integrative Bioscience, Okazaki National Research Institutes, Myodaiji, Okazaki, Aichi 444-8585, Japan
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39
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Mizutani Y, Kitagawa T. Mode Dependence of Vibrational Energy Redistribution in Nickel Tetraphenylporphyrin Probed by Picosecond Time-Resolved Resonance Raman Spectroscopy: Slow IVR to Phenyl Peripherals. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2002. [DOI: 10.1246/bcsj.75.965] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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40
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Mizutani Y, Kitagawa T. Vibrational Energy Relaxation of Metalloporphyrins in a Condensed Phase Probed by Time-Resolved Resonance Raman Spectroscopy. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2002. [DOI: 10.1246/bcsj.75.623] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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41
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Stoll LK, Zgierski MZ, Kozlowski PM. Density Functional Theory Analysis of Nickel Octaethylporphyrin Ruffling. J Phys Chem A 2001. [DOI: 10.1021/jp012416k] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lindy K. Stoll
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, and Steacie Institute for Molecular Science, National Research Council of Canada, Ottawa, Ontario, Canada K1A OR6
| | - Marek Z. Zgierski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, and Steacie Institute for Molecular Science, National Research Council of Canada, Ottawa, Ontario, Canada K1A OR6
| | - Pawel M. Kozlowski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, and Steacie Institute for Molecular Science, National Research Council of Canada, Ottawa, Ontario, Canada K1A OR6
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42
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Sato H, Chiba H, Tashiro H, Ozaki Y. Excitation wavelength-dependent changes in Raman spectra of whole blood and hemoglobin: comparison of the spectra with 514.5-, 720-, and 1064-nm excitation. JOURNAL OF BIOMEDICAL OPTICS 2001; 6:366-70. [PMID: 11516329 DOI: 10.1117/1.1380668] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2000] [Revised: 01/24/2001] [Accepted: 02/09/2001] [Indexed: 05/21/2023]
Abstract
Raman spectra of whole blood and oxy-hemoglobin (Hb) were measured under the same conditions with visible (514.5 nm) and near-infrared (NIR; 720 and 1064 nm) excitation, and the obtained spectra were compared in detail. The Raman spectrum of blood excited with visible light is dominated by very intense bands due to carotenoids, so that it was difficult to obtain information about Hb from the spectrum. The Raman spectra of whole blood and oxy-Hb excited with 720 nm light are very close to each other; both spectra are essentially Raman spectra of the heme chromophore that is preresonant with Q bands. Qualitative spectral analysis including band assignment and investigation of nature of resonance effect were carried out for the Raman spectra with 720 nm excitation. The spectra of whole blood and oxy-Hb excited with 1064 nm light contain contributions from nonresonance Raman spectra of the heme chromophore and Raman spectra of proteins. The 1064 nm excited spectra of blood and oxy-Hb are similar to each other but different in some features. For example, bands due to protein appear stronger in the spectrum of whole blood than in that of oxy-Hb which does not contain protein except globin part. The comparison between the 514.5, 720, and 1064 nm excited Raman spectra reveal that the excitation wavelength of 720 nm is more practical than that of visible light and 1064 nm in the Raman analysis of Hb, such as oxygenation, specially in situ measurement.
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Affiliation(s)
- H Sato
- Advanced Engineering Center, RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.
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Das TK, Couture M, Guertin M, Rousseau DL. Distal Interactions in the Cyanide Complex of Ferric Chlamydomonas Hemoglobin. J Phys Chem B 2000. [DOI: 10.1021/jp000452y] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tapan Kanti Das
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, and Department of Biochemistry and Microbiology, Faculty of Sciences and Engineering, Laval University, Quebec, G1K 7P4, Canada
| | - Manon Couture
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, and Department of Biochemistry and Microbiology, Faculty of Sciences and Engineering, Laval University, Quebec, G1K 7P4, Canada
| | - Michel Guertin
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, and Department of Biochemistry and Microbiology, Faculty of Sciences and Engineering, Laval University, Quebec, G1K 7P4, Canada
| | - Denis L. Rousseau
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, and Department of Biochemistry and Microbiology, Faculty of Sciences and Engineering, Laval University, Quebec, G1K 7P4, Canada
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Rush TS, Kozlowski PM, Piffat CA, Kumble R, Zgierski MZ, Spiro TG. Computational Modeling of Metalloporphyrin Structure and Vibrational Spectra: Porphyrin Ruffling in NiTPP. J Phys Chem B 2000. [DOI: 10.1021/jp000266s] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Thomas S. Rush
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, and Steacie Institute for Molecular Sciences, National Research Council of Canada, Ottawa, Ontario, Canada K1A OR6
| | - Pawel M. Kozlowski
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, and Steacie Institute for Molecular Sciences, National Research Council of Canada, Ottawa, Ontario, Canada K1A OR6
| | - Christine A. Piffat
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, and Steacie Institute for Molecular Sciences, National Research Council of Canada, Ottawa, Ontario, Canada K1A OR6
| | - Ranjit Kumble
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, and Steacie Institute for Molecular Sciences, National Research Council of Canada, Ottawa, Ontario, Canada K1A OR6
| | - Marek Z. Zgierski
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, and Steacie Institute for Molecular Sciences, National Research Council of Canada, Ottawa, Ontario, Canada K1A OR6
| | - Thomas G. Spiro
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, and Steacie Institute for Molecular Sciences, National Research Council of Canada, Ottawa, Ontario, Canada K1A OR6
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Mizutani Y, Uesugi Y, Kitagawa T. Intramolecular vibrational energy redistribution and intermolecular energy transfer in the (d, d) excited state of nickel octaethylporphyrin. J Chem Phys 1999. [DOI: 10.1063/1.480253] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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48
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Collman JP, Harford ST, Franzen S, Shreve AP, Woodruff WH. Resonance Raman and X-ray Crystallographic Studies of Intertriad Metal-Metal Bonds. 2. WRu and MoOs Porphyrin Dimers. Inorg Chem 1999; 38:2093-2097. [PMID: 11670991 DOI: 10.1021/ic9810337] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Solution ((1)H NMR, Evans method magnetic susceptibility, resonance Raman) and X-ray crystallographic spectroscopic studies of intertriad heterodimeric [(OEP)MoOs(OEP)] (3), [(OEP)WRu(OEP)] (4), [(OEP)MoOs(TPP)]PF(6) (5(+)), and [(OEP)WRu(TPP)]PF(6) (6(+)) metalloporphyrins are reported (OEP = 2,3,7,8,12,13,17,18-octaethylporphyrinato; TPP = 5,10,15,20-tetraphenylporphyrinato). Evans method magnetic susceptibility data indicate that 3 and 4 contain two unpaired electrons in the ground electronic configuration. Resonance Raman spectra of 3, 4, 5(+), and 6(+) suggest that WRu bonds are 5-10% stronger than corresponding MoOs species. Structural characterization of 5(+) and 6(+) demonstrates metal-metal bond lengths of 2.30 (WRu) and 2.24 (MoOs) Å, respectively. The possibility of a special stability associated with polar heterometallic multiple bonds is discussed.
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Affiliation(s)
- James P. Collman
- Department of Chemistry, Stanford University, Stanford, California 94305, and Los Alamos National Laboratory, Los Alamos, New Mexico 87545
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Collman JP, Harford ST, Franzen S, Marchon JC, Maldivi P, Shreve AP, Woodruff WH. Resonance Raman, X-ray Crystallographic, and Magnetic Susceptibility Studies of Metal-Metal-Bonded MoRu and WOs Porphyrin Dimers. 1. Evidence for an Unusual MO Diagram. Inorg Chem 1999; 38:2085-2092. [PMID: 11670990 DOI: 10.1021/ic981032e] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Solution (VT NMR, Evans method magnetic susceptibility, resonance Raman) and solid-state (SQUID magnetic susceptibility, X-ray crystallography) spectroscopic studies of intertriad heterodimeric [(OEP)MoRu(OEP)] (1), [(OEP)WOs(OEP)] (2), and [(OEP)MoRu(TPP)]PF(6) (3(+)) metalloporphyrins are reported (OEP = 2,3,7,8,12,13,17,18-octaethylporphyrinato; TPP = 5,10,15,20-tetraphenylporphyrinato). Solution and solid-state magnetic susceptibility data indicate that 1 and 2 contain two unpaired electrons in the ground electronic configuration. The presence of a delta bond in 3(+) has been confirmed by structural characterization. The experimental evidence is consistent with a molecular orbital ordering, sigma < pi < delta < pi < delta, which is different from that seen for homologous metalloporphyrin dimers with homometallic or intratriad heterometallic multiple metal-metal bonds. Resonance Raman data suggest that the heterometallic bonds are slightly stronger than isoelectronic homometallic species.
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Affiliation(s)
- James P. Collman
- Department of Chemistry, Stanford University, Stanford, California 94305, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, and Département de Recherche Fondamentale sur la Matière Condensée/SCIB, CEA-Grenoble, 38054 Grenoble, France
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Czarnecki K, Proniewicz LM, Fujii H, Ji D, Czernuszewicz RS, Kincaid JR. Insensitivity of Vanadyl−Oxygen Bond Strengths to Radical Type (2A1u vs 2A2u) in Vanadyl Porphyrin Cation Radicals. Inorg Chem 1999. [DOI: 10.1021/ic981369g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kazimierz Czarnecki
- Chemistry Department; Marquette University, Milwaukee, Wisconsin 53233, Chemical Physics Division, Department of Chemistry, and Regional Laboratory of Physicochemical Analysis and Structural Research, Jagiellonian University, 3 Ingardena Street, 30-060 Krakow, Poland, Institute for Molecular Science, Okazaki National Research Institutes, Okazaki 444, Japan, and Chemistry Department, University of Houston, Houston, Texas 77004
| | - Leonard M. Proniewicz
- Chemistry Department; Marquette University, Milwaukee, Wisconsin 53233, Chemical Physics Division, Department of Chemistry, and Regional Laboratory of Physicochemical Analysis and Structural Research, Jagiellonian University, 3 Ingardena Street, 30-060 Krakow, Poland, Institute for Molecular Science, Okazaki National Research Institutes, Okazaki 444, Japan, and Chemistry Department, University of Houston, Houston, Texas 77004
| | - Hiroshi Fujii
- Chemistry Department; Marquette University, Milwaukee, Wisconsin 53233, Chemical Physics Division, Department of Chemistry, and Regional Laboratory of Physicochemical Analysis and Structural Research, Jagiellonian University, 3 Ingardena Street, 30-060 Krakow, Poland, Institute for Molecular Science, Okazaki National Research Institutes, Okazaki 444, Japan, and Chemistry Department, University of Houston, Houston, Texas 77004
| | - David Ji
- Chemistry Department; Marquette University, Milwaukee, Wisconsin 53233, Chemical Physics Division, Department of Chemistry, and Regional Laboratory of Physicochemical Analysis and Structural Research, Jagiellonian University, 3 Ingardena Street, 30-060 Krakow, Poland, Institute for Molecular Science, Okazaki National Research Institutes, Okazaki 444, Japan, and Chemistry Department, University of Houston, Houston, Texas 77004
| | - Roman S. Czernuszewicz
- Chemistry Department; Marquette University, Milwaukee, Wisconsin 53233, Chemical Physics Division, Department of Chemistry, and Regional Laboratory of Physicochemical Analysis and Structural Research, Jagiellonian University, 3 Ingardena Street, 30-060 Krakow, Poland, Institute for Molecular Science, Okazaki National Research Institutes, Okazaki 444, Japan, and Chemistry Department, University of Houston, Houston, Texas 77004
| | - James R. Kincaid
- Chemistry Department; Marquette University, Milwaukee, Wisconsin 53233, Chemical Physics Division, Department of Chemistry, and Regional Laboratory of Physicochemical Analysis and Structural Research, Jagiellonian University, 3 Ingardena Street, 30-060 Krakow, Poland, Institute for Molecular Science, Okazaki National Research Institutes, Okazaki 444, Japan, and Chemistry Department, University of Houston, Houston, Texas 77004
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