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Dr. Vladimir Pelmentschikov

V. Pelmentschikov
Vladimir Pelmentschikov
Lupe [1]

Technische Universität Berlin
Fakultät II
Institut für Chemie
Sekretariat C 7
Straße des 17. Juni 135
10623 Berlin

E-Mail: pelmentschikov(at)gmail.com [2]
Telefon: +49 30 314 28008
Telefax: +49 30 314 21075

Raum: C 71
Gebäude C, Straße des 17. Juni 115

Rollen, Mitgliedschaften und Funktionen:

  • wiss. Mitarbeiter in der Arbeitsgruppe Prof. Dr. M. Kaupp [3]
  • Associate Editor, Journal of Proteolysis [4]

Research Topics:

  • My research is focused on quantum chemical studies of protein active sites. The areas of my interest are enzyme reaction mechanisms, electron paramagnetic resonance (EPR) and nuclear vibrational resonance spectra (NRVS) of metalloproteins and organometallic complexes.
  • Q-Spector python tool (under constant development) for post-analysis of the vibrational normal modes and other spectral properties (IR, VCD, NRVSs, UV-Visible, and KED diagrams) calculated by computational chemistry software (GAUSSIAN / TURBOMOLE / ADF / AMBER) and building the spectra using Gaussian / Lorentz broadening.

Publications List:

  • Terminal Hydride Species in [FeFe]-Hydrogenases Are Vibrationally Coupled to the Active Site Environment  C. Pham, D. Mulder, V. Pelmenschikov, P. King, M. Ratzloff, H. Wang, N. Mishra, E. Alp, J. Zhao, M. Hu, K. Tamasaku, Y. Yoda, S. Cramer Angew. Chem. Int. Ed. 2018, 57, 10605–10609, 10.1002/anie.201805144 [5]
  • High-Frequency Fe-H Vibrations in a Bridging Hybride Complex Characterized by NRVS and DFT V. Pelmenschikov, L. Gee, H. Wang, K. MacLeod, S. McWilliams, K. Skubi, S. Cramer, P. Holland Angew. Chem. Int. Ed. 2018, 57, 9367 -9371, 10.1002/anie.201804601 [6]
  • Sterically Stabilized Terminal Hydride of a Diiron Dithiolate M.R. Carlson, D.L. Gray, C.P. Richers, W. Wang, P.-H. Zhao, T.B. Rauchfuss, V. Pelmenschikov, C.C. Pham, L.B. Gee, H. Wang, S.P. Cramer Inorg. Chem. 2018, 57, 1988–2001, 10.1021/acs.inorgchem.7b02903 [7]
  • Reaction Coordinate Leading to H2 Production in [FeFe]-Hydrogenase Identified by Nuclear Resonance Vibrational Spectroscopy and Density Functional Theory V. Pelmenschikov, J.A. Birrell, C.C. Pham, N. Mishra, H. Wang, C. Sommer, E. Reijerse, C.P. Richers, K. Tamasaku, Y. Yoda, T.B. Rauchfuss, W. Lubitz, S.P. Cramer J. Am. Chem. Soc. 2017, 139, 16894–16902, 10.1021/jacs.7b09751 [8]
  • Direct Observation of an Iron-Bound Terminal Hydride in [FeFe]-Hydrogenase by Nuclear Resonance Vibrational Spectroscopy E.J. Reijerse, C.C. Pham, V. Pelmenschikov, R. Gilbert-Wilson, A. Adamska-Venkatesh, J.F. Siebel, L.B. Gee, Y. Yoda, K. Tamasaku, W. Lubitz, T.B. Rauchfuss, S.P. Cramer J. Am. Chem. Soc. 2017, 139, 4306-4309, 10.1021/jacs.7b0068 [9]
  • Characterization of the [3Fe–4S] 0/1+ cluster from the D14C variant of Pyrococcus furiosus ferredoxin via combined NRVS and DFT analyses L. Lauterbach, L.B. Gee, V. Pelmenschikov, F.E. Jenney Jr, S. Kamali, Y. Yoda, M.W.W. Adams, S.P. Cramer Dalton Trans. 2016, 45, 7215-7219, 10.1039/C5DT04760A [10]
  • The Mössbauer Parameters of the Proximal Cluster of Membrane-Bound Hydrogenase Revisited: A Density Functional Theory Study S.G. Tabrizi, V. Pelmenschikov, L. Noodleman, M. Kaupp J. Chem. Theory Comput. 2016, 12, 174-187, 10.1021/acs.jctc.5b00854 [11] 
  • Low frequency dynamics of the nitrogenase MoFe protein via femtosecond pump probe spectroscopy - Observation of a candidate promoting vibration M. Maiuri, I. Delfino, G. Cerullo, C. Manzoni, V. Pelmenschikov, Y. Guo, H. Wang, L.B. Gee, C.H. Dapper, W.E. Newton, S.P. Cramer J. Inorg. Biochem. 2015, 153, 128-135, 10.1016/j.jinorgbio.2015.07.005 [12]
  • Electronic Structure, Bonding, Spin Coupling, and Energetics of Polynuclear Iron–Sulfur Clusters – A Broken Symmetry Density Functional Theory Perspective K. H. Hopmann, V. Pelmenschikov, W.-G. Han Du, L. Noodleman, in Spin States in Biochemistry and Inorganic Chemistry: Influence on Structure and Reactivity (eds M. Swart and M. Costas) 2015, John Wiley & Sons, Ltd, Oxford, UK, 10.1002/9781118898277.ch13 [13]
  • Resonance Raman Spectroscopic Analysis of the [NiFe] Active Site and the Proximal [4Fe-3S] Cluster of an O2-Tolerant Membrane-Bound Hydrogenase in the Crystalline State E. Siebert, Y. Rippers, S. Frielingsdorf, J. Fritsch, A. Schmidt, J. Kalms, S. Katz, O. Lenz, P. Scheerer, L. Paasche, V. Pelmenschikov, U. Kuhlmann, M. A. Mroginski, I. Zebger, P. Hildebrandt J. Phys. Chem. B 2015, 119 (43), 13785, 10.1021/acs.jpcb.5b04119 [14]
  • Hydride bridge in [NiFe]-hydrogenase observed by nuclear resonance vibrational spectroscopy H. Ogata, T. Krämer, H. Wang, D. Schilter, V. Pelmenschikov, M. van Gastel, F. Neese, T. B. Rauchfuss, L. B. Gee, A. D. Scott, Y. Yoda, Y. Tanaka, W. Lubitz, S. P. Cramer Nat. Commun. 2015, 6, 7890, 10.1038/ncomms8890 [15]
  • Correlations between metal spin states and vibrational spectra of a trinuclear Fe(II) complex exhibiting spin crossover T. P. Gerasimova, S. A. Katsyuba, L. G. Lavrenova, V. Pelmenschikov, M. Kaupp J. Mol. Struct. 2015, 1101, 8-13, 10.1016/j.molstruc.2015.08.001 [16]
  • Docking and Migration of Carbon Monoxide in Nitrogenase: The Case for Gated Pockets from Infrared Spectroscopy and Molecular Dynamics L. B. Gee, I. Leontyev, A. Stuchebrukhov, A. D. Scott, V. Pelmenschikov, S. P. Cramer Biochemistry 2015, 54, 3314-3319, 10.1021/acs.biochem.5b00216 [17]
  • Structural Characterization of CO-Inhibited Mo-Nitrogenase by Combined Application of NRVS, EXAFS, and DFT: New Insights into the Effects of CO Binding and the Role of the Interstitial Atom A.D. Scott, V. Pelmenschikov, Y. Guo, L. Yan, H. Wang, S.J. George, C.H. Dapper, W.E. Newton, Y. Yoda, Y. Tanaka, S.P. Cramer J. Am. Chem. Soc. 2014, 136, 15942-15954, 10.1021/ja505720m [18]
  • Synthesis and vibrational spectroscopy of 57 Fe-labeled models of [NiFe] hydrogenase: first direct observation of a nickel–iron interaction D. Schilter, V. Pelmenschikov, H. Wang, F. Meier, L.B. Gee, Y. Yoda, M. Kaupp, T.B. Rauchfuss, S.P. Cramer Chem. Commun. 2014, 50, 13469-13472, 10.1039/C4CC04572F [19]
  • Reversible [4Fe-3S] cluster morphing in an O2-tolerant [NiFe] hydrogenase S. Frielingsdorf, J. Fritsch, A. Schmidt, M. Hammer, J. Löwenstein, E. Siebert, V. Pelmenschikov, T. Jaenicke, J. Kalms, Y. Rippers, F. Lendzian, I. Zebger, C. Teutloff, M. Kaupp, R. Bittl, P. Hildebrandt, B. Friedrich, O. Lenz, P. Scheerer Nature Chemical Biology 2014, 10, 378-385, 10.1038/nchembio.1500 [20]
  • The HydG Enzyme Generates an Fe(CO)2(CN) Synthon in Assembly of the FeFe Hydrogenase H-cluster J.M. Kuchenreuther, W.K. Myers, D.L.M. Suess, T.A. Stich, V. Pelmenschikov, S.A. Shiigi, S.P. Cramer, J.R. Swartz, R.D. Britt, S.J. George Science 2014, 343, 424-427, 10.1126/science.1246572 [21]
  • Redox-Dependent Structural Transformations of the [4Fe-3S] Proximal Cluster in O2-Tolerant Membrane-Bound [NiFe]-Hydrogenase: a DFT Study V. Pelmenschikov and M. Kaupp J. Am. Chem. Soc. 2013, 135, 11809-11823,  10.1021/ja402159u [22]
  • Characterization of [4Fe-4S] Cluster Vibrations and Structure in Nitrogenase Fe Protein at Three Oxidation Levels via Combined NRVS, EXAFS, and DFT Analyses D. Mitra, S.J. George, Y. Guo, S. Kamali, S. Keable, J.W. Peters, V. Pelmenschikov, D.A. Case, and S.P. Cramer J. Am. Chem. Soc. 2013, 135, 2530-2543, 10.1021/ja307027n [23]
  • IR-Monitored Photolysis of CO-Inhibited Nitrogenase: A Major EPR-Silent Species with Coupled Terminal CO Ligands L. Yan, V. Pelmenschikov, C.H. Dapper, A.D. Scott, W.E. Newton, and S.P. Cramer Chem. Eur. J.  2012, 18, 16349-16357, 10.1002/chem.201202072 [24]
  • Dynamics of the [4Fe-4S] Cluster in Pyrococcus furiosus D14C Ferredoxin via Nuclear Resonance Vibrational and Resonance Raman Spectroscopies, Force Field Simulations, and Density Functional Theory Calculations D. Mitra, V. Pelmenschikov, Y. Guo, D. A. Case, H. Wang, W. Dong, M.-L. Tan, T. Ichiye, F. E. Jenney, M. W. W. Adams, Y. Yoda, J. Zhao, S. P. Cramer Biochemistry 2011, 50, 5220-5235, 10.1021/bi200046p [25]
  • Fe-H/D stretching and bending modes in nuclear resonance vibrational, Raman and infrared spectroscopies: Comparisons of density functional theory and experiment V. Pelmenschikov, Y. Guo, H. Wang, S. P. Cramer, D. A. Case Faraday Discuss. 2011, 148, 409-420, 10.1039/C004367M [26]
  • Is There a Ni-Methyl Intermediate in the Mechanism of Methyl-Coenzyme M Reductase? S. Chen, V. Pelmenschikov, M. R. A. Blomberg, and P. E. M. Siegbahn J. Am. Chem. Soc. 2009, 131, 9912-9913, 10.1021/ja904301f [27]
  • Characterization of the Fe Site in Iron-Sulfur-Cluster-Free Hydrogenase (HMD) and of a Model Compound via Nuclear Resonance Vibrational Spectroscopy (NRVS) Y. Guo, H. Wang, Y. Xiao, S. Vogt, R. K. Thauer, S. Shima, P. I. Volkers, T. B. Rauchfuss, V. Pelmenschikov, D. A. Case, E. E. Alp, W. Sturhahn, Y. Yoda, and S. P. Cramer Inorg. Chem. 2008, 47, 3969-3977, 10.1021/ic701251j [28]
  • Ligand-bound S = 1/2 FeMo-Cofactor of Nitrogenase: Hyperfine Interaction Analysis and Implication for the Central Ligand X Identity V. Pelmenschikov, D. A. Case, L. Noodleman Inorg. Chem. 2008, 47, 6162-6172, 10.1021/ic7022743 [29]
  • Testing if the interstitial atom, X, of the nitrogenase molybdenum-iron cofactor is N or C: ENDOR, ESEEM, and DFT Studies of the S = 3/2 resting state in multiple environments D. Lukoyanov, V. Pelmenschikov, N. Maeser, M. Laryukhin, T.C. Yang, L. Noodleman, D.R. Dean, D.A. Case, L.C. Seefeldt, and B.M. Hoffman Inorg. Chem. 2007, 46, 11437-11439, 10.1021/ic7018814 [30]
  • Nickel Superoxide Dismutase Reaction Mechanism studied by Hybrid Density Functional Methods V. Pelmenschikov, P. E. M. Siegbahn J. Am. Chem. Soc. 2006, 128, 7466-7475, 10.1021/ja053665f [31]
  • Copper-Zinc Superoxide Dismutase: Theoretical Insights into the Catalytic Mechanism V. Pelmenschikov, P. E. M. Siegbahn. Inorg. Chem. 2005, 44, 3311-332, 10.1021/ic050018g [32]
  • Density Functional Calculations on Class III Ribonucleotide Reductase: Substrate Reaction Mechanism with Two Formates K.-B. Cho, V. Pelmenschikov, A. Grаslund, P. E. M. Siegbahn J. Phys. Chem. B. 2004, 108, 2056-2065, 10.1021/jp035280u [33]
  • Class I Ribonucleotide Reductase Revisited: The Effect of Removing a Proton on Glu441 V. Pelmenschikov, K.-B. Cho, P. E. M. Siegbahn J. Comput. Chem. 2004, 25, 311-321, 10.1002/jcc.10389 [34]
  • Catalysis by Methyl-Coenzyme M Reductase: a Theoretical Study for Heterodisulfide Product Formation V. Pelmenschikov, P. E. M. Siegbahn J. Biol. Inorg. Chem. 2003, 8, 653-662, 10.1007/s00775-003-0461-8 [35]
  • A Mechanism from Quantum Chemical Studies for Methane Formation in Methanogenesis V. Pelmenschikov, M. R. A. Blomberg, P. E. M. Siegbahn, R. H. Crabtree. J. Am. Chem. Soc. 2002, 124, 4039-4049, 10.1021/ja011664r [36]
  • Catalytic Mechanism of Matrix Metalloproteinases: Two-Layered ONIOM Study V. Pelmenschikov, P. E. M. Siegbahn Inorg. Chem. 2002, 41, 5659-5666,  10.1021/ic0255656 [37]
  • A Theoretical Study of The Mechanism for Peptide Hydrolysis by Thermolysin V. Pelmenschikov, M. R. A. Blomberg, P. E. M. Siegbahn J. Biol. Inorg. Chem. 2002, 7, 284-298, 10.1007/s007750100295 [38]
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