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Room: 303.210
Phone: +61 8 9266 7172
E-mail

Dr Karl J Jalkanen

Visiting Research Fellow

Field of interest

Spectroscopic Methods Used in Molecular Biophysics

Research Interests

Quantum mechanical calculation of spectra of biomolecules:

• Vibrational Spectroscopy
  • Vibrational Absorption Spectroscopy
  • Vibrational Circular Dichroism Spectroscopy
• Scattering Spectroscopy
  • Raman Scattering Spectroscopy
  • Raman Optical Activity
• Magnetic Resonance Spectroscopy
  • Nuclear Overhauser
  • Nuclear spin-spin Resonance

Main Collaborators

• Prof. Risto Nieminen, Helsinki University of Technology, Helsinki, Finland.
• Prof. Nicholas C. Handy, Cambridge University, Cambridge, England.
• Dr. Roger D. Amos, Australian Partnership for Advanced Computing National Facility, Australian National University, Canberra, Australia.
• Prof. Th. Frauenheim, University of Bremen, Germany.
• Prof. Sandor Suhai, German Cancer Research Center, Heidelberg, Germany.
• Prof. Henrik G. Bohr, Technical University of Denmark, Lyngby, Denmark.
• Prof. P.J. Stephens, University of Southern California, Los Angeles, California USA.
• Prof. Larry A. Nafie, Syracuse University, Syracuse, New York USA.
• Dr. Rebecca C. Wade, EMBL-Heidelberg, Heidelberg, Germany.
• Dr. Christiana Jung, MDC, Berlin-Buch, Germany
• Professor Lauence D. Barron, Department of Chemistry, University of Glasgow

Education

• BS in Chemistry, Michigan Technological University, May 1980.
• MS in Applied Mathematics, University of Southern California, Aug. 1988.
• Ph.D. in Chemistry, University of Southern California, Aug. 1989.

Appointments

• Postdoctoral Research Scientist, Potential Energy Functions Consortium (PEFC), Biosym Technologies, 9685 Scranton Road, San Diego, CA 92121 USA. 11.89-2.92.
• Postdoctoral Research Scientist, Applications Group, National Center for Supercomputing Applications (NCSA), University of Illinois at Urbana/Champaign (UIUC) , 405 N. Mathews Ave., Champaign/Urbana, IL 61801 USA.  3.92-7.94.
• Visiting Research Scientist, Department of Molecular Biophysics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany. 8.94-8.96.
• Visiting Dreyfus-Fellow Professor of Biochemistry/Chemistry, Calvin College, 3201 Burton Street S.E., Grand Rapids, MI USA. 9.96-5.97.
• Visiting Research Scientist, Department of Molecular Biophysics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany. 7.97-3.99.
• Visiting Research Scientist, Laboratory of Physics, Helsinki University of Technology (HUT), P.O. Box 1100, Otakaari 1 M, FIN-02015 HUT, Finland. 4.99-10.99.
• Visiting Professor, Department of Physicss, Technical University of Denmark, DK-2800 Lyngby, Denmark. 10.99-1.2000.
• Visiting Research Scientist, Laboratory of Physics, Helsinki University of Technology (HUT), P.O. Box 1100, Otakaari 1 M, FIN-02015, Finland. 1.2000-12.2000.
• Visiting Scholar and Research Scientist, Steinbeis Transfer Center for Genomics, Im Neuenheimer Feld 370/42, D-69120 Heidelberg, Germany. 1.2001-5.2001.
• Visiting Scholar and Research Scientist, Laboratory of Physics, Helsinki University of Technology (HUT), P.O. Box 1100, Otakaari 1M, FIN-02015 HUT, Finland. 6.2001-8.2001.
• Assistant Professor of Biophysics/Physics, Quantum Protein (QuP) Center, Technical University of Denmark, Building 309, DK-2800 Kgs. Lyngby, Denmark. 8.2001 to 8.2002.
• Associate Professor (Lektor) of Biophysics/Physics, Quantum Protein (QuP) Center, Technical University of Denmark, Building 309, DK-2800 Kgs. Lyngby, Denmark. 9.2002 to 8.2005 (on sabbatical leave from DTU since September 2005).
• Visiting Professor of Biophysics/Physics, Laboratory of Physics, Helsinki University of Technology, P.O. Box 1100, Otakaari 1 M, FIN-02015 HUT, Finland. 7.2005-9.2005.
• Visiting Research Fellow and Visiting Associate Professor of Biophysics/Physics/Chemistry, Nanochemistry Research Institute, Department of Applied Chemistry, Curtin University of Technology, P.O. Box U1987, Perth 6845, Western Australia. 10.2005 – present.

Recent publications

• ''Solution-Phase Conformations of N-Acetyl-N’-methyl-L-alaninamide from Vibrational Raman Optical Activity,'' J. Phys. Chem. 1996, 100, 2025-2034. Z. Deng, P. L. Polavarapu, S. J. Ford, L. Hecht, L. D. Barron, C. S. Ewig and K. Jalkanen.
• ''N-Acetyl-L-Alanine N’-Methylamide: A Density Functional Analysis of the Vibrational Absorption and Vibrational Circular Dichroism Spectra,'' Chem. Phys. 1996, 208, 81-116. K. J. Jalkanen and S. Suhai.
• ''Density Functional and Neural Network Analysis: Hydration Effects and Spectroscopic and Structural Correlations in Small Peptides and Amino Acids,'' Theoretical and Computational Methods in Genome Research, 1997, 255-277. K. J. Jalkanen, S. Suhai and H. Bohr.
• ''Derivation of Class II Force Fields: V. A Quantum Force Field for Amides, Peptides and Related Compounds,'' J. Comp. Chem. 1998, 19, 430-458. J. R. Maple, M.-J. Hwang, K. J. Jalkanen, T. P. Stockfisch and A. T. Hagler.
• ''Theortetical Study of aqueous N-Acetyl-L-Alanine N’-Methylamide: Structures, Raman, VCD and ROA Spectra,'' J. Phys. Chem. B 1998, 102, 2587-2602. Wen-Ge Han, K. J. Jalkanen, Marcus Elstner and Sandor Suhai.
• ''A Density Functional Study of the Structures and Vibrational Spectra of the Zwitterion L-Alanine in the Presence of Explicit Water Molecules,'' J. Phys. Chem. B 1998, 102, 5899-5913. Emadeddin Tajkhorshid, K. J. Jalkanen and Sandor Suhai.
• '' A Computational Study of M-M Multiple Bonding in (Ph2MMPh2)n, where M = B or Al, and n= 0, -1, or -2,'' Main Group Metal Chemistry 1998, 21, 219-224. E.L. Hamilton, J.G. Pruis, R.L. Dekock and K.J. Jalkanen.
• ''L-Alanyl-L-alanine in the zwitterionic state: structures determined in the presence of explict waters and with continuum models using density functional theory,'' Chem. Phys. 1999, 240, 63-77. M. Knapp-Mohammady, K. J. Jalkanen, F. Nardi, R. C. Wade and S. Suhai.
• ''A comparative study of MP2, B3LYP, RHF and SCC-DFTB force fields in predicting the vibrational spectra of N-acetyl-L-alanine-N‘-methylamide: VA and VCD spectra,'' Chem. Phys. 1999, 246, 13-36. H.G. Bohr, K.J. Jalkanen, M. Elstner, K. Frimand and S. Suhai.
• ''Metal-Metal Cooperativity Effects in Promoting C-H Bond Cleavage of a Methyl Group by an Adjacent Metal Center,'' J. Am. Chem. Soc. 1999, 121, 3666-3683. J.R. Torkelson, F.H. Antwi-Nsiah, R. McDonald, M. Cowie, J.G. Pruis, K.J. Jalkanen and R.L. DeKock.
• ''Hybrid SCC-DFTB/Molecular Mechanical Studies of H-Bonded Systems of N-Acetyl-(L-Ala)n N'-Methylamide Helices in Water Solution,'' Int. J. Quant. Chem. 2000, 78, 459-479. W.-G. Han, M. Elstner, K.J. Jalkanen, Th. Frauenheim and S. Suhai.
• ''Structures, vibrational absorption and vibrational circular dichroism spectra of L-alanine in aqueous solution: a density functional theory and RHF study,'' Chem. Phys. 2000, 255, 165-194.  K. Frimand, H. Bohr, K.J. Jalkanen, and S. Suhai.
• ''DFT studies on helix formation in N-acetyl-(L-alanyl)n N'-methyl amide for n = 1-20,'' Chem. Phys. 2000, 256, 15-27. M. Elstner, K.J. Jalkanen, M. Knapp-Mohammady, Th. Frauenheim and S. Suhai.
• ''Simulations and analysis of the Raman scattering and differential Raman scattering/Raman optical activity (ROA) spectra of amino acids, peptides and proteins in aqueous solution,'' Vestnik Moskovskogo Universiteta. Khimiya 2000, 41, 4-7. K.J. Jalkanen, R.M. Nieminen and J. Bohr.
• ''Energetics and structure of glycine and alanine based model peptides: Approximate SCC-DFTB, AM1 and PM3 methods in comparison with DFT, HF and MP2 calculations,'' Chem. Phys. 2001, 263, 203-219. M. Elstner, K.J. Jalkanen, M. Knapp-Mohammady, Th. Frauenheim and S. Suhai.
• ''A comparison of aqueous solvent models used in the calculation of the Raman and ROA spectra of L-alanine,'' Chem. Phys. 2001, 265, 125-151. K.J. Jalkanen, R.M. Nieminen, K. Frimand, J. Bohr, H. Bohr, R.C. Wade, E. Tajkhorshid and S. Suhai.
• ''Theoretical determination of the vibrational absorption and Raman spectra of 3-methylindole and 3-methylindole radicals,´´ Chem. Phys. 2001, 265, 13-35. S.W. Bunte, G.M. Jensen, K.L. McNesby, D.B. Goodin, C.F. Chabalowski, R.M. Nieminen, S. Suhai and K.J. Jalkanen.
• ''Neural-network analysis of the vibrational spectra of N-acetyl L-alanyl N'-methyl amide conformational states,'' Phys. Rev. E 2001, 64, 021905-1-13. H.G. Bohr, K. Frimand, K.J. Jalkanen, R.M. Nieminen and S. Suhai.
• ''Applications of neural network prediction of conformational states for small peptides from spectra and of fold classes,'' Computers and Chemistry 2001, 26, 65-77. H.G. Bohr, P. Røgen and K.J. Jalkanen.
• ''SCC-TB, DFT/B3LYP, MP2 and RHF study of ethylene oxide and propylene oxide structures, VA and VCD spectra,'' Chem. Phys. 2002, 279, 161-178. K. Frimand and K.J. Jalkanen.
• ''An analysis the vibrational absorption (VA) and the vibrational circular dichroism (VCD) spectra of isotopomers of L-Alanine in aqueous solution,'' Chem. Phys. 2002, 282, 219-235. S. Abdali, K.J. Jalkanen, R.M. Nieminen, S. Suhai and H.G. Bohr.
• ''A vibrational analysis of various isotopomers of L-Alanyl-L-Alanine in aqueous solution: vibrational absorption (VA), vibrational circular dichroism (VCD), Raman and Raman optical activity (ROA) spectra,'' Int. J. Quant. Chem. 2003, 92, 239-259. K.J. Jalkanen, R.M. Nieminen, M. Knapp-Mohammady and S. Suhai.
• ''Energetics, structures, vibrational frequencies, vibrational absorption, vibrational circular dichroism and Raman intensities of [Leu]enkephalin,'' J. Phys.: Condens. Matter 2003, 15, S1823-S1351. K.J. Jalkanen.
• ''Vibrational absorption spectra, DFT and SCC-DFTB conformational study and analyses of Leu-enkephalin,'' Phys. Chem. Chem. Phys. 2003, 5, 1295-1300. S. Abdali, T.A. Niehaus, K.J. Jalkanen, X. Ciao, L.A. Nafie, Th. Frauenheim, S. Suhai and H. Bohr.
• ''Conformational determination of Leu-enkephalin based on theoretical and
  experimental VA and VCD spectra analyses''  Phys. Chem. Chem. Phys. 2004, 6, 2434-2439. S.Abdali, K.J. Jalkanen, X. Ciao, L.A. Nafie and H. Bohr.
• ''Amino acids and small peptides as building blocks for proteins: comparative theoretical and spectroscopic studies,'' J. Mol. Structure (Theochem) 2004, 675, 61-77. K.J. Jalkanen, M. Elstner and S. Suhai.
• ''Electronic pathways in photoactivated repair of UV mutated DNA,'' Mod. Phys. Lett. B 2005, 19, 473-488. H. Bohr, K.J. Jalkanen and F. Bary Malik.
• ''Linear response properties required to simulate vibrational spectra of biomolecules in various media: (R)-Phenyloxirane,'' Adv. Quantum Chem. 2005, 50, 91-124. doi:10.1016/S0065-3276(05)50006-6 K.J. Jalkanen, V. W. Jürgensen and I.M. Degtyarenko.
• ''Spectrosopic studies of small biomolecules in condensed phases,'' Condensed Matter Theories, 2005, 20, eds. J. W. Clark, R. M. Panoff and H. Li (Nova Science Publishers, Hauppauge, NY), pp. 375-391. H. Bohr and K.J. Jalkanen [Link]
• ''The use of vibrational spectra to study protein and DNA structures, hydration, and binding of biomolecules: a combined theoretical and experimental approach,'' Int. J. Quantum Chem. 106:5 (2006) 1160-1198. doi:10.1002/qua.20863 K.J.Jalkanen, V.W. Jürgensen, A. Claussen, G.M. Jensen, A. Rahim, R.C. Wade, F. Nardi, C. Jung, R.M. Nieminen, I.M. Degtyarenko, F. Herrmann, M.Knapp-Mohammady, T. Niehaus, K. Frimand and S. Suhai.
• ''The VA, VCD, Raman and ROA spectra of tri-L-serine in aqueous solution,'' Physical Biology, 3, 2006, pp S63 - S 79, doi:10.1088/1478-3975/3/1/S07 V. W. Jürgensen and K.J. Jalkanen
• ''Direct Determination of Absolute Configuration of Methyl-Substituted Phenyloxiranes: A Combined Experimental and Theoretical Approach,'' J. Phys. Chem. A 110 (2006) 9123-9129, doi:10.1021/jp060154m. P. Fristrup, P.R. Lassen, C. Johannessen, D. Tanner, P.-O. Norrby, K.J. Jalkanen, and L. Hemmingsen
• ''L-Alanine in a Droplet of Water: A Density-Functional Molecular Dynamics Study,''
  J. Phys. Chem. B 111 (2007) 4227-4234, doi:10.1021/jp0676991. I.M. Degtyarenko, K.J. Jalkanen, A.A. Gurtovenko, and R.M. Nieminen
• ''A Festschrift in Honor of Philip J. Stephens' 65th Birthday,''
  Theor. Chem. Acc. 119 (2008) 1-3. doi:10.1007/s00214-007-0287-5.
  G.M. Jensen and K.J. Jalkanen.
• ''Direct determination of absolute configuration: a vibrational circular dichroism study on dimethyl-substituted phenyloxiranes synthesized by Shi epoxidation,''
  Theor. Chem. Acc. 119 (2008) 133-142. doi:10.1007/s00214-006-0186-1.
  P. Fristrup, P.R. Lassen, D. Tanner and K.J. Jalkanen.
  
• ''A combined theoretical and experimental study of the structure and vibrational absorption, vibrational circular dichroism, Raman and Raman optical activity spectra of the L-histidine zwitterion,''
  Theor. Chem. Acc. 119 (2008) 155-176. doi:10.1007/s00214-007-0276-8.
  E. Deplazes, W. van Bronswijk, F. Zhu, L.D. Barron, L. Ma, L.A. Nafie and K.J. Jalkanen.
• ''A configurational and conformational study of aframodial and its diasteriomers via experimental and theoretical VA and VCD spectroscopies,"
  Theor. Chem. Acc. 119 (2008) 177-190. doi:10.1007/s00214-007-0390-7.
  K.J. Jalkanen, J.D. Gale, P.R. Lassen, L. Hemmingsen, A. Rodarte, I.M. Degtyarenko, R.M. Nieminen, S. Brøgger Christensen, M. Knapp-Mohommady and S. Suhai.
• ''Role of hydration in determining the structure, and vibrational spectra of L-alanine and N-acetyl L-alanine N'-methyl amide in aqueous solution: a combined theoretical and experimental approach,''
  Theor. Chem. Acc. 119 (2008) 191-210. doi:10.1007/s00214-007-0361-z.
  K.J. Jalkanen, I.M. Degtyarenko, R.M. Nieminen, X. Cao, L.A. Nafie, F. Zhu and L.D. Barron.
• "Trans-1,2-dicyano cyclopropane and other cyano cyclopropane derivatives: A theoretical and experimental VA, VCD, Raman and ROA spectroscopic study.,"
  Theor. Chem. Acc. 119 (2008) 211-229. doi:10.1007/s00214-007-0391-6.
  K.J. Jalkanen, J.D. Gale, G.J. Jalkanen, D.F. McIntosh, A.A. El-Azhary, and G.M. Jensen.
• ''Classification of protein fold classes by knot theory and prediction of folds by neural networks: A combined theoretical and experimental approach,''
  Theor. Chem. Acc. 119 (2008) 265-274. doi:10.1007/s00214-007-0285-7.
  K. Ramnarayan, H.G. Bohr and K.J. Jalkanen.
• ''The aqueous and crystalline forms of L-alanine zwitterion,''
  J. Comp. Theor. Nanoscience 5 (2008) 277-285. preprint
  doi:10.1166/jctn.2008.003.
  I.M. Degtyarenko, K.J. Jalkanen, A.A. Gurtovenko and R.M. Nieminen.