Computational Molecular Biophysics
Jan H. Jensen, Research
Associate Professor (Skou Fellow)
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Department of
Chemistry Universitetsparken 5 Other
affiliations: Nano-Science Center |
E-mail: jhjensen@kemi.ku.dk |
Research in the Jensen group is in the area
of computational molecular biophysics
- at the intersection of molecular physics, quantum chemistry, and structural
biology and structural bioinformatics.
Our work involves, in roughly equal parts, theory/algorithm development and
computational modeling of protein chemistry.
[CV] [Research] [group members] [publications]
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A more up-to date description of research can be found here
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Theory and Algorithm Development Much of our work
is based on the I am also
“consulting” a little on a GUI to GAMESS called Avogadro |
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Protein pKa Prediction The chemistry of
biomolecules is intimately tied to their protonation states and, therefore,
to the pKa's of the ionizable functional groups in the molecules. We have developed
a QM/MM based methodology for the prediction of pKa's of ionizable
groups in proteins The QM/MM studies
have lead to quantitative structure/activity relationships which forms the
basis of our PROPKA program |
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NMR Chemical Shifts in Proteins NMR chemical
shifts provide a powerful experimental probe of hydrogen bonding within
proteins We have developed
a computational methodology for the accurate prediction of proton chemical
shifts in proteins We are using the
method to rationalize unusual NMR chemical shifts in proteins |
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Drug Design Inhibitors of certain
serine proteases are proven antitumor agents, and we are extending the
computational methodology for pKa predictions to the calculation
of inhibition constants, in order to aid the design for more potent and
selective drugs |
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Redox Potentials The redox
potential is a reflection of the electronic structure of the transition metal
atom, which in turn is influenced by the nature of the ligands and the
protein environment in a way that is not well understood. QM/MM methods
offer a unique opportunity to study redox potentials from first principles
and derive quantitative structure/activity rules governing redox potentials
in proteins. |
2008
67. Laura L. Parker,
Claudio J. Margulis, and Jan H. Jensen “Rationalization of the Difference in
Lifetime of Two Covalent Sialosyl-Enzyme Intermediates in Trypanosoma
rangeli Sialidase”,
Journal of Physical Chemistry B 2008, 112, 11808-11816.
66.Dmitri G. Fedorov,
Jan H, Jensen, Ramesh C. Deka, Kazuo Kitaura “Covalent bond fragmentation
suitable to describe surfaces in the fragment molecular orbital method” Journal
of Physical Chemistry A 2008, 112, 14093-14095
65. Annette Langkilde, Søren M. Kristensen, Leila Lo Leggio, Anne
Mølgaard, Jan H. Jensen, Andrew R. Houk, Jens-Christian Navarro Poulsen, Sakari
Kauppinen, and Sine Larsen “Short hydrogen bonds in
proteins: A case study of Rhamnogalacturonan acetylesterase” Acta
Crystallographica Section D 2008, 64, 851-863.
64. Aleksander Cehovin, Hector Mera, Jan H. Jensen, Kurt Stokbro
and Thomas B. Pedersen “Role
of the virtual orbitals and HOMO-LUMO gap in mean-field approximations to the
conductance of molecular junctions”, Physical Review B 2008, 77, 195432.
63. Jan H, Jensen “Calculating
pH and salt dependence of protein-protein binding” Current
Pharmaceutical Biotechnology, 2008, 9, 96-102. (Invited
contribution: special issue on protein-protein and protein-membrane
interactions.)
62. Delphine C. Bas, David M. Rogers, and Jan H. Jensen “Very fast prediction and
rationalization of pKa values of protein-ligand complexes” Proteins:
Structure, Function, and Bioinformatics 2008,73, 765-783.
61. Aaron C. Mason and Jan H. Jensen “Protein-Protein binding is often associated with changes in protonation state” Proteins: Structure, Function, and Bioinformatics 2008, 71, 81-91.
2007
60. Jonas Baltrusaitis, Jennifer D.
Schuttlefield, Elizabeth Zeitler, Jan H. Jensen and Vicki H. Grassian “Surface Reactions of Carbon Dioxide
at the Adsorbed Water – Oxide Interface” Journal of Physical Chemistry C 2007, 111, 14870-14880.
59. Jacob Kongsted, Ulf Ryde, James
Wydra, and Jan H. Jensen “Prediction
and rationalization of the pH-dependence of activity and stability of family 11
xylanases” Biochemistry 2007, 46, 13581-13592.
58. Jonas Baltrusaitis, Jennifer
Schuttelfield, Jan H. Jensen, and Vicki H. Grassian “FTIR Spectroscopy Combined with
Quantum Chemical Calculations to Investigate Adsorbed Nitrate on Aluminum Oxide
Surfaces in the Presence and Absence of Co-Adsorbed Water” Physical
Chemistry Chemical Physics 2007, 9, 4970-4981.
57. Junchao
Xia, Ryan P. Daly, Feng-Chuan Chuang, Laura L. Parker, Jan H. Jensen, and
Claudio J. Margulis “Sugar
folding: A novel structural prediction tool for oligosaccharides and
polysaccharides II” Journal of Chemical Theory and Computation
2007, 3, 1629-1643.
56. Junchao Xia, Ryan P. Daly, Feng-Chuan Chuang, Laura L.
Parker, Jan H. Jensen, and Claudio J. Margulis “Sugar folding: A novel structural
prediction tool for oligosaccharides and polysaccharides I” Journal of
Chemical Theory and Computation 2007, 3, 1620-1628.
55. Todd J. Dolinsky, Paul Czodrowski, Hui Li, Jan H. Jensen,
Jens E. Nielsen, Gerhard Klebe, Nathan A. Baker “PDB2PQR: Expanding and upgrading automated preparation of
biomolecular structures for molecular simulations”, Nucleic Acid
Research,
2007, 35, W522-W525.
54.Mark S. Gordon, Lyuda Slipchenko, Hui Li, and Jan H. Jensen “The effective fragment
potential: a general method for predicting intermolecular interactions” Annual
Reports in Computational Chemistry 3, 177-193, 2007.
2006
53. Pan-Fen Wang, Allen J. Flynn, Mor M. Naor, Jan H.
Jensen, Guanglei Cui, Kenneth M. Merz, Jr., George L. Kenyon and Michael J.
McLeish "Exploring the Role
of the Active Site Cysteine in Human Muscle Creatine Kinase" Biochemistry 2006, 45, 11464-11472.
Michael E. Colvin, Christopher J. Cramer, Clifford E. Dykstra,
Jan H. Jensen, Samuel Krimm, Jean-Louis Rivail, Ajit J. Thakkar, and Manuel
Yanez "Molecular
Quantum Mechanics to Biodynamics: Essential Connections" THEOCHEM
2006, 764, 1-8. (Viewpoint Article; Non-reviewed but still worth reading)
52. Laura L. Parker, Andrew R. Houk, and Jan H. Jensen "Cooperative Hydrogen Bonding Effects
are Key Determinants of Backbone Amide Proton Chemical Shifts in Proteins"
Journal of the American Chemical Society 2006, 128, 9863-9872.
51. Baoyu Hong, Majd Haddad, Frank
Maley, Jan H. Jensen, Amnon Kohen "Hydride transfer vs hydrogen radical
transfer in thymidylate synthase" Journal of the American Chemical
Society 2006, 128,
5636-5637.
50. Hui Li, Mark S. Gordon, and Jan
H. Jensen "Charge transfer
interactions in the effective fragment potential method", Journal
of Chemical Physics
2006, 124, 214108.
49. Jonas Baltrusaitis, Jan H.
Jensen, and Vicki H. Grassian "FTIR Spectroscopy Combined with
Isotope Labeling and Quantum Chemical Calculations to Investigate Bicarbonate
Formation Following Reaction of Carbon Dioxide with Surface Hydroxyl Groups on
Fe2O3 and Al2O3" Journal
of Physical Chemistry B 2006,
110, 12005-16.
48. Nathan Powers and Jan H. Jensen
"Chemically Accurate
Protein Structures: Validation of Protein NMR Structures by Comparison of
Measured and Predicted pKa Values" Journal of
Biomolecular NMR
2006, 35, 39-51.
(Recommended on Facultyof1000.)
47. Dmitri Fedorov, Katzuo Kitaura,
Hui Li, Jan H. Jensen, and Mark S. Gordon "The polarizable continuum model
(PCM) combined with the fragment molecular orbital method (FMO) " Journal
of Computational Chemistry, 27, 976-985.
46.
Melissa A. Porter, Jordan R. Hall, James C. Locke, Jan H. Jensen and Pablo A.
Molina "Amide Backbone
Interactions are the Prime Determinants of Carboxyl pKa Values at N-termini of
alpha-helices" Proteins: Structure, Function, and Bioinformatics, 63, 621 - 635.
2005
45. George A. Kraus, Ning Zhang,
Jingqiang Wei, and Jan H. Jensen "Regiochemical Control by Remote
Substituents. A Selective Synthesis of Angularly-Fused Ring Systems" European
Journal of Organic Chemistry 2005, 3040-3044.
44. Jan H. Jensen, Hui Li. Andrew D.
Robertson, and Pablo A. Molina "Prediction and Rationalization of Protein
pKa Values Using QM and QM/MM Methods", Journal of Physical Chemistry A 2005, 109, 6634-6643 (invited
Feature Article; 10th most accessed JPCA article July-Sept, 2005).
PDF
43. Hui Li, Andrew D. Robertson, and Jan H. Jensen "Very Fast Structure-Based Prediction and
Rationalization of Protein pKa Values" Proteins: Structure, Function, and Bioinformatics 2005, 61, 704-721. PDF.
2004
42. Mor M.
Naor and Jan H. Jensen "The Determinants of Cysteine pKa values in
Creatine Kinase and a1-Antitrypsin", Proteins: Structure, Function, and
Bioinformatics 2004, 57, 799-803.
PDF
41. Hui Li
and Jan H. Jensen "Improving the Accuracy and Efficiency of Geometry
Optimizations with the Polarizable Continuum Model: New Energy Gradients and
Molecular Surface Tesselation", Journal of Computational Chemistry, 2004, 25,
1449-1462. PDF
40. Hui
Li, Simon P. Webb, Joseph Ivanic, and Jan H. Jensen "The Determinants of
the Relative Reduction Potentials of Type-1 Copper Sites in Proteins" Journal
of the American Chemical Society 2004, 126, 8010-8019. PDF
39. Hui
Li, Andrew D. Robertson, and Jan H. Jensen "The Determinants of Carboxyl
pKa Values in Turkey Ovomucoid Third Domain" Proteins: Structure,
Function, and Bioinformatics, 2004, 55, 689-704. PDF (Recommended on Facultyof1000.)
2003
38. Pablo
A. Molina, Hui Li, and Jan H. Jensen "Intra-Protein Electrostatics From
First Principles: Divide-and-Conquer Methods for QM/MM Calculations" Journal
of Computational Chemistry, 2003, 24, 1971-1979. PDF
37. Pablo
A. Molina and Jan H. Jensen "A Predictive Model of Strong Hydrogen Bonding
in Proteins: The Nd1-H-Od1 Hydrogen Bond in Low-pH
a-Chymotrypsin and a-Lytic
Protease" Journal of Physical Chemistry B 2003, 107,
6226-6233. PDF
36.
Jui-Hsien Huang, Jeffrey J. Luci, Ting-Yu Lee, Dale C. Swenson, Jan H. Jensen,
and Louis Messerle "A Planar Tetracoordinate Carbon and Unusual Bonding in
an Organodimetallic Propynylidene Complex Arising from Double C-H Activation of
an Allene Ligand" Journal of the American Chemical Society 2003, 125,
1688-1689. PDF
35. Hui
Li, Christian S. Pomelli, and Jan H. Jensen "Continuum Solvation of Large
Molecules Described by QM/MM: Semi-Iterative Implementation of the PCM/EFP
Interface", Theoretical Chemistry Accounts 2003, 109, 71-84. PDF
34. Pablo
A. Molina, R. Steven Sikorski, and Jan H. Jensen, "NMR Chemical Shifts in
the Low-pH Form of a-Chymotrypsin. A QM/MM and ONIOM-NMR Study" Theoretical
Chemistry Accounts 2003, 109, 100-107. Special issue on QM/MM methods. PDF
2002
33. Amnon
Kohen and Jan H. Jensen "Secondary Swain-Schaad Relations as an Indication
for Tunneling in Enzymatic Reactions" Journal of the American Chemical Society 2002, 124,
3858-3864. PDF
32. Hui Li
and Jan H. Jensen "Partial Hessian Vibrational Analysis: the Localization
of the Molecular Vibrational Energy and Entropy" Theoretical Chemistry
Accounts 2002, 107, 211-219. PDF
31. Hui
Li, Alexander Hains, Joshua Everts, Andrew D. Robertson, and Jan H. Jensen
"The Prediction of Protein pKa's Using QM/MM: The pKa of Lysine 55 in
Turkey Ovomucoid Third Domain" Journal of Physical Chemistry B 2002,106, 3486
-3494.
PDF
2001
30. George
A. Kraus, N. Zhang, A. Melekhov, Jan H. Jensen "Regiochemical Control by
Remote Substituents. A Direct Synthesis of Tetrangulol" SYNLETT 2001,
pages 521-522.
29. Jan H.
Jensen "Intermolecular Exchange-Induction and Charge Transfer. Derivation
of Approximate Formulas Using Non-Orthogonal Localized Molecular Orbitals"
Journal of Chemical Physics 2001, 114, 8775-8783. PDF
28. Ryan
M. Minikis, Visvaldas Kairys, and Jan H. Jensen "Effect of Intra-Protein
Electrostatics Derived From First Principles: An Effective Fragment Potential
Method Study of the Proton Affinity of Lysine 55 and Tyrosine 20 in Turkey
Ovomucoid Third Domain" Journal of Physical Chemistry A 2001,105, 3829-3827. PDF
27. Mark
S. Gordon, Mark Freitag, Pradipta Bandyopadhyay, Jan H. Jensen, Visvaldas
Kairys, and Walter J. Stevens, "The Effective Fragment Potential Method: A
QM-based Approach to Modeling Environmental Effects in Chemistry," Journal
of Physical Chemistry A 2001, 105, 293-307. PDF
2000
26. Lynne
C. Remer and Jan H. Jensen, "Towards a General Theory of Hydrogen Bonding:
The Short, Strong Hydrogen Bond [HOH···OH]-", Journal of Physical
Chemistry A 2000, 104, 9266-9275. PDF
25.
Visvaldas Kairys and Jan H. Jensen, "QM/MM Boundaries Across Covalent
Bonds: A Frozen LMO Based Approach for the Effective Fragment Potential
Method," Journal of Physical Chemistry A 2000, 104,
6656-6665.
PDF
24. Mark
A. Freitag, Mark S. Gordon, Jan H. Jensen, and Walter J. Stevens
"Evaluation of Charge Penetration Between Distributed Multipolar
Expansions," Journal of Chemical Physics 2000, 112,
7300-7306. PDF
23. Ryan
M. Minikis and Jan H. Jensen, "Towards a General Theory of Hydrogen
Bonding: A Study of Hydrogen Bonds Involving H2O and HF", International
Journal of Quantum Chemistry 2000, 76, 341-358. Invited contribution
to the Klaus Ruedenberg honorary volumes. PDF
22. Mark
S. Gordon and Jan H. Jensen, "Perspective on "The Physical Nature of
the Chemical Bond" Ruedenberg K (1962) Rev Mod Phys 34: 326-376", Theoretical
Chemistry Accounts 2000, 103, 248-251.
1999
21.
Visvaldas Kairys and Jan H. Jensen, "Evaluation of the Charge Penetration
Energy Between Non-Orthogonal Molecular Orbitals Using the Spherical Gaussian
Overlap Approximation," Chemical Physics Letters 1999, 315,
140-144.
PDF
Graduate
and Postdoctoral Work
20. Mark
S. Gordon and Jan H. Jensen, "Wavefunctions and Chemical Bonding:
Interpretation", Encyclopedia of Computational Chemistry, Wiley, 1998,
pages 3198-3214. Selected for publication in Handbook of Molecular Physics and
Quantum Chemistry, 2003.
19.
Josemon Jacob, James H. Espenson, Jan H. Jensen, and Mark S. Gordon,
"1,3-Transposition of Allylic Alcohols Catalyzed by Methylrhenium
Trioxide", Organometallics, 1998, volume 17, pages 1835-1840.
18. Jan H.
Jensen and Mark S. Gordon, "An Approximate Formula for the Intermolecular
Pauli Repulsion Between Closed Shell Molecules II. Application to the Effective
Fragment Potential Method", Journal of Chemical Physics, 1998, volume 108,
pages 4772-4782.
17. Jan H.
Jensen and Mark S. Gordon, "An Approximate Formula for the Intermolecular
Pauli Repulsion Between Closed Shell Molecules", Molecular Physics, 1996,
volume 89, pages 1313-1325.
16. Mark
S. Gordon and Jan H. Jensen, "Understanding the Hydrogen Bond Using
Quantum Chemistry", Accounts of Chemical Research, 1996, volume 29, pages
536-543.
15. Paul
N. Day, Jan H. Jensen, Mark. S. Gordon, Simon P. Webb, Walter J. Stevens, David
R. Garmer, Harold Basch, and Drora Cohen, "An Effective Fragment Method
for Modeling Solvent Effects in Quantum Mechanical Calculations", Journal
of Chemical Physics, 1996, volume 105, pages 1968-1986.
14. Jan H.
Jensen, "Modeling Intermolecular Exchange Integrals Between Non-Orthogonal
Molecular Orbitals", Journal of Chemical Physics, 1996, volume 104, pages
7795-7796.
13. Jan H.
Jensen and Mark S. Gordon, "On the Number of Water Molecules Necessary to
Stabilize the Glycine Zwitterion", Journal of the American Chemical
Society, 1995, volume 117, pages 8159-8170.
12. Jan H.
Jensen and Mark S. Gordon, "Ab Initio Localized Charge Distributions:
Theory and a Detailed Analysis of the Water Dimer-Hydrogen Bond", Journal
of Physical Chemistry, 1995, volume 99, pages 8091-8107.
11. Kim K.
Baldridge, Jan H. Jensen, Nikita Matsunaga, Michael W. Schmidt, Mark S. Gordon,
Theresa L. Windus, Jerry A. Boatz, Thomas R. Cundari, "Applications of
Parallel GAMESS", ACS Symposium Series 592, American Chemical Society,
Washington, D.C., 1995. Chapter 3.
10. George
A. Kraus, Jun Li, Mark S. Gordon, and Jan H. Jensen, "Direct Total
Syntheses of Frenolicin B and Kalafungin via Highly Regioselective Diels-Alder
Reactions", Journal of Organic Chemistry, 1995, volume 60, pages
1154-1159.
9. Jan H.
Jensen, Paul N. Day, Mark S. Gordon, Harold Basch, Drora Cohen, David R.
Garmer, Morris Kraus, and Walter J. Stevens, "An Effective Fragment Method
for Modeling Intermolecular Hydrogen Bonding-Effects on Quantum Mechanical
Calculations", In Modeling the Hydrogen Bond, D. A. Smith, Ed. ACS
Symposium Series 569, American Chemical Society, Washington, D.C., 1994.
Chapter 9.
8. George
A. Kraus, Jun Li, Mark S. Gordon, and Jan H. Jensen, "Regiocontrol by
Remote Substituents. A Direct Total Synthesis of Racemic Hongconin", Journal
of Organic Chemistry, 1994, volume 59, pages 2219-2222.
7. Jan H.
Jensen, Keiji Morokuma, and Mark S. Gordon, "The Decomposition of
Ethylene: A Theoretical Study", Journal of Chemical Physics, 1994, volume
100, pages 1981-1987.
6. Michael
W. Schmidt, Kim K. Baldridge, Jerry A. Boatz, Steven T. Elbert, Mark S. Gordon,
Jan H. Jensen, Shiro Koseki, Nikita Matsunaga, Kiet A. Nguyen, Shujun Su,
Theresa L. Windus, Michel Dupuis, and John A. Montgomery, "The General
Atomic and Molecular Electronic Structure System", Journal of
Computational Chemistry, 1993, volume 14, pages 1347-1363.
5. George
A. Kraus, Jun Li, Mark S. Gordon, and Jan H. Jensen, "Regiocontrol by
Remote Substituents. An Enantioselective Total Synthesis of Frenolicin B via a
Highly Regioselective Diels-Alder Reaction", Journal of the American
Chemical Society, 1993, volume 115, pages 5859-5860.
4. Jan H.
Jensen, Kim K. Baldridge, and Mark S. Gordon, "The Uncatalyzed Peptide
Bond Formation in the Gas Phase", Journal of Physical Chemistry, 1992,
volume 96, pages 8340-8351.
3. Jan H.
Jensen and Mark S. Gordon, "The Conformational Potential Energy Surface of
Glycine: A Theoretical Study", Journal of the American Chemical Society,
1991, volume 113, pages 7917-7924.
2. Mark S.
Gordon, Marshall T. Carroll, Jan H. Jensen, Larry P. Davis, Larry W. Burggraf
and R. Martin Guidry, "The Nature of the Si-N Bond in Silatranes",
Organometallics, 1991, volume 10, pages 2657-2660.
1. Jan H.
Jensen and Mark S. Gordon, "Splicing I: Using Mixed Basis Sets in Ab Initio
Calculations", Journal of Computational Chemistry, 1991, volume 12, pages
421-426.