Jan Jensen's CV

Curriculum Vitae

JAN HALBORG JENSEN 
Department of Chemistry
University of Copenhagen
Universitetsparken 5
2100 Copenhagen
Denmark
Phone: +45 35 32 02 39
E-mail: jhjensen @ chem.ku.dk
Blog  Group Blog  Twitter  Google+  Youtube  Slideshare
My recent manuscript reviews

EDUCATIONAL AND PROFESSIONAL HISTORY
Professional and Academic Positions 
2011-present: Deputy Head of Department in charge of teaching
2009-present: Professor of Bio-Computational Chemistry, Department of Chemistry, University of Copenhagen
2006-2009: Associate Research Professor/Skou Fellow, Department of Chemistry, University of Copenhagen
2003-2006: Associate Professor of Chemistry and Applied Mathematical & Computational Sciences, University of Iowa
2002-2003: Assistant Professor, Interdisciplinary Graduate Degree Program in Applied Mathematical and Computational Sciences, University of Iowa.
1997-2003: Assistant Professor, Department of Chemistry, University of Iowa,
1996-1997: Postdoctoral Associate, Iowa State University

Higher Education 
1995: Ph.D. in Theoretical Chemistry from Iowa State University, Ames, Iowa.
1989: B. A. (ACS Chemistry Major - Departmental Honors Program, minor in Mathematics) from Concordia College, Moorhead, Minnesota; Magna Cum Laude.

Honors and Professional Activities 
2014 Panelist, Ministry of Higher Education and Science's annual meeting on education
2014 Roundtable discussion on good teaching, Ministry of Higher Education and Science
2013 Teacher of the Year (Årets Harald), University of Copenhagen
2013 A. Tovborg Jensen Award/Bjerrum-Brønsted-Lang Lecturer from the Royal Danish Academy of Science
2013-present, Review Editor Frontiers in Theoretical and Computational Chemistry
2012-present, Editor, Computational Chemistry Highlights
2010 Publication of Molecular Modeling Basics by CRC Press.
2009 Initiated Molecular Modeling Basics blog
2008 Co-organizer, Telluride Workshop on Force Field Development
2006-09 Skou Fellowship, Danish Research Council
2004 Visiting Scientist, Department of Chemistry, University of Copenhagen, Denmark
2004 Ad hoc member, Biodata Management and Analysis NIH Study Section
2004 Co-organizer, Symp. on Quantum/Classical Calculations, Fall National ACS Meeting
2000 Organizer, 33rd Midwest Theoretical Chemistry Meeting, Iowa City
2000 Richard G. Werth Lecturer, Concordia College
1999 Research Innovation Award, Research Corporation

Other Affiliations 

SOFTWARE
My group maintains the following programs (many of these can be downloaded here:https://github.com/jensengroup):
PROPKA: rapid prediction of protein pKa values.
PROPKA GUI: a VMD plugin for visualization of PROPKA results.
BioFET-SIM: a code for modeling signals of nano-BioFET sensors.
FragIt: a code for setting up FMO and EFMO calculations
Molecule Calculator a GUI for rapid calculating molecular properties (for teaching)
My group contributes code to the following programs:
GAMESS: the most widely used non-commercial quantum chemistry program
Avogadro: A GUI for quantum chemistry programs.

BLOGS

SELECT PRESENTATIONS
2014 Keynote speaker, Modelling Molecules and Materials – M3, UK Molecular Graphics and Modelling Society, Glasgow
2013 Invited talk at the 8th Congress of the International Society of Theoretical Chemical Physics, Budapest. Protein structure determination and refinement using QM-derived chemical shifts
2013 Bjerrum-Brønsted-Lang Lecture, University of Copenhagen Quantum biochemistry and the rise of semi-empirical methods and automation in quantum chemistry
Here is a more extensive list of talks

PUBLICATIONS AND CITATIONS
97 peer reviewed publications.
>18,500 citations, H-index of 38 (source: Google Scholar)

A list of publications with citations can be found at my Google Scholar page.
In preparation 
# Jimmy C. Kromann, Anders S. Christensen and Jan H. Jensen "The Fragment Molecular Orbital and Effective Fragment Molecular Orbital implementation of the HF-3c Method" manuscript in preparation.
# Anders S. Christensen, Lars A. Bratholm, Simon Olsson, Thomas Hamelryck, and Jan H. Jensen "Weighting of chemical shift evidence in Monte Carlo simulations of proteins" manuscript in preparation

Submitted 
* Ilke Ugur, Antoine Marion, Jan H. Jensen, and Gerald Monard "Rationalization of the pKa Values of Alcohols and Thiols Using Atomic Change Descriptors and Its Application to the Prediction of Amino acid pKa’s" Journal of Chemical Information and Modeling, submitted.

Publications
2014 
97. Jimmy C. Kromann, Anders S. Christensen, Casper Steinmann, Martin Korth, and Jan H. Jensen "A New Dispersion and Third-Generation Hydrogen Bonding Corrected PM6 Method: PM6-D3H+" PeerJ 2014, 2:e449 accepted. DOI  PeerJ Preprint
96. S. Upadyay, R. Frederiksen, N. Lloret, L. De Vico, P. Krogstrup, J. H. Jensen, K. Martinez, J. Nygård "Indium arsenide nanowire field-effect transistor for pH and biological sensing" Applied Physics Letters 2014,  104, 203504. DOI
95. Jan H. Jensen, Martin Willemöes, Jakob R. Winther, and Luca De Vico, "In silico prediction of mutant HIV-1 proteases cleaving a target sequence" PLoS ONE 2014 9(5): e958333. DOI arXiv
94. Anders S. Christensen, Thomas Hamelryck, and Jan H. Jensen "FragBuilder: An efficient Python library to setup quantum chemistry calculations on peptides models" PeerJ 2014 2:e277 DOI PeerJ PrePrints
93. Anders S. Christensen, Casper Steinmann, Dimitri G. Fedorov, and Jan H. Jensen "Hybrid RHF/MP2 geometry optimizations in the Effective Molecular Orbital Method" PLoS ONE 2014 9(2): e88800 DOI arXiv
2013 
* Martin R. Hediger, Karen L. Martinez, Jesper Nygård, Mads Brandbyge, Jan H. Jensen, Luca De Vico "BioFET-SIM: A Tool for the Analysis and Prediction of Signal Changes in Nanowire-Based Field Effect Transistor Biosensors" Nanoscale Sensors Lecture Notes in Nanoscale Science and Technology Volume 19, 2013, pp 55-86 DOI (not peer reviewed but still worth reading)
92. Anders S. Christensen, Troels E. Linnet, Mikael Borg, Kresten Lindorff-Larsen, Thomas Hamelryck, and Jan H. Jensen "Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics" PLoS ONE, 8(12): e84123 arXiv DOI
91. Martin P. Andersson, Jan H. Jensen and Susan L. S. Stipp "Predicting pKa for proteins using COSMO-RS" PeerJ 2013, 1:e198 DOI.
90. Martin R Hediger, Luca De Vico, Julie B Rannes, Christian Jäckel, Werner Besenmatter, Allan Svendsen, Jan H Jensen "In silico screening of 393 mutants facilitates enzyme engineering of amidase activity in CalB" PeerJ 2013, 1:e145 DOI arXiv
89. Martin R. Hediger, Casper Steinmann, Luca De Vico, Jan H. Jensen "A computational method for the systematic screening of reaction barriers in enzymes: Searching for Bacillus circulans xylanase mutants with greater activity towards a synthetic substrate." PeerJ 2013, 1:e111 DOI.
88. Casper Steinmann, Kristoffer Blædel, Anders S. Christensen, and Jan H. Jensen "Interface of the polarizable continuum model of solvation with semi-empirical methods in the GAMESS program", PLoS ONE 2013,8(7): e67725 DOI
87. Jan H. Jensen and Jimmy C. Kromann "The Molecule Calculator: A web-server for fast quantum mechanics-based estimation of molecular properties" Journal of Chemical Education 2013, 90,1093–1095. DOIarXiv
86. Spencer R. Pruitt, Casper Steinmann, Jan H. Jensen, Mark S. Gordon, "A Fully Integrated Fragment Molecular Orbital/Effective Fragment Potential Method" Journal of Chemical Theory and Computation (2013), 9, 2235–2249. DOI
85. Wouter Boomsma, Jes Frellsen, Tim Harder, Sandro Bottaro, Kristoffer E. Johansson, Pengfei Tian, Kasper Stovgaard, Christian Andreettaη, Simon Olsson, Jan Valentin, Lubomir D. Antonov, Anders S. Christensen, Mikael Borg, Jan H. Jensen, Kresten Lindorff-Larsen, Jesper Ferkinghoff-Borg, and Thomas Hamelryck "PHAISTOS: A Framework for Markov Chain Monte Carlo Simulation and Inference of Protein Structure" Journal of Computational Chemistry 2013, 34, 1697 DOI
84. Casper Steinmann, Dmitri G. Fedorov, Jan H. Jensen "Mapping Enzymatic Catalysis using the Effective Fragment Molecular Orbital Method: Towards all ab initio Biochemistry" PLoS ONE 2013, 8(4): e60602. DOI
83. Noémie Lloret, Rune Frederiksen, Thor C. Møller, Nathalie I. Rieben, Shivendra Upadhyay, Luca De Vico, Jan H. Jensen, Jesper Nygård, Karen L. Martinez "Effects of buffer composition and dilution on nanowire field-effect biosensors" Nanotechnology 2013, 24 035501. DOI
2012 
82. Martin R. Hediger, Luca De Vico, Allan Svendsen, Werner Besenmatter, Jan H. Jensen “A Computational Methodology to Screen Activities of Enzyme Variants” PLoS ONE 2012, 7(12): e49849.DOI arXiv
81. Martin R. Hediger, Jan H. Jensen, and Luca De Vico “BioFET-SIM Web Interface: Implementation and Two Applications” PLoS ONE 2012 7(10): e45379.DOI arXiv
80. Casper Steinmann, Mikael W. Ibsen, Anne S. Hansen, Jan H. Jensen "FragIt: A Tool to Prepare Input Files for Fragment Based Quantum Chemical Calculations" PLoS ONE 2012, 7(9):e44480DOI arXiv
79. Casper Steinmann, Dmitri G. Fedorov, and Jan H. Jensen “The Effective Fragment Molecular Orbital Method for Fragments Connected by Covalent Bonds” PLoS ONE 2012, 7(7):e41117.DOIarXiv
2011 
78. Chresten R. Søndergaard, Mats H. M. Olsson, Michal Rostkowski, and Jan H. Jensen "Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values" Journal of Chemical Theory and Computation 2011, 7, 2284–2295. DOI
77. Anders S. Christensen, Stephan P.A. Sauer, Jan H. Jensen "Definitive benchmark study of ring current effects on amide proton chemical shifts" Journal of Chemical Theory and Computation 2011, 7, 2078–2084. DOI video summary
76. Luca De Vico, Lars Iversen, Martin H. Sørensen, Mads Brandbyge, Jesper Nygård, Karen L. Martinez, Jan H. Jensen "Predicting and rationalizing the effect of surface charge distribution and orientation on nano-wire based FET bio-sensors" Nanoscale 2011, 3, 3635. DOI
75. Michal Rostkowski, Mats HM Olsson, Chresten R Søndergaard and Jan H Jensen "Graphical Analysis of pH-dependent Properties of Proteins predicted using PROPKA" BMC Structural Biology 2011 11:6. DOI.
74. Mats H. M. Olsson, Chresten R. Søndergaard, Michal Rostkowski, and Jan H. Jensen "PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions" Journal of Chemical Theory and Computation 2011, 7, 525-537. DOI.
73. Luca De Vico, Martin H. Sørensen, David M. Rogers, Mads Brandbyge, Brian S. Sørensen, Jesper Nygård, Lars Iversen, Karen L. Martinez and Jan H. Jensen “Quantifying signal changes in nano-wire based biosensors”, Nanoscale 2011, 3, 706-717. DOI.
2010 
72. Casper Steinmann, Dmitri G. Fedorov, and Jan H. Jensen “The Effective Fragment Molecular Orbital Method: A Merger of the Fragment Molecular Orbital and Effective Fragment Potential Methods” Journal of Physical Chemistry A 2010, 114, 8705-8712. DOI
71.Hui Li, Dmitri G. Fedorov, Takashi Nagata, Kazuo Kitaura, Jan H. Jensen, and Mark S. Gordon “Energy Gradients in Combined Fragment Molecular Orbital and Polarizable Continuum Model (FMO/PCM) Calculation”, Journal of Computational Chemistry 2010, 31, 778-790. DOI
70.Daniel D. Kemp, Jamie Rintelman, Mark S. Gordon, Jan H. Jensen “Exchange-repulson between effective fragment potentials and ab initio molecules” Theoretical Chemistry Accounts 2010, 125, 481-491. DOI
2009
69. Dmitri G. Fedorov, Pavel V. Avramov, Jan H. Jensen, and Kazuo Kitaura “Analytic gradient for the adaptive frozen orbital bond detachment in the fragment molecular orbital method” Chemical Physics Letters 2009, 477. 169-175. DOI
68. Jan H. Jensen and Hui Li “Calculation of reduction potentials and pKa values” invited contribution to Computational Inorganic and Bioinorganic Chemistry, Edited by Edward I. Solomon, Robert A. Scott, and R. Bruce King, John Wiley and Sons, Ltd, 2009, 109-122.
2008
67. 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, 11808–11816. DOI
66.Laura L. Parker, Ying-Hua Chung, 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, 14093-14095. DOI
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. DOI
64. 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).
63. Delphine C. Bas, David M. Rogers, and Jan H. Jensen “Very Fast Prediction and Rationalization of pKa Values for Protein-Ligand Complexes”, Proteins: Structure, Function, and Bioinformatics 2008, 73, 765-783. DOI
62. 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. DOI
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. DOI
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. DOI
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. DOI
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. DOI
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. DOI
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. DOI
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. DOI
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. DOI
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. DOI
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. DOI
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. DOI
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. DOI
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, 12005-12011. DOI
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. DOI
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 2006, 27, 976-985. DOI
46. Melissa A. Porter, Jordan R. Hall, James C. Locke, Jan H. Jensen and Pablo A. Molina “Amide proton hydrogen bonds are prime determinants of carboxyl pKa values at N-termini of alpha-helices” Proteins: Structure, Function, and Bioinformatics 2006, 63, 621-635. DOI
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 and 10th most accessed JPCA article, July-September 2005)
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.
2004
42. Mor M. Naor and Jan H. Jensen “The Determinants of Cysteine pKa values in Creatine Kinase and α1-Antitrypsin”, Proteins: Structure, Function, and Bioinformatics 2004, 57, 799-803.
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.
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.
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.
2003
38. Pablo A. Molina, Hui Li, and Jan H. Jensen “Intra-Protein Electrostatics Derived From First Principles: Divide-and-Conquer Approaches for QM/MM Calculations”, Journal of Computational Chemistry 2003, 24, 1971-1979.
37. Pablo A. Molina and Jan H. Jensen “A Predictive Model of Strong Hydrogen Bonding in Proteins: The Nδ1-H-Oδ1 Hydrogen Bond in Low-pH α-Chymotrypsin and α-Lytic Protease” Journal of Physical Chemistry B 2003, 107, 6226-6233.
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.
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.
34. Pablo A. Molina, R. Steven Sikorski, and Jan H. Jensen “NMR Chemical Shifts in the Low-pH Form of α-Chymotrypsin. A QM/MM and ONIOM-NMR Study” Theoretical Chemistry Accounts, 2003, 109, 100-107. Special issue on QM/MM Methods
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.
32. 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.
31. 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.
2001
30. George A. Kraus, N. Zhang, A. Melekhov, Jan H. Jensen “Regiochemical Control by Remote Substituents. A Direct Synthesis of Tetrangulol” SYNLETT 2001, 521-522.
29. Jan H. Jensen “Intermolecular Exchange-Induction and Charge Transfer. Derivation of Approximate Formulas Using on-Orthogonal Localized Molecular Orbitals” Journal of Chemical Physics 2001, 114, 8775-8783.
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.
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.
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.
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.
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.
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 issue.
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.
1998
20.Mark S. Gordon and Jan H. Jensen, “Wavefunctions and Chemical Bonding: Interpretation”, Encyclopedia of Computational Chemistry, Wiley, 1998, 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, 17, 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, 108, 4772-4782.
1996
17. Jan H. Jensen and Mark S. Gordon, “An Approximate Formula for the Intermolecular Pauli Repulsion Between Closed Shell Molecules”, Molecular Physics, 1996, 89, 1313-1325.
16. Mark S. Gordon and Jan H. Jensen, “Understanding the Hydrogen Bond Using Quantum Chemistry”, Accounts of Chemical Research, 1996, 29, 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, 105, 1968-1986.
14. Jan H. Jensen, “Modeling Intermolecular Exchange Integrals Between Non-Orthogonal Molecular Orbitals”, Journal of Chemical Physics, 1996, 104, 7795-7796.
1995
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, 117, 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, 99, 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, 60, 1154-1159.
1994
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, 59, 2219-2222.
7. Jan H. Jensen, Keiji Morokuma, and Mark S. Gordon, “The Decomposition of Ethylene: A Theoretical Study”, Journal of Chemical Physics, 1994, 100, 1981-1987.
1993
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, 14, 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, 115, 5859-5860.
1992
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, 96, 8340-8351.
1991
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, 113, 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, 10, 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, 12, 421-426.
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