Curriculum Vitae
JAN HALBORG JENSEN
JAN HALBORG JENSEN
Department of Chemistry
University of Copenhagen
Universitetsparken 5
2100 Copenhagen
Denmark
E-mail: jhjensen @ chem.ku.dk
University of Copenhagen
Universitetsparken 5
2100 Copenhagen
Denmark
E-mail: jhjensen @ chem.ku.dk
EDUCATIONAL AND PROFESSIONAL HISTORY
Professional and Academic Positions
Professional and Academic Positions
2009-present: Professor of Computational Chemistry, Department of Chemistry, University of Copenhagen
2011-2018: Deputy Head of Department in charge of teaching
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
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.
1989: B. A. (ACS Chemistry Major - Departmental Honors Program, minor in Mathematics) from Concordia College, Moorhead, Minnesota; Magna Cum Laude.
Other Affiliations
2022- Advisory Board Digital Discovery
2022- Editor-in-Chief PeerJ Physical Chemistry
2021- Editorial Board and Advisory Board, SciPost Chemistry
2019-2022 Editoral Board, PeerJ Physical Chemistry
2018- Scientific Advisory Board, ChemRxiv
2015 Co-organizer, 3rd Danish Protein Molecular Modellers Meeting
2015-2019 Educational Advisor, Department of Chemistry, Oslo University
2019-2022 Editoral Board, PeerJ Physical Chemistry
2018- Scientific Advisory Board, ChemRxiv
2015 Co-organizer, 3rd Danish Protein Molecular Modellers Meeting
2015-2019 Educational Advisor, Department of Chemistry, Oslo University
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
2013-2015, 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
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
2013-2015, 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
SELECT PRESENTATIONS
Invited speaker at numerous symposia or workshops and departmental seminars in North America, Europe, and Asia. Select recent or future presentations:2024 SCQC 2024 Scandinavian Community for Quantum Chemistry, DK
2023 Critical assessment of molecular machine learning workshop [ML4Molecules] (Keynote)
2023 Novo Nordisk, Måløv, DK
2022 Molecular Modeling and Drug Discovery Seminar Series, Montreal, CA
2022 RSC meeting on Ultra-Large Libraries, UK
PUBLICATIONS AND CITATIONS
131 peer reviewed publications.
>44,000 citations, H-index of 55 (source: Google Scholar)
ORCID: 0000-0002-1465-1010
131 peer reviewed publications.
>44,000 citations, H-index of 55 (source: Google Scholar)
ORCID: 0000-0002-1465-1010
Publications
2024
131. Julius Seumer and Jan H. Jensen "Beyond Predefined Ligand Libraries: A Genetic Algorithm Approach for De Novo Discovery of Catalysts for the Suzuki Coupling Reactions" PeerJ Physical Chemistry 2024, accepted. Preprint
130 Fengling Li et al. "CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson’s Disease Associated Protein" Journal of Chemical Information and Modeling 2024 Preprint DOI
129. Rasmus M. Borup, Nicolai Ree, Jan H. Jensen "pKalculator: A pKa predictor for CH bonds" Beilstein Journal of Organic Chemistry 2024, 20, 1614–1622. Preprint DOI
128. Magnus Strandgaard, Julius Seumer, Jan H. Jensen "Discovery of molybdenum based nitrogen fixation catalysts with genetic algorithms", Chemical Science 2024, 15, 10638 - 10650. Preprint DOI
127. Nicolai Ree, Andreas H. Göller, Jan H. Jensen Automated Quantum Chemistry for Estimating Nucleophilicity and Electrophilicity with Applications to Retrosynthesis and Covalent Inhibitors. Digital Discovery 2024, 3, 347–354. Preprint DOI
2023
126. Maria H. Rasmussen, Chenru Duan, Heather J. Kulik, and Jan H. Jensen "Uncertain of uncertainties? A comparison of uncertainty quantification metrics for chemical data sets" Journal of Cheminformatics 2023, 15:121. Preprint DOI
125. Magnus Strandgaard, Julius Seumer, Bardi Benediktsson, Arghya Bhowmik, Tejs Vegge, and Jan H. Jensen "Genetic algorithm-based re-optimization of the Schrock catalyst for dinitrogen fixation" PeerJ Physical Chemistry 2023, 5:e30. Preprint DOI
124. Maria H. Rasmussen, Julius Seumer, and Jan H. Jensen "Toward De Novo Catalyst Discovery: Fast Identification of New Catalyst Candidates for Alcohol-Mediated Morita-Baylis-Hillman Reactions" Angew. Chem., Int. Ed. 2023, 62, e202310580. Preprint DOI
123. Maria H. Rasmussen, Diana S. Christensen, Jan H. Jensen "Do machines dream of atoms? Crippen's logP as a quantitative molecular benchmark for explainable AI heatmaps" SciPost Chemistry 2023, 2, 002. Preprint DOI
122. Julius Seumer, Jonathan K.S. Hansen, Mogens Brøndsted Nielsen, Jan H. Jensen "Computational evolution of new catalysts for the Morita–Baylis–Hillman reaction", Angew. Chem., Int. Ed. 2023, 62, e202218565. Preprint DOI
2022
121. Nicolai Ree, Andreas Göller, Jan H. Jensen "What the Heck? – Automated regioselectivity calculations of palladium-catalyzed Heck reactions using quantum chemistry", ACS Omega 2022, 7, 49, 45617–45623. Preprint. DOI
120. Marc Garner, Mads Koerstz, Jan H. Jensen, Gemma C. Solomon "Substituent Control of σ-interference Effects in the Transmission of Saturated Molecules" ACS Physical Chemistry Au 2022 2, 4, 282–288. Preprint. DOI
119. Oliver Christensen, Rasmus Schlosser, Rasmus Nielsen, Jes Johannes, Mads Koerstz, Jan H. Jensen, Kurt V. Mikkelsen "A Neural Network Approach for Property Determination of Molecular Solar Cell Candidates" Journal of Physical Chemistry A 2022, 126, 1681-1688. DOI
118. Maria H. Rasmussen and Jan H. Jensen " Fast and automated identification of reactions with low barriers using meta-MD simulations" PeerJ Physical Chemistry 2022, 4:e22. DOI Preprint
117. Nicolai Ree, Andreas Göller, Jan H. Jensen "RegioML: Predicting the regioselectivity of electrophilic aromatic substitution reactions using machine learning" Digital Discovery 2022, 1, 108-114. DOI Preprint
2021
116. Nicolai Ree, Mads Koerstz, Kurt Mikkelsen, and Jan H. Jensen "Virtual screening of norbornadiene-based molecular solar thermal energy storage systems using a genetic algorithm" Journal of Chemical Physics 2021, 155, 184105. Preprint DOI
115. Mads Koerstz, Maria H. Rasmussen, Jan H. Jensen "Fast and automated identification of reactions with low barriers: the decomposition of 3-hydroperoxypropanal" SciPost Chemistry 2021, 1, 003. Preprint DOI
114. Casper Steinmann and Jan H. Jensen "Using a genetic algorithm to find molecules with good docking scores" PeerJ Physical Chemistry 2021, 3:e18 Preprint DOI
113. Nicolai Ree, Andreas Göller, Jan H. Jensen "RegioSQM20: Improved prediction of the regioselectivity of electrophilic aromatic substitutions" Journal of Cheminformatics 2021, 13:10. Preprint DOI
112. Mads Koerstz, Anders S. Christensen, Kurt V. Mikkelsen, Mogens B. Nielsen, Jan H. Jensen “High throughput virtual screening of 230 billion molecular solar heat battery candidates” PeerJ Physical Chemistry 2021, 3:e16. Preprint DOI
2020
111. Maria H. Rasmussen and Jan H. Jensen "Fast and automatic estimation of transition state structures using tight binding quantum chemical calculations" PeerJ Physical Chemistry 2020 2:e15. Preprint DOI
110. Emilie S. Henault, Maria H. Rasmussen, Jan H. Jensen Chemical space exploration: how genetic algorithms find the needle in the haystack PeerJ Physical Chemistry 2020 2:e11 Preprint DOI
2019
109. Jan H. Jensen "Graph-based genetic algorithm and generative model/Monte Carlo tree search for the exploration of chemical space" Chemical Science 2019, 10, 3567-3572 Preprint DOI
2018
108. Marc H. Garner, Mads Koerstz, Jan H. Jensen, and Gemma C. Solomon "The Bicyclo[2.2.2]octane Motif: A Class of Saturated Group 14 Quantum Interference Based Single-Molecule Insulators" Journal of Physical Chemistry Letters 2018, 9, 6941–6947. Preprint DOI
107. Jimmy Kromann, Casper Steinmann, and Jan H. Jensen "Improving Solvation Energy Predictions Using The SMD Solvation Method and Semiempirical Electronic Structure Methods" Journal of Chemical Physics 2018, 149, 104102. Preprint DOI
106. Dmitri G. Fedorov, Jimmy C. Kromann, Jan H. Jensen "Empirical corrections and pair interaction energies in the fragment molecular orbital method" Chemical Physics Letters 2018, 706, 328–333. Preprint DOI.
105. Jimmy C. Kromann, Anders S. Christensen, Alexander Welford, and Jan H. Jensen "Random Versus Systematic Errors in Reaction Enthalpies Computed Using Semiempirical and Minimal Basis Set Methods" ACS Omega 2018, 3, 4372–4377 Preprint DOI
104. Jimmy C. Kromann, Jan H. Jensen, Monika Kruszyk, Mikkel Jessing, and Morten Jørgensen "Fast and Accurate Prediction of the Regioselectivity of Electrophilic Aromatic Substitution Reactions" Chemical Science 2018, 9, 660–665. Preprint DOI
2017
103. Anders Christensen, Jimmy Kromann, Jan Jensen, and Qiang Cui "Intermolecular Interactions in the Condensed Phase: Evaluation of Semi-empirical Quantum Mechanical Methods" Journal of Chemical Physics 2017, 147, 161704. DOI
102. Jan H. Jensen, Christopher J. Swain, and Lars Olsen "Prediction of pKa values for drug-like molecules using semiempirical quantum chemical methods" Journal of Physical Chemistry A 2017, 121, 699–707. Preprint Data DOI
* Jan H. Jensen "Which method is more accurate? or errors have error bars" PeerJ Preprints 2017 5:e2693v1 DOI
101. Lars A. Bratholm and Jan H. Jensen "Protein Structure Refinement using a Quantum Mechanics-Based Chemical Shielding Predictor" Chemical Science 2017, 8, 2061–2072 Preprint Data DOI
2016
100. Jimmy C. Kromann, Frej A. N. Larsen, Hadeel Moustafa, and Jan H. Jensen "Prediction of pKa Values Using the PM6 Semiempirical Method" PeerJ 2016, 4:e2335. DOI Preprint data
99. Jimmy C. Kromann, Anders S. Christensen, Qiang Cui, and Jan H. Jensen "Towards a barrier height benchmark set for biologically relevant systems" PeerJ 2016, 4:e1994 DOI data Preprint
2015
* Jan H. Jensen "High Througput pKa Prediction Using Semi Empirical Methods" A proposal submitted to the Danish NSF (FTP). arXiv
98. Anders S. Larsen, Lars A. Bratholm, Anders S. Christensen, Maher Channir, and Jan H. Jensen "ProCS15: A DFT-based chemical shift predictor for backbone and Cβ atoms in proteins" PeerJ, 3:e1344 Preprint DOI code data
* Jan H. Jensen "My flipped classroom: what I did and how I did it" in Universitetspædagogiske praksisser, Peter Stray Jørgensen (red.) og Lotte Rienecker (red.) Samfundslitteratur, 2015 pg 157-174. Preprint (not peer reviewed but still worth reading).
97. Jan H. Jensen "Predicting accurate absolute binding energies in aqueous solution: thermodynamic considerations for electronic structure methods" PCCP 2015, 17, 12441-12451. DOI arXiv
96. Søs Torpenholt, Leonardo De Maria, Mats H. M. Olsson, Lars H. Christensen, Michael Skjøt, Peter Westh, Jan H. Jensen and Leila Lo Leggio "Effect of mutations on the thermostability of Aspergillus aculeatus β-1,4-galactanase" Computational and Structural Biotechnology Journal 2015, 13, 256–264. DOI
95. Lars A. Bratholm, Anders S. Christensen, Thomas Hamelryck, and Jan H. Jensen "Bayesian inference of protein structure from chemical shift data" PeerJ 2015, 3:e861. Preprint DOI
2014
94. 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 2014, 54, 2200-2013. DOI
93. 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. DOI PeerJ Preprint
92. 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
91. 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
2019
109. Jan H. Jensen "Graph-based genetic algorithm and generative model/Monte Carlo tree search for the exploration of chemical space" Chemical Science 2019, 10, 3567-3572 Preprint DOI
2018
108. Marc H. Garner, Mads Koerstz, Jan H. Jensen, and Gemma C. Solomon "The Bicyclo[2.2.2]octane Motif: A Class of Saturated Group 14 Quantum Interference Based Single-Molecule Insulators" Journal of Physical Chemistry Letters 2018, 9, 6941–6947. Preprint DOI
107. Jimmy Kromann, Casper Steinmann, and Jan H. Jensen "Improving Solvation Energy Predictions Using The SMD Solvation Method and Semiempirical Electronic Structure Methods" Journal of Chemical Physics 2018, 149, 104102. Preprint DOI
106. Dmitri G. Fedorov, Jimmy C. Kromann, Jan H. Jensen "Empirical corrections and pair interaction energies in the fragment molecular orbital method" Chemical Physics Letters 2018, 706, 328–333. Preprint DOI.
105. Jimmy C. Kromann, Anders S. Christensen, Alexander Welford, and Jan H. Jensen "Random Versus Systematic Errors in Reaction Enthalpies Computed Using Semiempirical and Minimal Basis Set Methods" ACS Omega 2018, 3, 4372–4377 Preprint DOI
104. Jimmy C. Kromann, Jan H. Jensen, Monika Kruszyk, Mikkel Jessing, and Morten Jørgensen "Fast and Accurate Prediction of the Regioselectivity of Electrophilic Aromatic Substitution Reactions" Chemical Science 2018, 9, 660–665. Preprint DOI
2017
103. Anders Christensen, Jimmy Kromann, Jan Jensen, and Qiang Cui "Intermolecular Interactions in the Condensed Phase: Evaluation of Semi-empirical Quantum Mechanical Methods" Journal of Chemical Physics 2017, 147, 161704. DOI
102. Jan H. Jensen, Christopher J. Swain, and Lars Olsen "Prediction of pKa values for drug-like molecules using semiempirical quantum chemical methods" Journal of Physical Chemistry A 2017, 121, 699–707. Preprint Data DOI
* Jan H. Jensen "Which method is more accurate? or errors have error bars" PeerJ Preprints 2017 5:e2693v1 DOI
101. Lars A. Bratholm and Jan H. Jensen "Protein Structure Refinement using a Quantum Mechanics-Based Chemical Shielding Predictor" Chemical Science 2017, 8, 2061–2072 Preprint Data DOI
2016
100. Jimmy C. Kromann, Frej A. N. Larsen, Hadeel Moustafa, and Jan H. Jensen "Prediction of pKa Values Using the PM6 Semiempirical Method" PeerJ 2016, 4:e2335. DOI Preprint data
99. Jimmy C. Kromann, Anders S. Christensen, Qiang Cui, and Jan H. Jensen "Towards a barrier height benchmark set for biologically relevant systems" PeerJ 2016, 4:e1994 DOI data Preprint
2015
* Jan H. Jensen "High Througput pKa Prediction Using Semi Empirical Methods" A proposal submitted to the Danish NSF (FTP). arXiv
98. Anders S. Larsen, Lars A. Bratholm, Anders S. Christensen, Maher Channir, and Jan H. Jensen "ProCS15: A DFT-based chemical shift predictor for backbone and Cβ atoms in proteins" PeerJ, 3:e1344 Preprint DOI code data
* Jan H. Jensen "My flipped classroom: what I did and how I did it" in Universitetspædagogiske praksisser, Peter Stray Jørgensen (red.) og Lotte Rienecker (red.) Samfundslitteratur, 2015 pg 157-174. Preprint (not peer reviewed but still worth reading).
97. Jan H. Jensen "Predicting accurate absolute binding energies in aqueous solution: thermodynamic considerations for electronic structure methods" PCCP 2015, 17, 12441-12451. DOI arXiv
96. Søs Torpenholt, Leonardo De Maria, Mats H. M. Olsson, Lars H. Christensen, Michael Skjøt, Peter Westh, Jan H. Jensen and Leila Lo Leggio "Effect of mutations on the thermostability of Aspergillus aculeatus β-1,4-galactanase" Computational and Structural Biotechnology Journal 2015, 13, 256–264. DOI
95. Lars A. Bratholm, Anders S. Christensen, Thomas Hamelryck, and Jan H. Jensen "Bayesian inference of protein structure from chemical shift data" PeerJ 2015, 3:e861. Preprint DOI
2014
94. 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 2014, 54, 2200-2013. DOI
93. 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. DOI PeerJ Preprint
92. 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
91. 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
90. 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
89. 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
89. 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)
88. 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
87. Martin P. Andersson, Jan H. Jensen and Susan L. S. Stipp "Predicting pKa for proteins using COSMO-RS" PeerJ 2013, 1:e198 DOI.
86. 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
85. 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.
84. 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
83. 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. DOI arXiv
82. 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
81. 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
80. 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
79. 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
88. 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
87. Martin P. Andersson, Jan H. Jensen and Susan L. S. Stipp "Predicting pKa for proteins using COSMO-RS" PeerJ 2013, 1:e198 DOI.
86. 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
85. 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.
84. 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
83. 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. DOI arXiv
82. 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
81. 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
80. 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
79. 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
78. 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
77. 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
76. 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
75. 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
77. 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
76. 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
75. 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
74. 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
73. 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
72. 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
71. 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.
70. 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.
69. 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. 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
71. 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.
70. 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.
69. 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
68. 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
67. 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
66. 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
65. 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
* 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
64. 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
63. 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
62. 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
61. Jan H. Jensen “Calculating pH and salt dependence of protein-protein binding” Current Pharmaceutical Biotechnology 2008, 9, 96-102.
60. 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
59. 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
58. 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
57. 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
56. 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
55. 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
54. 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
53. 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
52. 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
51.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
50. 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
49. 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
48. 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
47. 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
46. 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
45. 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
44. 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
43. 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
42. 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.
41. 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.
40. 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
39. 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.
38. 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.
37. 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.
36. 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
35. 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.
34. 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.
33. 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.
32. 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.
31. 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
30. 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.
29. 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.
28. 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
27. George A. Kraus, N. Zhang, A. Melekhov, Jan H. Jensen “Regiochemical Control by Remote Substituents. A Direct Synthesis of Tetrangulol” SYNLETT 2001, 521-522.
26. 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.
25. 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.
24. 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
23. 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.
22. 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.
21. 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.
20. 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.
19. 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
18. 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
* 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.
17.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.
16.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
15. 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.
14. Mark S. Gordon and Jan H. Jensen, “Understanding the Hydrogen Bond Using Quantum Chemistry”, Accounts of Chemical Research, 1996, 29, 536-543.
13. 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.
12. Jan H. Jensen, “Modeling Intermolecular Exchange Integrals Between Non-Orthogonal Molecular Orbitals”, Journal of Chemical Physics, 1996, 104, 7795-7796.
1995
11. 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.
10. 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.
* 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.
9. 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
* 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.
67. 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
66. 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
65. 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
* 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
64. 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
63. 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
62. 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
61. Jan H. Jensen “Calculating pH and salt dependence of protein-protein binding” Current Pharmaceutical Biotechnology 2008, 9, 96-102.
60. 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
59. 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
58. 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
57. 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
56. 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
55. 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
54. 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
53. 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
52. 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
51.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
50. 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
49. 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
48. 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
47. 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
46. 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
45. 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
44. 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
43. 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
42. 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.
41. 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.
40. 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
39. 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.
38. 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.
37. 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.
36. 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
35. 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.
34. 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.
33. 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.
32. 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.
31. 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
30. 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.
29. 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.
28. 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
27. George A. Kraus, N. Zhang, A. Melekhov, Jan H. Jensen “Regiochemical Control by Remote Substituents. A Direct Synthesis of Tetrangulol” SYNLETT 2001, 521-522.
26. 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.
25. 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.
24. 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
23. 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.
22. 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.
21. 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.
20. 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.
19. 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
18. 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
* 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.
17.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.
16.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
15. 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.
14. Mark S. Gordon and Jan H. Jensen, “Understanding the Hydrogen Bond Using Quantum Chemistry”, Accounts of Chemical Research, 1996, 29, 536-543.
13. 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.
12. Jan H. Jensen, “Modeling Intermolecular Exchange Integrals Between Non-Orthogonal Molecular Orbitals”, Journal of Chemical Physics, 1996, 104, 7795-7796.
1995
11. 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.
10. 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.
* 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.
9. 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
* 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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