Jan H. Jensen, PhD - Publications

Affiliations: 
Chemistry University of Copenhagen, København, Denmark 
Area:
biocomputational chemistry
Website:
http://synbio.ku.dk/research/researcher_profiles/jan_h_jensen/

88 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Garner MH, Koerstz M, Jensen JH, Solomon GC. The Bicyclo[2.2.2]octane Motif: A Class of Saturated Group 14 Quantum Interference Based Single-Molecule Insulators. The Journal of Physical Chemistry Letters. 6941-6947. PMID 30484655 DOI: 10.1021/Acs.Jpclett.8B03432  0.31
2018 Kromann JC, Steinmann C, Jensen JH. Improving solvation energy predictions using the SMD solvation method and semiempirical electronic structure methods. The Journal of Chemical Physics. 149: 104102. PMID 30219007 DOI: 10.1063/1.5047273  0.653
2018 Kromann JC, Jensen JH, Kruszyk M, Jessing M, Jørgensen M. Fast and accurate prediction of the regioselectivity of electrophilic aromatic substitution reactions. Chemical Science. 9: 660-665. PMID 29629133 DOI: 10.1039/C7Sc04156J  0.372
2018 Fedorov DG, Kromann JC, Jensen JH. Empirical corrections and pair interaction energies in the fragment molecular orbital method Chemical Physics Letters. 706: 328-333. DOI: 10.1016/J.Cplett.2018.06.025  0.372
2017 Christensen AS, Kromann JC, Jensen JH, Cui Q. Intermolecular interactions in the condensed phase: Evaluation of semi-empirical quantum mechanical methods. The Journal of Chemical Physics. 147: 161704. PMID 29096452 DOI: 10.1063/1.4985605  0.346
2017 Bratholm LA, Jensen JH. Protein structure refinement using a quantum mechanics-based chemical shielding predictor. Chemical Science. 8: 2061-2072. PMID 28451325 DOI: 10.1039/C6Sc04344E  0.33
2017 Jensen JH, Swain CJ, Olsen L. Prediction of pKa Values for Drug-Like Molecules Using Semiempirical Quantum Chemical Methods. The Journal of Physical Chemistry. A. PMID 28054775 DOI: 10.1021/Acs.Jpca.6B10990  0.304
2016 Kromann JC, Larsen F, Moustafa H, Jensen JH. Prediction of pKa values using the PM6 semiempirical method. Peerj. 4: e2335. PMID 27602298 DOI: 10.7717/Peerj.2335  0.354
2016 Kromann JC, Christensen AS, Cui Q, Jensen JH. Towards a barrier height benchmark set for biologically relevant systems. Peerj. 4: e1994. PMID 27168993 DOI: 10.7717/Peerj.1994  0.365
2015 Larsen AS, Bratholm LA, Christensen AS, Channir M, Jensen JH. ProCS15: a DFT-based chemical shift predictor for backbone and Cβ atoms in proteins. Peerj. 3: e1344. PMID 26623185 DOI: 10.7717/Peerj.1344  0.341
2015 Jensen JH. Predicting accurate absolute binding energies in aqueous solution: thermodynamic considerations for electronic structure methods. Physical Chemistry Chemical Physics : Pccp. 17: 12441-51. PMID 25901455 DOI: 10.1039/C5Cp00628G  0.337
2015 Bratholm LA, Christensen AS, Hamelryck T, Jensen JH. Bayesian inference of protein structure from chemical shift data. Peerj. 3: e861. PMID 25825683 DOI: 10.7717/Peerj.861  0.309
2014 Ugur I, Marion A, Parant S, Jensen JH, Monard G. Rationalization of the pKa values of alcohols and thiols using atomic charge descriptors and its application to the prediction of amino acid pKa's. Journal of Chemical Information and Modeling. 54: 2200-13. PMID 25089727 DOI: 10.1021/Ci500079W  0.344
2014 Kromann JC, Christensen AS, Steinmann C, Korth M, Jensen JH. A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H+. Peerj. 2: e449. PMID 25024918 DOI: 10.7717/Peerj.449  0.637
2014 Christensen AS, Steinmann C, Fedorov DG, Jensen JH. Hybrid RHF/MP2 geometry optimizations with the effective fragment molecular orbital method. Plos One. 9: e88800. PMID 24558430 DOI: 10.1371/Journal.Pone.0088800  0.647
2013 Pruitt SR, Steinmann C, Jensen JH, Gordon MS. Fully Integrated Effective Fragment Molecular Orbital Method. Journal of Chemical Theory and Computation. 9: 2235-2249. PMID 26583717 DOI: 10.1021/Ct4001119  0.778
2013 Christensen AS, Linnet TE, Borg M, Boomsma W, Lindorff-Larsen K, Hamelryck T, Jensen JH. Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics. Plos One. 8: e84123. PMID 24391900 DOI: 10.1371/Journal.Pone.0084123  0.383
2013 Andersson MP, Jensen JH, Stipp SL. Predicting pKa for proteins using COSMO-RS. Peerj. 1: e198. PMID 24244915 DOI: 10.7717/Peerj.198  0.318
2013 Hediger MR, Steinmann C, De Vico L, Jensen JH. 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. 1: e111. PMID 23904990 DOI: 10.7717/Peerj.111  0.613
2013 Steinmann C, Blædel KL, Christensen AS, Jensen JH. Interface of the polarizable continuum model of solvation with semi-empirical methods in the GAMESS program. Plos One. 8: e67725. PMID 23844075 DOI: 10.1371/Journal.Pone.0067725  0.624
2013 Steinmann C, Fedorov DG, Jensen JH. Mapping enzymatic catalysis using the effective fragment molecular orbital method: towards all ab initio biochemistry. Plos One. 8: e60602. PMID 23593259 DOI: 10.1371/Journal.Pone.0060602  0.634
2013 Hediger MR, Steinmann C, De Vico L, Jensen JH. A computational method for the systematic screening of reaction barriers in enzymes: Searching for Bacillus circulans xylanasemutants with greater activity towards a synthetic substrate Peerj. 2013. DOI: 10.7717/peerj.111  0.549
2013 Steinmann C, Fedorov DG, Jensen JH. Cross region fragmentation. Plos One. DOI: 10.1371/Journal.Pone.0060602.G003  0.548
2013 Jensen JH, Kromann JC. The molecule calculator: A web application for fast quantum mechanics-based estimation of molecular properties Journal of Chemical Education. 90: 1093-1095. DOI: 10.1021/Ed400164N  0.376
2013 Pruitt SR, Steinmann C, Jensen JH, Gordon MS. Fully integrated effective fragment molecular orbital method Journal of Chemical Theory and Computation. 9: 2235-2249. DOI: 10.1021/ct4001119  0.766
2012 Hediger MR, De Vico L, Svendsen A, Besenmatter W, Jensen JH. A Computational Methodology to Screen Activities of Enzyme Variants Plos One. 7. PMID 23284627 DOI: 10.1371/Journal.Pone.0049849  0.345
2012 Steinmann C, Ibsen MW, Hansen AS, Jensen JH. FragIt: A Tool to Prepare Input Files for Fragment Based Quantum Chemical Calculations Plos One. 7. PMID 23028546 DOI: 10.1371/Journal.Pone.0044480  0.643
2012 Steinmann C, Fedorov DG, Jensen JH. The effective fragment molecular orbital method for fragments connected by covalent bonds. Plos One. 7: e41117. PMID 22844433 DOI: 10.1371/Journal.Pone.0041117  0.681
2011 Christensen AS, Sauer SP, Jensen JH. Definitive Benchmark Study of Ring Current Effects on Amide Proton Chemical Shifts. Journal of Chemical Theory and Computation. 7: 2078-2084. PMID 26606479 DOI: 10.1021/Ct2002607  0.355
2011 Rostkowski M, Olsson MH, Søndergaard CR, Jensen JH. Graphical analysis of pH-dependent properties of proteins predicted using PROPKA. Bmc Structural Biology. 11: 6. PMID 21269479 DOI: 10.1186/1472-6807-11-6  0.312
2010 Steinmann C, Fedorov DG, Jensen JH. Effective fragment molecular orbital method: a merger of the effective fragment potential and fragment molecular orbital methods. The Journal of Physical Chemistry. A. 114: 8705-12. PMID 20446697 DOI: 10.1021/Jp101498M  0.663
2010 Li H, Fedorov DG, Nagata T, Kitaura K, Jensen JH, Gordon MS. Energy gradients in combined fragment molecular orbital and polarizable continuum model (FMO/PCM) calculation. Journal of Computational Chemistry. 31: 778-90. PMID 19569184 DOI: 10.1002/Jcc.21363  0.53
2010 Kemp DD, Rintelman JM, Gordon MS, Jensen JH. Exchange repulsion between effective fragment potentials and ab initio molecules Theoretical Chemistry Accounts. 125: 481-491. DOI: 10.1007/S00214-009-0660-7  0.758
2010 GORDON MS, CARROLL MT, JENSEN JH, DAVIS LP, BURGGRAF LW, GUIDRY RM. ChemInform Abstract: Nature of the Si-N Bond in Silatranes Cheminform. 22: no-no. DOI: 10.1002/chin.199144049  0.567
2009 Fedorov DG, Avramov PV, Jensen JH, Kitaura K. Analytic gradient for the adaptive frozen orbital bond detachment in the fragment molecular orbital method Chemical Physics Letters. 477: 169-175. DOI: 10.1016/J.Cplett.2009.06.072  0.424
2008 Fedorov DG, Jensen JH, Deka RC, Kitaura K. Covalent bond fragmentation suitable to describe solids in the fragment molecular orbital method. The Journal of Physical Chemistry. A. 112: 11808-16. PMID 18942816 DOI: 10.1021/Jp805435N  0.384
2008 Langkilde A, Kristensen SM, Lo Leggio L, Mølgaard A, Jensen JH, Houk AR, Navarro Poulsen JC, Kauppinen S, Larsen S. Short strong hydrogen bonds in proteins: a case study of rhamnogalacturonan acetylesterase. Acta Crystallographica. Section D, Biological Crystallography. 851-63. PMID 18645234 DOI: 10.1107/S0907444908017083  0.345
2008 Cehovin A, Mera H, Jensen JH, Stokbro K, Pedersen TB. Role of the virtual orbitals and HOMO-LUMO gap in mean-field approximations to the conductance of molecular junctions Physical Review B - Condensed Matter and Materials Physics. 77. DOI: 10.1103/Physrevb.77.195432  0.35
2007 Xia J, Daly RP, Chuang FC, Parker L, Jensen JH, Margulis CJ. Sugar Folding:  A Novel Structural Prediction Tool for Oligosaccharides and Polysaccharides 2. Journal of Chemical Theory and Computation. 3: 1629-43. PMID 26633232 DOI: 10.1021/Ct700034Q  0.345
2007 Xia J, Daly RP, Chuang FC, Parker L, Jensen JH, Margulis CJ. Sugar Folding:  A Novel Structural Prediction Tool for Oligosaccharides and Polysaccharides 1. Journal of Chemical Theory and Computation. 3: 1620-8. PMID 26633231 DOI: 10.1021/Ct700033Y  0.369
2007 Kongsted J, Ryde U, Wydra J, Jensen JH. Prediction and rationalization of the pH dependence of the activity and stability of family 11 xylanases. Biochemistry. 46: 13581-92. PMID 17960918 DOI: 10.1021/Bi7016365  0.533
2007 Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Research. 35: W522-5. PMID 17488841 DOI: 10.1093/Nar/Gkm276  0.339
2007 Gordon MS, Slipchenko L, Li H, Jensen JH. Chapter 10 The Effective Fragment Potential: A General Method for Predicting Intermolecular Interactions Annual Reports in Computational Chemistry. 3: 177-193. DOI: 10.1016/S1574-1400(07)03010-1  0.519
2006 Parker LL, Houk AR, Jensen JH. Cooperative hydrogen bonding effects are key determinants of backbone amide proton chemical shifts in proteins. Journal of the American Chemical Society. 128: 9863-72. PMID 16866544 DOI: 10.1021/Ja0617901  0.339
2006 Powers N, Jensen JH. Chemically accurate protein structures: validation of protein NMR structures by comparison of measured and predicted pKa values. Journal of Biomolecular Nmr. 35: 39-51. PMID 16791739 DOI: 10.1007/S10858-006-9003-3  0.306
2006 Li H, Gordon MS, Jensen JH. Charge transfer interaction in the effective fragment potential method. The Journal of Chemical Physics. 124: 214108. PMID 16774399 DOI: 10.1063/1.2196884  0.505
2006 Fedorov DG, Kitaura K, Li H, Jensen JH, Gordon MS. The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO). Journal of Computational Chemistry. 27: 976-85. PMID 16604514 DOI: 10.1002/Jcc.20406  0.542
2006 Porter MA, Hall JR, Locke JC, Jensen JH, Molina PA. Hydrogen bonding is the prime determinant of carboxyl pKa values at the N-termini of alpha-helices. Proteins. 63: 621-35. PMID 16447255 DOI: 10.1002/Prot.20879  0.315
2006 Colvin ME, Cramer CJ, Dykstra CE, Jensen JH, Krimm S, Rivail JL, Thakkar AJ, Yáñez M. Molecular quantum mechanics to biodynamics: Essential connections Journal of Molecular Structure: Theochem. 764: 1-8. DOI: 10.1016/J.Theochem.2006.01.037  0.309
2005 Jensen JH, Li H, Robertson AD, Molina PA. Prediction and rationalization of protein pKa values using QM and QM/MM methods. The Journal of Physical Chemistry. A. 109: 6634-43. PMID 16834015 DOI: 10.1021/Jp051922X  0.429
2004 Li H, Jensen JH. Improving the efficiency and convergence of geometry optimization with the polarizable continuum model: new energy gradients and molecular surface tessellation. Journal of Computational Chemistry. 25: 1449-62. PMID 15224389 DOI: 10.1002/Jcc.20072  0.321
2004 Li H, Webb SP, Ivanic J, Jensen JH. Determinants of the relative reduction potentials of type-1 copper sites in proteins. Journal of the American Chemical Society. 126: 8010-9. PMID 15212551 DOI: 10.1021/Ja049345Y  0.624
2004 Li H, Robertson AD, Jensen JH. The determinants of carboxyl pKa values in turkey ovomucoid third domain. Proteins. 55: 689-704. PMID 15103631 DOI: 10.1002/Prot.20032  0.354
2003 Molina PA, Li H, Jensen JH. Intraprotein electrostatics derived from first principles: divide-and-conquer approaches for QM/MM calculations. Journal of Computational Chemistry. 24: 1971-9. PMID 14531051 DOI: 10.1002/Jcc.10333  0.397
2003 Huang JH, Luci JJ, Lee TY, Swenson DC, Jensen JH, Messerle L. 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. 125: 1688-9. PMID 12580580 DOI: 10.1021/Ja020369J  0.301
2003 Molina PA, Jensen JH. 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. 107: 6226-6233. DOI: 10.1021/Jp0340663  0.348
2003 Li H, Pomelli CS, Jensen JH. Continuum solvation of large molecules described by QM/MM: A semi-iterative implementation of the PCM/EFP interface Theoretical Chemistry Accounts. 109: 71-84. DOI: 10.1007/S00214-002-0427-X  0.331
2003 Molina PA, Sikorski RS, Jensen JH. NMR chemical shifts in the low-pH form of α-chymotrypsin. A QM/MM and ONIOM-NMR study Theoretical Chemistry Accounts. 109: 100-107. DOI: 10.1007/S00214-002-0415-1  0.369
2002 Kohen A, Jensen JH. Boundary conditions for the Swain-Schaad relationship as a criterion for hydrogen tunneling. Journal of the American Chemical Society. 124: 3858-64. PMID 11942822 DOI: 10.1021/Ja016909E  0.336
2002 Li H, Hains AW, Everts JE, Robertson AD, Jensen JH. The prediction of protein pKa's using QM/MM: The pKa of lysine 55 in turkey ovomucoid third domain Journal of Physical Chemistry B. 106: 3486-3494. DOI: 10.1021/Jp013995W  0.367
2002 Li H, Jensen JH. Partial Hessian vibrational analysis: The localization of the molecular vibrational energy and entropy Theoretical Chemistry Accounts. 107: 211-219. DOI: 10.1007/S00214-001-0317-7  0.352
2001 Jensen JH. Intermolecular exchange-induction and charge transfer: Derivation of approximate formulas using nonorthogonal localized molecular orbitals Journal of Chemical Physics. 114: 8775-8783. DOI: 10.1063/1.1356017  0.368
2001 Minikis RM, Kairys V, Jensen JH. Accurate intraprotein electrostatics derived from first principles: An effective fragment potential method study of the proton affinities of lysine 55 and tyrosine 20 in turkey ovomucoid third domain Journal of Physical Chemistry A. 105: 3829-3837. DOI: 10.1021/Jp0032659  0.37
2001 Gordon MS, Freitag MA, Bandyopadhyay P, Jensen JH, Kairys V, Stevens WJ. The effective fragment potential method: A QM-based MM approach to modeling environmental effects in chemistry Journal of Physical Chemistry A. 105: 306-307.  0.701
2000 Freitag MA, Gordon MS, Jensen JH, Stevens WJ. Evaluation of charge penetration between distributed multipolar expansions Journal of Chemical Physics. 112: 7300-7306. DOI: 10.1063/1.481370  0.744
2000 Remer LC, Jensen JH. Toward a general theory of hydrogen bonding: The short, strong hydrogen bond [HOH⋯OH]- Journal of Physical Chemistry A. 104: 9266-9275. DOI: 10.1021/Jp002726N  0.364
2000 Kairys V, Jensen JH. QM/MM boundaries across covalent bonds: A frozen localized molecular orbital-based approach for the effective fragment potential method Journal of Physical Chemistry A. 104: 6656-6665. DOI: 10.1021/Jp000887L  0.409
2000 Gordon MS, Jensen JH. Perspective on "The physical nature of the chemical bond" Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta). 103: 248-251. DOI: 10.1007/s002149900034  0.363
2000 Gordon MS, Jensen JH. Perspective on “The physical nature of the chemical bond” Theoretical Chemistry Accounts. 103: 248-251. DOI: 10.1007/978-3-662-10421-7_25  0.464
2000 Minikis RM, Jensen JH. Toward a General Theory of Hydrogen Bonding: A Study of Hydrogen Bonds Involving H2O and HF International Journal of Quantum Chemistry. 76: 341-358. DOI: 10.1002/(Sici)1097-461X(2000)76:3<341::Aid-Qua4>3.0.Co;2-5  0.373
1999 Kairys V, Jensen JH. Evaluation of the charge penetration energy between non-orthogonal molecular orbitals using the Spherical Gaussian Overlap approximation Chemical Physics Letters. 315: 140-144. DOI: 10.1016/S0009-2614(99)01187-2  0.39
1998 Jensen JH, Gordon MS. An approximate formula for the intermolecular Pauli repulsion between closed shell molecules. II. Application to the effective fragment potential method The Journal of Chemical Physics. 108: 4772-4782. DOI: 10.1063/1.475888  0.512
1998 Jacob J, Espenson JH, Jensen JH, Gordon MS. 1,3-Transposition of Allylic Alcohols Catalyzed by Methyltrioxorhenium Organometallics. 17: 1835-1840. DOI: 10.1021/Om971115N  0.389
1996 Jensen J, Gordon M. An approximate formula for the intermolecular Pauli repulsion between closed shell molecules Molecular Physics. 89: 1313-1325. DOI: 10.1080/002689796173200  0.477
1996 Day PN, Jensen JH, Gordon MS, Webb SP, Stevens WJ, Krauss M, Garmer D, Basch H, Cohen D. An effective fragment method for modeling solvent effects in quantum mechanical calculations The Journal of Chemical Physics. 105: 1968–1986. DOI: 10.1063/1.472045  0.713
1996 Jensen JH. Modeling intermolecular exchange integrals between nonorthogonal molecular orbitals Journal of Chemical Physics. 104: 7795-7796. DOI: 10.1063/1.471485  0.367
1996 Gordon MS, Jensen JH. Understanding the Hydrogen Bond Using Quantum Chemistry Accounts of Chemical Research. 29: 536-543. DOI: 10.1021/Ar9600594  0.444
1995 Kraus GA, Li J, Gordon MS, Jensen JH. Direct Total Syntheses of Frenolicin B and Kalafungin via Highly Regioselective Diels-Alder Reactions The Journal of Organic Chemistry. 60: 1154-1159. DOI: 10.1021/Jo00110A017  0.385
1995 Jensen JH, Gordon MS. On the Number of Water Molecules Necessary To Stabilize the Glycine Zwitterion Journal of the American Chemical Society. 117: 8159-8170. DOI: 10.1021/Ja00136A013  0.461
1995 Jensen JH, Gordon MS. Ab Initio Localized Charge Distributions: Theory and a Detailed Analysis of the Water Dimer-Hydrogen Bond The Journal of Physical Chemistry. 99: 8091-8107. DOI: 10.1021/J100020A037  0.508
1994 Jensen JH, Morokuma K, Gordon MS. Pathways for H2 elimination from ethylene: A theoretical study The Journal of Chemical Physics. 100: 1981-1987. DOI: 10.1063/1.466550  0.48
1994 Kraus GA, Li J, Gordon M, Jensen JH. Regiocontrol by Remote Substituents. A Direct Total Synthesis of Racemic Hongconin The Journal of Organic Chemistry. 59: 2219-2222. DOI: 10.1021/Jo00087A044  0.388
1993 Kraus GA, Li J, Gordon MS, Jensen JH. Regiocontrol by remote substituents. An enantioselective total synthesis of frenolicin B via a highly regioselective Diels-Alder reaction Journal of the American Chemical Society. 115: 5859-5860. DOI: 10.1021/Ja00066A078  0.433
1993 Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JH, Koseki S, Matsunaga N, Nguyen KA, Su S, Windus TL, Dupuis M, Montgomery JA. General atomic and molecular electronic structure system Journal of Computational Chemistry. 14: 1347-1363. DOI: 10.1002/Jcc.540141112  0.74
1992 Jensen JH, Baldridge KK, Gordon MS. Uncatalyzed peptide bond formation in the gas phase The Journal of Physical Chemistry. 96: 8340-8351. DOI: 10.1021/J100200A025  0.642
1991 Gordon MS, Carroll MT, Jensen JH, Davis LP, Burggraf LW, Guidry RM. Nature of the silicon-nitrogen bond in silatranes Organometallics. 10: 2657-2660. DOI: 10.1021/Om00054A028  0.656
1991 Jensen JH, Gordon MS. Conformational potential energy surface of glycine: a theoretical study Journal of the American Chemical Society. 113: 7917-7924. DOI: 10.1021/Ja00021A015  0.44
1991 Jensen JH, Gordon MS. Splicing I: using mixed basis sets in AB Initio calculations Journal of Computational Chemistry. 12: 421-426. DOI: 10.1002/Jcc.540120403  0.424
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