All Stories

  1. A graph-based genetic algorithm and generative model/Monte Carlo tree search for the exploration of chemical space

    Article • Chemical Science, January 2019, Royal Society of Chemistry

    Jan H Jensen

  2. The Bicyclo[2.2.2]octane Motif: A Class of Saturated Group 14 Quantum Interference Based Single-Molecule Insulators

    Article • The Journal of Physical Chemistry Letters, November 2018, American Chemical Society (ACS)

    Jan H Jensen

  3. Searching for the origin of life using a computational search engine

    Article • September 2018, PeerJ

    Jan H Jensen

  4. Searching for the origin of life using a computational search engine

    Article • September 2018, PeerJ

    Jan H Jensen

  5. Improving solvation energy predictions using the SMD solvation method and semiempirical electronic structure methods

    Article • The Journal of Chemical Physics, September 2018, American Institute of Physics

    Jan H Jensen

  6. Empirical corrections and pair interaction energies in the fragment molecular orbital method

    Article • Chemical Physics Letters, August 2018, Elsevier

    Jan H Jensen

  7. Random versus Systematic Errors in Reaction Enthalpies Computed Using Semiempirical and Minimal Basis Set Methods

    Article • ACS Omega, April 2018, American Chemical Society (ACS)

    Jan H Jensen

  8. Fast and accurate prediction of the regioselectivity of electrophilic aromatic substitution reactions

    Article • Chemical Science, January 2018, Royal Society of Chemistry

    Jan H Jensen

  9. Intermolecular interactions in the condensed phase: Evaluation of semi-empirical quantum mechanical methods

    Article • The Journal of Chemical Physics, October 2017, American Institute of Physics

    Jan H Jensen

  10. Prediction of pKa Values for Druglike Molecules Using Semiempirical Quantum Chemical Methods

    Article • The Journal of Physical Chemistry A, January 2017, American Chemical Society (ACS)

    Jan H Jensen

  11. Which method is more accurate? or errors have error bars

    Article • January 2017, PeerJ

    Jan H Jensen

  12. Which method is more accurate? or errors have error bars

    Article • January 2017, PeerJ

    Jan H Jensen

  13. Protein structure refinement using a quantum mechanics-based chemical shielding predictor

    Article • Chemical Science, January 2017, Royal Society of Chemistry

    Jan H Jensen

  14. Prediction of pKa values for drug-like molecules using semiempirical quantum chemical methods

    Article • December 2016, PeerJ

    Jan H Jensen

  15. Prediction of pKa values for drug-like molecules using semiempirical quantum chemical methods

    Article • December 2016, PeerJ

    Jan H Jensen

  16. Prediction of pKa values for drug-like molecules using semiempirical quantum chemical methods

    Article • November 2016, PeerJ

    Jan H Jensen

  17. Protein structure refinement using a quantum mechanics-based chemical shielding predictor

    Article • September 2016, PeerJ

    Jan H Jensen

  18. Protein structure refinement using a quantum mechanics-based chemical shielding predictor

    Article • September 2016, PeerJ

    Jan H Jensen

  19. Prediction of pKa values using the PM6 semiempirical method

    Article • PeerJ, August 2016, PeerJ

    Jan H Jensen

  20. Prediction of pKa values using the PM6 semiempirical method

    Article • May 2016, PeerJ

    Jan H Jensen

  21. Prediction of pKa values using the PM6 semiempirical method

    Article • May 2016, PeerJ

    Jan H Jensen

  22. Towards a barrier height benchmark set for biologically relevant systems

    Article • PeerJ, May 2016, PeerJ

    Jan H Jensen

  23. Towards a barrier height benchmark set for biologically relevant systems

    Article • February 2016, PeerJ

    Jan H Jensen

  24. Towards a barrier height benchmark set for biologically relevant systems

    Article • February 2016, PeerJ

    Jan H Jensen

  25. Towards a barrier height benchmark set for biologically relevant systems

    Article • February 2016, PeerJ

    Jan H Jensen

  26. ProCS15: A DFT-based chemical shift predictor for backbone and Cβ atoms in proteins

    Article • August 2015, PeerJ

    Jan H Jensen

  27. ProCS15: A DFT-based chemical shift predictor for backbone and Cβ atoms in proteins

    Article • August 2015, PeerJ

    Jan H Jensen

  28. Bayesian inference of protein structure from chemical shift data

    Article • PeerJ, March 2015, PeerJ

    Jan H Jensen

  29. Predicting accurate absolute binding energies in aqueous solution: thermodynamic considerations for electronic structure methods

    Article • Physical Chemistry Chemical Physics, January 2015, Royal Society of Chemistry

    Jan H Jensen

  30. Effect of mutations on the thermostability of Aspergillus aculeatus β-1,4-galactanase

    Article • Computational and Structural Biotechnology Journal, January 2015, Elsevier

    Jan H Jensen, Leila Lo Leggio

  31. Rationalization of the p K a Values of Alcohols and Thiols Using Atomic Charge Descriptors and Its Application to the Prediction of Amino Acid p K a ’s

    Article • Journal of Chemical Information and Computer Sciences, August 2014, American Chemical Society (ACS)

    Jan H Jensen

  32. A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H+

    Article • PeerJ, June 2014, PeerJ

    Professor Martin Korth, Jan H Jensen

  33. Indium arsenide nanowire field-effect transistors for pH and biological sensing

    Article • Applied Physics Letters, May 2014, American Institute of Physics

    Jan H Jensen

  34. In Silico Prediction of Mutant HIV-1 Proteases Cleaving a Target Sequence

    Article • PLoS ONE, May 2014, PLOS

    Jan H Jensen

  35. FragBuilder: an efficient Python library to setup quantum chemistry calculations on peptides models

    Article • PeerJ, March 2014, PeerJ

    Jan H Jensen

  36. Hybrid RHF/MP2 Geometry Optimizations with the Effective Fragment Molecular Orbital Method

    Article • PLoS ONE, February 2014, PLOS

    Jan H Jensen

  37. Protein Structure Validation and Refinement Using Amide Proton Chemical Shifts Derived from Quantum Mechanics

    Article • PLoS ONE, December 2013, PLOS

    Jan H Jensen

  38. Predicting pK a for proteins using COSMO-RS

    Article • PeerJ, October 2013, PeerJ

    Jan H Jensen

  39. In silico screening of 393 mutants facilitates enzyme engineering of amidase activity in CalB

    Article • PeerJ, August 2013, PeerJ

    Jan H Jensen

  40. The Molecule Calculator: A Web Application for Fast Quantum Mechanics-Based Estimation of Molecular Properties

    Article • Journal of Chemical Education, August 2013, American Chemical Society (ACS)

    Jan H Jensen

  41. 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

    Article • PeerJ, July 2013, PeerJ

    Jan H Jensen

  42. Interface of the Polarizable Continuum Model of Solvation with Semi-Empirical Methods in the GAMESS Program

    Article • PLoS ONE, July 2013, PLOS

    Jan H Jensen

  43. Fully Integrated Effective Fragment Molecular Orbital Method

    Article • Journal of Chemical Theory and Computation, May 2013, American Chemical Society (ACS)

    Jan H Jensen

  44. PHAISTOS: A framework for Markov chain Monte Carlo simulation and inference of protein structure

    Article • Journal of Computational Chemistry, April 2013, Wiley

    Jan H Jensen

  45. Mapping Enzymatic Catalysis Using the Effective Fragment Molecular Orbital Method: Towards all ab initio Biochemistry

    Article • PLoS ONE, April 2013, PLOS

    Jan H Jensen

  46. Effects of buffer composition and dilution on nanowire field-effect biosensors

    Article • Nanotechnology, December 2012, Institute of Physics Publishing

    Jan H Jensen

  47. A Computational Methodology to Screen Activities of Enzyme Variants

    Article • PLoS ONE, December 2012, PLOS

    Jan H Jensen

  48. BioFET-SIM Web Interface: Implementation and Two Applications

    Article • PLoS ONE, October 2012, PLOS

    Jan H Jensen

  49. FragIt: A Tool to Prepare Input Files for Fragment Based Quantum Chemical Calculations

    Article • PLoS ONE, September 2012, PLOS

    Jan H Jensen

  50. The Effective Fragment Molecular Orbital Method for Fragments Connected by Covalent Bonds

    Article • PLoS ONE, July 2012, PLOS

    Jan H Jensen

  51. Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of p K a Values

    Article • Journal of Chemical Theory and Computation, July 2011, American Chemical Society (ACS)

    Jan H Jensen

  52. Definitive Benchmark Study of Ring Current Effects on Amide Proton Chemical Shifts

    Article • Journal of Chemical Theory and Computation, June 2011, American Chemical Society (ACS)

    Dr Stephan P. A. Sauer, Jan H Jensen

  53. PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical p K a Predictions

    Article • Journal of Chemical Theory and Computation, February 2011, American Chemical Society (ACS)

    Jan H Jensen

  54. Predicting and rationalizing the effect of surface charge distribution and orientation on nano-wire based FET bio-sensors

    Article • Nanoscale, January 2011, Royal Society of Chemistry

    Jan H Jensen

  55. Quantifying signal changes in nano-wire based biosensors

    Article • Nanoscale, January 2011, Royal Society of Chemistry

    Jan H Jensen

  56. Graphical analysis of pH-dependent properties of proteins predicted using PROPKA

    Article • BMC Structural Biology, January 2011, Springer Science + Business Media

    Jan H Jensen

  57. Effective Fragment Molecular Orbital Method: A Merger of the Effective Fragment Potential and Fragment Molecular Orbital Methods †

    Article • The Journal of Physical Chemistry A, August 2010, American Chemical Society (ACS)

    Jan H Jensen

  58. Exchange repulsion between effective fragment potentials and ab initio molecules

    Article • Theoretical Chemistry Accounts, November 2009, Springer Science + Business Media

    Jan H Jensen

  59. Analytic gradient for the adaptive frozen orbital bond detachment in the fragment molecular orbital method

    Article • Chemical Physics Letters, July 2009, Elsevier

    Jan H Jensen

  60. Energy gradients in combined fragment molecular orbital and polarizable continuum model (FMO/PCM) calculation

    Article • Journal of Computational Chemistry, January 2009, Wiley

    Jan H Jensen

  61. Covalent Bond Fragmentation Suitable To Describe Solids in the Fragment Molecular Orbital Method

    Article • The Journal of Physical Chemistry A, November 2008, American Chemical Society (ACS)

    Jan H Jensen

  62. Rationalization of the Difference in Lifetime of Two Covalent Sialosyl−Enzyme Intermediates of Trypanosoma rangeli Sialidase

    Article • The Journal of Physical Chemistry, November 2008, American Chemical Society (ACS)

    Jan H Jensen

  63. Short strong hydrogen bonds in proteins: a case study of rhamnogalacturonan acetylesterase

    Article • Acta Crystallographica Section D Biological Crystallography, July 2008, International Union of Crystallography

    Jan H Jensen, Leila Lo Leggio

  64. Very fast prediction and rationalization of pKa values for protein-ligand complexes

    Article • Proteins Structure Function and Bioinformatics, May 2008, Wiley

    Jan H Jensen

  65. Role of the virtual orbitals and HOMO-LUMO gap in mean-field approximations to the conductance of molecular junctions

    Article • Physical Review B, May 2008, American Physical Society (APS)

    Jan H Jensen

  66. Application driven software for chemistry

    Article • May 2008, Institute of Electrical & Electronics Engineers (IEEE)

    Jan H Jensen

  67. Calculating pH and Salt Dependence of Protein-Protein Binding

    Article • Current Pharmaceutical Biotechnology, April 2008, Bentham Science Publishers

    Jan H Jensen

  68. Protein-protein binding is often associated with changes in protonation state

    Article • Proteins Structure Function and Bioinformatics, April 2008, Wiley

    Jan H Jensen

  69. Prediction and Rationalization of the pH Dependence of the Activity and Stability of Family 11 Xylanases †

    Article • Biochemistry, November 2007, American Chemical Society (ACS)

    Jan H Jensen

  70. Surface Reactions of Carbon Dioxide at the Adsorbed Water−Oxide Interface

    Article • The Journal of Physical Chemistry C, October 2007, American Chemical Society (ACS)

    Jan H Jensen

  71. Sugar Folding:  A Novel Structural Prediction Tool for Oligosaccharides and Polysaccharides 2

    Article • Journal of Chemical Theory and Computation, July 2007, American Chemical Society (ACS)

    Jan H Jensen

  72. Sugar Folding:  A Novel Structural Prediction Tool for Oligosaccharides and Polysaccharides 1

    Article • Journal of Chemical Theory and Computation, July 2007, American Chemical Society (ACS)

    Jan H Jensen

  73. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations

    Article • Nucleic Acids Research, May 2007, Oxford University Press (OUP)

    Jan H Jensen

  74. FTIR spectroscopy combined with quantum chemical calculations to investigate adsorbed nitrate on aluminium oxide surfaces in the presence and absence of co-adsorbed water

    Article • Physical Chemistry Chemical Physics, January 2007, Royal Society of Chemistry

    Jan H Jensen

  75. Chapter 10 The Effective Fragment Potential: A General Method for Predicting Intermolecular Interactions

    Article • January 2007, Elsevier

    Jan H Jensen

  76. Exploring the Role of the Active Site Cysteine in Human Muscle Creatine Kinase †

    Article • Biochemistry, September 2006, American Chemical Society (ACS)

    Jan H Jensen

  77. Cooperative Hydrogen Bonding Effects Are Key Determinants of Backbone Amide Proton Chemical Shifts in Proteins

    Article • Journal of the American Chemical Society, August 2006, American Chemical Society (ACS)

    Jan H Jensen

  78. Charge transfer interaction in the effective fragment potential method

    Article • The Journal of Chemical Physics, June 2006, American Institute of Physics

    Jan H Jensen

  79. FTIR Spectroscopy Combined with Isotope Labeling and Quantum Chemical Calculations to Investigate Adsorbed Bicarbonate Formation Following Reaction of Carbon Dioxide with Surface Hydroxyl Groups on Fe2O3and Al2O3

    Article • The Journal of Physical Chemistry, June 2006, American Chemical Society (ACS)

    Jan H Jensen

  80. Molecular quantum mechanics to biodynamics: Essential connections

    Article • Journal of Molecular Structure THEOCHEM, May 2006, Elsevier

    Jan H Jensen

  81. Hydride Transfer versus Hydrogen Radical Transfer in Thymidylate Synthase

    Article • Journal of the American Chemical Society, May 2006, American Chemical Society (ACS)

    Jan H Jensen

  82. Chemically accurate protein structures: Validation of protein NMR structures by comparison of measured and predicted pK a values

    Article • Journal of Biomolecular NMR, May 2006, Springer Science + Business Media

    Jan H Jensen

  83. Hydrogen bonding is the prime determinant of carboxyl pKa values at the N-termini of α-helices

    Article • Proteins Structure Function and Bioinformatics, January 2006, Wiley

    Jan H Jensen

  84. The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO)

    Article • Journal of Computational Chemistry, January 2006, Wiley

    Jan H Jensen

  85. Very fast empirical prediction and rationalization of protein pKa values

    Article • Proteins Structure Function and Bioinformatics, October 2005, Wiley

    Jan H Jensen

  86. Prediction and Rationalization of Protein p K a Values Using QM and QM/MM Methods

    Article • The Journal of Physical Chemistry A, August 2005, American Chemical Society (ACS)

    Jan H Jensen

  87. Regiochemical Control by Remote Substituents - A Selective Synthesis of Angularly Fused Ring Systems

    Article • European Journal of Organic Chemistry, July 2005, Wiley

    Jan H Jensen

  88. Determinants of the Relative Reduction Potentials of Type-1 Copper Sites in Proteins

    Article • Journal of the American Chemical Society, June 2004, American Chemical Society (ACS)

    Jan H Jensen

  89. The determinants of carboxyl pKa values in turkey ovomucoid third domain

    Article • Proteins Structure Function and Bioinformatics, March 2004, Wiley

    Jan H Jensen

  90. Improving the efficiency and convergence of geometry optimization with the polarizable continuum model: New energy gradients and molecular surface tessellation

    Article • Journal of Computational Chemistry, January 2004, Wiley

    Jan H Jensen

  91. Determinants of cysteine pKa values in creatine kinase and α1-antitrypsin

    Article • Proteins Structure Function and Bioinformatics, January 2004, Wiley

    Jan H Jensen

  92. Intraprotein electrostatics derived from first principles: Divide-and-conquer approaches for QM/MM calculations

    Article • Journal of Computational Chemistry, October 2003, Wiley

    Jan H Jensen

  93. NMR chemical shifts in the low-pH form of a-chymotrypsin. A QM/MM and ONIOM-NMR study

    Article • Theoretical Chemistry Accounts, April 2003, Springer Science + Business Media

    Jan H Jensen

  94. Continuum solvation of large molecules described by QM/MM: a semi-iterative implementation of the PCM/EFP interface

    Article • Theoretical Chemistry Accounts, March 2003, Springer Science + Business Media

    Jan H Jensen

  95. A Planar Tetracoordinate Carbon and Unusual Bonding in an Organodimetallic Propynylidene Complex Arising from Double C−H Activation of an Allene Ligand

    Article • Journal of the American Chemical Society, February 2003, American Chemical Society (ACS)

    Jan H Jensen

  96. The Prediction of Protein p K a 's Using QM/MM:  The p K a of Lysine 55 in Turkey Ovomucoid Third Domain

    Article • The Journal of Physical Chemistry, April 2002, American Chemical Society (ACS)

    Jan H Jensen

  97. Partial Hessian vibrational analysis: the localization of the molecular vibrational energy and entropy

    Article • Theoretical Chemistry Accounts, April 2002, Springer Science + Business Media

    Jan H Jensen

  98. Boundary Conditions for the Swain−Schaad Relationship as a Criterion for Hydrogen Tunneling

    Article • Journal of the American Chemical Society, April 2002, American Chemical Society (ACS)

    Jan H Jensen

  99. Intermolecular exchange-induction and charge transfer: Derivation of approximate formulas using nonorthogonal localized molecular orbitals

    Article • The Journal of Chemical Physics, May 2001, American Institute of Physics

    Jan H Jensen

  100. Modeling intermolecular exchange integrals between nonorthogonal molecular orbitals

    Article • The Journal of Chemical Physics, May 1996, American Institute of Physics

    Jan H Jensen

  101. Applications of Parallel GAMESS

    Article • May 1995, American Chemical Society (ACS)

    Jan H Jensen

  102. Direct Total Syntheses of Frenolicin B and Kalafungin via Highly Regioselective Diels-Alder Reactions

    Article • The Journal of Organic Chemistry, March 1995, American Chemical Society (ACS)

    Jan H Jensen

  103. Effective Fragment Method for Modeling Intermolecular Hydrogen-Bonding Effects on Quantum Mechanical Calculations

    Article • May 1994, American Chemical Society (ACS)

    Jan H Jensen

  104. General atomic and molecular electronic structure system

    Article • Journal of Computational Chemistry, November 1993, Wiley

    Jan H Jensen

  105. Splicing I: Using mixed basis sets inab initio calculations

    Article • Journal of Computational Chemistry, May 1991, Wiley

    Jan H Jensen