Publications

Ph.D. Dissertation

   M. Haranczyk - "Algorithms and Software Tools for Exploration of Chemical Spaces, Charge Distributions, and Solvation Effects. Applications thereof to DNA Fragments." - University of Gdansk, Poland, 2008. Click here to download.
Advisor: Prof. Maciej Gutowski
Referees: Prof. Lucjan Piela (University of Warsaw, Poland) and Prof. Jozef A. Liwo (University of Gdansk, Poland)

Books and book chapters

   J. Rak, K. Mazurkiewicz, M. Kobylecka, P. Storoniak, M. Haranczyk, I. Dabkowska, R.A. Bachorz, M. Gutowski, D. Radisic, S.T. Stokes, S.N. Eustis, D. Wang, X. Li, Y.J. Ko, K. H. Bowen - "Stable Valence Anions of Nucleic Acid Bases and DNA Strand Breaks Induced by Low Energy Electrons" in Radiation Induced Molecular Phenomena in Nucleic Acid: A Comprehensive Theoretical and Experimental Analysis in the book series Challenges and Advances in Computational Chemistry and Physics edited by M. K. Shukla, J. Leszczynski and published by Springer (2008), pp. 619-667.

Research Articles (h-index: 20)

1. R.L. Martin, L.-C. Lin, K. Jariwala, B. Smit, M. Haranczyk - "Mail-order MOFs: designing isoreticular MOF-5 analogues comprising commercially available organic molecules" - Journal of Physical Chemistry C - in press

2. R.L. Martin, M. Haranczyk - "Exploring frontiers of high surface area metal-organic frameworks" - Chemical Science 4 (2013) 1781-1785

3. F. Yan, M. Lartey, K. Damodaran, E. Albenze, R. Thompson, J. Kim, M. Haranczyk, H. Nulwala, D. Luebke, B. Smit - "Understanding the effect of side groups in ionic liquids on carbon-capture properties: a combined experimental and theoretical effort" - Physical Chemistry and Chemical Physics (PCCP) 15 (2013) 3264-3272

4. R. L. Martin, Prabhat, D.D. Donofrio, J.A. Sethian, M. Haranczyk - "Accelerating analysis of void space in porous materials on multicore and GPU platforms" - International Journal of High Performance Computing Applications 26 (2012)

5. M. Haranczyk, P. Urbaszek, E.G. Ng, T. Puzyn - "Combinatorial x Computational x Cheminformatics Approach to Characterization of Congeneric Libraries of Organic Pollutants" - Journal of Chemical Information and Modeling 52 (2012) 2902-2909.

6. R.L. Martin, T.F. Willems, L-C. Lin, J. Kim, J. Swisher, B. Smit, M. Haranczyk -" Similarity-driven Discovery of Porous Materials for Adsorption-based Separations" - ChemPhysChem 13 (2012) 13, 3595 - 3597

7. J. Kim, L.-C. Lin, R.L. Martin, J. Swisher, M. Haranczyk, B. Smit - "Large-scale Computational Screening of Zeolites for Ethane/Ethene Separation" - Langmuir Langmuir 28 (2012) 11914-11919

8. L-C. Lin, A. Berger, R.L. Martin, J. Kim, J. Swisher, K. Jariwala, C.H. Rycroft, A. Bhown, M.W. Deem, M. Haranczyk, B. Smit, B. - In silico screening for carbon capture materials - Nature Materials - 11 (2012) 633-641

9. J. Kim, R.L. Martin, O. Ruebel, M. Haranczyk, B. Smit - High-throughput Characterization of Porous Materials Using Graphics Processing Units - Journal of Chemical Theory Computation 8 (2012) 1684-1693

10. R.L. Martin, B. Smit, M. Haranczyk - "Addressing challenges of identifying geometrically diverse sets of crystalline porous materials" - Journal of Chemical Information and Modeling 52 (2012) 308-318

11. T.F. Willems, C.H. Rycroft, M. Kazi, J.C. Meza, M. Haranczyk - "Algorithms and tools for high-throughput geometry-based analysis of crystalline porous materials" - Microporous and Mesoporous Materials 149 (2012) 134-141

12. M. Haranczyk, R. L. Martin, Prabhat, J.A. Sethian - "Computational Approaches for the High-Throughput Analysis of Porous Materials for Energy-related Applications" - Proceedings of the 2011 SciDAC Conference

13. J. Kim, A. Koniges, R. L. Martin, M. Haranczyk, J. A. Swisher, B. Smit - "GPU Computational Screening of Carbon Capture Materials" - Proceedings of the 2011 SciDAC Conference

14. R. L. Martin, Prabhat, D.D. Donofrio, J.A. Sethian, M. Haranczyk - "Accelerating analysis of void space in porous materials on multicore and GPU platforms" - International Journal of High Performance Computing Applications - in press

15. N.E.R. Zimmermann, M. Haranczyk, M. Sharma, B. Liu, B. Smit, F.J. Keil, - "Adsorption and Diffusion in Zeolites: The Pitfall of Isotypic Crystal Structures" - Molecular Simulations 37 (2011) 986-989

16. K. Beketayev, G. H. Weber, M. Haranczyk, P-T. Bremer, M. Hlawitschka, B. Hamann - "Topology-based Visualization of Transformation Pathways in Complex Chemical Systems" - Computer Graphics Forum 30 (2011) 663-672

17. T. Puzyn, A. Gajewicz, A. Rybacka, M. Haranczyk - "Global vs. local QSPR models for Persistent Organic Pollutants: Balancing between predictivity and economy" - Structural Chemistry 22 (2011) 873-884

18. T. Puzyn, M. Haranczyk, N. Suzuki, T. Sakurai - "Estimating persistence of brominated and chlorinated organic pollutants in air, water, soil and sediments with the QSPR-based classification scheme" - Molecular Diversity 15 (2011) 173-188

19. M. Haranczyk, J.A. Sethian - "Automatic structure analysis in high-throughput characterization of porous materials" -Journal of Chemical Theory and Computation 6 (2010) 3472-3480

20. Y. Jae Ko, H. Wang, D. Radisic, S. T. Stokes, S. N. Eustis, K. H. Bowen, K. Mazurkiewicz, P. Storoniak, A. Kowalczyk, M. Haranczyk, M. Gutowski, J. Rak - "Barrier-Free Proton Transfer Induced by Electron Attachment to the Complexes between 1 Methylcytosine and Formic Acid" - Molecular Physics 108 (2010) 2621-2631

21. P. Storoniak, K. Mazurkiewicz, M. Haranczyk, M. Gutowski, J. Rak, S. N. Eustis,Y. Jae Ko, H. Wang, K. H. Bowen - "The anionic (9-methyladenine)-(1-methylthymine) base pair solvated by formic acid. A computational and photoelectron spectroscopy study" - J. Phys. Chem. B 114 (2010) 11353-11362.

22. M. Haranczyk, T. Puzyn, E. Ng - "On Enumeration of Congeners of Common Persistent Organic Pollutants" - Environmental Pollution 158 (2010) 2786-2789

23. M. Haranczyk, M. Gutowski - "Combinatorial-Computational-Chemoinformatics (C3) approach to finding and analyzing low-energy tautomers" - Journal of Computer Aided Molecular Design 24 (2010) 627-638

24. A. Mostrag, T. Puzyn, M. Haranczyk - "Modeling the overall persistence and environmental mobility of sulfur-containing polychlorinated organic compounds" - Environmental Science and Pollution Research 17 (2010) 470-477.

25. K. Theisen, B. Smit, M. Haranczyk - "Chemical Hieroglyphs: Abstract Depiction of Complex Void Space Topology of Nanoporous Materials" - Journal of Chemical Information and Modeling 50 (2010) 461-469.

26. M. Haranczyk, J.A. Sethian - "Navigating molecular worms inside chemical labyrinths" - Proceedings of National Academy of Science (PNAS) 106 (2009) 21472-21477

27. A. Gajewicz, M. Haranczyk, T. Puzyn - "Predicting logarithmic values of the subcooled liquid vapor pressure of halogenated persistent organic pollutants with QSPR: How different are chlorinated and brominated congeners?" - Atmospheric Environment 44 (2010) 1428-1436.

28. E.J. Gardiner, V.J. Gillet, M. Haranczyk, J. Hert, J.D. Holliday, N. Malim, Y. Patel, P. Willett - "Turbo Similarity Searching: Evaluation of Virtual-Screening Performance" - Statistical Analysis and Data Mining 2 (2009) 103-114

29. A. Al Khalifa, M. Haranczyk, J. Holliday - "Comparison of Non-binary Similarity Coefficients for Similarity Searching, Clustering and Compound Selection" -Journal of Chemical Information and Modelling 49 (2009) 1193-1201

30. S. Kamerlin, M. Haranczyk, A. Warshel - "Are mixed explicit/implicit solvation models reliable for studying phosphate hydrolysis? A comparative study of continuum, explicit and mixed solvation models" - ChemPhysChem 10 (2009) 1125-1134

31. W. Yu, L. Liang, Z. Lin, S. Ling, M. Haranczyk, M. Gutowski - Comparison of Some Representative DFT and WFT Methods for the Studies of Amino Acids - Journal of Computational Chemistry - 30 (2009) 589-600

32. S. Kamerlin, M. Haranczyk, A.Warshel - "Progresses in Ab Initio QM/MM Free Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of pKa, Redox Reactions and Solvation Free Energies" - Journal of Physical Chemistry B - 113 (2009) 1253-1272 (Featured on the cover)

33. R. Bachorz, G. Lupica, M. Gutowski, M. Haranczyk - "Electrostatic Potential Maps of Damaged DNA Studied by Image Analysis Tools. 8-Oxoguanine and Abasic Site Lesions" - Journal of Molecular Modeling - 15 (2009) 817-827

34. M. Haranczyk, M. Gutowski, A. Warshel - Solvation free energies of molecules. The most stable anionic tautomers of uracil -Physical Chemistry Chemical Physics - 10 (2008) 4442-4448 (Featured on the cover)

35. S.N. Eustis, D. Radisic, K.H. Bowen, R.A. Bachorz, M. Haranczyk, G.K. Schenter, M. Gutowski - Electron-Driven Acid-Base Chemistry: Proton Transfer from Hydrogen Chloride to Ammonia - Science 319 (2008) 936-939 (Featured on the cover)

36. M. Haranczyk, J. Holliday, P. Willett, M. Gutowski - Structure and Singly Occupied Molecular Orbital Analysis of Anionic Tautomers of Guanine - Journal of Computational Chemistry 29 (2008) 1277-1291 - (Featured on the cover)

37. M. Haranczyk, T. Puzyn, P. Sadowski - ConGENER - A Tool for Modeling of the Congeneric Sets of Environmental Pollutants - QSAR and Combinatorial Science 27 (2008) 826-833

38. T. Puzyn, N. Suzuki, M. Haranczyk, J. Rak - Calculation of quantum-mechanical descriptors for QSPR at the DFT level is unnecessary? - Journal of Chemical Information and Modeling 48 (2008) 1174-1180

39. T. Puzyn, N. Suzuki, M. Haranczyk - How do the partitioning properties of polyhalogenated POPs change when chlorine is replaced with bromine? - Environmental Science and Technology 42 (2008) 5189-5195

40. A. V. Pisliakov, P. K. Sharma, Z. T. Chu, M. Haranczyk, A. Warshel - Electrostatic Basis for the Unidirectionality of the Primary Proton Transfer in Cytochrome c Oxidase -Proceedings of National Academy of Science (PNAS) 105 (2008) 7726-7731

41. E. Rosta, M. Haranczyk, Z.T. Chu, A. Warshel - Accelerating QM/MM Free Energy Calculations: Representing the Surroundings by an Updated Mean Charge Distribution -Journal of Physical Chemistry B 112 (2008) 5680-5692

42. M. Haranczyk, M. Gutowski - Visualization of molecular orbitals and the related electron densities - Journal of Chemical Theory and Computation 4 (2008) 689-693

43. M. Haranczyk, J. Holliday - Comparison of Similarity Coefficients for Clustering and Compound Selection - Journal of Chemical Information and Modeling 48 (2008) 498-508

44. M. Haranczyk, M. Gutowski - Effect of excess electron and one water molecule on relative stability of the canonical and zwitterionic tautomers of glycine -Journal of Chemical Physics 128 (2008) 125101-125112 (Selected for the April 1, 2008 issue of Virtual Journal of Biological Physics Research published by American Institute of Physics)

45. M. Haranczyk, G. Lupica, I. D¹bkowska, M. Gutowski - Cylindrical Projection of Electrostatic Potential and Image Analysis Tools for Damaged DNA. The Substitution of Thymine with Thymine Glycol - Journal of Physical Chemistry B 112 (2008) 2198-2206

46. M. Haranczyk, M. Gutowski, X. Li, K.H. Bowen - Bound anionic states of adenine. Theoretical and photoelectron spectroscopy study -Proceedings of National Academy of Science (PNAS) 104 (2007) 4804-4807

47. M. Haranczyk, M. Gutowski, X. Li, K.H. Bowen - Adiabatically bound anions of guanine - Journal Physical Chemistry B 111 (2007) 14073-14076

48. X. Li, K.H. Bowen M. Haranczyk, R.A. Bachorz, K. Mazurkiewicz, J. Rak, M. Gutowski - Photoelectron spectroscopy of adiabatically bound valence anions of rare tautomers of the nucleic acid bases - Journal of Chemical Physics 127 (2007) 174309

49. K. Mazurkiewicz, M. Haranczyk, P. Storoniak, M. Gutowski, J. Rak, D. Radisic, S.N. Eustis, D. Wang, K.H. Bowen - Intermolecular proton transfer induced by excess electron attachment to adenine-(formic acid)n (n=2,3) hydrogen-bonded complexes - Chemical Physics 342 (2007) 215-222

50. M. Haranczyk, M. Gutowski - Quantum Mechanical Energy -Based Screening of Combinatorially Generated Library of Tautomers. TauTGen: A Tautomer Generator Program - Journal of Chemical Information and Modeling 47 (2007) 686-694.

51. K. Mazurkiewicz, M. Haranczyk, M. Gutowski, J. Rak, D. Radisic, S. N. Eustis, D. Wang, K.H. Bowen, Jr. - Valence anions in complexes of adenine and 9-methyladenine with formic acid - stabilization by intermolecular proton transfer - Journal of American Chemical Society (JACS) 129 (2007) 1216-1224.

52. M. Haranczyk, J.H. Miller, M. Gutowski - Differences in Electrostatic Potential around DNA Fragments Containing Adenine and 8-oxo-Adenine. An Analysis Based on Regular Cylindrical Projection - Journal of Molecular Graphics and Modelling 26 (2007) 282-289

53. K. Mazurkiewicz, M. Haranczyk, M. Gutowski, J. Rak - Can an excess electron localise on a purine moiety in the adenine-thymine Watson-Crick base pair? A computational study - International Journal of Quantum Chemistry 107 (2007) 2224-2232

54. M. Haranczyk, M. Gutowski - Differences in Electrostatic Potential Around DNA Fragments Containing Guanine and 8-oxo-Guanine -Theoretical Chemistry Accounts 117 (2007) 291-296.

55. S. Ling, W. Yu, Z. Huang, Z. Lin, M. Haranczyk, M. Gutowski - Gaseous Arginine Conformers and Their Unique Intramolecular Interactions - Journal of Physical Chemistry A 104 (2006) 12282-12291.

56. M. Haranczyk, M. Gutowski - Finding Adiabatically Bound Anions of Guanine through Combinatorial-Computational Approach - Angewandte Chemie Int. Ed. 44 (2005) 6585-6588.

57. J.H. Miller, A. Aceves, M. Nerst, M. Haranczyk, M. Gutowski, E. Vorpagel, M. Dupuis - Structure and Energetics of Clustered Damage Sites -Radiation Research 164 (2005) 582-585

58. M. Haranczyk, J. Rak and M. Gutowski - Stabilization of very rare tautomers of 1-methylcytosine by an excess electron - Journal of Physical Chemistry A 109 (2005) 11495-11503

59. M. Haranczyk, J. Rak, M. Gutowski, D. Radisic, S.T. Stokes, K.H. Bowen - Intermolecular proton transfer In anionic complexes of uracyl with alcohols - Journal of Physical Chemistry B 109 (2005) 13383-13391.

60. R.A. Bachorz, M. Haranczyk, I. Dabkowska, J. Rak and M Gutowski - Anion of the formie acid dimer as a model for intermolecular proton transfer induced by a p* excess electron -Journal of Chemical Physics 122 (2005) 204304

61. M. Haranczyk, M. Gutowski - Valence and dipole-bound anions of the most stable tautomers of guanine - The Journal of the American Chemical Society (JACS) 127 (2005) 699-706

62. M. Haranczyk, J. Rak, M. Gutowski, D. Radisic, S.T. Stokes, J.M. Nilles, and K.H. Bowen, Jr. - Effect of Hydrogen Bonding on Barrier-Free Proton Transfer in Anionic Complexes of Uracil with Weak Acids: (U...HCN)^- versus (U...H₂S)^- - The Jortner Special Issue of the Israel Journal of Chemistry 44 (2004) 157-170

63. M. Haranczyk, M. Gutowski - Fluorine-Substituted Phenols as Probes to Study Intermolecular Proton Transfer Induced by Excess Electron Attachment to Uracil-Phenol Complexes -Internet Electronic Journal of Molecular Design 3 (2004) 368-378

64. M. Haranczyk, I. Dabkowska, J. Rak, M. Gutowski, M. Nilles, S. Stokes, D. Radisic, K.H. Bowen, Jr. - Excess Electron Attachment Induces Barrier-Free Proton Transfer in Anionic Complexes of Thymine and Uracil with Formic Acid - The Journal of Physical Chemistry B 108 (2004) 6919-6921

65. M. Haranczyk, R. Bachorz, J. Rak, M. Gutowski, D. Radisic, M. Nilles and K. H. Bowen, Jr. - Excess Electron Attachment Induces Barrier-Free Proton Transfer in Binary Complexes of Uracil with H₂Se or H₂S but not with H₂O - The Journal of Physical Chemistry B 107 (2003) 7889-7895

66. M. Haranczyk, P.C. Burgers and P.J.A. Ruttink - Catalysis models for the enolization of the acetaldehyde radical cation - Int. J. of Mass Spectrometry 220 (2002) 53-67