Mark P. Waller


Google Scholar, ORCID ID

43. Surajit Nandi, Suzanne R. McAnanama-Brereton, Mark P. Waller, Anakuthil Anoop
A Tabu-search Based Strategy for Modeling Molecular Aggregates and Binary Reactions
Computational and Theoretical Chemistry (2017) accepted
42. Marwin H. S. Segler, Mike Preuss, Mark P. Waller
Towards ‘AlphaChem’: Chemical Synthesis Planning with Tree Search and Deep Neural Network Policies, International Conference on Learning Representations 2017, Workshop Track.
arXiv:1702.00020
41. Marwin H.S. Segler, Thierry Kogej, Christian Tyrchan, Mark P. Waller
Generating Focussed Molecule Libraries for Drug Discovery with Recurrent Neural Networks
arXiv:1701.01329 (2017)
40. Marwin H.S. Segler, Mark P. Waller
Neural-Symbolic Machine Learning for Retrosynthesis and Reaction Prediction
Chemistry – A European Journal (2017) in press
DOI: 10.1002/chem.201605499
39. Min Zheng, Mark P. Waller
ChemPreview: Toward an Augmented Reality-based Molecular Interface
Journal of Molecular Graphics and Modelling (2017) 73, 18-23
DOI: 10.1016/j.jmgm.2017.01.019
38. Min Zheng, Jeffrey Reimers, Mark P. Waller, and Pavel Afonine
Q|R: Quantum-based Refinement
Acta Crystallographica Section D (2017) D73, 45-52
DOI: 10.1107/S2059798316019847
37. Jack Yang, Mark P. Waller
A Hybrid Dimer Swarm Optimizer
Computational and Theoretical Chemistry (2017) 1102, 98-104.
DOI: 10.1016/j.comptc.2016.12.019
36. Min Zheng, Mark P. Waller
Toward more efficient density-based adaptive QM/MM methods
Int J. Quant. Chem (2017) e25336
DOI: qua.25336
35. Marwin H. S. Segler and Mark P. Waller
Modelling Chemcial Reasoning to Predict and Invent Reactions
Chem. Eur. J. (2017), 23, 1–12
DOI: chem.201604556
34. Min Zheng, Mark P. Waller
Adaptive QM/MM Methods
WIREs Comput. Mol. Sci. (2016)
DOI: 10.1002/wcms.1255
33. Phillip Scharf, Biswarup Jash, Jissy A. Kuriappan, Mark P. Waller, Jens Müller
Sequence-Dependent Duplex Stabilization of a Metal-Mediated Based Pair.
Chem. Eur. J. (2016) 22, 295-301.
DOI: 10.1002/chem.201503405
32. Sadhana Kumbhar, Saibal Jana, Anakuthil Anoop, Mark P. Waller
Cooperativity in Bimetallic Glutathione Complexes.
J. Mol. Graph. Model. (2015) accepted
DOI: 10.1016/j.jmgm.2015.05.003
31. Malte Behrends, Stefan Wagner, Klaus Kopka, Otmar Schober, Michael Schäfers, Sadhana Kumbhar, Mark P. Waller , Günter Haufe
New matrix metalloproteinase inhibitors based on c-fluorinated a-aminocarboxylic and a-aminohydroxamic acids.
Bioorg. Med. Chem. (2015) 23, 3809-3818.
DOI: 10.1016/j.bmc.2015.03.078
30. Stefanie C. Lange, Jan Unsleber, Patrik Druücker, Hans-Joachim Galla, Mark P. Waller, Bart Jan Ravoo
pH response and molecular recognition in a low molecular weight peptide hydrogel.
Org. Biomol. Chem. (2015) 13, 561-569
DOI: 10.1039/c4ob02069c
29. Mark P. Waller, Sadhana Kumbhar, Jack Yang
A Density Based Adaptive QM/MM Method
ChemPhysChem (2014) 15, 3218–3225
DOI: 10.1002/cphc.201402105
28. Melanie Rauschenberg, Sateesh Bandaru, Mark P. Waller, Bart Jan Ravoo
Peptide Based Carbohydrate Receptors
Chem. Eur. J. (2014) 20, 2779-2782.
DOI: 10.1002/chem.201303777
27. Hendrik Frisch, Jan P. Unsleber, David Lüdeker, Martin Peterlechner, Gunther Brunklaus,  Mark P. Waller, Pol Besenius
pH-Switchable Ampholytic Supramolecular Co-Polymers
Angew. Chem. Int. Ed. (2013) 52, 10097–10101.
DOI:10.1002/anie.201303810
26. Thomas Dresselhaus, Nadine D. Weikart, Henning D. Mootz, Mark P. Waller
Naturally and synthetically linked lys48 diubiquitin: a QM/MM study
RSC Advances (2013) 3, 16122-16129.
DOI:10.1039/C3RA42649A
25. Sadhana Kumbhar, Silke Johannsen, Roland K. O. Sigel, Mark P. Waller, Jens Müller
A QM/MM refinement of an experimental DNA structure with metal-mediated base pairs 
J. Inorg. Biochem. (2013) 127, 203–210.
DOI:10.1016/j.jinorgbio.2013.03.009
24. Thomas Dresselhaus, Jack Yang, Sadhana Kumbhar, Mark P. Waller
A Hybrid Metaheuristic Approach for Non-Local Optimization of Molecular Systems 
J. Chem. Theory Comput., (2013) 9, 2137–2149. 
DOI:10.1021/ct301079m
23. Mark P. Waller, Thomas Dresselhaus, Jack Yang
JACOB: An Enterprise Framework for Computational Chemistry  
J. Comput. Chem., (2013) 34, 1420-1428.
DOI:10.1002/jcc.23272
22. Jack Yang, Mark P. Waller, 
A Systematic Approach to Identify Cooperatively Bound Homotrimers 
J. Phys. Chem. A, (2013) 117, 174−182
DOI:10.1021/jp310067m
21. Jack Yang, Mark P. Waller, 
JACOB: A Dynamic Database for Computational Chemistry Benchmarking 
J. Chem. Inf. Model. (2012) 52, 3255-3262
DOI:10.1021/ci300374g
20. Jack Yang, Mark P. Waller, 
Revealing noncovalent interactions in quantum crystallography: Taurine revisited  
J. Comput. Chem (2012) 34, 466–470
DOI:10.1002/jcc.23155
19. Jens Voskuhl, Mark P. Waller , Sateesh Bandaru, Boryslav A. Tkachenko, Carlo Fregonese, Birgit Wibbeling, Peter R. Schreiner and Bart Jan Ravoo
Nanodiamonds in sugar rings: an experimental and theoretical investigation of cyclodextrin–nanodiamond inclusion complexes  
Org. Biomol. Chem. (2012) 10, 4524-4530
DOI:10.1039/C2OB06915F
18. Mark P. Waller, Holger Kruse, Christian Mück-Lichtenfeld and Stefan Grimme
Investigating inclusion complexes using quantum chemical method.  
Chem. Soc. Rev. (2012) 41, 3119–312
DOI:10.1039/c2cs15244d
17. Sadhana Kumbhar, Frank D. Fischer, Mark P. Waller
Assessment of Weak Intermolecular Interactions Across QM/MM Noncovalent Boundaries. 
J. Chem. Inf. Model. (2012) 52, 93–98
DOI:10.1021/ci200406s
16. Mark P. Waller, Stefan Grimme
Weak Intermolecular Interactions: A Supermolecular Approach. 
Handbook of Computational Chemistry / Leszczynski, Jerzy, editor(s).
Berlin Heidelberg : Springer-Verlag, (2012) 443-466.
15. K. R. Geethalakshmi, Mark P. Waller, Walter Thiel, Michael Bühl,
51V NMR chemical shifts calculated from QM/MM models of Peroxo-forms of Vanadium Haloperoxidases. 
J. Phys. Chem. B (2009) 13, 4456–4465.
DOI:10.1021/jp8109308
14. Mark P. Waller, K. R. Geethalakshmi, Michael Bühl,
51V NMR Chemical Shifts from Quantum-Mechanical/Molecular-Mechanical Models of Vanadium Bromoperoxidase. 
J. Phys. Chem. B (2008) 112, 5813-5823.
DOI:10.1021/jp800580n
13. Mark P. Waller, Michael Bühl, K. R. Geethalakshmi, Dongqi Wang, and Walter Thiel,
51V NMR Chemical Shifts Calculated from QM/MM Models of Vanadium Chloroperoxidase.
Chem. Eur. J. (2007) 13, 4723–4732.
DOI:10.1002/chem.200700295
12. Mark P. Waller, Michael Bühl,
Vibrational Corrections to Geometries of Transition Metal Complexes from Density Functional Theory 
J. Comput. Chem. (2007) 28, 1531–1537.
DOI:10.1002/jcc.20678
11. Mark P. Waller, Heiko Braun, Nils Hojdis, Michael Bühl,
Geometries of Second-Row Transition-Metal Complexes from Density-Functional Theory. 
J. Chem. Theory Comput. (2007) 3, 2234-2242.
DOI:10.1021/ct700178y
10. K. R. Geethalakshmi, Mark P. Waller, and Michael Bühl,
The Presumption of Innocence? A DFT-Directed Verdict on Oxidized Amavadin and Vanadium Catecholate Complexes. 
Inorg. Chem. (2007) 46, 11297−11307.
DOI:10.1021/ic701650y
9. Jacob Overgaard, Mark P. Waller, Ross Piltz, James A. Platts Paul Emseis, Peter A. Williams, Peter Leverett, David E. Hibbs.
Experimental and theoretical charge density distribution of two ternary Co(III) complexes of aromatic acids
J. Phys. Chem. A, (2007), 111, 10123–10133.
DOI:10.1021/jp068621n
8. Mark P. Waller, Sian T. Howard, James A. Platts, Ross O. Piltz, David J. Willock, David E. Hibbs,
Novel Properties from Experimental Charge Densities: An Application to the Zwitterionic Neurotransmitter Taurine. 
Chem. Eur. J. (2006) 12, 7603–7614.
DOI:10.1002/chem.200600392 
7. Mark P. Waller, Arturo Robertazzi, David E. Hibbs, Peter A. Williams, Jamie A. Platts,
Use of DFT for prediction of π-stacking interactions: Applications to benzenes, pyridines, and DNA bases. 
J. Comput. Chem. (2006) 27, 491-504.
DOI:10.1002/jcc.20363
6. Thomas Starke-Peterkovic, Nigel Turner,Mark F. Vitha, Mark P. Waller, David E. Hibbs, Ronald J. Clarke,
Cholesterol increases the dipole potential of lipid membranes via its intrinsic dipole moment.  
Biophys. J. (2006) 90, 4060-4070.
DOI:10.1529/biophysj.105.074666
5. David E. Hibbs, Sian T. Howard, Jeremy Huke, Mark P. Waller,
A new orbital-based-method for the analysis of experimental molecular charge densities: an application to (Z)-N-methyl-C-phenylnitrone.  
Phys. Chem. Chem. Phys. (2005) 7, 1772-1778.
DOI:10.1039/b416614k
4. David E. Hibbs, Jacob Overgaard, James A. Platts, Mark P. Waller, Michael B. Hursthouse,
Experimental and Theoretical Charge Density Studies of Tetrafluorophthalonitrile and Tetrafluoroisophthalonitrile. 
J. Phys. Chem. B (2004) 108, 3663-3672.
DOI:10.1021/jp037700l
3. Jacob Overgaard, Mark P. Waller, James A. Platts, David E. Hibbs,
Influence of crystal effects on molecular charge densities in a study of 9-ethynyl-9-fluorenol.  
J. Phys. Chem. A (2003) 107, 11201-11208.
DOI:10.1021/jp036269x
2. Mark P. Waller, David E. Hibbs, Jacob Overgaard, Jane R. Hanrahan, Trevor W. Hambley,
Flavone.
Acta Cryst., Section E: Structure Reports (2003) E59(6),767-768.
DOI:10.1107/S160053680300730X
1. David E. Hibbs, Jane R. Hanrahan, Micahel B. Hursthouse, David W. Knight, Jacob Overgaard, Peter O. Turner, Ross O. Piltz, Mark P. Waller,
Experimental and theoretical charge distribution in (Z)-N-methyl-C-phenylnitrone.  
Organic & Biomolecular Chemistry (2003) 1, 1034-1040.
DOI: 10.1039/b210698a