[65] Beierlein, F.,Horn, A.H.C., Sticht, H., Mokhir, A.. and Imhof, P.
In Silico Study of Camptothecin-Based Pro-Drugs Binding to Human Carboxylesterase 2
Biomolecules 14 (2024) 153

[64] Klemt, I.; Reshetnikov, V.; Dutta, S.; Bila, G.; Bilyy, R.; Cuartero, I.C.; Hidalgo, A.; Wünsche, A.; Böhm, M.; Wondrak, M.; Kunz-Schughart, L.A., Tietze, R., Beierlein, F., Imhof, P., Gensberger-Reid, S., Pischetsrieder, M., Körber, M., Jost, T., Mokhir, A.  A concept of dual-responsive prodrugs based on oligomerization-controlled reactivity of ester groups: An improvement of cancer cells versus neutrophils selectivity of camptothecin. RSC Med. Chem. (2024)

[63] Gorriz, R.F., Volkenandt, S., and Imhof, P.
Protonation-State Dependence of Hydration and Interactions in the Two Proton-Conducting Channels of Cytochrome c Oxidase
Int. J. Mol. Sci. 24 (2023) 10464

[62] Volkenandt, S. and Imhof, P.
Comparison of Empirical Zn²⁺ Models in Protein–DNA Complexes
Biophysica 3 (2023) 214-330.

[61] Maity, A., Mathur, N., Imhof, P., Singh, N.
Structural analysis of DNA molecule in a confined shell
Physica A: Statistical Mechanics and its Applications (2023) 128382

[60] Gorriz, R.F. and Imhof, P.
Interplay of Hydration and Protonation Dynamics in the K-channel of Cytochrome c Oxidase
Biomolecules 12 (2022) 1615

[59] Mardt, A., Gorriz, R.F., Ferraro, F., Ulrich, P., Zahran, M., Imhof, P.
Effect of a U:G mispair on the water around DNA
Biophysical Chemistry 283 (2022) 106779

[58] Beierlein, F., Volkenandt, S., Imhof, P.
Oxidation Enhances Binding of Extrahelical 5-Methyl-Cytosines by Thymine DNA Glycosylase
J. Phys. Chem. B 126 (2022) 1188-1201

[57] Volkenandt, S., Beierlein, F., Imhof, P.
Interaction of Thymine DNA Glycosylase with Oxidised 5-Methyl-cytosines in Their Amino- and Imino-Forms.
Molecules 26 (2021) 5728.

[56] Bicak, B., Kecel Gunduz, S. , Budama Lilinc, Y., Imhof, P., Gok, B., Akman, G., Ozel, A. E.
Structural, Spectroscopis, in Silico, in Vitro and DNA Binding Evaluations of Tyrosyl-Lysyl-Threonine
Journal of Biomolecular Structure and Dynamics (TBSD) (2021)  https://doi.org/10.1080/07391102.2021.1968499

[55] Absmeier, E., Vester, K., Ghane, T.,  Burakovskiy, D., Milon, P., Imhof, P., Rodnina, M.V., Santos, K.F., Wahl, M.C.
Long-range allostery mediates cooperative adenine nucleotide binding by the Ski2-like RNA helicase Brr2
J. Biol. Chem.  297 (2021) 100829

[54] Hassan,I., Ferraro, F., and Imhof, P.
Effect of the Hydration Shell on the Carbonyl Vibration in the Ala-Leu-Ala-Leu Peptide
Molecules 26  (2021) 2148

[53] Oliveira de Santana, Q.L., Santos Evangelista, T.C., Imhof, P., Baptista Ferreira, S.,  Fernández-Bolaños, J.G., Sydnes, M.O., Lopéz, O. and Lindbäck, E.
Tacrine-sugar mimetic conjugates as enhanced cholinesterase inhibitors
Org. Biomol. Chem. 19 (2021) 2322-2337

[52] Stegmaier, V., Gorriz, R.F., and Imhof, P.
Protonation Dynamics in the K-Channel of Cytochrome c Oxidase estimated from Molecular Dynamics Simulations
Processes 9 (2021) 265

[51] Robalo,  Mendes de Oliveira, D. Imhof, P., Ben-Amotz, D., and Vila Verde, A.
Quantifying how step-wise fluorination tunes local solute hydrophobicity, hydration shell thermodynamics and the quantum mechanical contributions of solute–water interactions
Phys. Chem. Chem. Phys. 22  (2020) 22997

[50] Reidelbach, M. and Imhof, P.
Proton transfer in the D-channel of cytochrome c oxidase modeled by a transition network approach.
Biochimica et Biophysica Acta (BBA) General Subjects 1864 (2020) 129614

[49] Haltenhof,T., Kotte, A., de Bortoli, F., Schiefer, S., Meinke, S., Emmerichs. A.-K., Petermann, K.K.,  Timmermann, B.,  Franz, A., Wahl, M.C., Imhof, P., Preußner, M., and Heyd, F.
A conserved kinase-based body temperature sensor globally controls alternative splicing and gene expression .
Mol. Cell 78 (2020) 57-69

[48] Bagherpoor Helabad, M.,, Volkenandt, S., and Imhof, P. .
Molecular Dynamics Simulations of a Chimeric Androgen Receptor Protein (SPARKI) Confirm the Importance of the Dimerization Domain on DNA Binding Specificity .
Frontiers in Molecular Biosciences 7 (2020) 4

[47] Robalo, J.R., Streacker, L.M.,  Mendes de Oliveira, D. Imhof, P., Ben-Amotz, and D. Vila Verde, A.
Hydrophobic but Water-Friendly: Favorable Water–Perfluoromethyl Interactions Promote Hydration Shell Defects
J. Am. Chem. Soc. 141 (2019) 15856-15868

[46] Krachtus, D., Smith, J.C., and Imhof, P.
Quantum Mechanical/Molecular Mechanical Analysis of the Catalytic Mechanism of Phosphoserine Phosphatase
Molecules 23 (2018) 3342

[45] Reidelbach, M., Weber, M., and Imhof, P.
Prediction of perturbed proton transfer networks
Plos ONE.13 (2018) e0207718

[44] Kanaan, N. and Imhof, P.
Interactions of the DNA Repair Enzyme Human Thymine DNA Glycosylase with cognate and non-cognate DNA
Biochemistry 57 (2018) 5654–5665

[43] Hassan,I., Donati, L., Stensitzki, T., Keller, B.G., Heyne, K., and Imhof, P.
The Vibrational Spectrum of the hydrated Alanine-Leucine Peptide in the Amide region from IR experiments and First Principles Calculations
Chem. Phys. Lett. 698  (2018) 227-223

[42] Ghane, T., Gorriz, R.F., Wrzalek, S., Volkenandt, S., Delatieh, F. Reidelbach, M., and Imhof, P.
Hydrogen-Bonded Network and Water Dynamics in the D-channel of Cytochrome c Oxidase
The Journal of Membrane Biology 251 (2018), 299-314

[41] Batebi, H., Dragelj, J. and Imhof, P.
Role of AP-endonuclease (Ape1) active site residues in stabilization of the reactant enzyme-DNA comples
Proteins:Structure, Function, and Bioinformatics 86 (2018) 439-453

[40] Bagherpoor Helabad, M., Ghane, T., Reidelbach, M., Woelke, A. L., Knapp, E. W., and Imhof, P.
Protonation-state dependent communication in Cytochrome c Oxidase
Biophysical J. 113 (2017) 817-828 (Corrected version of this paper)

[39] Batebi, H. and Imhof, P.
Phosphodiester hydrolysis computed for cluster models of enzymatic active sites.
Theor. Chem. Acc. 135 (2016) 262

[38] Schöne, S., Jurk, M., Bagherpoor Helabad, M., Dror, I., Lebars, I., Kieffer, B., Imhof, P., Rohs, R., Vingron, M., Thomas-Chollier, M., and Meijsing, S.
Sequences flanking the core binding site modulate glucocorticoid receptor structure and activity
Nat. Commun. 7 (2016) 12621

[37] Reidelbach, M., Betz, F., Mäusle, R. M., and Imhof, P.
Proton transfer pathways in an aspartate-water cluster sampled by a network of discrete states
Chem. Phys. Lett. 659 (2016) 169-175

[36] Imhof,P.

A Networks Approach to Modeling Enzymatic Reactions
in Methods in Enzymology: Computational approaches for studying Enzyme Mechanism, (ed. G. A. Voth), 578 (2016) chapter 11, p.249-271

[35] Kanaan, N., Crehuet, R., and Imhof,P.
Mechanism of the Glycosidic Bond Cleavage of Mismatched Thymine in Human Thymine DNA Glycosylase Revealed by Classical Molecular Dynamics and Quantum Mechanical/Molecular Mechanical Calculations
J. Phys. Chem. B 119 (2015) 12365-12380

[34] Bagherpoor Helabad, M., Kanaan, N., and Imhof, P.
Base Flip in DNA Studied by Molecular Dynamics Simulations of Differently-Oxidized Forms of Methyl-Cytosine
  Int. J. Mol. Sci 15 (2014) 11799-11816

[33] Ivchenko, O., Bachert, P., and Imhof, P.
Umbrella sampling of proton transfer in a creatine-water system
Chem. Phys. Lett 600 (2014) 51-55

[32] Ivchenko, O., Whittleston, C.S., Carr, J.M., Imhof, P., Goerke, S., Bachert, P. and Wales, D.J.
Proton Transfer Pathways, Energy Landscape, and Kinetics in Creatine–Water Systems
J. Phys. Chem. B 118 (2014) 1969–1975

[31] Vasu, K., Nagamalleswar, E., Zahran, M., Imhof, P., Xu, S.-Y., Zhu, Z., Chan, S.-H. and Nagaraja, V.
Increasing cleavage specificity and activity of restriction endonuclease KpnI
Nucl. Acid. Res. 41 (2013) 9812-9824

[30] Imhof, P. and Zahran, M.
The effect of a G:T mispair on the dynamics of DNA
Plos ONE 8 (2013) e53305

[29] Imhof, P.
A computational study of the absorption spectra of the photoconvertible fluorescent protein EosFP in different protonation states
J. Chem. Theory Comput. 8 (2012) 4828-4836

[28] Held. M, Imhof, P., Keller, B. and Noe, F.
Modulation of a Ligand's Energy Landscape and Kinetics by the Chemical Environment
J. Phys. Chem. B 116 (2012) 13597-13607

[27] Berezniak, T., Jäschke, A. and Smith, J. C and Imhof, P.
Stereoselection in the Diels-Alderase Ribozyme: A Molecular Dynamics Study
J. Comp. Chem. 33 (2012) 1603-1614

[26] Zahran, M., Berezniak, T., Imhof, P. and Smith, J. C.
Role of Magnesium Ions in DNA Recognition by the EcoRV Restriction Endonuclease,
FEBS Letters 585 (2011) 2739-2743

[25] Parks, J. M., Imhof, P. and Smith, J. C.
Modelling Enzyme Catalysis by Computer Simulations
Istvan T. Horvath (ed.), Encyclopedia of Catalysis, John Wiley & Sons Ltd.

[24] Berezniak, T., Zahran, M., Imhof, P., Jäschke, A. and Smith, J. C.
Magnesium-Dependent Active-Site Conformational Selection in the Diels-Alderase Ribozyme
J. Am. Chem. Soc, 132 (2010) 12587-12596

[23] Zahran, M., Daidone, I., Smith, J. C., and Imhof, P.
Mechanism of DNA recognition by the Restriction Enzyme EcoRV
J. Mol. Biol., 401 (2010) 415-432

[22] Imhof, P., Fischer, S. and Smith, J. C.
Catalytic Mechanism of DNA Backbone Cleavage by the Restriction Enzyme EcoRV: A Quantum Mechanical/Molecular Mechanical Analysis
Biochemistry, 48 (2009) 9061-9075

[21] Zahran, M., Imhof, P., and Smith, J. C.
Sequence specific DNA recognition by EcoRV
Hansmann, U. H., Meinke, J. H., Mohanty, S., Nadler, W., and Zimmermann, O. (eds.), From Computational Biophysics to Systems Biology 2008 (CBSB08), Jülich, vol. 40, (2008) pp. 417–420, Proceedings, NIC Series Juelich

[20] Imhof, P., Noé, F., Fischer, S., and Smith, J. C.
AM1/d parameters for magnesium in metalloenzymes
J. Chem. Theory Comput., 2 (2006) 1050–1056

[19] Jagoda, M., Warzeska, S., Pritzkow, H., Wadepohl, H., Imhof, P., Smith, J. C., and Krämer, R.
Catalytic transesterification of dialkyl phosphates by a bioinspired dicopper(II) macrocyclic complex
J. Am. Chem. Soc, 127 (2005) 15061–15070

[18] Imhof, P., Fischer, S., Krämer, R., and Smith, J. C.
Density functional theory analysis of dimethylphosphate hydrolysis: effect of solvation and nucleophile variation
J. Mol. Struct. (Theochem), 713 (2005) 1–5

[17] Imhof, P., Krügler, D., Brause, R., and Kleinermanns, K.
Geometry change of simple aromatics upon electronic excitation obtained from Franck-Condon fits of dispersed fluorescence spectra
J. Chem. Phys., 121 (2004) 2598–2610

[16] Bühl, M., Schurhammer, R., and Imhof, P.
Peroxovanadate imidazole complexes as catalysts for olefin epoxidation: Density functional study of dynamics, 51V NMR chemical shifts, and mechanism
J. Am. Chem. Soc., 126 (2004) 3310–3320

[15] Bühl, M., Imhof, P., and Repisky, M.
Rovibrational corrections to transition metal NMR shielding constants
Chem Phys Chem, 5 (2004) 410–414

[14] Spangenberg, D., Imhof, P., and Kleinermanns, K.
The S1 state geometry of phenol determined by simultaneous Franck Condon and rotational constants fits
Phys. Chem. Chem. Phys., 5 (2003) 2505–2514

[13] Imhof, P., Brause, R., and Kleinermanns, K.
Determination of ground state vibrational frequencies of jet-cooled resorcinol by means of dispersed fluorescence spectroscopy and ab Initio calculations
J. Mol. Spec., 201 (2002) 65–70

[12] Imhof, P. and Kleinermanns, K.
Dispersed fluorescence spectroscopy of pchlorophenol
Phys. Chem. Chem. Phys., 4 (2002) 264–170

[11] Nir, E., Janzen, C., Imhof, P., Kleinermanns, K., and de Vries, M. S.
Pairing of the nucleobases guanine and cytosine in the gas phase studied by IR–UV doubleresonance spectroscopy and ab initio calculations
Phys. Chem. Chem. Phys., 4 (2002) 732–739

[10] Nir, E., Janzen, C., Imhof, P., Kleinermanns, K., and de Vries, M. S.
Pairing of the nucleobase guanine studied by IR–UV double-resonance spectroscopy and ab initio calculations
Phys. Chem. Chem. Phys., 4 (2002) 740–750.

[9] Nir, E., Janzen, C., Imhof, P., Kleinermanns, K., and de Vries, M. S.
Guanine tautomerism revealed by UV–UV and IR–UV hole burning spectroscopy
J. Chem. Phys., 115 (2001) 4604–4611

[8] Imhof, P. and Kleinermanns, K.
Dispersed fluorescence spectra and ab initio calculations of o-Cyanophenol
J. Phys. Chem. A, 105 (2001) 8922–8925

[7] Imhof, P. and Kleinermanns, K.
Dispersed fluorescence spectra of chlorobenzene
Chem. Phys., 270 (2001) 227–236

[6] Roth, W., Imhof, P., and Kleinermanns, K.
Laser induced dispersed fluorescence spectroscopy and ab initio calculations of p-cyanophenol
Phys. Chem. Chem. Phys., 3 (2001) 1806

[5] Nir, E., Imhof, P., Kleinermanns, K., and deVries, M. S.
REMPI spectroscopy of laser desorbed guanosines
J. Am. Chem. Soc., 122 (2000) 8091–809

[4] Roth, W., Imhof, P., Gerhards, M., Schumm, S., and Kleinermanns, K.
Reassignment of ground and first excited state vibrations in phenol
Chem. Phys., 252 (2000) 247–256

 [3] Spangenberg, D., Imhof, P., Roth, W., Janzen, C., and Kleinermanns, K.
Phenol-(ethanol)₁ isomers studied by double-resonance spectroscopy and ab initio calculations
J. Phys. Chem.A, 103 (1999) 5918–5924

 [2] Imhof, P., Roth, W., Janzen, C., Spangenberg, D., and Kleinermanns, K.
Hydrogen-bonded phenol-acid clusters studied by vibrational resolved laser spectroscopy
and ab initio calculations - I. Formic acid
Chem. Phys., 242 (1999) 141–151

 [1] Imhof, P., Roth, W., Janzen, C., Spangenberg, D., and Kleinermanns, K.
Hydrogen-bonded phenol-acid clusters studied by vibrational resolved laser spectroscopy
and ab initio calculations - II. Acetic acid
Chem. Phys., 242 (1999) 153–159