Bakowies, D. ,
" ATOMIC-2 protocol for thermochemistry "
J. Chem. Theory Comput. 2022, 18, 4142-4163.
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Computer code available.
Bakowies D., "Ab initio thermochemistry with ATOMIC-2"     DOI: 10.5281/zenodo.5780172

Bakowies, D.; von Lilienfeld, O. A. ,
" Density functional geometries and zero-point energies in ab initio thermochemical treatments of compounds with first-row atoms (H, C, N, O, F) "
J. Chem. Theory Comput. 2021, 17(8), 4872-4890.
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Bakowies, D. ,
" Estimating systematic error and uncertainty in ab initio thermochemistry: II. ATOMIC(hc) enthalpies of formation for a large set of hydrocarbons "
J. Chem. Theory Comput. 2020, 16(1), 399-426.
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Bakowies, D. ,
" Estimating systematic error and uncertainty in ab initio thermochemistry. I. Atomization energies of hydrocarbons in the ATOMIC(hc) protocol "
J. Chem. Theory Comput. 2019, 15(10), 5230-5251.
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Tahchieva, D. N.; Bakowies, D.; Ramakrishnan R.; von Lilienfeld, O. A. ,
" Torsional potentials of glyoxal, oxalyl halides, and their thiocarbonyl derivatives: Challenges for popular density functional approximations "
J. Chem. Theory Comput. 2018, 14(9), 4806-4817.
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Bakowies, D. ,
" Simplified wave function models in thermochemical protocols based on bond separation reactions "
J. Phys. Chem. A 2014, 118(50), 11811-11827.
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Bakowies, D. ,
" Assessment of density functional theory for thermochemical approaches based on bond separation reactions "
J. Phys. Chem. A 2013, 117(1), 228-243.
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Bakowies, D. ,
" Ab initio thermochemistry with high-level isodesmic corrections: Validation of the ATOMIC protocol for a large set of compounds with first-row atoms (H, C, N, O, F) "
J. Phys. Chem. A 2009, 113(43), 11517-11534.
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Bakowies, D. ,
" Ab initio thermochemistry using optimal-balance models with isodesmic corrections: The ATOMIC protocol "
J. Chem. Phys. 2009, 130, 144113/1-21.
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Free Download Copyright Notice: Copyright (2009) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The article appeared in the Journal of Chemical Physics (citation above) and may be found at the journal webpage .

Bakowies, D. ,
" Ab initio thermochemistry of large molecules "
Scientific Report of the Swiss National Supercomputing Centre (2006/2007) 2008, 32-35.
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Bakowies, D. ,
" Accurate extrapolation of electron correlation energies from small basis sets "
J. Chem. Phys. 2007, 127, 164109/1-12
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Free Download Copyright Notice: Copyright (2007) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The article appeared in the Journal of Chemical Physics (citation above) and may be found at the journal webpage .

Bakowies, D. ,
" Extrapolation of electron correlation energies to finite and complete basis set targets "
J. Chem. Phys. 2007, 127, 084105/1-23.
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Free Download Copyright Notice: Copyright (2007) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The article appeared in the Journal of Chemical Physics (citation above) and may be found at the journal webpage .

van Gunsteren, W. F.; Bakowies, D.; Baron, R. et al.,
" Biomolecular modeling: Goals, problems, perspectives "
Angew. Chem. Int. Ed. 2006, 45, 4064-4092, Angew. Chem. 2006, 118, 4168-4198.
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Bakowies, D. ,
" Atomization energies from ab initio calculations without empirical corrections "
Scientific Report of the Swiss National Supercomputing Centre 2005, 14-17.
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Christen, M.; Hünenberger, P. H.; Bakowies, D. et al.,
" The GROMOS software for biomolecular simulation: GROMOS05 "
J. Comput. Chem. 2005, 26, 1719-1751.
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Chandrasekhar, I.; Bakowies, D.; Glättli, A.; Hünenberger, P.; Pereira, C.; van Gunsteren, W. F.,
" Molecular dynamics simulation of lipid bilayers with GROMOS96: Application of surface tension "
Mol. Simul. 2005, 31, 543-548.
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Baron, R.; Bakowies, D.; van Gunsteren, W. F.,
" Principles of carbopeptoid folding: A molecular dynamics simulation study "
J. Peptide Sci. 2005, 11, 74-84.
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Baron, R.; Bakowies, D.; van Gunsteren, W. F.,
" Carbopeptoid folding: Effects of stereochemistry, chain length, and solvent "
Angew. Chem. Int. Ed. 2004, 43, 4055-4059, Angew. Chem. 2004, 116, 4147-4151.
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Daura, X.; Bakowies, D.; Seebach, D.; Fleischhauer, J.; van Gunsteren, W. F.; Krüger, P.,
" Circular dichroism spectra of β-peptides: Sensitivity to molecular structure and effects of motional averaging "
Eur. Biophys. J. 2003, 32, 661-670.
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Bakowies, D.
" Biomolekulare Reality-Simulationen "
Nachr. Chem. 2003, 51, 788-793.
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Bakowies, D.
" Trendbericht Theoretische Chemie 2002: Kraftfelder für biomolekulare Simulationen "
Nachr. Chem. 2003, 51, 325-327.
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Bakowies, D.
" Analyzing solvent in protein cavities: Methods and application to fatty acid binding protein "
Annual Report of the Competence Center for Computational Chemistry, ETH Zürich 2003, 24-43.
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(Technical Report on a Feature Project)

Baron, R.; Bakowies, D.; van Gunsteren, W. F.; Daura, X.,
" β-peptides with different secondary-structure preferences: How different are their conformational spaces? "
Helv. Chim. Acta 2002, 85, 3872-3882.
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Bakowies, D.; van Gunsteren, W. F.,
" Water in protein cavities: A procedure to identify internal water and exchange pathways and application to fatty acid binding protein "
Proteins 2002, 47, 534-545.
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Bakowies, D.; van Gunsteren, W. F.,
" Simulations of apo and holo-fatty acid binding protein: Structure and dynamics of protein, ligand and internal water "
J. Mol. Biol. 2002, 315, 713-736.
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Gunsteren, W. F.; Bakowies, D.; Bürgi, R. et al.,
" Molecular dynamics simulation of biomolecular systems "
Chimia 2001, 55, 856-860.
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van Gunsteren, W. F.; Bakowies, D.; Damm, W.; Hansson, T; Stocker, U.; Daura, X.,
" Practical aspects of simulation studies of biomolecular systems "
in Dynamics, structure and function of biological macromolecules,
edited by Jardetzky, O. and Finucane, M., NATO ASI Series A315, IOS Press, Amsterdam, 2001, pp. 1-26.
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Kollman, P. A.; Kuhn, B.; Donini, O.; Peräkylä, M.; Stanton, R.; Bakowies, D.,
" Elucidating the nature of enzyme catalysis utilizing a new twist on an old methodology: Quantum mechanical - free energy calculations on chemical reactions in enzymes and in aqueous solution "
Acc. Chem. Res. 2001, 34, 72-79.
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Bakowies, D.; Kollman, P. A.,
" Theoretical study of base-catalyzed amide hydrolysis: Gas and aqueous phase hydrolysis of formamide "
J. Am. Chem. Soc. 1999, 121, 5712-5726.
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Stanton, R. V.; Peräkylä, M.; Bakowies, D.; Kollman, P. A.,
" Combined ab initio and free energy calculations to study reactions in enzymes and solution: Amide hydrolysis in trypsin and aqueous solution "
J. Am. Chem. Soc. 1998, 120, 3448-3457.
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Bakowies, D.; Thiel, W.,
" Hybrid models for combined quantum mechanical and molecular mechanical approaches "
J. Phys. Chem. 1996, 100, 10580-10594.
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Bakowies, D.; Thiel, W.,
" Semiempirical treatment of electrostatic potentials and partial charges in combined quantum mechanical and molecular mechanical approaches "
J. Comput. Chem. 1996, 17, 87-108.
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Bakowies, D.; Bühl, M.; Patchkovskii, S.; Thiel, W.,
" Theoretical studies on giant fullerenes and on endohedral fullerene complexes "
in Fullerenes: Recent advances in the physics and chemistry of fullerenes and related materials, Vol. 3, edited by Ruoff, R. S. and Kadish, K. M., The Electrochemical Society, Pennington, NJ, 1996, pp. 901-910.
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Bakowies, D.; Bühl, M.; Thiel, W.,
" A density functional study on the shape of C₁₈₀ and C₂₄₀ fullerenes "
Chem. Phys. Lett. 1995, 247, 491-493.
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Bakowies, D.; Bühl, M.; Thiel, W.,
" Can large fullerenes be spherical ? "
J. Am. Chem. Soc. 1995, 117, 10113-10118.
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Slanina, Z.; François, J.-P.; Kolb, M.; Bakowies, D.; Thiel, W.,
" Calculated relative stabilities of C₈₄ "
Fullerene Sci. Techn.  1993, 1, 221-230.
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Slanina, Z.; François, J.-P.; Bakowies, D.; Thiel, W.,
" Fullerene C₇₈ isomers: Temperature dependence of their calculated relative stabilities "
J. Mol. Struct.: THEOCHEM 1993, 279, 213-216.
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Bakowies, D.; Kolb, M.; Thiel, W.; Richard, S.; Ahlrichs, R.; Kappes, M. M.,
" Quantum chemical study of C₈₄ fullerene isomers "
Chem. Phys. Lett. 1992, 200, 411-417.
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Bakowies, D.; Gelessus, A.; Thiel, W.,
" Quantum chemical study of C₇₈ fullerene isomers "
Chem. Phys. Lett. 1992, 197, 324-329.
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Slanina, Z.; Adamowicz, L.; Bakowies, D.; Thiel, W.,
" Fullerene C₅₀ isomers: Temperature-induced interchange of relative stabilities "
Thermochim. Acta 1992, 202, 249-254.
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Bakowies, D.; Thiel, W.,
" Theoretical study of Buckminsterfullerene derivatives C₆₀X_n (X=H, F; n = 2, 36, 60) "
Chem. Phys. Lett. 1992, 192, 236-242.
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Bakowies, D.; Thiel, W.,
" MNDO study of large carbon clusters "
J. Am. Chem. Soc. 1991, 113, 3704-3714.
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Bakowies, D.; Thiel, W.,
" Theoretical infrared spectra of large carbon clusters "
Chem. Phys. 1991, 151, 309-321.
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