Publications
Insights into the Variations of Kinetic and Potential Energies in a Multi-Bond Reaction: The Reaction Electronic Flux Perspective
Villegas-Escobar, N. J. Mol. Model. 2024, 30 (8), 262.
11-Jul-2024
Molecular Environment Modulates CO2 Liberation from Carboxy-Biotin
Murillo-Lopez, J. A.; Villegas-Escobar, N.; Vogt-Geisse, S.; Vöhringer-Martinez, E. J. Phys. Chem. B 2024, 128 (22), 5327–5335.
21-May-2024
Grid: A Python Library for Molecular Integration, Interpolation, Differentiation, and More
Tehrani, A.; Yang, X. D.; Martínez-González, M.; Pujal, L.; Hernández-Esparza, R.; Chan, M.; Vöhringer-Martinez, E.; Verstraelen, T.; Ayers, P. W.; Heidar-Zadeh, F. Journal of Chemical Physics 2024, 160 (17), 172503.
03-May-2024
The Tale of HORTON: Lessons Learned in a Decade of Scientific Software Development
Chan, M.; Verstraelen, T.; Tehrani, A.; Richer, M.; Yang, X. D.; Kim, T. D.; Vöhringer-Martinez, E.; Heidar-Zadeh, F.; Ayers, P. W. . Journal of Chemical Physics 2024, 160 (16), 162501.
23-Apr-2024
Nonbonded Force Field Parameters from MBIS Partitioning of the Molecular Electron Density Improve Binding Affinity Predictions of the T4-Lysozyme Double Mutant
Macaya, L.; González, D.; Vöhringer-Martinez, E. Journal Chemical Information Modeling 2024.[ChemRXiv]
28-Mar-2024
Infrared Spectroscopy Reveals Metal-Independent Carbonic Anhydrase Activity in Crotonyl-CoA Carboxylase/Reductase
Gomez, A.; Tinzl, M.; Stoffel, G.; Westedt, H.; Grubmüller, H.; Erb, T. J.; Vöhringer-Martinez, E.; Stripp, S. T. Chemical Science 2024, 15 (13), 4960–4968..
29-Feb-2024
Air- and Water-Stable Heteroleptic Copper (I) Complexes Bearing Bis(Indazol-1-Yl)Methane Ligands: Synthesis, Characterisation, and Computational Studies
Moreno-da Costa, D.; Zúñiga-Loyola, C.; Droghetti, F.; Robles, S.; Villegas-Menares, A.; Villegas-Escobar, N.; Gonzalez-Pavez, I.; Molins, E.; Natali, M.; Cabrera, A. R. Molecules 2023, 29 (1), 47.
18-Dec-2023
Conformational Dynamics of the Most Efficient Carboxylase Contributes to Efficient CO2 Fixation
Gomez, A.; Erb, T. J.; Grubmüller, H.; Vöhringer-Martinez, E. Journal Chemical Information Modeling 2023, 63 (24), 7807–7815. [ChemRXiv]
04-Dec-2023
Covalent Adduct Formation as a Strategy for Efficient CO2 Fixation in Crotonyl-CoA Carboxylases/Reductases
Recabarren, R.; Tinzl, M.; Saez, D. A.; Gomez, A.; Erb, T. J.; Vöhringer-Martinez, E. ACS Catalysis 2023, 13 (9), 6230–6241.[ChemRXiv]
21-Apr-2023
High-Level Coupled-Cluster Study on Substituent Effects in H2 Activation by Low-Valent Aluminyl Anions
Villegas-Escobar, N.; Hoobler, P. R.; Toro-Labbé, A.; Schaefer, H. F. J. Phys. Chem. A 2023, 127 (4), 956–965
23-Jan-2023
Diverse Cooperative Reactivity at a Square Planar Aluminium Complex and Catalytic Reduction of CO2
Shaves, C. L.; Villegas‐Escobar, N.; Clark, E. R.; Riddlestone, I. M. Chem. Eur. J. 2023, 29 (16), e202203806
13-Dec-2022
Ene-Adducts from 1,4-Dihydropyridines and α,β-Unsaturated Nitriles: Asynchronous Transition States Displaying Aromatic Features.
Saez, D. A.; Vogt-Geisse, S.; Vöhringer-Martinez, E. Org. Biomol. Chem. 2022, 20 (44), 8662–8671. .
14-Oct-2022
Nonbonded Force Field Parameters from Minimal Basis Iterative Stockholder Partitioning of the Molecular Electron Density Improve CB7 Host–Guest Affinity Predictions
Duván González, Luis Macaya, Carlos Castillo-Orellana, Toon Verstraelen, Stefan Vogt-Geisse, Esteban Vöhringer-Martinez Journal of Chemical Information and Modeling 2022, 62 (17), 4162–4174.
12-Sep-2022
Binding Energy Evaluation Platform: A Database of Quantum Chemical Binding Energy Distributions for the Astrochemical Community
Giulia Bovolenta, Stefan Vogt-Geisse, Stefano Bovino, Tommaso Grassi Astrophysical Journal Supplement Series 2022, 262 (1), 17.
24-Aug-2022
Constrained iterative Hirshfeld charges: A variational approach
Leila Pujal, Maximilian van Zyl, Esteban Vöhringer-Martinez, Toon Verstraelen, Patrick Bultinck, Paul W Ayers, Farnaz Heidar-Zadeh Journal of Chemical Physics 2022, 156 (19), 194109.
21-May-2022
Intersubunit Coupling Enables Fast CO2-Fixation by Reductive Carboxylases
Hasan DeMirci, Yashas Rao, Gabriele M Stoffel, Bastian Vögeli, Kristina Schell, Aharon Gomez, Alexander Batyuk, Cornelius Gati, Raymond G Sierra, Mark S Hunter, E Han Dao, Halil I Ciftci, Brandon Hayes, Fredric Poitevin, Po-Nan Li, Manat Kaur, Kensuke Tono, David Adrian Saez, Samuel Deutsch, Yasuo Yoshikuni, Helmut Grubmüller, Tobias J Erb, Esteban Vöhringer-Martinez, Soichi Wakatsuki ACS Central Science 2022, 8 (8), 1091–1101.
25-Apr-2022
Molecular Environment-Specific Atomic Charges Improve Binding Affinity Predictions of SAMPL5 Host–Guest Systems
González, D.; Macaya, L.; Vöhringer-Martinez, E. Journal of Chemical Information. Modeling. 2021, 61 (9), 4462–4474.
31-Oct-2021
Long-Range Structural Defects by Pathogenic Mutations in Most Severe Glucose-6-Phosphate Dehydrogenase Deficiency
Horikoshi, N.; Hwang, S.; Gati, C.; Matsui, T.; Castillo-Orellana, C.; Raub, A. G.; Garcia, A. A.; Jabbarpour, F.; Batyuk, A.; Broweleit, J.; Xiang, X.; Chiang, A.; Broweleit, R.; Vöhringer-Martinez, E.; Mochly-Rosen, D.; Wakatsuki, S. . Proceedings National Academy Sciences USA 2021, 118 (4), e2022790118.
26-Jan-2021
IOData : A Python Library for Reading, Writing, and Converting Computational Chemistry File Formats and Generating Input Files
Verstraelen, T.; Adams, W.; Pujal, L.; Tehrani, A.; Kelly, B. D.; Macaya, L.; Meng, F.; Richer, M.; Hernández‐Esparza, R.; Yang, X. D.; Chan, M.; Kim, T. D.; Cools‐Ceuppens, M.; Chuiko, V.; Vöhringer‐Martinez, E.; Ayers, P. W.; Heidar‐Zadeh, F.. Journal Computational Chemistry 2021, 42 (6), 458–464.
27-Dec-2020
High level ab initio binding energy distribution of molecules on interstellar ices: Hydrogen fluoride
Bovolenta, G.; Bovino, S.; Vöhringer-Martinez, E.; Saez, D. A.; Grassi, T.; Vogt-Geisse*, S. High Level Ab Initio Binding Energy Distribution of Molecules on Interstellar Ices: Hydrogen Fluoride. Molecular Astrophysics, 2020, 21, 100095. [ChemRxiv link]
20-Dec-2020
A novel framework for studying the impact of binding energy distributions on the chemistry of dust grains
T. Grassi, S. Bovino, P. Caselli, G. Bovolenta, S. Vogt-Geisse and B. Ercolano A novel framework for studying the impact of binding energy distributions on the chemistry of dust grains Astronomy & Astrophysics, 643 (2020) A155 [ARxiv link]
18-Nov-2020
Electronic structure benchmark calculations of CO2 fixing elementary chemical steps in RuBisCO using the projector‐based embedding approach
Douglas‐Gallardo, O. A.; Shepherd, I.; Bennie, S. J.; Ranaghan, K. E.; Mulholland*, A. J.; Vöhringer‐Martinez*, E. Electronic Structure Benchmark Calculations of CO2 Fixing Elementary Chemical Steps in RuBisCO Using the Projector‐based Embedding Approach. Journal of Computational Chemistry , 2020, 41 (24), 2151–2157. [ChemRxiv link]
08-Jul-2020
DFT benchmark study of the O–O bond dissociation energy in peroxides validated with high-level ab initio calculations
Carmona, D., Jaque, P., Vöhringer-Martinez, E.*, DFT benchmark study of the O–O bond dissociation energy in peroxides validated with high-level ab initio calculations, Theoretical Chemistry Accounts 2020, 139, 102. [ChemRxiv link]
04-Jun-2020
SAMPL6 Octanol–water partition coefficients from alchemical free energy calculations with MBIS atomic charges
Riquelme, M, Vöhringer-Martinez*, E,. SAMPL6 Octanol–water partition coefficients from alchemical free energy calculations with MBIS atomic charges, Journal of Computer-Aided Molecular Design, 2020, 34, 327-334. [ChemRxiv link]
20-Jan-2020
Atom-Condensed Fukui Function in Condensed Phases and Biological Systems and Its Application to Enzymatic Fixation of Carbon Dioxide
Oller, J., Saez, D., Vöhringer-Martinez, E.*, Atom Condensed Fukui Function for Condensed Phases and Biological Systems and its Application to enzymatic Fixation of Carbon Dioxide, Journal of Physical Chemistry A (Paul Geerlings Festschrift) 2020, 124 (5), 849-857. [ChemRxiv link]
17-Jan-2020
Four amino acids define the CO2 binding pocket of enoyl-CoA carboxylases/reductases
Gabriele M. M. Stoffel, David Adrian Saez, Hasan DeMirci, Bastian Vögeli, Yashas Rao, Jan Zarzycki, Yasuo Yoshikuni, Soichi Wakatsuki*, Esteban Vöhringer-Martinez*, Tobias J. Erb*, Proceedings of the National Academy of Sciences USA, 2019 116 (28) 13964-13969
26-Jun-2019
Awakening the Sleeping Carboxylase Function of Enzymes: Engineering the Natural CO2-Binding Potential of Reductases
Bernhardsgrütter, I., Schell, K., Peter, D., Borjian, F., Saez, D., Vöhringer- Martinez, E., Erb, T. J. Journal of the American Chemical Society 2019, 141, 25, 9778–9782
12-Jun-2019
“Conformational sampling and polarization of Asp26 in pKa calculations of thioredoxin”
A. Gomez, E Vöhringer-Martinez, Proteins: Structure, Function, and Bioinformatics. 2019, 87, 6, 467-477 [ChemRxiv link]
04-Feb-2019
“Communication: Photoinduced carbon dioxide binding with surface-functionalized silicon quantum dots”
O. A. Douglas-Gallardo, C. G. Sánchez, E Vöhringer-Martinez
J. Chem. Phys. 2018, 148, 141102 [ChemRxiv link]
21-Dec-2018
“Global and local reactivity descriptors based on quadratic and linear energy models for α,β-unsaturated organic compounds”
Javier Oller, Patricia Pérez, Paul W. Ayers, Esteban Vöhringer-Martinez
Int. J. Quantum Chem. 2018, e25706. [ChemRxiv link]
22-Oct-2018
“Catalytic Reaction Mechanism in Native and Mutant Catechol-O-methyltransferase from the Adaptive String Method and Mean Reaction Force Analysis”
D. A. Saez, K. Zinovjev, I. Tunon, E Vöhringer-Martinez
J. Phys. Chem. B. 2018, 122, 8861 [ChemRxiv link]
27-Sep-2018
“Hydration Free Energies in the FreeSolv Database Calculated with Polarized Iterative Hirshfeld Charges”
M. Riquelme, A. Lara, D. Mobley, T. Verstraelen, A. Matamala, E. Vöhringer-Martinez
J. Chem. Inf. Mod. 2018, 58, 9, 1779-1797. [ChemRxiv link]
24-Sep-2018
“Partition coefficients of methylated DNA bases obtained from free energy calculations with molecular electron density derived atomic charges”
A. Lara, M. Riquelme, E. Vöhringer-Martinez,
J. Comp. Chem. 2018, 39, 22, 1728-1737 [ChemRxiv link]
24-Aug-2018
“Information-Theoretic Approaches to Atoms-in-Molecules: Hirshfeld Family of Partitioning Schemes”
F. Heidar-Zadeh, P. Ayers, T. Verstraelen, I. Vinogradov, E. Vöhringe-Martinez, P. Bultinck
J. Phys. Chem. A 2018, 122, 17, 4219-4245
03-Mar-2018
“High level potential energy surface and mechanism of Al(CH3)2OCH3-promoted lactone polymerization: initiation and propagation”
S. Vogt-Geisse, R. A. Mata, A. Toro-Labbé
Phys. Chem. Chem. 2017, 18, 8989
07-Mar-2017
“Conformational Substrate Selection Contributes to the Enzymatic Catalytic Reaction Mechanism of Pin1”
E. Vöhringer-Martinez, C. Dörner
J. Chem. Phys. B 2016, 120, 49, 12444-12453
15-Dec-2016
“The local response of global descriptors”
F. Heidar-Zadeh, S. Fias, E. Vöhringer-Martinez, T. Verstraelen, P. Ayers
Theor. Chem. Acc. 2016, 136, 19
23-Nov-2016
“Determination of pulsation periods and other parameters of 2875 stars classified as MIRA in the All Sky Automated Survey (ASAS)”
N. Vogt, A. Contreras-Quijada, I. Fuentes-Morales, S. Vogt-Geisse, C. Arcos, C. Abarca, C. Agurto-Gangas, M. Caviedes, H. DaSilva, J. Flores, V. Gotta, F. Peñaloza, K. Rojas, J. I. Villaseñor
Astrophys. J. Supp. 2016, 227, 6
20-Sep-2016
“An explicit approach to conceptual density functional theory descriptors of arbitrary order
F. Heidar-Zader, M. Richer, S.Fias, R. Miranda-Quintana, M. Chan, M. Franco-Pérez,C. González-Espinoza, T. Kim, C. Lanssens A. Pat, X. Yang, E. Vöhringer-Martinez, C. Cárdenas, T. Verstraelen, P. Ayers
Chem. Phys. Lett. 2016, 660, 307-312
01-Sep-2016
“The effect of the environment on the methyl transfer reaction mechanism between trimethylsulfonium and phenolate”
D. A. Saez, S. Vogt-Geisse, R. Inostroza-Rivera, T. Kubar, M. Elstner, A. Toro-Labbe, E Vöhringer-Martinez
Phys. Chem. Chem. Phys. 201, 18, 24033
27-Jul-2016
“Chemical potential and reaction electronic flux in symmetry controlled reactions
S.Vogt-Geisse, A. Toro-Labbé
J. Compt.Chem. 2016, 37, 1794
18-Jun-2016
“Symmetry adapted reaction electronic flux in cycloaddition reactions”
N. Villegas-Escobar, S. Vogt-Geisse, S. Gutiérrez-Oiva, A. Toro-Labbé
Theor. Chem. Acc. 2016, 135, 191
14-Jun-2016
“Kudi: A free open-source python library for the analysis of properties along reaction paths”
S. Vogt-Geisse
J.Mol. Mod. 2016, 22 ,110
06-May-2016
“Extending the halogen-bonded supramolecular synthon concept to 1,3,4-oxadiazole derivatives”
P. Hidalgo, S. Leal, C. Jimenez, E. Vöhringer-Martinez, B. Herrera, J. Pasan, C. Ruiz-Perez, D. Bruce
CrsytEngCom 2015, 188, 1, 42-47
07-Jan-2016
“A consistent S-Adenosylmethionine force field improved by dynamic Hirshfeld-I atomic charges for biomolecular simulation”
D. A. Saez, E Vöhringer-Martinez
J. Comp. Aided Mol. Des. 2015, 29, 951
15-Aug-2015
“Electronic structure benchmark calculations of inorganic and biochemical carboxylation reactions”
O. A. Douglas-Gallardo, D. A. Saez, S. Vogt-Geisse, E. Vöhringer-Martinez
J. Comput. Chem. 2019, 40, 1401 [ChemRxiv link]
15-May-2015
