Class-202

Class-101

Vogt Lab

Astrochemistry: Understanding the chemistry of the interstellar medium is key for various astrophyiscal processes like star formations or  Astrobiology.  In our group we apply electronic structure and density functional theory methods in order to obtain highly accurate estimates of binding energies of small molecules on interstellar icy mantels.

Undergraduate Teaching

The members of QCMM teach several undergarduate and graduate level phyiscal chemistry and programing clases courses. Some of those courses are:

Molecular Dynamics

Electroncic Structure and Chemical Reactivity

Physical Chemistry I (Thermodynamics)

Physical Chemistry III (Quantum Chemistry and Statisical Mecanics)

Elements of Physical Chemistry (Thermodynamics and Cinetics)

Introduction to Python Programing

Introduction to Python Programing with Applications in Chemistry

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]

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]

Github: An open-source python library for the analysis of properties along reaction paths

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]

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]

Congratulations to Dr. Esteban Vöhringer-Martinez on his new grant of joint Max Planck and ANID research.

Congratulations to Dr. Maximiliano Riquelme, on his PhD degree and his new job in the Universidad de Valdivia!

An interview in the magazine Vortice with our Italian PhD student Giulia Bovolenta about doing a PhD in Universidad de Concepción

Dr. Stefan Vogt-Geisse is on a sabbatical leave in the Georgia Institute of Technology. He will be back in March of 2019.

QCMM members Prof. Esteban Vöhringer-Martinez and Dr. David Saez are co-authors on an article published in the in the Journal of American Chemical Society.

“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]

Python in Chemistry Workshop With lectures of Dr. Toon Verstraelen (Best Coding Practices in Python.) , Dr. Fernaz Heidar (Chemtools) and Dr. Paul Ayers (Horton). Also with a special lecture of Dr. Christopher Rowley.

QCMM @ 44th International Congress of Theoretical Chemists of Latin Expression, Santiago de Chile 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]

“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]

“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]

“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]

“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]

Dr. Stefan Vogt gave a talk in the University of Ohio State and at the Georgia Institute of Technology. “Exploring chemistry with second layer software. Examples and applications”

Dr. Voehringer Martinez gave a talk at the conference. “Computer Simulation of Biological Membraners and Free Energy Calculation of Biological Systems”.

“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

“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

“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

“The local response of global descriptors”

F. Heidar-Zadeh, S. Fias, E. Vöhringer-Martinez, T. Verstraelen, P. Ayers
Theor. Chem. Acc. 2016, 136, 19

“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

“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

“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

“Chemical potential and reaction electronic flux in symmetry controlled reactions

S.Vogt-Geisse, A. Toro-Labbé
J. Compt.Chem. 2016, 37, 1794

“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

“Kudi: A free open-source python library for the analysis of properties along reaction paths”

S. Vogt-Geisse
J.Mol. Mod. 2016, 22 ,110

“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

“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

“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]