Escudo de la República de Colombia Escudo de la República de Colombia

Our Group

Research in our Lab concentrates on the development, computational implementation and application of theoretical methods to investigate a wide variety of molecular phenomena. Our research involves mainly the development of the Any Particle Molecular Orbital method and its application to the study of molecular properties; molecular quantum dynamics and control; bioinorganic role of metal cations; quantum treatment of peptides among others. Most of our research is carried out employing our LOWDIN software package. If you would like to know more about our research, please click here


Our team is composed by professionals from different disciplines such as computer sciences, physics, mathematics and chemistry. We are always looking for enthusiastic students to join our lab. If you are interested in undergraduate or graduate studies in quantum and computational chemistry, please contact us.


FACULTY





Jorge Alí-Torres, Ph.D

Assistant Professor
Department of Chemistry
Unidad Camilo Torres
Bloque 9. Oficina 3B2
Telephone: +57 1 3165000 Ext. 10608
Email: jialit@unal.edu.co
Universidad Nacional de Colombia
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Johan Galindo, Ph.D

Assistant Professor
Department of Chemistry
Unidad Camilo Torres
Bloque 9. Oficina 1B2
Telephone: +57 1 3165000 Ext. 10643
Email: jfgalindoc@unal.edu.co
Universidad Nacional de Colombia
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Andrés Reyes, Ph.D.

Professor of Chemistry
Department of Chemistry
Unidad Camilo Torres
Bloque 9. Oficina 3B1
Telephone: +57 1 3165000 Ext. 10616
Email: areyesv@unal.edu.co
Universidad Nacional de Colombia
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Álvaro Valdes, Ph.D

Associate Professor
Department of Physics
Unidad Camilo Torres
Bloque 9. Oficina 3B2-1
Telephone: +57 1 3165000 Ext. 13057
Email: avaldesl@unal.edu.co
Universidad Nacional de Colombia
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STUDENTS





Mauricio Rodas, M.Sc.

Doctoral Student (2011- )
- LOWDIN-CUDA code.
- Geometrical Isotope Effects on Hydrogen bonds.
- Positronic chemistry.

Personal website


Ismael Ortiz, M.Sc.

Doctoral Student (2014- )
- Semi empirical methods based on MO
and TB.

- Exotic particles.

Personal website


Félix Moncada, M.Sc.

Doctoral Student (2014- )
- DFT.
- Exotic particles.

Personal website


Orlando Carrillo, M.Sc.

Doctoral Student (2018- )
- Nanoconfined molecules.
Personal website




Adrian Orjuela

Doctoral Student (2019- )
- Quantum and computational chemistry.
- Bioinformatics.
- Multi-scale methods.



Carlos E. Gaitán

M.Sc. Student (2015- )
- Positronic chemistry.
- Exotic particles.

Personal website


Luisa Espín

M.Sc. Student (2018- )
- Multi-scale Modeling.


William Quintero, M.Sc.

Researcher
- Computational calculations of molecular properties.
- Confined systems.

Personal website




Diego Chaparro, M.Sc.

Researcher
- Alzheimer’s disease.
- Multifunctional metal-binding agents.
- Conceptual DFT.

Personal website

Weekly Seminars


2020


Date
Speaker
Title
Oct. 23 - 2020
Adrián Leonardo Orjuela Rocha, Ph.D. studentAproximación al diseño de fármacos asistido por computadora
Oct. 09 - 2020
Francisco Nuñez Zarur, Ph.D.Quantifying the role of ring strain on the reactivity of supported single-site catalysts
Sep. 17 - 2020
Chonny Herrera AcevedoSelection of antileishmanial sesquiterpene lactones from SistematX database using a combined ligand‑/structure‑based virtual screening approach
Sep. 11 - 2020
Leidy Diana Ardila LealEstudio de estabilidad a tiempo real y estabilidad acelerada correlacionados con análisis de dinámica molecular de la lacasa rPOXA 1B de Pleorotus ostreatus
Sep. 04 - 2020
Jorge Puello Silva, Ph.D. studentEstructura electrónica y molecular de complejos de amiloide beta (Aβ) con Fe+2/+3 (Fe+2/+3-Aβ) asociados a la enfermedad de Alzheimer. Una revisión del estado del arte
Aug. 28 - 2020
Orlando Carrillo Bohórquez, Ph.D. candidateEstudio computacional de moléculas nano-confinadas: agua en fulerenos
Aug. 21 - 2020
Félix S. Moncada A., Ph.D. candidateA modified Colle-Salvetti correlation functional for electron-positron correlation
Mar. 13 - 2020
Nicolás Puentes Díaz, Undergraduate studentLigandos tipo Salen como posibles agentes farmacológicos en la enfermedad de Alzheimer



Previous Seminars





For more information about the weekly seminars write to lfespind@unal.edu.co.

Events

Research

The Born-Oppenheimer approximation (BOA) is one the most fundamental approximations of molecular physics and chemistry. This approximation has been used successfully in many research areas ranging from spectroscopy to quantum chemistry. In fact, the use of this approximation in quantum chemistry has made possible the study of molecular systems containing thousands of electrons and nuclei. However, quantum chemistry methods based on the BOA still fail  to include nuclear quantum effects (NQE) on the molecular electronic structure, because the BOA completely uncouples the electronic and nuclear degrees of freedom. For most chemical systems these effects beyond the BOA are very small. However, for systems containing light or delocalized nuclei, they may be very important. In order to study NQE with a method that goes beyond the BOA, we have developed the LOWDIN Software package. This code is the result of the fusion of the Any  Particle Molecular Orbital (APMO) and PARAKATA software packages. As a result, LOWDIN is capable performing nuclear-electronic molecular orbital calculations at HF  (RHF, UHF and ROHF), MP2, and DFT levels of theory. In addition, LOWDIN has implemented the electronic propagator and auxiliary density perturbation theory methods Developers Team: Edwin F. Posada, Jonathan Romero, Felix Moncada Collaborators:  Roberto Flores-Moreno, Sergio Gonzalez.


    Publications

  1. Á. Valdés, O. Carrillo-Bohórquez, and R. Prosmiti. “Fully Coupled Quantum Treatment of Nanoconfined Systems: A Water Molecule inside a Fullerene C60 ”. J. Chem. Theory Comput., 14 (12), 6521–6531, (2018).
  2. T. Nelson, D. Ondarse-Alvares, N. Oldani, B. Rodriguez-Hernandez, L. Alfonso-Hernandez, J.F. Galindo, V. Kleiman, S. Fernandez-Alberti, A. Roitberg and S. Tretiak. “Coherent exciton-vibrational dynamics and energy transfer in conjugated organics”. Nat Commu., 9, 2316, (2018).
  3. J. Charry, M. Varella and A. Reyes. “Binding matter with antimatter: the covalent positron bond”. J. Angew. Chem. Int. Ed. 57, 8859-8864, (2018).
  4. E. Posada, F. Moncada and A. Reyes. “The any particle molecular orbital grid-based Hartree-Fock (APMO-GBHF) approach”. J. Chem. Phys., 148 (8), 084113, (2018).
  5. D. Chaparro, and J. Alí-Torres. “Assessment of the Isodesmic Method in the Calculation of Standard Reduction Potential of Copper Complexes”. J. Mol. Model., 23 (283), 1-8, (2017).
  6. L. Pedraza-Gonzalez, J. Charry, W. Quintero, J. Alí-Torres, and A. Reyes. "Fast and Accurate Prediction of Proton Affinities: Revisiting the Extended Koopmans’ Theorem for Protons”. Phys. Chem. Chem. Phys., (19), 25324-25333. (2017) .
  7. J. Charry, L. Pedraza-González and A. Reyes. "On the physical interpretation of the nuclear molecular orbital energy", J. Phys. Chem. 146, 214103 (2017).
  8. F. Moncada, R. Flores-Moreno, A. Reyes. "Theoretical calculation of polarizability isotope effects", J Mol Model, 23: 90, (2017).
  9. L. Pedraza-González, J.F. Galindo, R. González, and A. Reyes, "Revisiting the Dielectric Constant Effect on the Nucleophile and Leaving Group of Prototypical Backside SN2 Reactions: A Reaction Force and Atomic Contribution Analysis". J. Phys. Chem. A., (2016).
  10. Y. Tsukamoto, Y. Ikabata, J. Romero, A. Reyes and H. Nakai, "The divide-and-conquer second-order proton propagator method based on nuclear orbital plus molecular orbital theory for the efficient computation of proton binding energies". Phys. Chem. Chem. Phys., 18, 27422-27431, (2016).
  11. L. Pedraza-González, J. Romero, J. Alí-Torres and A. Reyes, "Prediction of proton affinities of organic molecules using the any-particle molecular-orbital second-order proton propagator approach". Phys. Chem. Chem. Phys., 18, 27185-27189, (2016).
  12. R. D. Guerrero, C. A. Arango, and A. Reyes, "Analytical Optimal Pulse Shapes Obtained with the aid of Genetic Algorithms: Controlling the Photoisomerization Yield of Retinal". J. Chem. Phys, 145, 031101 (2016)
  13. A. Mirats, J. Alí-Torres, L. Rodríguez-Santiago, and M. Sodupe, “Stability of transient Cu+-A?(1–16) species and influence of coordination and peptide configuration on superoxide formation”, Theor. Chem. Acc., 135(3), 1-9, (2016).
  14. J. Alí-Torres, A. Mirats, J. Maréchal, L. Rodríguez-Santiago and M.Sodupe, “Modeling Cu2+-A? Complexes from Computational Approaches”, AIP Advances, 5 (9), 092402, (2015).
  15. A. Mirats, J. Alí-Torres, L. Rodríguez-Santiago, M. Sodupe and G. La Penna, “Dioxygen Activation in the Cu-Amyloid Complex”, Phys. Chem. Chem. Phys, 17, 27270-27274, (2015).
  16. L. Rodríguez-Santiago, J. Alí-Torres, P. Vidossich and M. Sodupe, “Coordination properties of a metal chelator clioquinol to Zn2+ studied by static DFT and ab initio molecular dynamics”, Phys. Chem. Chem. Phys, 17, 13582-13589, (2015).
  17. C. Rodríguez-Rodríguez, M. Telpoukhovskaia, J. Alí-Torres, L. Rodríguez-Santiago, Y. Manso, G. Bailey, J. Hidalgo, M. Sodupe and C. Orvig, “Thioflavin-based molecular probes for application in Alzheimer's disease: from in silico to in vitro models”, Metallomics, 7, 83-92. (2015)
  18. R. D. Guerrero, C. A. Arango, A. Reyes, Analytical optimal pulse shapes obtained with the aid of genetic algorithms, J. Chem. Phys, J. Chem. Phys., 143, 124108 (2015)
  19. E. Posada, F. Moncada, A. Reyes. "Negative Muon Chemistry: The Quantum Muon Effect and the Finite Nuclear Mass Effect", J. Phys. Chem. A, 118 (40), pp 9491–9499 (2014)
  20. J. Romero, J. Charry, R. Flores-Moreno, M.T. do. N. Varella, and A. Reyes. "Calculation of positron binding energies using the generalized any particle propagator theory", J. Chem. Phys., 141, 114103 (2014)
  21. H. J. Bohórquez, A. Reyes. "The atomic Pauli energy grows exponentially with the electronic localization", Mol. Phys., 112, 416-421 (2014)
  22. R.D. Guerrero, C. Arango, A. Reyes,"Optimal control of wave-packets: a semiclassical approach", Mol. Phys., 112, 408-415 (2014)
  23. J. Charry, J. Romero, M.T. do N. Varella, A. Reyes. "Calculation of positron binding energies of amino acids with the any-particle molecular-orbital approach", Phys. Rev. A., 89, 052709 (2014)
  24. J. Romero, J. Charry, H. Nakai, A. Reyes. "Improving quasiparticle second order electron propagator calculations with the spin-component-scaled technique", Chem. Phys. Lett. 591, 82–87 (2014)
  25. R. Flores-Moreno, E. F. Posada, F. Moncada, J. Romero, J. Charry, M. A. Díaz-Tinoco, S. A. Gonzáles, N. F. Aguirre, A. Reyes, "LOWDIN: The Any Particle Molecular Orbital Code", Int. J. Quantum Chem., 114(1), 50-56 (2014)
  26. J. Romero, A. Restrepo, A. Reyes, "Solvent isotope effects on the hydration of alkaline cations: H/D secondary isotope effects on electrostatic interactions.", Mol. Phys. Let., 112(3-4), 518-525 (2014)
  27. R. Fernandez-Maestre, A. Reyes, H.H. Hill, Explaining the Drift Behavior of Caffeine and Glucosamine After Addition of Ethyl Lactate in the Buffer Gas of an Ion Mobility Spectrometer, Bull. Korean Chem. Soc., 35 1023 (2014).
  28. S. Pan, D. Moreno, J. L. Cabellos, J. Romero, A. Reyes, G. Merino, P. K. Chattaraj. "In Quest of Strong Be-Ng Bonds Among the Neutral Ng-Be Complexes", J. Phys. Chem. A., 118(2), 487-494 (2014)
  29. S. Pan, S. Jalife, J. Romero, A. Reyes, G. Merino, and P. K. Chattaraj. "Attractive Xe-Li interaction in Li-decorated clusters", Comp. Theor. Chem, 1021, 62-69 (2013)
  30. N.F. Aguirre, E.F. Posada, P. Villareal, G. Delgado-Barrio, M. Biczysko, A. Mitrushchenkov, A. Reyes, M.P. de Lara-Castells, "Including nuclear quantum effects into highly correlated electronic structure calculations", J. Chem. Phys., 138, 184113 (2013)
  31. A. Reyes, P. A. Cuervo, F. Orozco, R. Abonia, M. Duque-Norena, P. Perez, E. Chamorro. "Theoretical investigation of the selectivity in intramolecular cyclizations of some 2'-aminochalcones to dihydroquinolin-8-ones and indolin-3-ones", J. Mol. Model., 19(9), 3611-3618(2013)
  32. M. Díaz-Tinoco, J. Romero, J. V. Ortiz, A. Reyes, R. Flores-Moreno. "A generalized any particle propagator theory: prediction of proton affinities and acidity properties with the proton propagator"., J. Chem. Phys. 138, 194108 (2013)
  33. F. S. Moncada, S. D. Cruz, A. Reyes, "Electronic properties of atoms and molecules containing one and two negative muons", Chem. Phys. Lett., 570, 16 (2013)
  34. J. Gonzalez, E. Florez, J. Romero, A. Reyes, A. Restrepo, "Microsolvation of Mg2+, Ca2+: strong influence of formal charges in hydrogen bonding networks", J. Mol. Model., 19(4), 1763 (2013)
  35. K. Pineda-Urbina, R.D. Guerrero, A. Reyes, Z. Gomez-Sandoval, R. Flores-Moreno, "Shape entropy's response to molecular ionization", J. Mol. Model., 19(4), 1677 (2013)
  36. S. Pan, M. Contreras, J. Romero, A. Reyes, G. Merino, P. K. Chattaraj, "C5Li7+ and O2Li5+ as Noble Gas Trapping Agents", Chem. Eur. J. 19(7), 2322, (2013)
  37. F. Moncada, L.S. Uribe, J. Romero, A. Reyes, "Hydrogen Isotope Effects on Covalent and Noncovalent Interactions: the Case of Protonated Rare Gas Clusters", Int. J. Quantum Chem. 113(10), 1556, (2013)
  38. J. Romero, E. Posada, R. Flores-Moreno, A. Reyes, "A generalized any particle propagator theory: Assessment of nuclear quantum effects on electron propagator calculations", J. Chem. Phys., 137, 074105 (2012)
  39. F. S. Moncada, E. Posada, R. Flores, A. Reyes, "Non-Born-Oppenheimer Self-Consistent Field Calculations with Cubic Scaling", Chemical Physics. 400 103-107 (2012)
  40. F. Moncada, D. Cruz, A. Reyes, "Muonic alchemy: transmuting elements with the inclusion of negative muons", Chem. Phys. Letters. 539-540, 209-213 (2012)
  41. N. Nuñez, A. Reyes, R. Quevedo, "Hydrogen Bond Assisted Synthesis of Azacyclophanes from L-tyrosine Derivatives", Tetrahedron Lett. 53, 530 (2012)
  42. D. Moreno, S. A. González, A. Reyes, "Turning Symmetric an Asymmetric Hydrogen Bond with the Inclusion of Nuclear Quantum Effects", J. Chem. Phys., 134 024115 (2011)
  43. J. Romero, A. Reyes, J. David, and A. Restrepo, "Understanding Microsolvation of Li+:Structural and Energetical Analyses", Phys. Chem. Chem. Phys. 13, 15264 (2011)
  44. E. F. Posada, F. Moncada and A. Reyes, "Optimizacion del Paquete Computacional para el Cálculo de Estructura Nucleo-electronica APMO", Rev. Colomb. Quim. 40 35 (2011)
  45. S. A. González, A. Reyes, "Nuclear Quantum Effects on the He2H+ Complex With the Nuclear Molecular Orbital Approach", Int. J. Quant. Chem. 110 689 (2010)
  46. R. Quevedo, I. Ortiz and A. Reyes, "Synthesis and Conformational Analysis of Azacyclophanes from L-Tyrosine", Tetrahedron Lett. 51 1216 (2010)
  47. F. Moncada, S. A. González, A. Reyes, "First Principles Investigation of Hydrogen Isotope Effects in [XSO4H2SO4X]- (X = H,K) Complexes", Mol. Phys., 108 1545 (2010)
  48. D. V. Moreno, S. A. González and A. Reyes, ''Secondary Hydrogen Isotope Effects on the Structure and Stability of Cation-π Complexes (Cation = Li+, Na+, K+ and π= Acetylene, Ethylene, Benzene), J. Phys. Chem. A, 114 9231 (2010)
  49. J. Romero, A. Reyes and J. Wist, "Secondary Deuterium Isotope Effects on the Acidity of Glycine", Spectrochim. Acta. Part A, 77 845 (2010)
  50. A. Rivera, D. Moyano, M. Maldonado, J. Rios-Motta, A. Reyes, "FTIR and DFT Studies of the Proton Affnity of Small Aminal Cages", Spectrochim. Acta, Part A, 74 588 (2009)
  51. S. A. González, A. Reyes, "Implementación del método del gradiente analítico de la energía en al teoría del orbital molecular nuclear y electrónico", Rev. Colom. Quim. 38, 109 (2009)
  52. N. Forero, S. A. Gonzalez, A. Reyes, "Estudio teórico del efecto isotópico de hidrógeno en el aducto borano-carbonilo", Rev. Colom. Quim. 38, 135 (2009)
  53. I. Ortiz, S. A. González, A. Reyes, "Estudio del efecto de isótopo de hidrógeno en los complejos MH· · · HF (M: Li,Na)", Rev. Colom. Quim. 38, 143 (2009)
  54. S. A. González, N. F. Aguirre, A. Reyes "APMO: A Computer Program Based on the Electronic and non-Electronic Molecular Orbital Theory for Studies of Nuclear Quantum Effects", Rev. Colomb. Quim. 37, 93 (2008)
  55. S. A. González, N. F. Aguirre, A. Reyes "Theoretical Investigation of Isotope Effects: The Any-Particle Molecular Orbital Code", Int. J. Quant. Chem. 108, 1742 (2008)
  56. G. A. Parada, D. Fernández, A. Reyes, M. F. Suárez and L. Fadini "Síntesis y estudio teórico DFT de compuestos de Ru(II) con ligantes ferrocenílicos para aplicaciones electroquímicas", Rev. Colomb. Quim. 36, 186 (2007)
  57. A. B. Pacheco, B. Thorndyke, A. Reyes, and D. A. Micha "Quantum Dynamics of an Excited Alkali Atom in a Noble Gas Cluster: Lithium Attached to a Helium Cluster", J. Chem. Phys. 127, 244504 (2007)
  58. A. B. Pacheco, A. Reyes, D. A. Micha. "First Principles Dynamics of Light Emission in Alkali Atom - Noble Gas Atom Collisions at 10keV", J. Chem. Phys. 125, 154313 (2006)
  59. A. B. Pacheco, A. Reyes, D. A. Micha. "First Principles Dynamics of Light Emission and Absorption during Alkali Atom - Noble Gas Atom Interactions", Phys. Rev. A. 74, 062714 (2006)

Gallery

  • Sanibel 2012
  • Encuentro Nacional de Químicos Teóricos y Computacionales 2012
  • Encuentro Nacional de Químicos Teóricos y Computacionales 2014
  • Photodynamics 2012
  • QUITEL 2012
  • QUITEL 2014