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The LOWDIN code: A software package for the study of Nuclear Quantum Effects

Abstract: 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. 

For further information see: LOWDIN PROJECT  

Developers Team : Edwin F. PosadaJonathan Romero, Felix Moncada
Collaborators: Roberto Flores-Moreno, Sergio Gonzalez.

Computational simulations of bioinorganic processes 

Abstract: We use state-of-the-art computational methods to gain insights into the role of metal cations on the development of neurodegenerative diseases, in special Alzheimer’s disease

Researcher: Jorge Alí-Torres
Collaborators: Mariona Sodupe and Luis Rodríguez-Santiago.

Any Particle Molecular Orbital computer package (APMO) 

Abstract: The current version of the APMO code is an implementation of the nuclear orbital and molecular orbital approaches (NMO) at the Hartree-Fock level of theory. Currently, we have applied the APMO code to a variety of systems to elucidate the isotope effects on electronic wave functions, geometries, dipole moments and electron densities. Although our current version of the code is slower than regular electronic structure packages, our code is robust enough to treat any system containing any combination of quantum particles (i.e. electrons, nuclei, positrons, muons, etc) within a Hartree-Fock  scheme. 

Researcher: Sergio González, Néstor F. Aguirre, Edwin F. Posada.

Computer-aided molecular design

Abstract:  Using a combination of bioinformatics and quantum chemical methods we design new agents with potential application in metal-promoted neurodegenerative disease.

Researcher: Jorge Alí-Torres
Collaborators: Cristina Rodríguez-Rodríguez.

Positrons and positronium chemistry

Abstract: Positrons are being employed in new analytical techniques for medical and material sciences, encouraging the study of the interaction between positrons and molecular systems. We are exploring the chemistry behind systems comprising positrons, electrons and nuclei employing the APMO approach.

Quantum treatment of peptide systems

Abstract:  We apply quantum chemical methods for studying peptide chemistry: secondary structures, interaction with metal cations, and molecular and aggregating properties.

Researcher: Jorge Alí-Torres
Collaborators: Hugo J. Bohórquez.

Semiclassical study of the optimal control of molecular rotors laser pulses

Abstract: Optimal quantum control may lead us to the manipulation of molecular motions, and the enhancement or inhibition of a given chemical reaction. Most of the quantum control schemes used today employ the interaction of the molecules with light as the control mechanism. Therefore, a key aspect to make quantum control processes possible is to produce light pulses with specific characteristics. Among all the techniques designed to produce light, pulse shaping has become the most versatile. This technique involves the accurate control over the amplitude, phase, frequency and/or interpulse separation of laser light. We are interested in study the key physical aspects of the semiclassical dynamics of molecular rotors interacting with laser pulses. Studying the effects of optical pulses on the fundamental phase-space, and spectral structures of a molecular rotor.

Researcher: Rubén Darío Guerrero, Carlos Arango.

Computational calculations of molecular properties

Abstract:  Calculation of molecular properties, such as, pKa, affinity constants, proton affinities, standard reduction potentials, among others, are computationally challenging. In this research line, we develop computational protocols for calculating these physicochemical properties.

Researcher: Jorge Alí-Torres, Carlos Cárdenas, Laura Pedraza.

Conductor-like screening model for any particle (COSMO-APMO)

Abstract: At the begining all tools developed from quantum mechanics was limited to study one molecule in vacuo. The information obtained are really usefull to understand the behavior of molecules on gas phase, but as we know, the most the chemical processes are carried out on presence of solvent molecules. To take account of the solute-solvent interaction we are working on development of a new method based on conductor-like screaning model (COSMO) that allows calculations for any particle.

Researcher: Danilo González

Fragment molecular orbital method for any particle.

Abstract: The fragment molecular orbital method (FMO) was developed by K. Kitaura and coworkers in 1999. The main use of FMO is to compute very large molecular systems by dividing them into fragments and performing ab initio or density functional quantum-mechanical calculations of fragments and their dimers. my work focus on the development of a new method of FMO for any particle, employing the APMO metodology, APMO allow treat system containing any combination of quantum particles (i.e. electrons, nuclei, positrons, muons, etc) within a Hartree-Fock scheme. My job will focus on the study of polymers systems with positronium , with the purpose of studying defects in these materials and it's implementation on the Lowdin code.

Researcher: Ronald González

Generalized Propagator Theory

Abstract: In quantum chemistry, the propagator formalism has been applied to study the electron ionization phenomena. Using the APMO wavefunction as starting point, I am extending propagator theory to study the ionization of any type of particle (protons, positron, muons). Our method also let us to assess NQE in electron ionization energies.

Researcher: Jonathan Romero.

Multicomponent DFT

Abstract: The multicomponent density functional theory (DFT) is the extension of the electronic DFT to systems with multiple quantum species. We are developing a DFT method based on the Any Particle Molecular Orbital (APMO) theory.

Researcher: Felix Moncada, Jorge Charry
Collaborators:Roberto Flores-Moreno

Endohedral Fullerenes

Abstract: Endohedral fullerenes are fullerenes that have additional atoms, ions, or clusters enclosed. In many cases, the guests are not chemically bonded to the cage, as in HenC60, and therefore are delocalized inside the cage. A system like this can be thought as a particle trapped in a box.
We studying the quantum nature of the trapped particles, using a modified version of the APMO method.

Speed-Up LOWDIN with GPUs and including methods of NMO-QM/MM

Abstract: This job is intended primarily LOWDIN implement the ability to perform calculations in parallel using the computing power of graphics processing units (GPUs) and incorporate HF, UHF, ROHF, DFT, DFT multicomponent, MP2 calculations for simple point, numerical and analytical derivatives for calculating properties, equilibrium geometries and transition states and molecular dynamics methods.

Negative Muons Chemistry

Abstract: Negative muons are negatively charged particles with 206 times the mass of an electron. The chemical properties of atoms and molecules containing these particles were rarely investigated in the last century. However, In recent years a couple of papers have presented measurements of reaction rates for the collisional process He(μ) + H2 → He(μ)H + H, increasing the interest on the chemistry of these exotic systems.

We are studying from a theoretical perspective, based on the Any Particle Molecular Orbital method, the chemical properties of muonic atoms and molecules.

Past Research

Implementation of an interface between APMO and MOLPRO software packages for the study of nuclear quantum effects with high-correlated electronic wave functions (APMOLPRO).

Abstract: The APMO code is an implementation of the nuclear and molecular orbital approach where electrons and nuclei of molecular systems are described simultaneously with molecular orbitals at Hartree-Fock and second-order Möller-Pleset levels of theory. The APMO-MOLPRO interface extends the applicability of the APMO code by allowing to correlate the electronic structure part at higher levels of ab-initio theory and describe the nuclear response to electronic correlation effects.

The interface APMO-MOLPRO has been fully implemented into the MOLPRO package version 2009.1. It is necessary to have the APMO package installed, make a few changes to the source code of MOLPRO, include the source file of the interface (apmo.f) and recompile the main MOLPRO program. All parameters that control the calculation are selected directly from the MOLPRO input file.

Researchers : Edwin F. Posada, Nestor Aguirre, María del Pilar Lara

Electronic regions in atoms, molecules and complexes

Abstract: Chemical understanding can benefit from localization functions that are able to describe both, core electrons and valence electrons as well. The logarithmic derivative of the electron density provides such information. This tool identifies the critical points of any given molecule. 

Researcher:  Hugo Bohorquez

Electronic structure of confined systems at high-level of theory with LOWDIN

Abstract: Endohedral fullerenes are compounds that contain an atom, ion, molecule, or cluster inside the fullerene cage. To study these systems under electronic-structure methodologies, we add an external potential to the one-particle Hamiltonian of the confined atoms, in order to simulate the interaction with the fullerene cage. Due to the reduction in number or particles of the system we can perform high-level of theory calculations like MP2 or Full-CI with large basis set, and study the confinement effect in the electronic wavefunction of the confined system.

Photo-detachment Spectroscopy of Triatomic Colinear Systems (XHY, X,Y=Cl,Br,I) and Argon Microsolvation Effects using Ab-Initio Potentials.

Abstract: The potential energy surfaces (PES) available today for describing the systems XHY are of the LEPS type. It is well known that these surfaces only describe the general characteristics of the systems, and microsolvation effects can't be studied using these PES .To solve this problem, we are currently constructing numerical potential energy surfaces using regular electronic structure theories.

To simulate the photodetachment spectra we use discrete variable representation to determine the nuclear quantum states and the Franck-Condon principle to obtain the intensity of the peaks.

Universidad Nacional de Colombia
Unidad Camilo Torres - Bloque 9 Oficina 2B2
Calle 44 #45-67
Bogotá D.C. - Colombia