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.

Jorge AlíTorres, 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 Read more...  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 Read more...  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 Read more...  Álvaro Valdes, Ph.D Associate Professor Department of Physics Unidad Camilo Torres Bloque 9. Oficina 3B21 Telephone: +57 1 3165000 Ext. 13057 Email: avaldesl@unal.edu.co Universidad Nacional de Colombia Read more... 


Mauricio Rodas, M.Sc. Doctoral Student (2011 )  LOWDINCUDA 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  Adrian Orjuela Doctoral Student (2019 )  Quantum and computational chemistry.  Bioinformatics.  Multiscale methods. 
Carlos E. Gaitán M.Sc. Student (2015 )  Positronic chemistry.  Exotic particles. Personal website  Luisa Espín M.Sc. Student (2018 )  Multiscale Modeling.  William Quintero, M.Sc. Researcher  Computational calculations of molecular properties.  Confined systems. Personal website  Diego Chaparro, M.Sc. Researcher  Alzheimer’s disease.  Multifunctional metalbinding agents.  Conceptual DFT. Personal website 
Adrián Leonardo Orjuela Rocha, Ph.D. student  Aproximación al diseño de fármacos asistido por computadora  
Francisco Nuñez Zarur, Ph.D.  Quantifying the role of ring strain on the reactivity of supported singlesite catalysts  
Chonny Herrera Acevedo  Selection of antileishmanial sesquiterpene lactones from SistematX database using a combined ligand‑/structure‑based virtual screening approach  
Leidy Diana Ardila Leal  Estudio de estabilidad a tiempo real y estabilidad acelerada correlacionados con análisis de dinámica molecular de la lacasa rPOXA 1B de Pleorotus ostreatus  
Jorge Puello Silva, Ph.D. student  Estructura 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  
Orlando Carrillo Bohórquez, Ph.D. candidate  Estudio computacional de moléculas nanoconfinadas: agua en fulerenos  
Félix S. Moncada A., Ph.D. candidate  A modified ColleSalvetti correlation functional for electronpositron correlation  
Nicolás Puentes Díaz, Undergraduate student  Ligandos tipo Salen como posibles agentes farmacológicos en la enfermedad de Alzheimer 
Laura Valencia, Undergraduate student  Clasificación de semioquímicos de la familia scarabaeidae (orden: coleoptera) por medio de descriptores moleculares  
Laura Sepúlveda, Undergraduate student  Predicción del efecto del solvente sobre las bandas IR en el NMetilacetamida, usando machine learning  
Ruben Dario Guerrero, Ph.D.  Automatic generation of computational kernels for integralsdriven electronic structure on accelerator cards  
Adrián Leonardo Orjuela Rocha, Ph.D. student  Aspectos computacionales para el estudio del hierro en la enfermedad de Alzheimer  
Lina Peña, Undergraduate student  Modelamiento de fuerzas mecánicas en biología  
Diego Milanés, Ph.D.  Experimento LHCb  
Sol Mejía, Ph.D.  Effect of Charge and Phosphine Ligands on the Electronic Structure of the Au_{8} Cluster  
Jhon Zapata Rivera, Ph.D.  The CASSCF/PT2 approaches: an ab initio method for highly accurate calculation of absorption spectrum  
Adrián Leonardo Orjuela Rocha, Ph.D. student  Estudio computacional de la desagregación de fibras amiloides  
Diego Fernando Chaparro Gutierrez, M.Sc.  Ligandos quelantes derivados de isatina y su potencial aplicación como agentes terapéuticos en la enfermedad de Alzheimer  
Luisa Fernanda Espín Delgado, M.Sc. student  Predicción de la propensión de péptidos a formar agregados tipo amiloide mediante cálculos DFT  
León Mauricio Velásquez Márquez, Ph.D.  Propuesta de estudios computacionales en las reacciones de valorización de glicerol mediante procesos catalíticos  
Gina Marcela Hincapié Trivino, Ph.D.  Activación de metanol sobre óxidos mixtos derivados de hidrotalcitas para reacciones de transesterificación  
Orlando Carrillo Bohórquez, Ph.D. student  Estudio de los niveles rovibracionales y translacionales de una molécula de agua en fulerenos: sistemas H_{2}O@C_{60} y H_{2}O@C_{70}  
Félix S. Moncada A., Ph.D. candidate  Nuclearelectron correlation functionals from the ColleSalvetti formulation  
Edwin Arley Baquero Velasco, Ph.D.  C(sp^{3})–H Bond Activation of Sulfonated (NHC)Pt Complexes in Gas–Phase: An Experimental and DFT Study  
Stefany Botero Rodríguez  M.Sc. student  Identification of conserved structured regions for ncRNA within the coding region for the four serotypes of Dengue Virus and their biological diversity association  
Santiago Antolínez Cortés, Undergraduate student  Estudio mecanocuántico de los estados rovibracionales del sistema F^{}H_{2}O  
Carlos Andres Maya Aguirre, D.Sc. Student  Unal Instituto de Biotecnología  IBUN (Bogotá)  Interaction between PDI and Integrin αvβ3; a Docking and Molecular Dynamics study 
Johant Lakey, Center for Biodiversity and Drug Discovery, (INDICASAT AIP), Panamá  Assessment of Novel Curcumin Derivatives and Carotenoids as Potent Inhibitors of Amyloid? Aggregation and Inflammation in Alzheimer's Drug Discovery  
Stefany Botero Rodríguez  M.Sc. Student  Modelo integrado para la caracterización in silico del efecto de la diversidad genética sobre regiones estructuradas codificantes y no codificantes del virus del Dengue.  
Chonny Herrera Acevedo, M.Sc.  Estudios quimioinformáticos diseñados para seleccionar lactonas sesquiterpénicas con potencial actividad antichagásica y leishmanicida.  
Yonatan Zuleta Ochoa, D.Sc. Student  Semiclassical propagation in phase space with decoherence and dissipation  
Arturo Perez, M.Sc. Student  Modelo de Hubbard extendido  
Julian Arcila, M.Sc.  Anyons in the context of ultracold atoms 
Pietro Vidossich, Universidad de los Andes  Computational Design of Artificial Metalloenzymes for Enantioselective Catalysis  
Félix Moncada, PhD Student  Development of a Multicomponent WavefunctioninDensityFunctionalTheory Embedding Methodology to Include Correlation Between Electrons and Positrons, Muons or Nuclei in Molecular Systems  
Julián David Baquero Contreras, M.Sc. Student  Estudios computacionales de sistemas con metal? Sinucleína y su posible relación con la enfermedad de Parkinson  
Raúl Rodríguez Segundo, D.Sc. Student  Desarrollo de potenciales de interacción ionagua a partir de primeros principios  
Edwin Fernando Posada, D.Sc. Student  Desarrollo e implementación de un método libre de base para el estudio de efectos cuánticos nucleares (NuAPMO: Numerical Any Particle Molecular Orbital)  
Carlos Andrés Ortiz Mahecha  M.Sc. Student  Extensión de la teoría de Coupled Cluster Singles Doubles bajo el método del orbital molecular para cualquier partícula (APMO) usando el formalismo de segunda cuantización y su aplicación en sistemas positrónicos.  
Adrian Leonardo Orjuela Rocha. Undergraduate.  Estudio computacional de la interacción de moléculas provenientes de frutas tropicales colombianas con receptores de amargo (TAS2R´s)  
William David Quintero Martínez, M.Sc. Student.  Implementación del potencial de Lennard Jones en el paquete computacional LOWDIN y su aplicación en el estudio de gases nobles confinados en fullerenos  
Carlos Esteban Gaitán Caicedo, M.Sc. Student.  Efecto de la variación de masa de una partícula con carga positiva en sistemas moleculares utilizando el esquema APMO.  
Alejandro Peña Torres.  Dynamics of N_{2} on W(100) including van der Waals interactions: Energy dissipation effects.  
Carlos Esteban Gaitán Caicedo, M.Sc. Student.  Efecto de la variación de masa de una partícula con carga positiva en sistemas moleculares.  
Adriana Cabrera, M.Sc. Student.  Estudio de moléculas de CO_{2} dentro de hidrato clatratos y el paquete computacional VASP  
Orlando Carrillo Bohorquez, M.Sc. Student.  Dinámica Molecular Ab Initio y el Paquete Computacional CP2K  
William David Quintero Martinez, M.Sc. Student.  Potencial de Lennard Jones en el estudio teórico de átomos de gases nobles confinados en fullerenos  
Ismael Ortiz, Doctoral student.  Cálculo de interacciones entre sistemas moleculares gigantes y especies cuánticas exóticas con DFTB+  
Diego Chaparro, M.Sc. Student.  Cálculo computacional de potenciales de reducción para complejos de cobre  
Carlos Andres Ortiz Mahecha, M.Sc. Student.  Extensión de la teoría de Coupled Cluster Singles Doubles bajo el método del orbital molecular para cualquier partícula (APMO) usando el formalismo de segunda cuantización y su aplicación en sistemas positrónicos  
Mikko Muuronen. Ph.D.  First ElectronProton Transfer of Water Oxidation on Small TiO_{2} Nanoparticles  
Edwin Fernando Posada. Doctoral student.  Gridbased Numerical Any Particle Molecular Orbital (NAPMO)  
Carlos Andres Ortiz Mahecha, M.Sc. Student.  Extension of Coupled Cluster Singles Doubles and perturbative triples under Any Particle Molecular Orbital (APMO) theory and its implementation in LOWDIN program  
Orlando Carrillo Bohorquez, M.Sc. Student.  Quantum and Thermodynamic Study of Linear and Tshaped Isomers of the HeBr2 Complex.  
Juvenal Yosa, Ph.D  Phosphorylationdependent Molecular Switches, the PleD Protein Case. 
Diego Chaparro, M.Sc. Student  Cálculo computacional de potenciales de reducción para complejos de cobre.  
Félix S. Moncada. Doctoral student.  Estado actual y perspectivas del DFT multicomponente en Lowdin.  
Edwin Fernando Posada. Doctoral student.  Negative muon chemistry: The quantum muon effect and the finite nuclear mass effect.  
Carlos Andrés Ortiz Mahecha, M. Sc. Student.  Direct product decomposition approach for symmetry exploitation in coupled cluster singles doubles under APMO method.  
Ray Marín, Ph.D.  Transitioning from theoretical chemistry to personalised medicine  
Carlos Benavides, Ph.D.  Beyond the Pauli exclusion principle  
Rubén Guerrero, Doctoral student.  Semiclassical study of the optimal control of molecular rotors in tilted fields.  
Laura Milena Pedraza Gonzalez, M. Sc. Student.  Análisis de la unión de positrones a moléculas empleando el método del orbital molecular para cualquier tipo de partícula (APMO).  
Carlos Andrés Ortiz Mahecha, M. Sc. Student.  Extension of second quantization methods in Coupled Cluster Theory to treat any quantum particles.  
Ph.D. Fabián Lopez.  Quimiogenómica computacional.  
Ruben Guerrero, Graduated student.  Towards Nonadiabatic molecular dynamics on GPUs.  
Yosslen Aray, PhD.  Simulación de materiales y sistemas complejos utilizando mecánica cuántica, dinámica molecular y mesoscópica.  
Jorge Charry, M.Sc.  Symbolic algebra for the formulation of multicomponent propagator equations: a Python code.  
Francisco Nuñez Zarur, Ph.D.  Alkane metathesis with Tahydrides: Insights into the mechanism through molecular DFT calculations.  
Lorena Novoa Aponte, Ph.D. candidate.  CtpF: una ATPasa tipo P involucrada en el transporte de Ca^{2+} a través de la membrana plasmática de Mycobacterium tuberculosis.  
Alexander Sinitsyne, Ph.D.  Manyparticle systems: Kinetic approach  
Sol Milena Mejía Chica, Ph.D.  Understanding the azeotropic diethyl carbonate–water mixture by structural and energetic characterization of DEC(H_{2}O)n heteroclusters  
Isaias Lans, Ph.D.  Application of FiniteTemperature String Method to the Study of Hydride Transfer Between Anabaena FNR and NADP ^{+}/H  
Edwin Fernando Posada, Doctoral student.  Improving Performance of Basissetfree Hartreefock Calculations Through Gridbased Massively Parallel Techniques 
Cristian Buendía Atencio, Ph.D.  Bond additivity corrections (BAC): Empirical procedures for improving ab initio energetics  
Rubén Guerrero, Doctoral student  A Novel Heuristic Strategy to Attain onthefly Quantum Optimal Control  
Saul Daniel Cruz Lemus, Doctoral student  Caracterización de kesterita (Cu_{2}ZnSnS_{4}) utilizando espectroscopia de rayos X asistida por radiación sincrotrón para elucidar estructura electrónica  
Laura Milena Pedraza, M.Sc. student  Caracterización de la unión de protones y positrones a moléculas empleando la teoría del orbital molecular para cualquier partícula  
Ismael Ortiz Verano, Doctoral student  Density Functional Tight Binding, sus implementaciones, ventajas y perspectivas  
Jorge A. Charry, M.Sc. student  Desarrollo e implementación de un método de funciones gaussianas explícitamente correlacionadas bajo el esquema de orbitales moleculares para cualquier partícula, APMO.  
Danilo González Forero, M.Sc. student  Implementación de un Modelo de Solvatación Implícita Para Cualquier Partícula en LOWDIN.  
Ruben Dario Guerrero Mancilla, Doctoral student  The implementation of the Full multiple spawning method in the HELIOS package.  
Juvenal Yosa Reyes, Ph.D  Phosphorylationdependent Molecular Switches, the PleD Protein Case.  
Jorge A. Charry, M.Sc. Student  Two particles propagator theory.  
Dr. Néstor F. Aguirre  Descripción estadística de procesos de fragmentación con M3C y Generación de armónicos de alto orden en superficies.  
Maicol A. Ochoa Daza, Ph.D.  Transporte electrónico a través de moléculas en contacto con cuerpos macroscópicos. Una aplicación en optoelectrónica molecular.  
Alejandro Peña, M.Sc. Student  Development of coupled cluster methods employing the any particle molecular orbital approach and its implementation in LOWDIN program.  
Matheus Rodríguez, M.Sc. Student  Implementation of Energy Density Analysis EDAGrid in LOWDIN.  
Julian Baquero Contreras, Undergraduate Student  Variación de la topología de la densidad de carga y el potencial electrostático molecular en razón del cambio conformacional de una molécula.  
Thomas Heine, Ph.D  Transition metal chalcogenides: ultrathin inorganic materials with tunable eletronic properties.  
Camilo Andrés Espejo Pabon, Ph.D  Electronic structure of MoS2 under uniaxial compression. An application of the Wannier functions approach to van der Waals interactions in DFT.  
Mauricio Rodas, Doctoral Student.  Implementación del método QM/MM a través de una interfaz entre los paquetes AMBER y LOWDIN.  
Juan Pablo Villabona Monsalve, Ph.D.  Dinámica ultrarápida de estados electrónicos excitados: estudios por espectroscopia láser con resolución temporal y métodos abinitio multiconfiguracionales  
Danilo González, MSc Student.  Implementación de un Modelo de Solvatación Implícita Para Cualquier Partícula en LOWDIN  
Rubén Dario Guerrero, Doctoral Student.  A Novel Heuristic Strategy to Attain Quantum Optimal Control  
Carlos A. Ortíz Mahecha, MSc. Student.  Predicción de índices de acidez para reacciones en carbaniones usando el propagador protónico  
Felipe Valencia, Ph. D.  Revisiting carbon Schwarzites  
Márcio T. do N. Varella, Ph. D.  Transient Anion and Positronic States  
F. Javier Torres, Ph. D.  Incorporation of weak interactions in the computational simulation of nanosystems  
Hugo Bohórquez, Ph. D.  Tools for Quantum Multiscale Modeling  
Johan Galindo Cruz, Ph. D.  Energy Transfer Mechanism in the 2G1mEPer Unsymmetric Dendrimer  
Ramón Valencia Maturana, Ph. D.  Estructura Electrónica y Reactividad de Fulerenos Endohédricos/Cálculos de Estructura Electrónica en Compuestos Orgánicos para Baterias Solares 
Rubén Dario Guerrero, Grad. Student  Optimal quantum control of cistrans isomerization in retinal.  
Alejandro Peña Torres, MSc Student  Multidimensional PES determination for N_2 reacting on a tungsten surface using the modified shepard interpolation method.  
Jose Mauricio Rodas, Grad. Student  Molecular Mechanics on LOWDIN: UFF single point energies implementation  
Johan Galindo, PhD.  Electronic Excited State Specific IR Spectra for Phenylene Ethynylene Dendrimer Building Blocks  
Ronald González, MSc Student  Implementación de un método de orbitales moleculares de fragmentos para cualquier partícula en el programa LOWDIN  
Raymundo Hernández, Grad Student  Cálculo de Estructura Electrónica en Moleculas Diatómicas Confinadas  
Rubén Dario Guerrero, Grad Student  Towards NonMarkovian Optimal Quantum Control of Molecular Electronic States Employing KadanoffBaym Equations  
Matheus Rodríguez, MSc Student  Extensión teórica e implementación computacional en el programa LOWDIN del método de descomposición de energía por densidades (EDA) para cualquier partícula.  
Andy Zapata, MSc Student  Programación de la densidad electrónica en tarjetas gráficas.  
Carlos Ortiz, Undergrad Student  Estudio de la absorción y emisión en el ultravioleta visible de derivados de 3amino1Hisocromen1ona.  
Laura Pedraza, MSc Student  Revisiting the role of nucleophile, leaving group and solvent effect in backside SN2 reactions (Y  + CH3X ? YCH3 + X ; X,Y= F, Cl, Br, I): An atomic contribution study  
Jorge Ali Torres, PhD  Computational Modelling of Copper Complexes Relevant to Alzheimer Disease  
Juvenal Yosa Reyes, PhD  Multisurface Adiabatic Reactive Molecular Dynamics  
Francisco Núñez Zarur, PhD  Mechanism of ethylene polymerization by Cr(III) sites supported on silica: insights from DFT calculations 
The BornOppenheimer 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 nuclearelectronic 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 FloresMoreno, Sergio Gonzalez.
Abstract  
We implemented a systematic procedure for treating the quantal rotations by including all translational and vibrational degrees of freedom for any triatomic bent molecule in any embedded or confined environment, within the MCTDH framework. Fully coupled quantum treatments were employed to investigate unconventional properties in nanoconfined molecular systems. In this way, we facilitate a complete theoretical analysis of the underlying dynamics that enables us to compute the energy levels and the nuclear spin isomers of a single water molecule trapped in a C_{60} fullerene cage. The key point lies in the full 9D description of both nuclear and electronic degrees of freedom, as well as a reliable representation of the guest–host interaction. The presence of occluded impurities or inhomogeneities due to noncovalent interactions in the interfullerene environment could modify aspects of the potential, causing significant coupling between otherwise uncoupled modes. Using specific nmode model potentials, we obtained splitting patterns that confirm the effects of symmetry breaking observed by experiments in the ground orthoH_{2}O state. Further, our investigation reveals that the first rotationally excited states of the encapsulated ortho and paraH_{2}O have also raised their 3fold degeneracy. In view of the complexity of the problem, our results highlight the importance of accurate and computational demanding approaches for building up predictive models for such nanoconfined molecules.
Read more ... 
Abstract  
Coherence, signifying concurrent electronvibrational dynamics in complex natural and manmade systems, is currently a subject of intense study. Understanding this phenomenon is important when designing carrier transport in optoelectronic materials. Here, excited state dynamics simulations reveal a ubiquitous pattern in the evolution of photoexcitations for a broad range of molecular systems. Symmetries of the wavefunctions define a specific form of the nonadiabatic coupling that drives quantum transitions between excited states, leading to a collective asymmetric vibrational excitation coupled to the electronic system. This promotes periodic oscillatory evolution of the wavefunctions, preserving specific phase and amplitude relations across the ensemble of trajectories. The simple model proposed here explains the appearance of coherent excitonvibrational dynamics due to nonadiabatic transitions, which is universal across multiple molecular systems. The observed relationships between electronic wavefunctions and the resulting functionalities allows us to understand, and potentially manipulate, excited state dynamics and energy transfer in molecular materials.
Read more ... 
Abstract  
We report sufficient theoretical evidence of the energy stability of the e^{+}H_{2}^{2} molecule, formed by two H^{} anions and one positron. Analysis of the electronic and positronic densities of the latter compound undoubtedly points out the formation of a positronic covalent bond between the otherwise repelling hydride anions. The lower limit for the bonding energy of the e^{+}H_{2}^{2} molecule is 74 kJ/mol (0.77 eV), accounting for the zeropoint vibrational correction. The formation of a non electronic covalent bond is fundamentally distinct from positron attachment to stable molecules, as the latter process is characterized by a positron affinity, analogous to the electron affinity.
Read more ... 
Abstract  
The any particle molecular orbital gridbased HartreeFock approach (APMOGBHF) is proposed as an initial step to perform multicomponent postHartreeFock, explicitly correlated, and density functional theory methods without basis set errors. The method has been applied to a number of electronic and multispecies molecular systems. Results of these calculations show that the APMOGBHF total energies are comparable with those obtained at the APMOHF complete basis set limit. In addition, results reveal a considerable improvement in the description of the nuclear cusps of electronic and nonelectronic densities.
Read more ... 
Abstract  
Molecular phenomena involving electron transfer and reduction/oxidation processes are of the utmost importance in chemistry. However, accurate computational calculations of standard reduction potentials (SRPs) for transition metal complexes are still challenging. For this reason, some computational strategies have been proposed in order to overcome the main limitations in SRP calculations for copper complexes. However, these strategies are limited to particular coordination spheres and do not represent a general methodology. In this work, we present standard reduction potential calculations for copper complexes in aqueous solution covering a wide range of coordination spheres. These calculations were performed using the M062X density functional, and by employing the direct and isodesmic approaches. Result analysis reveals that values obtained with the use of the isodesmic method are in better agreement with experimental values than those obtained from the direct method (mean unsigned error 0.39 V with the direct and 0.08 V with the isodesmic method). This approach provides values with errors comparable to the experimental uncertainty due to the proper cancellation of computational errors. These results strongly suggest the isodesmic approach as an adequate methodology for the calculation of SRPs for copper complexes with diverse coordination spheres. Graphical Abstract Comparison between direct and isodesmic methods in the calculation of standard reduction potentials for copper complexes using DFT methods.
Read more ... 
Abstract  
In this work we propose schemes based on the extended Koopmans' theorem for quantum nuclei (eKT), in the framework of the any particle molecular orbital approach (APMO/KT), for the quantitative prediction of gas phase proton affinities (PAs). The performance of these schemes has been tested on a set of 300 organic molecules containing diverse functional groups. The APMO/KT scheme scaled by functional group (APMO/KTSCFG) displays an overall mean absolute error of 1.1 kcal mol?1 with respect to experimental data. Its performance in PA calculations is similar to that of postHartree–Fock composite methods or that of the APMO second order proton propagator (APMO/PP2) approach. The APMO/KTSCFG scheme is also employed to predict PAs of polyfunctional molecules such as the Nerve Agent VX and the 20 common ?amino acids, finding excellent agreement with available theoretical and/or experimental data. The accuracy of the predictions demonstrates that the APMO/KTSCFG scheme is a lowcost alternative to adiabatic methods for the calculation of accurate PAs. One of the most appealing features of the APMO/KTSCFG scheme, is that PAs can be derived from one singlepoint APMO Hartree–Fock calculation.
Read more ... 
Abstract  
Recently, several groups have extended and implemented molecular orbital (MO) schemes to simultaneously obtain wave functions for electrons and selected nuclei. Many of these schemes employ an extended HartreeFock approach as a first step to find approximate electronnuclear wave functions and energies. Numerous studies conducted with these extended MO methodologies have explored various effects of quantum nuclei on physical and chemical properties. However, to the best of our knowledge no physical interpretation has been assigned to the nuclear molecular orbital energy (NMOE) resulting after solving extended HartreeFock equations. This study confirms that the NMOE is directly related to the molecular electrostatic potential at the position of the nucleus.
Read more ... 
Abstract  
We propose a scheme to estimate hydrogen isotope effects on molecular polarizabilities. This approach combines the any particle molecular orbital method, in which both electrons and H/D nuclei are described as quantum waves, with the auxiliary density perturbation theory, to calculate analytically the polarizability tensor. We assess the performance of method by calculating the polarizability isotope effect for 20 molecules. A good correlation between theoretical and experimental data is found. Further analysis of the results reveals that the change in the polarizability of a XH bond upon deuteration decreases as the electronegativity of X increases. Our investigation also reveals that the molecular polarizability isotope effect presents an additive character. Therefore, it can be computed by counting the number of deuterated bonds in the molecule.
Read more ... 
Abstract  
The solvent effect on the nucleophile and leaving group atoms of the prototypical F^{?} + CH_{3}Cl ? CH_{3}F + Cl^{?} backside bimolecular nucleophilic substitution reaction (SN2) is analyzed employing the reaction force and the atomic contributions methods on the intrinsic reaction coordinate (IRC). Solvent effects were accounted for using the polarizable continuum solvent model. Calculations were performed employing eleven dielectric constants, ?, ranging from 1.0 to 78.5, to cover a wide spectrum of solvents. The reaction force data reveals that the solvent mainly influences the region of the IRC preceding the energy barrier, where the structural rearrangement to reach the transition state occurs. A detailed analysis of the atomic role in the reaction as a function of ? reveals that the nucleophile and the carbon atom are the ones that contribute the most to the energy barrier. In addition, we investigated the effect of the choice of nucleophile and leaving group on the ?E_{0} and ?E‡ of Y^{?} + CH_{3}X ? YCH_{3} + X^{?} (X,Y= F, Cl, Br, I) in aqueous solution. Our analysis allowed us to find relationships between the atomic contributions to the activation energy and leaving group ability and nucleophilicity.
Read more ... 
Abstract  
An efficient computational method to evaluate the binding energies of many protons in large systems was developed. Proton binding energy is calculated as a corrected nuclear orbital energy using the secondorder proton propagator method, which is based on nuclear orbital plus molecular orbital theory. In the present scheme, the divideandconquer technique was applied to utilize local molecular orbitals. This use relies on the locality of electronic relaxation after deprotonation and the electron–nucleus correlation. Numerical assessment showed reduction in computational cost without the loss of accuracy. An initial application to model a protein resulted in reasonable binding energies that were in accordance with the electrostatic environment and solvent effects.
Read more ... 
Abstract  
We assess the performance of the recently developed anyparticle molecularorbital secondorder proton propagator (APMO/PP2) scheme [M. DíazTinoco, J. Romero, J. V. Ortiz, A. Reyes and R. FloresMoreno, J. Chem. Phys., 2013, 138, 194108] on the calculation of gas phase proton affinities (PAs) of a set of 150 organic molecules comprising several functional groups: amines, alcohols, aldehydes, amides, ketones, esters, ethers, carboxylic acids and carboxylate anions. APMO/PP2 PAs display an overall mean absolute error of 0.68 kcal mol?1 with respect to experimental data. These results suggest that the APMO/PP2 method is an alternative approach for the quantitative prediction of gas phase proton affinities. One novel feature of the method is that a PA can be obtained from a single calculation of the optimized protonated molecule.
Read more ... 
Abstract  
We recently proposed a Quantum Optimal Control (QOC) method constrained to build pulses from analytical pulse shapes [R. D. Guerrero et al., J. Chem. Phys. 143(12), 124108 (2015)]. This approach was applied to control the dissociation channel yields of the diatomic molecule KH, considering three potential energy curves and one degree of freedom. In this work, we utilized this methodology to study the strong field control of the cistrans photoisomerization of 11cis retinal. This more complex system was modeled with a Hamiltonian comprising two potential energy surfaces and two degrees of freedom. The resulting optimal pulse, made of 6 linearly chirped pulses, was capable of controlling the population of the trans isomer on the ground electronic surface for nearly 200 fs. The simplicity of the pulse generated with our QOC approach offers two clear advantages: a direct analysis of the sequence of events occurring during the driven dynamics, and its reproducibility in the laboratory with current laser technologies.
Read more ... 
Abstract  
Accumulation of Cu^{2+} redox active metal cations has been associated with the oxidation damage observed in the development of Alzheimer disease. Copper ions can interact with accumulated amyloid? (A?) peptides and mediate the toxicity of the peptide through the catalytic production of H_{2}O_{2}. The first step of this catalytic process is the reduction of Cu^{2+}A? complex and the activation of O_{2} by the reduced species. This work addresses the stability of the reduced complexes and superoxide formation by Cu^{+}A? (1–16) complexes. We have considered the experimentally proposed coordination spheres for Cu^{2+}A? (1–16) which includes the terminal amino group, two His and the CO from Asp1 (complex I), three histidines and the CO of Ala2 (complex IIa), and one His, the NH2 terminus, the deprotonated amide nitrogen and carbonyl oxygen of Ala2 (complex IIc). Results from ab initio molecular dynamics calculations show that, after reduction of the square planar Cu^{2+}A? complex, decoordination of the O atom occurs in the first steps and tricoordinated structures are stable during the simulation time scale, thereby being prone to O_{2} activation. Quantum chemical calculations on small models and Cu^{+}A? (1–16) interacting with O_{2} indicate that the preference for O_{2} activation follow the order IIc > IIa > I. In all these cases energy barriers for superoxide formation are less than 4 kcal mol?1 and thus kinetically favorable. Comparison of small model systems and Cu^{+}A? (1–16) have pointed out that peptide configuration may significantly influence the O_{2} activation through second sphere interactions.
Read more ... 
Abstract  
Amyloid plaques formation and oxidative stress are two key events in the pathology of the Alzheimer disease (AD), in which metal cations have been shown to play an important role. In particular, the interaction of the redox active Cu^{2+} metal cation with A? has been found to interfere in amyloid aggregation and to lead to reactive oxygen species (ROS). A detailed knowledge of the electronic and molecular structure of Cu^{2+}A? complexes is thus important to get a better understanding of the role of these complexes in the development and progression of the AD disease. The computational treatment of these systems requires a combination of several available computational methodologies, because two fundamental aspects have to be addressed: the metal coordination sphere and the conformation adopted by the peptide uponcopper binding. In this paper we review the main computational strategies used to deal with the Cu^{2+}A? coordination and build plausible Cu^{2+}A? models that will afterwards allow determining physicochemical properties of interest, such as their redox potential.
Read more ... 
Abstract  
We investigate, by means of densityfunctional theory, the binding of dioxygen to Cu(I)–amyloid ? (A?), one of the first steps in the oxidation of ascorbate by dioxygen. Cu, A?, ascorbate and dioxygen are all present in the synapse during neurodegeneration, when the above species can trigger an irreversible oxidative stress inducing the eventual death of neurons. The binding of dioxygen to Cu(I) is possible and its role in dioxygen activation of Cu ligands and of residues in the first coordination sphere is described in atomic detail. Dioxygen is activated when a microenvironment suitable for a squareplanar Cu^{2+} coordination is present and a negatively charged group like Asp 1 carboxylate takes part in the Cu coordination anti to O_{2}.
Read more ... 
Abstract  
Several lines of evidence supporting the role of metal ions in amyloid aggregation, one of the hallmarks of Alzheimer's disease (AD), have turned metal ion chelation into a promising therapeutic treatment. The design of efficient chelating ligands requires proper knowledge of the electronic and molecular structure of the complexes formed, including their hydration properties. Among various potential chelators, clioquinol (5chloro7iodo8hydroxyquinoline, CQH) has been evaluated with relative success in in vitro experiments and even in phase 2 clinical trials. Clioquinol interacts with Zn(II) to lead to a binary metal/ligand 1:2 stoichiometric complex in which the phenolic group of CQH is deprotonated, resulting in Zn(CQ)_{2} neutral complexes, to which additional water molecules may coordinate. In the present work, the coordinative properties of clioquinol in aqueous solution have been analyzed by means of static, minimal cluster based DFT calculations and explicit solvent ab initio molecular dynamics simulations. Results from static calculations accounting for solvent effects by means of polarized continuum models suggest that the preferred metal coordination environment is tetrahedral Zn(CQ)_{2}, whereas ab initio molecular dynamics simulations point to quasi degenerate penta Zn(CQ)_{2}(H_{2}O) and hexa Zn(CQ)_{2}(H_{2}O)_{2} coordinated complexes. The possible reasons for these discrepant results are discussed.
Read more ... 
Abstract  
Alzheimer's disease (AD) is a neurological disease of confusing causation with no cure or prevention available. The definitive diagnosis is made postmortem, in part through the presence of amyloidbeta plaques in the brain tissue, which can be done with the small molecule thioflavinT (ThT). Plaques are also found to contain elevated amounts of metal ions Cu(II) and Zn(II) that contribute to the neurotoxicity of amyloidbeta (A?). In this paper, we report in silico, in vitro, and ex vivo studies with ThTderived metal binders 2(2hydroxyphenyl)benzoxazole (HBX), 2(2hydroxyphenyl)benzothiazole (HBT) and their respective iodinated counterparts,HBXI and HBTI. They exhibit low cytotoxicity in a neuronal cell line, potential blood–brain barrier penetration, and interaction with A? fibrils from senile plaques present in human and transgenic mice AD models. Molecular modelling studies have also been undertaken to understand the prospective ligand–A? complexes as well as to rationalize the experimental findings. Overall, our studies demonstrate that HBX, HBT, HBXI, and HBTI are excellent agents for future use in in vivo models of AD, as they show in vitro efficacy and biological compatibility. In addition to this, we present the glycosylated form of HBX (GBX), which has been prepared to take advantage of the benefits of the prodrug approach. Overall, the in vitro and ex vivo assays presented in this work validate the use of the proposed ThTbased drug candidate series as chemical tools for further in vivo development.
Read more ... 
Abstract  
We propose a methodology to design optimal pulses for achieving quantum optimal control on molecular systems. Our approach constrains pulse shapes to linear combinations of a fixed number of experimentally relevant pulse functions. Quantum optimal control is obtained by maximizing a multitarget fitness function using genetic algorithms. As a first application of the methodology, we generated an optimal pulse that successfully maximized the yield on a selected dissociation channel of a diatomic molecule. Our pulse is obtained as a linear combination of linearly chirped pulse functions. Data recorded along the evolution of the genetic algorithm contained important information regarding the interplay between radiative and diabatic processes. We performed a principal component analysis on these data to retrieve the most relevant processes along the optimal path. Our proposed methodology could be useful for performing quantum optimal control on more complex systems by employing a wider variety of pulse shape functions.
Read more ... 
Abstract  
The anyparticle molecular orbital method at the full con?guration interaction level has been employed to study atoms in which one electron has been replaced by a negative muon. In this approach electrons and muons are described as quantum waves. A scheme has been proposed to discriminate nuclear mass and quantum muon e?ects on chemical properties of muonic and regular atoms. This study reveals that the di?erences in the ionization potentials of isoelectronic muonic atoms and regular atoms are of the order of millielectronvolts. For the valence ionizations of muonic helium and muonic lithium the nuclear mass e?ects are more important. On the other hand, for 1s ionizations of muonic atoms heavier than beryllium, the quantum muon e?ects are more important. In addition, this study presents an assessment of the nuclear mass and quantum muon e?ects on the barrier of He? + H2 reaction.
Read more ... 
Abstract  
We recently extended the electron propagator theory to any type of quantum species based in the framework of the AnyParticle Molecular Orbital (APMO) approach [J. Romero, E. Posada, R. FloresMoreno, and A. Reyes, J. Chem. Phys.137, 074105 (2012)]. The generalized any particle molecular orbital propagator theory (APMO/PT) was implemented in its quasiparticle second order version in the LOWDIN code and was applied to calculate nuclear quantum effects in electron binding energies and proton binding energies in molecular systems [M. DíazTinoco, J. Romero, J. V. Ortiz, A. Reyes, and R. FloresMoreno, J. Chem. Phys.138, 194108 (2013)]. In this work, we present the derivation of third order quasiparticle APMO/PT methods and we apply them to calculate positron binding energies (PBEs) of atoms and molecules. We calculated the PBEs of anions and some diatomic molecules using the second order, third order, and renormalized third order quasiparticle APMO/PT approaches and compared our results with those previously calculated employing configuration interaction (CI), explicitly correlated and quantum Montecarlo methodologies. We found that renormalized APMO/PT methods can achieve accuracies of ?0.35 eV for anionic systems, compared to FullCI results, and provide a quantitative description of positron binding to anionic and highly polar species. Third order APMO/PT approaches display considerable potential to study positron binding to large molecules because of the fifth power scaling with respect to the number of basis sets. In this regard, we present additional PBE calculations of some small polar organic molecules, amino acids and DNA nucleobases. We complement our numerical assessment with formal and numerical analyses of the treatment of electronpositron correlation within the quasiparticle propagator approach.
Read more ... 
Abstract  
We investigate the Pauli energy in atoms and molecules as a measure of electron localisation. Our results indicate that the Pauli energy has an exponential dependence on the number of localised electrons. This relationship yields to a kinetic energy density expression that depends on the electron density ?(r) and the pair density ?2(r, r?). The proposed equation shows certain advantages over a similar orbitalfree kinetic energy functional recently proposed by Delle Site and coworkers. The methodology introduced here is a novel approach for exploring electronic quantities with a partition scheme that might be useful for research in density functional theory.
Read more ... 
Abstract  
We studied the optimal quantum control of a molecular rotor in tilted laser fields using the timesliced Herman–Kluk propagator for the evaluation of the optimal pulse and the light–dipole interaction as the control mechanism. The proposed methodology was used to study the effects of an optimal pulse on the evolution of a wavepacket in a doublewell potential and in the effective potential of a molecular rotor in a collinear tilted fields setup. The amplitude and frequency of the control pulse were obtained in such a way that the transition probability between two rotational wavepackets was maximised.
Read more ... 
Abstract  
We report positron binding energies (PBEs) for the 20 standard amino acids in the global minimum, hydrogenbonded, and zwitterionic forms. The calculations are performed at the anyparticle molecularorbital (APMO) HartreeFock (HF), Koopmans' theorem (KT), secondorder MöllerPlesset (MP2), and secondorder propagator (P2) levels of theory. Our study reveals that the APMO KT and APMO P2 methods generally provide higher PBEs than the APMO HF and APMO MP2 methods, respectively, with only a fraction of the computational costs of the latter. We also discuss the impact of the choice of the positronic center on the PBEs and propose a simple and inexpensive procedure, based on the condensed Fukui functions of the parent molecules, to select the most suitable expansion center. The results reported so far indicate that APMO KT and APMO P2 methods are convenient options for a qualitative or semiquantitative analysis of positron binding in medium to large polyatomic systems.
Read more ... 
Abstract  
A simple modification of the quasiparticle second order electron propagator (EP2) method based on the spincomponentscaled technique is proposed. In this new approach, the second order contributions to the selfenergy of same and opposite spins are scaled by empirical parameters. Comparison with EP2 and higher order approaches for different sets of molecules reveals that the costfree spincomponentscaled technique reduces average errors of EP2 up to 51%, thereby increasing its reliability and applicability for the calculation of electron binding energies in molecular systems.
Read more ... 
Abstract  
LOWDIN is a computational program that implements the Any Particle Molecular Orbital (APMO) method. The current version of the code encompasses Hartree–Fock, secondorder Møller–Plesset, configuration interaction, density functional, and generalized propagator theories. LOWDIN input file offers a unique flexibility, allowing users to exploit all the programs' capabilities to study systems containing any type and number of quantum species. This review provides a basic introduction to LOWDIN's key computational details and capabilities.
Read more ... 
Abstract  
We investigate H/D secondary isotope effects on the binding energies of water alkaline cation complexes, Alk^{+}(X_{2}O)_{n} (X = H, D; Alk = Li, Na, K; n = 1 ? 4), using the any particle molecular orbital approach. Our results reveal that deuteration reduces water’s capacity to solvate alkaline cations. An explanation to this behaviour is proposed in terms of the observed changes in distances, partial charges, electrostatic potentials and polarisation induced by deuteration.
Read more ... 
Abstract  
Abstract  
The global minimum geometries of BeCN_{2} and BeNBO are linear BeN–CN and BeN–BO, respectively. The Be center of BeCN_{2} binds He with the highest Be–He dissociation energy among the studied neutral He–Be complexes. In addition, BeCN_{2} can be further tuned as a better noble gas trapper by attaching it with any electronwithdrawing group. Taking BeO, BeS, BeNH, BeNBO, and BeCN_{2} systems, the study at the CCSD(T)/def2TZVP level of theory also shows that both BeCN_{2} and BeNBO systems have higher noble gas binding ability than those related reported systems. ΔG values for the formation of NgBeCN_{2}/NgBeNBO (Ng = Ar–Rn) are negative at room temperature (298 K), whereas the same becomes negative at low temperature for Ng = He and Ne. The polarization plus the charge transfer is the dominating term in the interaction energy.
Read more ... 
Abstract  
Xebinding ability of starshaped C_{5}Li_{7}^{+} cluster and O_{2}Li_{5}^{+} superalkali cluster is studied using the MP2 method. Both C_{5}Li_{7}^{+} and O_{2}Li_{5}^{+} clusters are found to bind with maximum twelve Xe atoms. We have also studied a series of Li decorated clusters for Xebinding. All these clusters show good Xebinding ability. Generally, monocationic clusters have greater binding ability with Xe atoms than the neutral clusters. In addition, a charged Li center binds Xe atoms with better dissociation energy and enthalpy than those with He through Kr. The electron transfer from Xe atoms to Li centers plays a crucial role in binding. The relative contribution of different interaction energy terms towards total interaction energy is analyzed via energy decomposition analysis (EDA). The stability of these Xeloaded clusters is analyzed in terms of the dissociation energies and reaction enthalpies.
Read more ... 
Abstract  
An interface between the APMO code and the electronic structure package MOLPRO is presented. The any particle molecular orbital APMO code [González et al., Int. J. Quantum Chem. 108, 1742 (2008)]10.1002/qua.21584 implements the model where electrons and light nuclei are treated simultaneously at HartreeFock or secondorder MöllerPlesset levels of theory. The APMOMOLPRO interface allows to include highlevel electronic correlation as implemented in the MOLPRO package and to describe nuclear quantum effects at HartreeFock level of theory with the APMO code. Different model systems illustrate the implementation: ^{4}He_{2} dimer as a protype of a weakly bound van der Waals system; isotopomers of [He–H–He]^{+} molecule as an example of a hydrogen bonded system; and molecular hydrogen to compare with very accurate nonBornOppenheimer calculations. The possible improvements and future developments are outlined.
Read more ... 
Abstract  
The selectivity of the intramolecular cyclizations of a series of 2’–aminochalcones was investigated with an approach that combines spin–polarized conceptual density functional theory and energy calculations. To that aim, condensed–to–atoms electrophilic Fukui functions, f NN +(r), were utilized as descriptors of the proclivity for nucleophilic attack of the NH2 group on the unsaturated ? and ? carbons. The results of our model are in excellent agreement with the experimental available evidence permitting us in all cases to predict when the cyclization processes led to the formation of 5–exo and 6–endo products.
Read more ... 
Abstract  
We have recently extended the electron propagator theory to the treatment of any type of particle using an AnyParticle Molecular Orbital (APMO) wavefunction as reference state. This approach, called APMO/PT, has been implemented in the LOWDIN code to calculate correlated binding energies, for any type of particle in molecular systems. In this work, we present the application of the APMO/PT approach to study proton detachment processes. We employed this method to calculate proton binding energies and proton affinities for a set of inorganic and organic molecules. Our results reveal that the secondorder proton propagator (APMO/PP2) quantitatively reproduces experimental trends with an average deviation of less than 0.41 eV. We also estimated proton affinities with an average deviation of 0.14 eV and the proton hydration free energy using APMO/PP2 with a resulting value of ?270.2 kcal/mol, in agreement with other results reported in the literature. Results presented in this work suggest that the APMO/PP2 approach is a promising tool for studying proton acid/base properties.
Read more ... 
Abstract  
AnyParticle Molecular Orbital/HartreeFock (APMO/HF) calculations are performed for a variety of atoms and simple diatomic molecular systems containing one and two negative muons (?). In these calculations electrons and muons are described quantum mechanically whereas nuclei are treated as point charges. Our results for atoms containing n=1,2 negative muons reveal that electronic properties such as electronic densities and ionization potentials shift to those of allelectron atoms with atomic numbers Zn. In the case of diatomic molecules these muonic effects are more diverse ranging from transmutation of atomic properties to drastic changes in equilibrium geometries and energies.
Read more ... 
Abstract  
A stochastic exploration of the quantum conformational spaces in the microsolvation of divalent cations with explicit consideration of up to six solvent molecules [Mg(H_{2}O)_{n})]^{2+}, (n=3, 4, 5, 6) at the B3LYP, MP2, CCSD(T) levels is presented. We find several cases in which the formal charge in Mg^{2+} causes dissociation of water molecules in the first solvation shell, leaving a hydroxide ion available to interact with the central cation, the released proton being transferred to outer solvation shells in a Grotthus type mechanism; this particular finding sheds light on the capacity of Mg^{2+} to promote formation of hydroxide anions, a process necessary to regulate proton transfer in enzymes with exonuclease activity. Two distinct types of hydrogen bonds, scattered over a wide range of distances (1.35–2.15 Å) were identified. We find that in inner solvation shells, where hydrogen bond networks are severely disturbed, most of the interaction energies come from electrostatic and polarization+charge transfer, while in outer solvation shells the situation approximates that of pure water clusters.
Read more ... 
Abstract  
In this work we define a shape entropy by calculating the Shannon's entropy of the shape function. This shape entropy and its linear response to the change in the total number of electrons of the molecule are explored as descriptors of bonding properties. Calculations on selected molecular systems were performed. According to these, shape entropy properly describes electron delocalization while its linear response to ionization predicts changes in bonding patterns. The derivative of the shape entropy proposed turned out to be fully determined by the shape function and the Fukui function.
Read more ... 
Abstract  
The noblegastrapping ability of the starshaped C_{5}Li_{7}^{+} cluster and O_{2}Li_{5}^{+} superalkali cluster is studied by using ab initio and density functional theory (DFT) at the MP2 and M052X levels with 6311+G(d,p) and 6311+G(d) basis sets. These clusters are shown to be effective noblegastrapping agents. The stability of noblegasloaded clusters is analyzed in terms of dissociation energies, reaction enthalpies, and conceptual DFTbased reactivity descriptors. The presence of an external electric field improves the dissociation energy.
Read more ... 
Abstract  
We investigate hydrogen isotope and nuclear quantum effects on geometries and binding energies of small protonated rare gas clusters (Rg_{n}X^{+}, Rg = He, Ne, Ar, X = H, D, T, and n = 1–3) with the any particle molecular orbital (APMO) MP2 level of theory (APMO/MP2). To gain insight on the impact of nuclear quantum effects on the different interactions present in the Rg_{n}X^{+} systems, we propose an APMO/MP2 energy decomposition analysis scheme. For RgH^{+} ions, isotopic substitution leads to an increase in the stability of the complex, because polarization and charge transfer contributions increase with the mass of the hydrogen. In the case of Rg_{2}H^{+} complexes, isotopic substitution results in a shortening and weakening of the rare gashydrogen ion bond. For Rg_{3}X^{+} complexes, the isotope effects on the rare gas binding energy are almost negligible. Nevertheless, our results reveal that subtle changes in the charge distribution of the Rg_{2}X^{+} core induced by an isotopic substitution have an impact on the geometry of the Rg_{3}X^{+} complex.
Read more ... 
Abstract  
In this work we propose an extended propagator theory for electrons and other types of quantum particles. This new approach has been implemented in the LOWDIN package and applied to sample calculations of atomic and small molecular systems to determine its accuracy and performance. As a first application of the method we have studied the nuclear quantum effects on electron ionization energies. We have observed that ionization energies of atoms are similar to those obtained with the electron propagator approach. However, for molecular systems containing hydrogen atoms there are improvements in the quality of the results with the inclusion of nuclear quantum effects. An energy term analysis has allowed us to conclude that nuclear quantum effects are important for zero order energies whereas propagator results correct the electron and electronnuclear correlation terms. Results presented for a series of nalkanes have revealed the potential of this method for the accurate calculation of ionization energies of a wide variety of molecular systems containing hydrogen nuclei. The proposed methodology will also be applicable to exotic molecular systems containing positrons or muons.
Read more ... 
Abstract  
An efficient nuclear molecular orbital methodology is presented. This approach combines an auxiliary density functional theory for electrons (ADFT) and a localized Hartree product (LHP) representation for the nuclear wave function. A series of test calculations conducted on small molecules exposed that energy and geometry errors introduced by the use of ADFT and LHP approximations are small and comparable to those obtained by the use of electronic ADFT. In addition, sample calculations performed on (HF)_{n} chains disclosed that the combined ADFT/LHP approach scales cubically with system size (n) as opposed to the quartic scaling of Hartree–Fock/LHP or DFT/LHP methods. Even for medium size molecules the improved scaling of the ADFT/LHP approach resulted in speedups of at least 5x with respect to Hartree–Fock/LHP calculations. The ADFT/LHP method opens up the possibility of studying nuclear quantum effects on large size systems that otherwise would be impractical.
Read more ... 
Abstract  
In this work we present a theoretical study of atoms in which one electron has been replaced by a negative muon. We have treated these muonic systems with the Any Particle Molecular Orbital method. A comparison between the electronic and muonic radial distributions revealed that muons are much more localized than electrons. Therefore, the muonic cloud is screening effectively one positive charge of the nucleus. Our results have revealed that by replacing an electron in an atom by a muon there is a transmutation of the electronic properties of that atom to those of the element with atomic number Z1.
Read more ... 
Abstract  
Spectroscopic and computational studies reveal that a dimer of two units of Ltyrosine derivatives, joined by intermolecular hydrogen bonds, acts as a template in the synthesis of azacyclophanes from Ltyrosine derivatives and formaldehyde via double Mannich type reaction. When the reaction is performed with ltyrosine, the absence of this template leads to linear products. A new azacyclophane (benzoxazinephane) was synthesized by condensation of Ltyrosine isopropyl ester and formaldehyde.
Read more ... 
Abstract  
Nuclear quantum effects (NQE) on the geometry, energy, and electronic structure of the [CN·L·NC]^{?} complex (L = H, D, T) are investigated with the recently developed APMO/MP2 code. This code implements the nuclear molecular orbital approach (NMO) at the Hartree–Fock (HF) and MP2 levels of theory for electrons and quantum nuclei. In a first study, we examined the H/D/T isotope effects on the geometry and electronic structure of the CNH molecule at NMO/HF and NMO/MP2 levels of theory. We found that when increasing the hydrogen nuclear mass there is a reduction of the RNH bond distance and an increase of the electronic population on the hydrogen atom. Our calculated bond distances are in good agreement with experimental and other theoretical results. In a second investigation, we explored the hydrogen NQE on the geometry of [CNHNC]^{?} complex at the NMO/HF and NMO/MP2 levels of theory. We discovered that while a NMO/HF calculation presented an asymmetric hydrogen bond, the NMO/MP2 calculation revealed a symmetric Hbond. We also examined the H/D/T isotope effects on the geometry and stabilization energy of the [CNHNC]^{?} complex. We noted that gradual increases in hydrogen mass led to reductions of the RNN distance and destabilization of the hydrogen bond (Hbond). A discussion of these results is given in terms of the hydrogen nuclear delocalization effects on the electronic structure and energy components. To the best of our knowledge, this is the first ab initio NMO study that reveals the importance of including nuclear quantum effects in conventional electronic structure calculations for an enhanced description of stronglowbarrier Hbonded systems.
Read more ... 
Abstract  
A stochastic exploration of the quantum conformational space for the (H_{2O})_{n}Li^{+}, n = 3, 4, 5 complexes produced 32 molecular clusters at the B3LYP/6–311++G** and MP2/6–311++G** levels. The first solvation shell is predicted to comprise a maximum of 4 water molecules. Energy decomposition analyses were performed to determine the relationship between the geometrical features of the complexes and the types of interactions responsible for their stabilization. Our findings reveal that electrostatic interactions are major players determining the structures and relative stabilities of the clusters. The formal charge on the Li atom leads to two distinct types of hydrogen bonds, scattered in a wide range of distances (1.61–2.32 Å), in many cases affording Hbonds that are considerably larger and considerably shorter than those in pure water clusters (typically 1.97 Å).
Read more ... 
Abstract  
This paper describes the optimization of the overall calculation scheme and the implementations of an efficient system for calculate molecular integrals in the APMO software package (Any Particle Molecular Orbital). APMO is an implementation of the nuclear and electronic molecular orbital (NEMO) method at HatreeFock (HF) and MP2 levels of theory. In this method, both nuclei and electrons are represented as wave functions, which allow the study of phenomena where nuclear quantum effects are important, such as isotope effects, hydrogen bonding, proton transfer, and others. This optimization reached a marked decrease in global and molecular integrals calculation times and enabled the use of basis functions with angular momenta higher than d and allowed the calculation of systems with more than eight atoms. This paper also presents the application of the NEMO method to the study of the isotope effect on mono and dihydrated complexes of copper (I) and zinc (II). For these
systems, we found that the substitution of a proton with a deuteron nucleus weakens the metaloxygen bond.

Abstract  
The nuclear quantum effects (NQE) on the geometries and energies of the HeH^{+} and He_{2}H^{+} complexes and their hydrogen isotopologues are investigated with the recently developed APMO/MP2 code. This code implements the Nuclear Molecular Orbital Approach (NMO) at a MP2 level of theory for electrons and quantum nuclei. In a first investigation of NQE on HeH^{+}, we have observed a reduction in the bond distance as the mass of the hydrogen isotope is increased. Our calculated bond distances are in good agreement with experiment. We have also studied the H/D/T isotope effects on the geometry, total energy and stabilization energy of HeHHe^{+}. We have also determined the relation between nuclear mass and delocalization and found that the lighter the nucleus the more delocalized it is. Our results demonstrate the importance of including nuclear quantum effects in these systems. To our knowledge, these are the first reported results on isotope effects on the HeH^{+} and He_{2}H^{+} complexes using a NMO method.
Read more ... 
Abstract  
The synthesis of a new azacyclophane formed by two ltyrosine units joined by two methylene bridges is presented. The structural and conformational characteristics are briefly discussed. Spectroscopic and theoretical data reveal a syn structure with two intramolecular hydrogen bonds.
Read more ... 
Abstract  
Hydrogen isotope effects on geometries, total energies, nuclear and electronic wave functions of the [HO_{3}SO–H–OSO_{3}H]^{} and [KO_{3}SO–H–OSO_{3}K]^{} complexes are investigated with the NEO/HF method. This method determines both electronic and nuclear wave function simultaneously. A discussion of the isotope effects is provided and used to explain the hydrogen isotope effects on the phase transition temperatures in hydrogen bonded ferroelectric materials, K_{3}H(SO_{4})_{2} and K_{3}D(SO_{4})_{2}.
Read more ... 
Abstract  
Secondary hydrogen isotope effects on the geometries, electronic wave functions and binding energies of cation?π complexes (cation = Li^{+}, Na^{+}, K^{+} and π= acetylene, ethylene, benzene) are investigated with NEO/HF and NEO/MP2 methods. These methods determine both electronic and nuclear wave functions simultaneously. Our results show that an increase of the hydrogen nuclear mass leads to the elongation of the cation?π bond distance and the decrease in its binding energy. An explanation to this behavior is given in terms of the changes in the πmolecule electronic structure and electrostatic potential induced by isotopic substitutions.
Read more ... 
Abstract  
Secondary deuterium isotope effects (IE) on the acidity (pK_{a}) of glycine were measured by ^{13}C NMR titration. It was found that deuteration decreases the pK_{a} by 0.034 ± 0.002. The experimental data are supported by theoretical calculations, which, in turn, allowed to relate the acidity decrease to the lowering of glycine vibrational frequencies upon deuteration.
Read more ... 
Abstract  
The proton affinity scale of small aminal cages was investigated using experimental and theoretical methodologies. The formation constant (Kf) was determined for 1:1 hydrogenbonded complexes between pfluorophenol (PFP) and some aminal cage type (B) in CCl4 at 298 K using FTIR spectrometry. Then, the total interaction energy (E_{PFF?B}), the energy of protonation (E_{HB+}), the HOMO–LUMO GAP values and the Fukui index were calculated using the DFT/B3LYP/631G(d,p) level of theory as theoretical descriptors. The values of the formation constant and energy changes vary with the tetrahedral character of the nitrogen lone pair. Good correlation between experimental and theoretical scales was observed, evidence for the existence of a relationship between the total energy of interaction calculated by structural parameters and the proton affinity in this series.
Read more ... 
Abstract  
In order to optimize the average geometries of molecular systems using the nuclear and electronic molecular orbital theory (NEMO), we have deducted the expression for calculating the analytical gradient of the energy in the HartreeFock theory, for any kind quantum specie. The implementation was done within the computational package APMO (AnyParticle Molecular Orbital) and in order to verify the correct implementation of the method, we have calculated the model molecules H_{2}, HF and H_{2}O, with numerical and analytical methods. With the use of analytical derivatives within of the OMME formalism, we will have a more efficient calculation of the nuclearelectronic structure of molecular systems with the APMO package.
Read more ... 
Abstract  
We have investigated the hydrogen isotope effect on the geometry, the electronic structure and the stability of the boranecarbonile adduct, by using the nuclearelectronic molecular orbital method (NEMO) which has been implemented in the APMO software. We have found that an increase of the mass of the hydrogen isotope reduces the boronhydrogen and carbonoxygen bond lengths while increasing the boroncarbon distance. In this study, the stability of the adduct has been analyzed in terms of formation energies and BC bond distances. We have found that the increase of the isotope mass weakens the BC bond. We tried to give an explaination to this phenomenon based on Lewis acidity concept but it predicted the wrong results. A reactivity model based on the energy differences of borane LUMO orbitais offered a correct explaination to this effect.
Read more ... 
Abstract  
We have carried out a theoretical investigacion of the hydrogen isotope effects on the geometry, the electronic charge distribution, the relative stability and the energy of formation of linear complexes of the type MXYF and all their hydrogen istopologues (M = Li, Na; X, Y= H, D, T). For this study we have utilized the APMO software at a nucleoelectronic HartreeFock level of theory. Our results are agreement with other reported theoretical data based on conventional electronic structure methods.
Read more ... 
Abstract  
With the aim of studying phenomena where atomic nuclei have a quantal behavior, we have developed the APMO (AnyParticle Molecular Orbital) software package. This implements the nuclear and electronic molecular orbital approach (NEMO) at a HartreeFock level of theory, where both nuclei and electrons are represented as wave functions.
To verify the correct implementation of the method, a number of electronic and nuclearelectronic calculations were carried out on H2 and LiH molecules. The calculated energy components follow the trends and are of the same order of magnitude of similar calculations reported in the literature.
In contrast to other packages that implement the NEMO approach, ours is designed to allow for studying systems with any number of quantum particles.
Read more ... 
Abstract  
To study the hydrogen isotope effects in a series of diatomic molecules and water dimers we have created the any particle molecular orbital computer package (APMO). The current version of the APMO code is an implementation of the nuclear orbital and molecular orbital approaches (NMO) at the HartreeFock level of theory. We have applied the APMO code to a variety of systems to elucidate the isotope effects on electronic wave functions, geometries and hydrogen bonds. We have studied the isotope effect on the dipole moments, electron densities and geometries of hydrogen molecule, lithium hydride and hydrogen fluoride and we have observed a reduction in the bond distance as the mass of the hydrogen isotopes is increased. This observation is in agreement with experimental data. We have also studied the primary and secondary isotope effects on the hydrogen bond of water dimers and we have observed that the hydrogenbond becomes weaker as the mass of the bonded hydrogen is increased. This trend has been observed by other authors. In contrast, the hydrogen bond becomes stronger when the mass of secondary hydrogens is increased. Our trends for secondary effects are in agreement with other theoretical and experimental studies. To our knowledge these are the first reported results on the secondary isotope effect on the hydrogen bond of water dimers using a NMO method. The applications presented in this paper demonstrate that the APMO code is highly suitable for the investigation of isotope effects in molecular systems containing a variety of quantum nuclei
Read more ... 
Abstract  
Novel ruthenium(II) complexes with ferrocenylic and/or phosphinic ligands of the type [RuCl2(PP)(NN)], with PP = 1,1’ bis(diphenylphosphino)ferrocene (dppf) or 1,2dipheylphospinoethane (dppe) and NN = 3,3’dicarboxyl 2,2’bipyridine (3,3’ dcbpy) or 2,2’bipyridine (bpy) were synthesized and characterized. DFT studies of these compounds allowed to explain some experimental aspects, leading to a theoretical design of modified Ru(II) ferrocenylic complexes in order to be used as a dye for Photosensitized Solar Cells. The ligands and the complexes were characterized by 1H y 31P – NMR, UVVis, IR and Cyclic and differential pulse voltammetries.
Read more ... 
Abstract  
An alkali atom–noble gas cluster system is considered as a model for solvation effects in optical spectra, within a quantumclassical description based on the density operator of a manyatom system and its partial Wigner transform. This leads to an eikonaltimedependent molecular orbital treatment suitable for a timedependent description of the coupling of light emission and atom dynamics in terms of the timedependent electric dipole of the whole system. As an application, we consider an optically excited lithium atom as the dopant in a helium cluster at 0.5?K. We describe the motions of the excited Li atom interacting with a cluster of He atoms and calculate the timedependent electric dipole of the Li–He99 system during the dynamics. The electronic Hamiltonian is taken as a sum of threebody Li–He diatomic potentials including electronic polarization and repulsion, with ldependent atomic pseudopotentials for Li and He, while we use a modified pair potential for He–He. The calculations involve the coupling of 12 quantum states with 300 classical degrees of freedom. We present results for the dynamics and spectra of a Li atom interacting with a model cluster surface of He atoms and also interacting with a droplet of He. We have found that the Li atom is attracted or repulsed from the He surface, depending on the orientation of its 2p orbitals. The spectra and dynamics of Li inside and at the surface of a cluster are found to be strongly dependent on its electronic states, its velocity direction, and whether light is present during emission or not.
Read more ... 
Abstract  
The absorption of light during atomic collisions is treated by coupling electronic excitations, treated quantum mechanically, to the motion of the nuclei described within a short de Broglie wavelength approximation, using a density matrix approach. The timedependent electric dipole of the system provides the intensity of light absorption in a treatment valid for transient phenomena, and the Fourier transform of timedependent intensities gives absorption spectra that are very sensitive to details of the interaction potentials of excited diatomic states. We consider several sets of atomic expansion functions and atomic pseudopotentials, and introduce new parametrizations to provide light absorption spectra in good agreement with experimentally measured and ab initio calculated spectra. To this end, we describe the electronic excitation of the valence electron of excited alkali atoms in collisions with noble gas atoms with a procedure that combines ldependent atomic pseudopotentials, including two and threebody polarization terms, and a treatment of the dynamics based on the eikonal approximation of atomic motions and timedependent molecular orbitals. We present results for the collision induced absorption spectra in the Li–He system at 720?K, which display both atomic and molecular transition intensities.
Read more ... 
Abstract  
Collisioninduced light emission during the interaction of an alkalimetal atom and a noblegas atom is treated within a firstprinciples, or direct, dynamics approach that calculates a timedependent electric dipole for the whole system, and spectral emission cross sections from its Fourier transform. These cross sections are very sensitive to excited diatomic potentials and a source of information on their shape. The coupling between electronic transitions and nuclear motions is treated with atomic pseudopotentials and an electronic density matrix coupled to trajectories for the nuclei. A recently implemented pseudopotential parametrization scheme is used here for the ground and excited states of the LiHe system, and to calculate statetostate dipole moments. To verify the accuracy of our new parameters, we recalculate the integral cross sections for the LiHe system in the keV energy regime and obtain agreement with other results from theory and experiment. We further present results for the emission spectrum from 10 keV Li(2s)+He collisions, and compare them to experimental values available in the region of light emitted at 300–900 nm.
Read more ... 