## Andrés Reyes

**Professor of Chemistry**

Departamento de Química

Universidad Nacional de Colombia

Unidad Camilo Torres

Bloque 9. Oficina 3B1

Calle 44 #45-67

Bogotá, Colombia

**Curriculum Vitae**

- B.Sc. in Chemistry, 1997, Universidad del Valle, Cali, Colombia
- Ph.D. in Chemistry, 2003, University of Florida, Gainesville, USA
- Postdoc, 2003-2005, Penn State University, University Park, USA
- Associate professor, 2005-2013, Universidad Nacional de Colombia, Bogota, Colombia
- Professor of Chemistry, 2013-present, Universidad Nacional de Colombia, Bogotá, Colombia

Publications

- Félix Moncada, Roberto Florez-Moreno and Andrés Reyes, Theoretical Calculation of Polarizability Isotope Effects JMMO, 2017,
## 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 X-H 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.

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- Laura Pedraza-González, Johan F. Galindo, Ronald González, and Andrés 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,
## 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, ε, 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 ε 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.

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- Yusuke Tsukamoto, Yasuhiro Ikabata, Jonathan Romero, Andrés Reyes and Hiromi 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., 2016, 18, 27422-27431
## 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 second-order proton propagator method, which is based on nuclear orbital plus molecular orbital theory. In the present scheme, the divide-and-conquer 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.

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- Laura Pedraza-González, Jonathan Romero, Jorge Alí-Torresa and Andrés Reyes, Prediction of proton affinities of organic molecules using the any-particle molecular-orbital second-order proton propagator approach. Phys. Chem. Chem. Phys., 2016, 18, 27185-27189
## Abstract

We assess the performance of the recently developed any-particle molecular-orbital second-order proton propagator (APMO/PP2) scheme [M. Díaz-Tinoco, J. Romero, J. V. Ortiz, A. Reyes and R. Flores-Moreno, 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.

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- 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)
## 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 cis-trans photoisomerization of 11-cis 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.

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- 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)
## 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 multi-target 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.

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- 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)
## Abstract

The any-particle molecular orbital method at the full conﬁguration 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 eﬀects on chemical properties of muonic and regular atoms. This study reveals that the diﬀerences 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 eﬀects are more important. On the other hand, for 1s ionizations of muonic atoms heavier than beryllium, the quantum muon eﬀects are more important. In addition, this study presents an assessment of the nuclear mass and quantum muon eﬀects on the barrier of Heμ + H2 reaction.

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- 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)
## Abstract

We recently extended the electron propagator theory to any type of quantum species based in the framework of the Any-Particle Molecular Orbital (APMO) approach [J. Romero, E. Posada, R. Flores-Moreno, 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. Díaz-Tinoco, J. Romero, J. V. Ortiz, A. Reyes, and R. Flores-Moreno, 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 Full-CI 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 electron-positron correlation within the quasiparticle propagator approach.

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- H. J. Bohórquez, A. Reyes. "The atomic Pauli energy grows exponentially with the electronic localization", Mol. Phys., 112, 416-421 (2014)
## 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 ρ(r) and the pair density ρ2(r, r′). The proposed equation shows certain advantages over a similar orbital-free kinetic energy functional recently proposed by Delle Site and co-workers. 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.

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- R.D. Guerrero, C. Arango, A. Reyes,"Optimal control of wave-packets: a semiclassical approach", Mol. Phys., 112, 408-415 (2014)
## Abstract

We studied the optimal quantum control of a molecular rotor in tilted laser fields using the time-sliced 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 wave-packet in a double-well 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 wave-packets was maximised.

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- 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)
## Abstract

We report positron binding energies (PBEs) for the 20 standard amino acids in the global minimum, hydrogen-bonded, and zwitterionic forms. The calculations are performed at the any-particle molecular-orbital (APMO) Hartree-Fock (HF), Koopmans' theorem (KT), second-order Möller-Plesset (MP2), and second-order 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.

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- 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)
## Abstract

A simple modification of the quasiparticle second order electron propagator (EP2) method based on the spin-component-scaled technique is proposed. In this new approach, the second order contributions to the self-energy 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 cost-free spin-component-scaled 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.

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- 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)
## Abstract

LOWDIN is a computational program that implements the Any Particle Molecular Orbital (APMO) method. The current version of the code encompasses Hartree–Fock, second-order 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.

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- 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
## 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.

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- 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).
## Abstract

- 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)
## 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 electron-withdrawing group. Taking BeO, BeS, BeNH, BeNBO, and BeCN_{2}systems, the study at the CCSD(T)/def2-TZVP 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.

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- 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)
## Abstract

Xe-binding ability of star-shaped C_{5}Li_{7}^{+}cluster and O_{2}Li_{5}^{+}super-alkali 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 Xe-binding. All these clusters show good Xe-binding 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 Xe-loaded clusters is analyzed in terms of the dissociation energies and reaction enthalpies.

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- 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)
## 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 Hartree-Fock or second-order Möller-Plesset levels of theory. The APMO-MOLPRO interface allows to include high-level electronic correlation as implemented in the MOLPRO package and to describe nuclear quantum effects at Hartree-Fock 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 non-Born-Oppenheimer calculations. The possible improvements and future developments are outlined.

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- 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)
## 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 α and β 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.

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- 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)
## Abstract

We have recently extended the electron propagator theory to the treatment of any type of particle using an Any-Particle 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 second-order 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.

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- 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)
## Abstract

Any-Particle Molecular Orbital/Hartree-Fock (APMO/HF) calculations are performed for a variety of atoms and simple diatomic molecular systems containing one and two negative muons (μ). 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 all-electron atoms with atomic numbers Z-n. 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.

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- J. Gonzalez, E. Florez, J. Romero, A. Reyes, A. Restrepo, "Microsolvation of Mg
^{2+}, Ca^{2+}: strong influence of formal charges in hydrogen bonding networks", J. Mol. Model., 19(4), 1763 (2013)## 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.

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- 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)
## 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.

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- S. Pan, M. Contreras, J. Romero, A. Reyes, G. Merino, P. K. Chattaraj, "C
_{5}Li_{7}^{+}and O_{2}Li_{5}^{+}as Noble Gas Trapping Agents", Chem. Eur. J. 19(7), 2322, (2013)## Abstract

The noble-gas-trapping ability of the star-shaped C_{5}Li_{7}^{+}cluster and O_{2}Li_{5}^{+}super-alkali cluster is studied by using ab initio and density functional theory (DFT) at the MP2 and M05-2X levels with 6-311+G(d,p) and 6-311+G(d) basis sets. These clusters are shown to be effective noble-gas-trapping agents. The stability of noble-gas-loaded clusters is analyzed in terms of dissociation energies, reaction enthalpies, and conceptual DFT-based reactivity descriptors. The presence of an external electric field improves the dissociation energy.

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- 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)
## 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 gas-hydrogen 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.

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- 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)
## 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 electron-nuclear correlation terms. Results presented for a series of n-alkanes 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.

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- 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)
## 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.

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- F. Moncada, D. Cruz, A. Reyes, "Muonic alchemy: transmuting elements with the inclusion of negative muons", Chem. Phys. Letters. 539-540, 209-213 (2012)
## 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 Z-1.

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- N. Nuñez, A. Reyes, R. Quevedo, "Hydrogen Bond Assisted Synthesis of Azacyclophanes from L-tyrosine Derivatives", Tetrahedron Lett. 53, 530 (2012)
## Abstract

Spectroscopic and computational studies reveal that a dimer of two units of L-tyrosine derivatives, joined by intermolecular hydrogen bonds, acts as a template in the synthesis of azacyclophanes from L-tyrosine derivatives and formaldehyde via double Mannich type reaction. When the reaction is performed with l-tyrosine, the absence of this template leads to linear products. A new azacyclophane (benzoxazinephane) was synthesized by condensation of L-tyrosine isopropyl ester and formaldehyde.

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- 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)
## 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 RN-H 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 H-bond. 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 (H-bond). 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 strong-low-barrier H-bonded systems.

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- J. Romero, A. Reyes, J. David, and A. Restrepo, "Understanding Microsolvation of Li
^{+}:Structural and Energetical Analyses", Phys. Chem. Chem. Phys. 13, 15264 (2011)## 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 H-bonds that are considerably larger and considerably shorter than those in pure water clusters (typically 1.97 Å).

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- 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)
## 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 Hatree-Fock (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 metal-oxygen bond.

- S. A. González, A. Reyes, "Nuclear Quantum Effects on the He
_{2}H^{+}Complex With the Nuclear Molecular Orbital Approach", Int. J. Quant. Chem. 110 689 (2010)## 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.

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- R. Quevedo, I. Ortiz and A. Reyes, "Synthesis and Conformational Analysis of Azacyclophanes from L-Tyrosine", Tetrahedron Lett. 51 1216 (2010)
## Abstract

The synthesis of a new azacyclophane formed by two l-tyrosine 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.

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- F. Moncada, S. A. González, A. Reyes, "First Principles Investigation of Hydrogen Isotope Effects in [XSO
_{4}−H−SO_{4}X]^{−}(X = H,K) Complexes", Mol. Phys., 108 1545 (2010)## 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}.

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- 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)## 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 π-molecule electronic structure and electrostatic potential induced by isotopic substitutions.

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- J. Romero, A. Reyes and J. Wist, "Secondary Deuterium Isotope Effects on the Acidity of Glycine", Spectrochim. Acta. Part A, 77 845 (2010)
## 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.

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- 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)
## 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 hydrogen-bonded complexes between p-fluorophenol (PFP) and some aminal cage type (B) in CCl4 at 298 K using FT-IR 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/6-31G(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.

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- 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)
## 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 Hartree-Fock theory, for any kind quantum specie. The implementation was done within the computational package APMO (Any-Particle 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 nuclear-electronic structure of molecular systems with the APMO package.

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- 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)
## Abstract

We have investigated the hydrogen isotope effect on the geometry, the electronic structure and the stability of the borane-carbonile adduct, by using the nuclear-electronic 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 boron-hydrogen and carbon-oxygen bond lengths while increasing the boron-carbon distance. In this study, the stability of the adduct has been analyzed in terms of formation energies and B-C bond distances. We have found that the increase of the isotope mass weakens the B-C 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.

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- 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)
## 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 M-X-Y-F and all their hydrogen istopologues (M = Li, Na; X, Y= H, D, T). For this study we have utilized the APMO software at a nucleo-electronic Hartree-Fock level of theory. Our results are agreement with other reported theoretical data based on conventional electronic structure methods.

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- 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)
## Abstract

With the aim of studying phenomena where atomic nuclei have a quantal behavior, we have developed the APMO (Any-Particle Molecular Orbital) software package. This implements the nuclear and electronic molecular orbital approach (NEMO) at a Hartree-Fock 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 nuclear-electronic 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.

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- 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)
## 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 Hartree-Fock 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 hydrogen-bond 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

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- 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)
## 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 1,2-dipheylphospinoethane (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, UV-Vis, IR and Cyclic and differential pulse voltammetries.

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- 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)
## Abstract

An alkali atom–noble gas cluster system is considered as a model for solvation effects in optical spectra, within a quantum-classical description based on the density operator of a many-atom system and its partial Wigner transform. This leads to an eikonal-time-dependent molecular orbital treatment suitable for a time-dependent description of the coupling of light emission and atom dynamics in terms of the time-dependent 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 time-dependent electric dipole of the Li–He99 system during the dynamics. The electronic Hamiltonian is taken as a sum of three-body Li–He diatomic potentials including electronic polarization and repulsion, with l-dependent 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.

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- 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)
## 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 time-dependent electric dipole of the system provides the intensity of light absorption in a treatment valid for transient phenomena, and the Fourier transform of time-dependent 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 l-dependent atomic pseudopotentials, including two- and three-body polarization terms, and a treatment of the dynamics based on the eikonal approximation of atomic motions and time-dependent 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.

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- 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)
## Abstract

Collision-induced light emission during the interaction of an alkali-metal atom and a noble-gas atom is treated within a first-principles, or direct, dynamics approach that calculates a time-dependent 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 state-to-state 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.

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- A. Reyes, M. V. Pak, and S. Hammes-Schiffer "Investigation of Isotope Effects with the Nuclear-Electronic Orbital Method", J. Chem. Phys. 123, 014303 (2005)
## Abstract

This paper addresses fundamental issues that arise in the application of the nuclear-electronic orbital (NEO) approach to systems with equivalent quantum nuclei. Our analysis illustrates \ that Hartree-Fock nuclear wave functions do not provide physically reasonable descriptions of systems comprised of equivalent low-spin fermions or equivalent bosons. The physical basis for this breakdown is tha\ t the ionic terms dominate due to the localized nature of the nuclear orbitals. Multiconfigurational wave functions that include only covalent terms provide physically reasonable descriptions of these types of \ systems. The application of the NEO approach to a variety of chemical systems is presented to elucidate the isotope effects on the geometries and electronic wave functions. Deuteration of hydrogen halides, wate\ r, ammonia, and hydronium ion decreases the bond length and the magnitude of negative partial atomic charge on the heavy atom. These results are consistent with experimental spectroscopic data. Deuteration at t\ he beta position for formate anion and a series of amines increases the magnitude of negative partial atomic charge on the protonation site for the unprotonated species. This observation is consistent with the \ experimentally observed increase in basicity upon deuteration at the beta position for carboxylic acids and amines.

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- A. Reyes, and D. A. Micha "Dynamics of Electronic Excitation in collisions of Alkali Atoms with Noble-Gas Atoms Using Atomic Core Potentials", J. Chem. Phys. 119, 12308 (2003)
## Abstract

The electronic excitation of the valence electron of alkali atoms in collisions with noble gas atoms has been studied with a procedure that combines l-dependent pseudopotentials including two and three-body polarization terms and a first principles description of the dynamics based on the eikonal approximation of atomic motions and time-dependent molecular orbitals. We discuss the effects of the atomic basis set size on the calculations. We present results for interaction potentials and couplings, the time-dependence of atomic populations, and state-to-state integral cross sections in the keV range. Our results for Li–He, Li–Ne, Na–He, and Na–Ne are in very good agreement with other theoretical and experimental data.

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- A. Reyes, and D. A. Micha "Dynamics of spin-orbit recoupling in collisions of Alkali Atoms with Noble-Gas Atoms Using Atomic Core Potentials", J. Chem. Phys. 119, 12316 (2003)
## Abstract

Spin–orbit recoupling in alkali-rare-gas atom colliding pairs is developed within a first principles description of the quantum dynamics introducing l-dependent pseudopotentials and including two and three-body polarization terms and the spin–orbit interatomic potential. The treatment combines an eikonal (or short wavelength) approximation for the nuclear motion and time-dependent molecular orbitals to provide interatomic potentials, their nonadiabatic couplings, and state populations during interactions. The time evolution of recoupling of angular momenta in alkali-rare-gas atom thermal collisions is described and computational aspects of spin–orbit coupling in terms of pseudopotentials are presented. Results for potentials arising from the spin–orbit splitting of the 2P states of Li and Na are presented along with cross sections for fine-structure transitions at 400 K and 450 K. The agreement with experiment and other theories is very good.

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- A. Reyes, D. A. Micha, and K. Runge "First Principles Dynamics of Li+He Collisional Excitation Using Atomic Core Potentials", Chem. Phys. Letters 363, 441 (2002)
## Abstract

A ﬁrst principles description of electronic excitation in Li–He colliding pairs is developed introducing l-dependent pseudopotentials and including two- and three-body polarization terms. The treatment combines an eikonal approximation and time-dependent molecular orbitals to provide interatomic potentials, their non-adiabatic couplings, and state populations during interactions. We discuss the eﬀects of the basis set size on the calculations, and compare our results with experiment and other calculations. Our integral cross-sections obtained with a large basis set are in excellent agreement with experiment.

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