Junia Melin - Academia.edu (original) (raw)

Papers by Junia Melin

arXiv: Biomolecules, 2016

A simple model to predict the directionality of vibrational energy flow at molecular level is pre... more A simple model to predict the directionality of vibrational energy flow at molecular level is presented. This model is based on a vibrational energy propagation analysis using ab intio molecular dynamics and the Fukui function and local softness reactivity indexes derived from DFT. By using this simple conceptual model we are giving a cogent rationale to previous theoretical and experimental reports of asymmetrical vibrational energy diffusion in proteins and energetic materials. We proposed here three basic rules for the Vibrational Energy Relaxation in molecules: (i) the vibrational energy flows form a soft site to a hard site but not in the opposite direction, (ii) when vibrational energy is injected directly to a hard site, it is trapped in this site, and (iii) if the vibrational energy is pump in a polarizable site and two sites with different softness are available, the energy will propagate to the softest one.

Journal of Chemical Physics, Jun 15, 2005

Vertical excitation energies of the Rydberg radical H3O are inferred from ab initio electron prop... more Vertical excitation energies of the Rydberg radical H3O are inferred from ab initio electron propagator calculations on the electron affinities of H3O+. The adiabatic ionization energy of H3O is evaluated with coupled-cluster calculations. These predictions provide optimal parameters for the molecular-adapted quantum defect orbital method, which is used to determine oscillator strengths. Given that the experimental spectrum of H3O does not seem to be available, comparisons with previous calculations are discussed. A simple model Hamiltonian, suitable for the study of bound states with arbitrarily high energies is generated by these means.

Journal of Chemical Theory and Computation, Feb 16, 2007

A new general-purpose reactivity indicator is derived. Unlike existing indicators, this indicator... more A new general-purpose reactivity indicator is derived. Unlike existing indicators, this indicator can describe the reactivity of molecules that lie between the electrostatic (or charge) control and electron-transfer (or frontier-orbital) control paradigms. Depending on the parameters in the indicator, it describes electrostatic control (where the electrostatic potential is the appropriate indicator), electron-transfer control (where the Fukui function's potential is the appropriate indicator), and intermediate cases (where linear combinations of the electrostatic potential and the Fukui function's potential are appropriate indicators). Our analysis gives some insight into the origins of the local hard/soft-acid/base principle. The "minimum Fukui function" rule for hard reagents also emerges naturally from our analysis: if (1) a reaction is strongly electrostatically controlled and (2) there are two sites that are equally favorable from an electrostatic standpoint, then the most reactive of the electrostatically equivalent sites is the site with the smallest Fukui function. An analogous electrostatic potential rule for soft reagents is also introduced: if (1) a reaction is strongly electron-transfer-controlled and (2) there are two sites where the Fukui function's potential are equivalent, then the most reactive of the Fukuiequivalent sites will be the one with greatest electrostatic potential (for electrophilic attack on a nucleophile) or smallest electrostatic potential (for nucleophilic attack on an electrophile).

The Journal of Physical Chemistry a, 2003

The Journal of Physical Chemistry A, 2004

... Junia Melin, Felipe Aparicio, Venkatesan Subramanian, Marcelo Galván, * and Pratim K.... more ... Junia Melin, Felipe Aparicio, Venkatesan Subramanian, Marcelo Galván, * and Pratim K. Chattaraj* §. Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, AP POSTAL 55-534, México DF 09340 ...

Photochemical & Photobiological Sciences, 2008

All chemicals were obtained from Acros Organics, unless noted otherwise. 400 MHz and 200 MHz Vari... more All chemicals were obtained from Acros Organics, unless noted otherwise. 400 MHz and 200 MHz Varian NMR-spectrometer and a Nicolet Protégé 460 FT-IR spectrometer were used in this study. We thank the Analytical Laboratory of Dr. Ruth Welti at KSU for recording the mass spectra of our compound employing an Applied Biosystems API-4000 triple quadrupole mass spectrometer with electrospray and APCI sources. Fluorenone-9-hydrazone (2) Hydrazine hydrate (6.024g, 0.12 mol of H 4 N 2) was added drop-wise to a suspension of 9-fluorenone (20.0 g, 0.11 mol) in ethanol (200 ml) at RT. An exothermic reaction was observed, which subsided after 15 min. The reaction mixture was refluxed overnight and then allowed to cool down to RT. After 12 h, the precipitate (yellow needles) was separated by filtration and recrystallized from anhydrous ethanol. Yield: 15.5 g, 72.2%. The purity of compound (2) was confirmed by using TLC (silica, mobile phase: n-hexane/ethyl acetate 4/1 v/v, R f =0.14).

The Journal of Physical Chemistry A, 1997

Journal of molecular modeling, 2016

We elucidate the regioselectivity of nucleophilic attack on substituted benzenesulfonates, quinol... more We elucidate the regioselectivity of nucleophilic attack on substituted benzenesulfonates, quinolines, and pyridines using a general-purpose reactivity indicator (GPRI) for electrophiles. We observe that the GPRI is most accurate when the incoming nucleophile resembles a point charge. We further observe that the GPRI often chooses reactive "dead ends" as the most reactive sites as well as sterically hindered reactive sites. This means that care must be taken to remove sites that are inherently unreactive. Generally, among sites where reactions actually occur, the GPRI identifies the sites in the molecule that lead to the kinetically favored product(s). Furthermore, the GPRI can discern which sites react with hard reagents and which sites react with soft reagents. Because it is currently impossible to use the mathematical framework of conceptual DFT to identify sterically inaccessible sites and reactive dead ends, the GPRI is primarily useful as an interpretative, not a pre...

Theoretical and Computational Chemistry, Dec 31, 2007

The Journal of Physical Chemistry a, Nov 1, 2007

Ab initio and density-functional theory calculations for a family of substituted acetylenes show ... more Ab initio and density-functional theory calculations for a family of substituted acetylenes show that removing electrons from these molecules causes the electron density along the C-C bond to increase. This result contradicts the predictions of simple frontier molecular orbital theory, but it is easily explained using the nucleophilic Fukui function-provided that one is willing to allow for the Fukui function to be negative. Negative Fukui functions emerge as key indicators of redox-induced electron rearrangements, where oxidation of an entire molecule (acetylene) leads to reduction of a specific region of the molecule (along the bond axis, between the carbon atoms). Remarkably, further oxidization of these substituted acetylenes (one can remove as many as four electrons!) causes the electron density along the C-C bond to increase even more. This work provides substantial evidence that the molecular Fukui function is sometimes negative and reveals that this is due to orbital relaxation.

Journal of molecular modeling, 2015

We present a critical discussion related to the recent definition of the intrinsic reactivity ind... more We present a critical discussion related to the recent definition of the intrinsic reactivity index, IRI, (Tetrahedron Lett. 2013, 54, 339-342; Tetrahedron 2013, 69, 4247-4258) formulated to describe both, electrophilicity (charge acceptance) and nucleophilicity (charge donation) reactivities. We here stress that such an IRI model, based on the quantity μ/η, should be properly related to theoretical approximations associated to the change in the global electronic energy of a given chemical system under interaction with a suitable electron bath (Gazquez JL et al. J Phys Chem A 2007, 111, 1966-1970). Further, the limitations of the IRI model are presented by emphasizing that the intrinsic relative scales of electrophilicity and nucleophilicity within a second-order perturbation approach must account for the further stabilization of the two interacting species (Chamorro E et al. J Phys Chem A 2013, 117, 2636-2643).

Theoretical and Computational Chemistry, 2007

A double Rydberg anion (DRA) consists of a stable cationic core and two electrons in a diffuse Ry... more A double Rydberg anion (DRA) consists of a stable cationic core and two electrons in a diffuse Rydberg orbital. These anions correspond to a local minimum on a potential energy surface where more stable isomers may exist. Experimental and theoretical works have contributed to a better understanding of the unusual electronic structure of these molecules. With electron propagator calculations and analysis of the electron localization function, some relationships between electronic structure and reactivity in DRAs are considered. J. Melin et al. HH bonding relationships between diffuse s functions. Such phase relationships and the predominance of diffuse s functions on hydrogens explained the sharpness of the corresponding photoelectron peak. This description also validated the use of the term double Rydberg anion (DRA), 2 4 for two electrons are found in a Rydberg-like orbital that is distributed on the periphery of a closed-shell cation, NH + 4 . Several theoretical works were published on other simple hydrides and, in addition to tetrahedral NH − 4 DRAs have been found 5−13 for C 3v OH − 3 and tetrahedral PH − 4 . Geometry optimizations of C 3v SH − 3 and linear structures of FH − 2 and ClH − 2 encountered transition states (TS) instead of DRA minima. The same study provided harmonic vibrational frequencies for NH − 4 OH − 3 , and PH − 4 . Recent calculations on NH 3 R − and OH 2 R − anions, where R = CH 3 NH 2 OH, and F, have identified other stable anions of this type. 14 Here, AH n substituents replace hydrogens from the parent species, tetrahedral NH − 4 , and C 3v OH − 3 . Dyson orbitals for electron detachments from stable anions such as NH 3 CH − 3 are delocalized over the periphery of the entire species. This result extends previous studies where large molecular cations were found to accommodate a diffuse, Rydberg electron that is spread over the periphery of the entire cationic kernel. 15 Covalent and ionic bonding that involves Rydberg-like orbitals has been explored as well. 16 Experiments with higher resolution on N 2 H −17 7 were quickly followed by electron propagator calculations 18 that confirmed the existence of an anion-molecule complex, H − NH 3 2 , and two DRAs with vertical electron-detachment energies placed symmetrically about the position of the low-energy peak in the NH − 4 spectrum. One of these N 2 H − 7 species is a complex consisting of the tetrahedral DRA and a coordinated ammonia molecule. The other features a hydrogen bond between two N atoms in a structure that resembles the N 2 H + 7 NH + 4 -NH 3 complex. The Dyson orbital for anion electron detachment in the latter isomer is localized on the three nonbridging hydrogens attached to the ammonium fragment's N atom. Vibrational satellites of each of the three vertical peaks also were assigned. Agreement of equally high quality was obtained for vibrational satellites seen in the NH − 4 spectrum. These works established the existence of a novel variety of electron pair in DRAs. Extensions of traditional electron pair concepts are clearly needed for these anions. The electron localization function (ELF) 19 is an interesting and robust descriptor of chemical bonding, which has been successfully applied to a wide variety of molecular systems. 20−24 This function, which is based on a topological analysis of a quantum function related to Pauli repulsion, describes the degree of localization (or delocalization) of electron pairs within the molecular space.

Theoretical Chemistry Accounts, 2007

The extended Koopmans' theorem is related to Fukui function, which measures the change in electro... more The extended Koopmans' theorem is related to Fukui function, which measures the change in electron density that accompanies electron attachment and removal. Two approaches are used, one based on the extended Koopmans' theorem differential equation and the other based directly on the expression of the ionized wave function from the extended Koopmans' theorem. It is observed that the Fukui function for electron removal can be modeled as the square of the first Dyson orbital, plus corrections. The possibility of useful generalizations to the extended Koopmans' theorem is considered; some of these extensions give approximations, or even exact expressions, for the Fukui function for electron attachment.

The Journal of Physical Chemistry A, 2006

Various decouplings of the electron propagator have been employed to provide theoretical comparis... more Various decouplings of the electron propagator have been employed to provide theoretical comparison to experimental electron detachment energies for the pyrrolide, imidazolide, and pyrazolide anions. Predictions for isoelectronic anions in which CH groups are replaced by N atoms also are reported. The ab initio electron propagator results agree closely with experimental values, and the associated Dyson orbitals provide a detailed catalog of bonding changes as the number and positions of N atoms vary within the set of pentagonal aromatic anions.

The Journal of Physical Chemistry A, 2007

Several decouplings of the electron propagator, including the relatively new P3+ approximation fo... more Several decouplings of the electron propagator, including the relatively new P3+ approximation for the selfenergy, have been used to calculate vertical electron detachment energies of tautomeric forms of closedshell, pentagonal, aromatic anions in which ring carbons without bonds to hydrogens appear. This study extends previous work in which the most stable forms of anionic, five-member rings with one to five nitrogens were considered. Whereas the lowest electron detachment energies sometimes are assigned by Koopmans's theorem results to π orbital vacancies, electron propagator calculations always obtain σ orbital vacancies for the ground states of the doublet radicals. Higher electron detachment energies that correspond to excited doublets with π vacancies also are presented. The predicted transition energies are in good agreement with low-intensity peaks in recent anion photoelectron spectra that have been assigned to less stable, tautomeric forms of these anions. * Corresponding authors. (J.V.O.) and mmishra@iitb.ac.in (M.K.M.).

The Journal of Physical Chemistry A, 2003

A reactivity picture developed within the spin-polarized density functional theory defined in the... more A reactivity picture developed within the spin-polarized density functional theory defined in the E{N, N S , V(r)} space is discussed. The reactivity model including changes in the total number of electrons N, the spin number (unpaired electron number) N S , and the external potential V(r) is tested against two chemical processes involving radical species. They are the hydrogenation reaction of the succinimidyl radical and the Bergman cyclization. Although the former reaction appears to be mostly driven by the spin potential, a quantity measuring the variations in electronic energy with respect to the spin multiplicity changes; the latter presents highly electrocyclic character without significant spin-polarization effects.

Tetrahedron, 2004

The hydride transfer process between the isoalloxazine moiety of flavins and the nicotinamide moi... more The hydride transfer process between the isoalloxazine moiety of flavins and the nicotinamide moiety of NAD(P)H has been explored by using density functional theory based reactivity index in the 1-methylnicotinamide -lumiflavine model system. Based on crystallographic data available, we have found that the group softness index helps to locate and orientate reactive regions in these interacting molecules while the electrophilicity index successfully describes the reactivity pattern of this system. q

Physical Chemistry Chemical Physics, 2007

Ayers, Parr, and Pearson recently showed that insight into the hard/soft acid/base (HSAB) princip... more Ayers, Parr, and Pearson recently showed that insight into the hard/soft acid/base (HSAB) principle could be obtained by analyzing the energy of reactions in hard/soft exchange reactions, i.e., reactions in which a soft acid replaces a hard acid or a soft base replaces a hard base [J. Chem. Phys., 2006, 124, 194107]. We show, in accord with the maximum hardness principle, that the hardness increases for favorable hard/soft exchange reactions and decreases when the HSAB principle indicates that hard/soft exchange reactions are unfavorable. This extends the previous work of the authors, which treated only the &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;quot;double hard/soft exchange&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;quot; reaction [P. K. Chattaraj and P. W. Ayers, J. Chem. Phys., 2005, 123, 086101]. We also discuss two different approaches to computing the hardness of molecules from the hardness of the composing fragments, and explain how the results differ. In the present context, it seems that the arithmetic mean of fragment softnesses is the preferable definition.