Dual Descriptor Research Articles

Nucleophilicity and electrophilicity of silylenes from a molecular electrostatic potential and dual descriptor perspectives

Nucleophilicity and elecrophilicity of mono and disubstituted silylenes are analyzed using the molecular electrostatic potential and the dual descriptor Δ f ( r → ) , defined within the so called conceptual DFT. A set of 32 compounds has been chosen which can be classified into 4 groups or families based on a linear relationship between the molecular electrostatic potential measured in the electrophilic (empty 3 p z orbital) V A and nucleophilic (lone pair) V min regions around of the silicon atom. The electrophilic and nucleophilic character of silylenes given by | V A - V min | is connected to the orbital-resolved dual descriptor Δ f 3 p z through the π -electron donating property of the substituent.

Conceptual Density Functional Theory and Some Recent Developments

Conceptual density functional theory(DFT),also called Density Functional Reactivity Theory or Chemical DFT,is the chemical reactivity theory of DFT.Its framework and some recent developments of Conceptual DFT are briefly reviewed in this article.Introduced in more detail are the reactivity indices such as electronegativity,hardness,softness,Fukui function,electrophilicity index,as well as principles derived from them.Two representative recent developments,the dual descriptor and steric effect quantification,are succinctly summarized.A personal prospective on the future of Conceptual DFT is provided at the end.

Building Block and Building Rule: Dual Descriptor Method for Biological Sequence Analysis

AbstractThe emergence of “Systems Biology” in recent years highlights the systematic viewpoint of bio-system modeling. Building on such a background, Dual Descriptor Method, a generic methodology for biological sequence analysis is proposed. From a systematic perspective, Dual Descriptor is defined as a two element set of Composition Weight Map and Position Weight Function which aim at reflecting the composition and permutation information of a sequence. An alternate training algorithm is provided to get an optimum description of the building patterns of the sequences. In this paper, dual descriptor method has been applied to the analysis of two typical problems of molecular biology: gene identification and the prediction of protein function. Satisfactory and insightful results are achieved. Owing to the generality of this methodology, dual descriptor method has wide application perspective for many problems of pattern recognition, especially those involved in “Systems Biology”.

Dual descriptors within the framework of spin-polarized density functional theory

Spin-polarized density functional theory (SP-DFT) allows both the analysis of charge-transfer (e.g., electrophilic and nucleophilic reactivity) and of spin-polarization processes (e.g., photophysical changes arising from electron transitions). In analogy with the dual descriptor introduced by Morell et al. [J. Phys. Chem. A 109, 205 (2005)], we introduce new dual descriptors intended to simultaneously give information of the molecular regions where the spin-polarization process linking states of different multiplicity will drive electron density and spin density changes. The electronic charge and spin rearrangement in the spin forbidden radiative transitions S(0)-->T(n,pi(*)) and S(0)-->T(pi,pi(*)) in formaldehyde and ethylene, respectively, have been used as benchmark examples illustrating the usefulness of the new spin-polarization dual descriptors. These quantities indicate those regions where spin-orbit coupling effects are at work in such processes. Additionally, the qualitative relationship between the topology of the spin-polarization dual descriptors and the vertical singlet triplet energy gap in simple substituted carbene series has been also discussed. It is shown that the electron density and spin density rearrangements arise in agreement with spectroscopic experimental evidence and other theoretical results on the selected target systems.

Calculation of Fukui Functions Without Differentiating to the Number of Electrons. 3. Local Fukui Function and Dual Descriptor

An alternative approach for the calculation of DFT-based reactivity descriptors involving derivatives of the energy with respect to the number of electrons and the external potential is further evaluated. Using functional derivatives with respect to the external potential, the finite difference approximation was avoided for the local calculation of the Fukui functions and the dual descriptor. A relevant set of molecules has been calculated after the optimization of computational parameters. It is shown that the new approach correctly predicts the nucleophilic attack on CH2O, the formation of CO metal complexes, the regioselectivity of monosubstituted benzenes, and the softest nucleophilic site in some ambident nucleophiles.

On the Nature of the Active Site in bis(imino)Pyridyl Iron, a Catalyst for Olefin Polymerization

Global and local descriptors of chemical reactivity and selectivity are used in order to characterize the nature of the active species of bis(imino)pyridyl iron, a catalyst for olefin polymerization. It is shown that chemical potential, hardness, electrophilicity, as well as the dual and multiphilic descriptors for chemical reactivity and selectivity, are adequate for characterizing the global and local reactivity trends of this organo-metallic complex. Most theoretical evidence presented in this paper indicates that the catalyst of Fe+3 seems to be more active for olefin polymerization than that of Fe+2. However, when the cocatalyst is considered, catalysts of Fe+2 and Fe+3 present similar electrophilic activity to orientate the nucleophilic attack. It is observed that this activity is well localized at the metallic center in the ferric species whereas it appears to be more delocalized on the ligands of the ferrous species.

Conceptual DFT: the chemical relevance of higher response functions

In recent years conceptual density functional theory offered a perspective for the interpretation/prediction of experimental/theoretical reactivity data on the basis of a series of response functions to perturbations in the number of electrons and/or external potential. This approach has enabled the sharp definition and computation, from first principles, of a series of well-known but sometimes vaguely defined chemical concepts such as electronegativity and hardness. In this contribution, a short overview of the shortcomings of the simplest, first order response functions is illustrated leading to a description of chemical bonding in a covalent interaction in terms of interacting atoms or groups, governed by electrostatics with the tendency to polarize bonds on the basis of electronegativity differences. The second order approach, well known until now, introduces the hardness/softness and Fukui function concepts related to polarizability and frontier MO theory, respectively. The introduction of polarizability/softness is also considered in a historical perspective in which polarizability was, with some exceptions, mainly put forward in non covalent interactions. A particular series of response functions, arising when the changes in the external potential are solely provoked by changes in nuclear configurations (the "R-analogues") are also systematically considered. The main part of the contribution is devoted to third order response functions which, at first sight, may be expected not to yield chemically significant information, as turns out to be for the hyperhardness. A counterexample is the dual descriptor and its R analogue, the initial hardness response, which turns out to yield a firm basis to regain the Woodward-Hoffmann rules for pericyclic reactions based on a density-only basis, i.e. without involving the phase, sign, symmetry of the wavefunction. Even the second order nonlinear response functions are shown possibly to bear interesting information, e.g. on the local and global polarizability. Its derivatives may govern the influence of charge on the polarizability, the R-analogues being the nuclear Fukui function and the quadratic and cubic force constants. Although some of the higher order derivatives may be difficult to evaluate a comparison with the energy expansion used in spectroscopy in terms of nuclear displacements, nuclear magnetic moments, electric and magnetic fields leads to the conjecture that, certainly cross terms may contain new, intricate information for understanding chemical reactivity.

Rationalization of Diels–Alder reactions through the use of the dual reactivity descriptor Δf(r)

In this work, the dual descriptor of chemical reactivity, an electronic density-based index, is used to study both the regioselectivity and the stereoselectivity of Diels-Alder reactions. The descriptor has been designed to simultaneously delineate the nucleophilic and electrophilic sites within a molecule. Subsequent pairing between the nucleophilic and electrophilic regions of the reagents predicts the major adducts in all cases studied. Specifically, the descriptor predicts the generation of a ortho-regioisomer when a diene monosubstitued at position 1 by an Electron Donating Group (EDG)/Electron Withdrawing Group (EWG), reacts with a dienophile monosubtituted by an EWG/EDG. Under the same conditions, if the diene is monosubstituted by either an EWG or an EDG at position 2, formation of the para-oriented adduct is predicted. This approach also provides insight into the stereoselectivity. For example, secondary interactions between the non-reactive regions of the reactants explain why the endo stereoisomer is preferred.

A conceptual DFT study of hydrazino peptides: Assessment of the nucleophilicity of the nitrogen atoms by means of the dual descriptor Δ f( r)

Hydrazinopeptides are pseudopeptide molecules containing a N N bond. To understand the compared reactivity as a nucleophile of the two nitrogen atoms included in this moiety with respect to the surrounding rest of the molecule, a conceptual DFT study is carried on with the analysis of the dual descriptor Δ f( r) in a series of molecules, at the B3LYP/6-31G(d,p) level. The dual descriptor is a tool based on the Principle of Maximal Hardness within the framework of conceptual DFT which characterises the nucleophilic and electrophilic areas within a molecule.

Multiphilic Descriptor for Chemical Reactivity and Selectivity

In line with the local philicity concept proposed by Chattaraj et al. (Chattaraj, P. K.; Maiti, B.; Sarkar, U. J. Phys. Chem. A. 2003, 107, 4973) and a dual descriptor derived by Morell, Grand and Toro-Labbé, (J. Phys. Chem. A 2005, 109, 205), we propose a multiphilic descriptor. It is defined as the difference between nucleophilic (omega(k)+) and electrophilic (omega(k)-) condensed philicity functions. This descriptor is capable of simultaneously explaining the nucleophilicity and electrophilicity of the given atomic sites in the molecule. Variation of these quantities along the path of a soft reaction is also analyzed. Predictive ability of this descriptor has been successfully tested on the selected systems and reactions. Corresponding force profiles are also analyzed in some representative cases. Also, to study the intra- and intermolecular reactivities another related descriptor, namely, the nucleophilicity excess (Deltaomega(g)-/+) for a nucleophile over the electrophilicity in it, has been defined and tested on all-metal aromatic compounds.

Characterization of the reactive conformations of protonated histamine through the reaction force analysis and the dual descriptor of chemical reactivity

A theoretical study of the conformational dependence of energy and electronic properties of neutral and protonated histamine tautomers was performed with the aim of modelling its interaction with an hypothetical receptor. Analysis of chemical potential, electrophilicity, dipole moment, at the global level, as well as the dual descriptor por chemical reactivity, at local level, indicate that the π tautomer presents the right conformation and reactivity behavior to interact with the receptor.

Use of cDNA‐AFLP for transcript profiling in narrow genetic pools; for example, cucumber (Cucumis sativusL.)

AbstractA cDNA‐AFLP transcript profiling was employed to examine three representative tissues (seedling, ovary and leaf) of nine Korean cucumber (Cucumis sativusL.) F1hybrids. Differential accumulation of transcript‐derived fragments (TDFs) was detected in 92 profiles. Genetic distance‐based cluster analysis partitioned these hybrids into four main groupings, consistent with their phenotypic relationships. Although several polymorphic profiles were confirmed by reverse transcriptase polymerase chain reaction (RT‐PCR) analysis, many were not reproducible, indicating that a large portion of the observed polymorphisms were based on sequence variation of transcripts rather than expression of variation. Thus, it is proposed that cDNA‐AFLP profiling be based on a dual descriptor system (sequence and expression). Data indicate that such a system would provide an efficient genetic marker system for identifying polymorphisms in narrow genetic pools.

New Dual Descriptor for Chemical Reactivity

In this paper, a new dual descriptor for nucleophilicity and electrophilicity is introduced. The new index is defined in terms of the variation of hardness with respect to the external potential, and it is written as the difference between nucleophilic and electrophilic Fukui functions, thus being able to characterize both reactive behaviors. It is shown that the new descriptor correctly predicts the site reactivity induced by different donor and acceptor groups in substituted phenyl molecules. Also, the Dunitz-Burgi attack on ketones and aldehydes has been revisited to illustrate the stereoselective capability of this new index. Finally, its predictive ability has been tested successfully on different series of conjugated and nonconjugated carbonyl compounds.