Expanding horizons in conceptual density functional theory: Novel ensembles and descriptors to decipher reactivity patterns.

Conceptual density functional theory (CDFT) and the quantum reactivity descriptors stemming from it have proven to be valuable tools for understanding the chemical behavior of molecules. This article is presented as being intrinsically of dual character. In a first part, it briefly reviews, in a deliberately didactical way, the main ensembles in CDFT, while the second half presents two additional ensembles, where the chemical hardness acts as a natural variable, and their respective reactivity descriptors. The evaluation of these reactivity descriptors on common organic chemical reagents are presented and discussed.

Influence of an Oriented External Electric Field on the Mechanism of Double Proton Transfer between Pyrazole and Guanidine: from an Asynchronous Plateau Transition State to a Synchronous or Stepwise Mechanism.

The double proton transfer (DPT) reaction between pyrazole and guanidine, a concerted reaction but strongly asynchronous and presenting a "plateau transition region", has been theoretically reinvestigated in the presence of an external uniform electric field. First, we computed the reaction path by DFT and proposed a very detailed description of the constitutive electronic events, based on the ELF topology and the bond evolution theory. Then, we studied the effect of an oriented external electric field (OEEF) on the reaction mechanism, for an OEEF oriented along the proton transfer axis. We observe that in one direction, the DPT reaction can be transformed into a stepwise reaction, going through a stabilized single proton transferred intermediate. Contrarily, the two proton transfers occur simultaneously when the electric field is applied in the opposite direction. In the latter case, the order in which the two protons are transferred in the same elementary step can even be reversed if the OEEF is intense enough. Finally, it has been shown that the evolution of the double proton transfer reaction in the presence of an electric field could be quantitatively anticipated by analyzing the ELF value at the bifurcation point between V(A, H) proton donor and V(B) proton acceptor of the double hydrogen bonded complex in the entrance channel.

Probing the in-air growth of large area of 3D functional structures into a 2D supramolecular nanoporous network.

Surface-confined host-guest chemistry at the air/solid interface is used for trapping a functionalized 3D Zn-phthalocyanine complex into a 2D porous supramolecular template allowing the large area functionalization of an sp2-hybridized carbon-based substrate as evidenced by STM, resonance Raman spectroscopy, and water contact angle measurements.

Femtosecond Fluorescence Upconversion Study of a Naphthalimide-Bithiophene-Triphenylamine Push-Pull Dye in Solution.

There is a high interest in the development of new push-pull dyes for the use in dye sensitized solar cells. The pronounced charge transfer character of the directly photoexcited state is in principle favorable for a charge injection. Here, we report a time-resolved fluorescence study of a triphenylamine-bithiophene-naphthalimide dye in four solvents of varying polarity using fluorescence upconversion. The recording of femtosecond time-resolved fluorescence spectra corrected for the group velocity dispersion allows for a detailed analysis discriminating between spectral shifts and total intensity decays. After photoexcitation, the directly populated state (S1/FC) evolves toward a relaxed charge transfer state (S1/CT). This S1/CT state is characterized by a lower radiative transition moment and a higher nonradiative quenching. The fast dynamic shift of the fluorescence band is well described by solvation dynamics in polar solvents, but less so in nonpolar solvents, hinting that the excited-state relaxation process occurs on a free energy surface whose topology is strongly governed by the solvent polarity. This study underlines the influence of the environment on the intramolecular charge transfer (ICT) process, and the necessity to analyze time-resolved data in detail when solvation and ICT occur simultaneously.

A topological study of chemical bonds under pressure: solid hydrogen as a model case.

It is now well recognized that a fundamental understanding of the rules that govern chemistry under pressure is still lacking. Hydrogen being the "simplest" element as well as a central core to high pressure physics, we undertake a general study of the changes in the chemical bonding under pressure. We start from a simple trimer unit that has been found in high pressure phases, whose behavior has been found to reveal the basics of hydrogen polymerization under pressure. Making use of bond analysis tools, mainly the NCI (noncovalent interactions) index, we show that polymerization takes place in three steps: dipolar attraction, repulsion and bond formation. The use of a 1D Wigner-Seitz radius allowed us to extend the conclusions to 3D networks and to analyze their degree of polymerization. On the one hand, this approach provides new insight into the polymerization of hydrogen. On the other hand, it shows that complicated molecular solids can be understood from cluster models, where correlated methods can be applied, main differences in solid state arising at the transition points, where breaking/forming of bonds happens at once instead of continuously like in the cluster model.

UV-induced formation of the thymine-thymine pyrimidine (6-4) pyrimidone photoproduct--a DFT study of the oxetane intermediate ring opening.

The mechanism by which the hypothetical oxetane/azetidine intermediate formed during the photochemical process leading to pyrimidine (6-4) pyrimidone photoproducts when DNA is submitted to UV radiation opens is investigated computationally by DFT using a 5'-TT-3' dinucleoside monophosphate as a structural model. First, the feasibility of an intramolecular mechanism involving one proton transfer inducing opening of the oxetane ring is examined. It results in a very high Gibbs energy of activation (+166 kJ mol(-1)) and quite a low Gibbs energy of reaction (-35 kJ mol(-1)). The protonation state of the phosphate group is shown to have little effect while the bulk effect of an aqueous environment modeled by the Polarizable Continuum Model method lowers slightly the activation barrier (by about 10-20 kJ mol(-1)), not enough to explain the fact that the oxetane intermediate is not observed experimentally. Then the catalytic effect of water molecules on the reaction pathway is studied by including either 1 or 2 assisting water molecules in the chemical system. The resulting activation barrier is considerably lowered and in the most favorable situation - a phosphate group deprotonated and 2 assisting water molecules - the Gibbs energy activation is as low as +44 kJ mol(-1) and the Gibbs energy of reaction is quite favorable: -79 kJ mol(-1), suggesting that in biological systems the oxetane ring opening process proceeds with explicit intervention of water molecules from the environment.

WH(n) under pressure.

An initial observation of the formation of WH under pressure from W gaskets surrounding hydrogen in diamond anvil cells led to a theoretical study of tungsten hydride phases. At P = 1 atm no stoichiometry is found to be stable with respect to separation into the elements, but as the pressure is raised WH(n) (n = 1-6, 8) stoichiometries are metastable or stable. WH and WH(4) are calculated to be stable at P > 15 GPa, WH(2) becomes stable at P > 100 GPa and WH(6) at P > 150 GPa. In agreement with experiment, the structure computed for WH is anti-NiAs. WH(2) shares with WH a hexagonal arrangement of tungsten atoms, with hydrogen atoms occupying octahedral and tetrahedral holes. For WH(4) the W atoms are in a distorted fcc arrangement. As the number of hydrogens rises, the coordination of W by H increases correspondingly, leading to a twelve-coordinated W in WH(6). In WH(8) H(2) units also develop. All of the hydrides considered should be metallic at high pressure, though the Fermi levels of WH(4) and WH(6) lie in a deep pseudogap. Prodded by these theoretical studies, experiments were then undertaken to seek phases other than WH, exploring a variety of experimental conditions that would favor further reaction. Though a better preparation and characterization of WH resulted, no higher hydrides have as yet been found.

A fresh look at dense hydrogen under pressure. I. an introduction to the problem, and an index probing equalization of H-H distances.

In the first of a series of four papers on hydrogen under pressure, and its transitions from an initiating molecular state, we begin by defining carefully the problem, and setting the distance scale of interactions of protons and electrons in molecular aggregates of the first of the elements. Following a review of the experimental situation, in particular the phase diagram of hydrogen, in as much as it is known, and the behavior of its vibrons and rotons, we move onto the setting up of a numerical laboratory for probing the underlying physics and chemistry of interactions in hydrogen as the pressure increases. The laboratory consists of the preferred static structures emerging from calculations on the system in the range of 1 atm to 500 GPa, those of Pickard and Needs. The intermolecular (inter-pair) H···H separations naturally decrease with increasing pressure, first rapidly so, then more slowly. The intramolecular (intra-pair) H-H distances vary over a much smaller scale (0.05 Å) as the pressure increases, first decreasing, then increasing, and finally decreasing. We define an equalization function to gauge the approach to equality of the first neighbor and shortest next neighbor H (proton) separations in this numerical laboratory. And we find that metallization is likely to occur before bond equalization.

A fresh look at dense hydrogen under pressure. II. Chemical and physical models aiding our understanding of evolving H-H separations.

In order to explain the intricate dance of intramolecular (intra-proton-pair) H-H separations observed in a numerical laboratory of calculationally preferred static hydrogen structures under pressure, we examine two effects through discrete molecular models. The first effect, we call it physical, is of simple confinement. We review a salient model already in the literature, that of LeSar and Herschbach, of a hydrogen molecule in a spheroidal cavity. As a complement, we also study a hydrogen molecule confined along a line between two helium atoms. As the size of the cavity/confining distance decreases (a surrogate for increasing pressure), in both models the equilibrium proton separation decreases and the force constant of the stretching vibration increases. The second effect, which is an orbital or chemical factor, emerges from the electronic structure of the known molecular transition metal complexes of dihydrogen. In these the H-H bond is significantly elongated (and the vibron much decreased in frequency) as a result of depopulation of the σ(g) bonding molecular orbital of H(2), and population of the antibonding σ(u)∗ MO. The general phenomenon, long known in chemistry, is analyzed through a specific molecular model of three hydrogen molecules interacting in a ring, a motif found in some candidate structures for dense hydrogen.

A fresh look at dense hydrogen under pressure. III. Two competing effects and the resulting intra-molecular H-H separation in solid hydrogen under pressure.

A preliminary discussion of the general problem of localization of wave functions, and the way it is approached in theoretical condensed matter physics (Wannier functions) and theoretical chemistry (localized or fragment orbitals) is followed by an application of the ideas of Paper II in this series to the structures of hydrogen as they evolve under increasing pressure. The idea that emerges is that of simultaneously operative physical (reduction of available space by an increasingly stiff wall of neighboring molecules) and chemical (depopulation of the σ(g) bonding molecular orbital of H(2), and population of the antibonding σ(u)∗ MO) factors. The two effects work in the same direction of reducing the intermolecular separation as the pressure increases, but compete, working in opposite directions, in their effect on the intramolecular (nearest neighbor, intra-pair) distance. We examine the population of σ(g) and σ(u)∗ MOs in our numerical laboratory, as well as the total electron transfer (small), and polarization (moderate, where allowed by symmetry) of the component H(2) molecules. From a molecular model of two interacting H(2) molecules we find a linear relationship between the electron transfer from σ(g) to σ(u)∗ of a hydrogen molecular fragment and the intramolecular H-H separation, and that, in turn, allows us to estimate the expected bond lengths in H(2) under pressure if the first effect (that of simple confinement) was absent. In essence, the intramolecular H-H separations under pressure are much shorter than they would be, were there no physical/confinement effect. We then use this knowledge to understand how the separate E and PV terms contribute to hydrogen phase changes with increasing pressure.

A fresh look at dense hydrogen under pressure. IV. Two structural models on the road from paired to monatomic hydrogen, via a possible non-crystalline phase.

In this paper, we examine the transition from a molecular to monatomic solid in hydrogen over a wide pressure range. This is achieved by setting up two models in which a single parameter δ allows the evolution from a molecular structure to a monatomic one of high coordination. Both models are based on a cubic Bravais lattice with eight atoms in the unit cell; one belongs to space group Pa3, the other to space group R3m. In Pa3 one moves from effective 1-coordination, a molecule, to a simple cubic 6-coordinated structure but through a very special point (the golden mean is involved) of 7-coordination. In R3m, the evolution is from 1 to 4 and then to 3 to 6-coordinate. If one studies the enthalpy as a function of pressure as these two structures evolve (δ increases), one sees the expected stabilization of minima with increased coordination (moving from 1 to 6 to 7 in the Pa3 structure, for instance). Interestingly, at some specific pressures, there are in both structures relatively large regions of phase space where the enthalpy remains roughly the same. Although the structures studied are always higher in enthalpy than the computationally best structures for solid hydrogen - those emerging from the Pickard and Needs or McMahon and Ceperley numerical laboratories - this result is suggestive of the possibility of a microscopically non-crystalline or "soft" phase of hydrogen at elevated pressures, one in which there is a substantial range of roughly equi-enthalpic geometries available to the system. A scaling argument for potential dynamic stabilization of such a phase is presented.

Use of the dual potential to rationalize the occurrence of some DNA lesions (pyrimidic dimers).

Exploiting the locality of the chemical potential of an excited state when it is evaluated using the ground state Density Functional Theory (DFT), a new local descriptor for excited states has been proposed (J. Chem. Theory Comput.2009, 5, 2274). This index is based on the assumption that the relaxation of the electronic density toward that of the ground state drives the chemical reactivity of excited states. The sign of the descriptor characterizes the electrophilic or nucleophilic behavior of atomic regions. Through an exact excited state DFT formalism provided by Gross, Oliveira, and Kohn, a mathematical argument is given for this descriptor only for the first excited state. It is afterward used to rationalize the occurrence and the regioselectivity of some DNA lesions based on the [2 + 2] cycloaddition between two adjacent bases.

Is an elementary reaction step really elementary? Theoretical decomposition of asynchronous concerted mechanisms.

In this paper the primitive process concept is used to reproduce and explain the potential energy profile of an asynchronous concerted mechanism. The number of primitive processes constituting such a mechanism can be deduced from the study of the influence of the number of electrons on the potential energy profile of the elementary step. The study of a particular example indicates that the position of the transition states of the primitive processes constituting an asynchronous concerted mechanism seems not to be affected by the number of electrons in the system. This implies that the maximum hardness and minimum electrophilicity principles are valid for primitive processes but not for asynchronous concerted mechanisms. It appears that a potential energy profile with a shoulder before the transition state, and a reaction force profile with more than two extrema together with a hardness profile presenting a minimum shifted with respect to the transition state are thus indicators of the presence of an asynchronous concerted mechanism.

Hydrolytic deamination of 5,6-dihydrocytosine in a protic medium: a theoretical study.

The mechanism for the deamination reaction of 5,6-dihydrocytosine with H(2)O in a protic medium was investigated by DFT calculations at the B3LYP/6-311G(d,p) level of theory as a model reaction for the deamination reaction of 5,6-saturated cytosine derivatives. Two pathways were found. Pathway dhA, which can explain the deamination in a protic medium at acidic pH, and pathway dhBt, more representative of the reaction in a protic medium at neutral pH. Pathway dhA is a two-step mechanism initiated by the nucleophilic addition of a water molecule to carbon C4 of N3-protonated 5,6-dihydrocytosine with the assistance of a second water molecule, followed by elimination of an ammonium cation to form 5,6-dihydrouracil. The nucleophilic addition is rate-determining with an activation free energy of 116.0 kJ/mol in aqueous solution. Pathway dhBt is a four-step mechanism which starts with the water-assisted tautomerization of 5,6-dihydrocytosine to form the imino tautomer. This intermediate undergoes nucleophilic addition of water to carbon C4, which after protonation eliminates an ammonium cation, as in pathway dhA. The nucleophilic addition is again rate-determining, with an activation free energy of 113.3 kJ/mol in aqueous solution. The latter value is about 25 kJ/mol lower than its counterpart for cytosine, in agreement with the experimental observation that 5,6-saturated cytosine derivatives exhibit a much shorter lifetime in aqueous solution than their unsaturated counterparts. The evaluation of reactivity indices derived from conceptual DFT leads to the conclusion that this lower activation free energy can be attributed to a larger local electrophilic power of carbon C4 in 5,6-saturated derivatives.

Minimum electrophilicity principle: an analysis based upon the variation of both chemical potential and absolute hardness.

In this work, the minimum electrophilicity principle (MEP), assessed by either the electrophilicity power or the DeltaNmax, is mathematically analysed through the variation of both chemical potential and chemical hardness. It appears that the decrease of the electrophilicity power and the decrease of the DeltaNmax are ruled by similar expressions in which both the chemical potential and the absolute hardness should increase. A reduced expression at constant chemical potential shows that the MEP and the maximum hardness principle are equivalent. However it pops up from the monitoring of chemical processes such as bond formation and redox reactions that the variation of the chemical potential is the most important term.

Mechanism of nitric oxide induced deamination of cytosine.

A five-step mechanism is proposed for the NO -induced deamination of cytosine. It has been investigated using DFT calculations, including both explicit water molecules and a bulk solvent model to mimic an aqueous environment. According to this mechanism, cytosine first undergoes tautomerization with the assistance of a water molecule from the bulk. A NO(+) cation produced by the autooxidation of NO is subsequently added to the exocyclic imino group of the cytosine imine tautomer. The resulting adduct is able to undergo a tautomerization step with the participation of a water molecule to produce a cytosine in which a -N(2)OH group is attached to carbon C4. Protonation of the oxygen of the latter gives a water molecule which dissociates instantaneously, leading to a pyrimidinic diazonium cation. This constitutes the rate-determining step of the mechanism with an activation free energy of 92.6 kJ mol(-1). The last step, which is highly exergonic, represents the driving force of the reaction. It is the substitution of the -N(2)(+) terminal group by a water molecule which simultaneously allows the transfer of one of the two hydrogens to the bulk. Thus, the two products of the reaction consist of a nitrogen molecule and the enol tautomer of uracil in equilibrium with the keto form.

Hydrolytic deamination of 5-methylcytosine in protic medium--a theoretical study.

The mechanism for the deamination reaction of 5-methylcytosine with H2O in protic medium was investigated using DFT calculations at the B3LYP/6-311G(d,p) level of theory. Two pathways were found. Pathway 5mA is a two-step mechanism where the N3-protonated 5-MeCyt undergoes a nucleophilic attack to carbon C4 by a water dimer before the elimination of an ammonium cation. Pathway 5mB is a three-step mechanism where neutral 5-MeCyt is directly attacked by a water dimer. The resulting intermediate is then protonated to allow the elimination of an ammonium cation. Both pathways lead to the formation of thymine in interaction with an ammonium cation and a water molecule. Pathway 5mA can explain the spontaneous deamination of 5-MeCyt in protic medium at acidic pH, whereas pathway 5mB is more representative of the deamination in protic medium at neutral pH. The nucleophilic addition of the water dimer is rate-determining in both pathways and is associated with an activation free energy in aqueous solution of 137.4 kJ/mol for pathway 5mA and 134.1 kJ/mol for pathway 5mB. This latter value is in agreement with the experimental observation that 5-MeCyt deaminates four- to fivefold faster than Cyt at neutral pH. Both electrostatic and electron-transfer contributions appear to have significant importance. In vacuum, the former one dominates when the substrate is positively charged and the latter one when it is neutral.

Characterization of the Chemical Behavior of the Low Excited States through a Local Chemical Potential.

Exploiting the locality of the chemical potential of an excited state when it is evaluated using the ground-state density functional theory (DFT), a new descriptor for excited states has been proposed. This index is based on the assumption that the relaxation of the electronic density drives the chemical reactivity of excited states. The sign of the descriptor characterizes the electrophilic or nucleophilic behavior of the atomic regions. A relation between the new descriptor and the dual descriptor is derived and provides a posteriori justification of its use to rationalize the Woodward-Hoffmann rules for photochemical reactions within the conceptual DFT. Finally, the descriptor is successfully applied to some [2 + 2] photocycloadditions, like Paterno-Büchi reactions.

Theoretical study of cytosine deamination from the perspective of the reaction force analysis.

A theoretical study of two different mechanisms for the spontaneous deamination of cytosine is presented. In the first mechanism, a tetrahedral intermediate results in a two-step mechanism whereas in the second one, it is the result of a concerted step. In this work a link is made between the two pathways through the study of the evolution along the reaction coordinates of chemical concepts such as chemical potential, hardness and electronic populations within the framework of the reaction force analysis. The reaction force profile suggests that the concerted mechanism is composed of two asynchronous events. The observation of the reaction force profile appears as an easy way to identify asynchronous concerted steps and as a privileged tool to study the more or less asynchronous character of chemical reactions.

Formation of cross-linked adducts between guanine and thymine mediated by hydroxyl radical and one-electron oxidation: a theoretical study.

The role of local geometric and stereo-electronic effects in tuning the preference for different cross-linked adducts between thymine and purinic bases has been analyzed by a computational approach rooted in density functional theory. Our study points out that G--T and T--G tandem lesions are produced according to the same mechanism as A--T and T--A intrastrand adducts, and in both cases purine--T adducts are preferred rather than the opposite sequences. Moreover, use of conceptual DFT tools allows the rationalization of the preferential occurrence of G--T and T--G tandem lesions in place of their A--T and T--A counterparts.