Fisher Information Study in Position and Momentum Spaces for Elementary Chemical Reactions

Differential Shannon Entropies and Mutual Information in a Curve Crossing System: Adiabatic and Diabatic Decompositions

The differential Shannon entropy provides a measure for the localization of a wave function. We regard the vibrational wave packet motion in a curve crossing system and calculate time-dependent entropies. Using a numerical example, we analyze how localization inside diabatic and adiabatic states can be accessed and discuss the differences between these two representations. In order to do so, we extend the usual entropy definition and introduce novel state-selective entropies. These quantities contain information on the form of the nuclear density components on the one hand and on the state population on the other, and it is shown how the contribution of the population can be removed. Having the state-selective entropies at hand, two additional functions derived from these, namely, the conditional entropy and the mutual information, are determined and compared. We find that these quantities relate closely to correlation effects rooted in different electronic properties of the system.

Differential Shannon entropies and correlation measures for Born-Oppenheimer electron-nuclear dynamics: numerical results and their analytical interpretation

We study the Born-Oppenheimer dynamics within a model for a coupled electron-nuclear motion. Differential Shannon entropies are calculated from the time-dependent probability densities of the combined system and, using single particle densities, entropies for the electronic and nuclear degrees of freedom are derived. These functions provide information on details of the wave packet motion. From the entropies, we determine the mutual information which characterizes particle correlations. This quantity is compared to other measures of electron-nuclear entanglement. Numerical results are interpreted within an analytically solvable approach, and it is documented how these functions depend on properties of the Born-Oppenheimer wave function and, in particular, how dynamical effects like wave packet focusing and dispersion influence the correlation between the particles.

Converting genetic information to non-equilibrium cellular thermodynamics in enzyme-catalyzed reactions

Living systems use genomic information to maintain a stable highly ordered state far from thermodynamic equilibrium but the specific mechanisms and general principles governing the interface of genetics and thermodynamics has not been extensively investigated. Genetic information is quantified in unitless bits termed "Shannon entropy", which does not directly relate to thermodynamic entropy or energy. Thus, it is unclear how the Shannon entropy of genetic information is converted into thermodynamic work necessary to maintain the non-equilibrium state of living systems. Here we investigate the interface of genetic information and cellular thermodynamics in enzymatic acceleration of a chemical reaction S + E → E S → E + P , where S and E are substrate and enzyme, E S is the enzyme substrate complex and P product. The rate of any intracellular chemical reaction is determined by probability functions at macroscopic (Boltzmann distribution of the reactant kinetic energies governed by temperature) or microscopic (overlap of reactant quantum wave functions) scales - described, respectively, by the Arrhenius and Knudsen equations. That is, the reaction rate, in the absence of a catalyst, is governed by temperature which determines the kinetic energy of the interacting molecules. Genetic information can act upon a when the encoded string of amino acids folds into a 3-deminsional structure that permits a lock/key spatial matching with the reactants. By optimally superposing the reactants' wave functions, the information in the enzyme increases the reaction rate by up to15 orders of magnitude under isothermal conditions. In turn, the accelerated reaction rate alters the intracellular thermodynamics environment as the products are at lower Gibbs free energy which permits thermodynamic work W m a x = - Δ G . Mathematically and biologically, the critical event that allows genetic information to produce thermodynamic work is the folding of the amino acid string specified by the gene into a 3-dimensional shape determined by its lowest energy state. Biologically, this allows the amino acid string to bind substrate and place them in an optimal spatial orientation. These key-lock are mathematically characterized by Kullback-Leibler Divergence and the interactions with the reaction channel now represent Fisher Information (the second derivative Kullback-Leibler divergence), which can take on the units of the process to which it is applied. Interestingly, Shannon is typically derived by "coarse graining" Shannon information. Thus, living system, by acting at a quantum level, "fine grain" Shannon information.

3D Information-Theoretic Analysis of the Simplest Hydrogen Abstraction Reaction

We investigate the course of an elementary chemical reaction from the perspective of information theory in 3D space through the hypersurface of several information-theoretic (IT) functionals such as disequilibrium (D), Shannon entropy (S), Fisher information (I), and the complexity measures of Fisher-Shannon (FS) and López-Mancini-Calbet (LMC). The probe for the study is the hydrogenic identity abstraction reaction. In order to perform the analysis, the reactivity pattern of the reaction is examined by use of the aforementioned functionals of the single-particle density, which is analyzed in position (r) and momentum (p) spaces. The 3D analyses revealed interesting reactivity patterns in the neighborhood of the intrinsic reaction coordinate (IRC) path, which allow to interpret the reaction mechanism for this reaction in a novel manner. In addition, the chemically interesting regions that have been characterized through the information functionals and their complexity measures are depicted and analyzed in the framework of the three-dimensional structure of the information-theoretical data of a chemical reaction, that is, the reactant/product (R/P) complexes, the transition state (TS), and the ones that are only revealed through IT measures such as the bond-cleavage energy region (BCER), the bond-breaking/forming (B-B/F) region, and the spin-coupling (SC) process. Furthermore, focus has been placed on the diagonal part of the hypersurface of the IT functionals, aside from the IRC path itself, with the purpose of analyzing the dissociation process of the triatomic transition-state complex that has revealed other interesting features of the bond-breaking (B-B) process. In other respects, it is shown throughout the combined analyses of the 3D structure of the IT functionals in conjugated spaces that the chemically significant regions occurring at the onset of the TS are completely characterized by information-theoretic aspects of localizability (S), uniformity (D), and disorder. Further, novel regions of low complexity seem to indicate new boundaries for chemically stable complex molecules. Finally, the study reveals that the chemical reaction occurs at low-complexity regions, where the concurrent phenomena take place: bond-breaking/forming (B-B/F), bond-cleavage energy reservoirs (BCER), spin-coupling (SC), and transition state (TS).

Spherical-Symmetry and Spin Effects on the Uncertainty Measures of Multidimensional Quantum Systems with Central Potentials

The spreading of the stationary states of the multidimensional single-particle systems with a central potential is quantified by means of Heisenberg-like measures (radial and logarithmic expectation values) and entropy-like quantities (Fisher, Shannon, Rényi) of position and momentum probability densities. Since the potential is assumed to be analytically unknown, these dispersion and information-theoretical measures are given by means of inequality-type relations which are explicitly shown to depend on dimensionality and state's angular hyperquantum numbers. The spherical-symmetry and spin effects on these spreading properties are obtained by use of various integral inequalities (Daubechies-Thakkar, Lieb-Thirring, Redheffer-Weyl, ...) and a variational approach based on the extremization of entropy-like measures. Emphasis is placed on the uncertainty relations, upon which the essential reason of the probabilistic theory of quantum systems relies.

Resultant Information Descriptors, Equilibrium States and Ensemble Entropy †

In this article, sources of information in electronic states are reexamined and a need for the resultant measures of the entropy/information content, combining contributions due to probability and phase/current densities, is emphasized. Probability distribution reflects the wavefunction modulus and generates classical contributions to Shannon’s global entropy and Fisher’s gradient information. The phase component of molecular states similarly determines their nonclassical supplements, due to probability “convection”. The local-energy concept is used to examine the phase equalization in the equilibrium, phase-transformed states. Continuity relations for the wavefunction modulus and phase components are reexamined, the convectional character of the local source of the resultant gradient information is stressed, and latent probability currents in the equilibrium (stationary) quantum states are related to the horizontal (“thermodynamic”) phase. The equivalence of the energy and resultant gradient information (kinetic energy) descriptors of chemical processes is stressed. In the grand-ensemble description, the reactivity criteria are defined by the populational derivatives of the system average electronic energy. Their entropic analogs, given by the associated derivatives of the overall gradient information, are shown to provide an equivalent set of reactivity indices for describing the charge transfer phenomena.

Information-Theoretic Descriptors of Molecular States and Electronic Communications between Reactants

The classical (modulus/probability) and nonclassical (phase/current) components of molecular states are reexamined and their information contributions are summarized. The state and information continuity relations are discussed and a nonclassical character of the resultant gradient information source is emphasized. The states of noninteracting and interacting subsystems in the model donor-acceptor reactive system are compared and configurations of the mutually-closed and -open equidensity orbitals are tackled. The density matrices for subsystems in reactive complexes are used to describe the entangled molecular fragments and electron communications in donor-acceptor systems which determine the entropic multiplicity and composition of chemical bonds between reactants.

N-Derivatives of Shannon entropy density as response functions

The exact first and second order partial derivatives of Shannon entropy density with respect to the number of electrons at constant external potential are introduced as new descriptors for prediction of the active sites of a molecule. The derivatives, which are a measure of the inhomogeneity of electron density, are calculated both exactly (from analytical forms) and approximately (using the finite difference method) for some molecular systems. According to the maximum entropy principle, the extreme value of the first order derivative on the surface of a given molecule should determine the active sites of the molecule in electrophilic and nucleophilic attack. The second order derivative indicates where the Shannon entropy is more concentrated or depleted during the electron exchange. Although these derivatives on the surfaces of helium and neon atoms are uniform, the corresponding values for argon, krypton and xenon atoms are not. This could explain the greater tendency of heavy noble gas atoms to form stable compounds. A dual descriptor is also defined as the difference between the left and right first order derivatives of Shannon entropy density, which allows one to simultaneously predict the preferable sites for electrophilic and nucleophilic attack over the system at point r. Therefore, the reactivity of an atom in a molecule requires the non-uniformity of the first and second order derivatives of Shannon entropy density on the surface of that atom.

Resultant Information Description of Electronic States and Chemical Processes †

General variations of electronic states are discussed, and the state "vertical" and "horizontal" displacements are explored. Quantum dynamics of the wave function modulus and phase components is examined, and the associated continuity relations are summarized. The probability and current contributions to overall information-theoretic (IT) descriptors of the state global and gradient entropy/information content are identified. These resultant measures are used to determine the phase equilibria in molecular systems. The currents corresponding to the entropy- and information-optimum phases are explored, the classical (probability) and nonclassical (current) flows in molecular information systems are identified, and probability interpretation of equidensity orbitals yielding the prescribed electron density is given. The physical equivalence of variational principles for the electronic energy and resultant gradient-information in open systems is stressed. It implies that their populational derivatives have the same capacity in describing charge transfer phenomena in molecules and their fragments. Illustrative application in determining thermodynamic equilibria and optimum charge transfer in molecular systems is discussed, and implications of the molecular virial theorem for bond-formation process and chemical reactions are investigated. The crucial role of the resultant gradient-information in chemical bonding is emphasized, and the Hammond postulate of reactivity theory is shown to be indexed by the reaction-coordinate derivative of electronic kinetic energy at the transition-state complex.

Understanding Electronic Structure and Chemical Reactivity: Quantum-Information Perspective

Several applications of quantum mechanics and information theory to chemical reactivity problems are presented with emphasis on equivalence of variational principles for the constrained minima of the system electronic energy and its kinetic energy component, which also determines the overall gradient information. Continuities of molecular probability and current distributions, reflecting the modulus and phase components of molecular wavefunctions, respectively, are summarized. Resultant measures of the entropy/information descriptors of electronic states, combining the classical (probability) and nonclassical (phase/current) contributions, are introduced, and information production in quantum states is shown to be of a nonclassical origin. Importance of resultant information descriptors for distinguishing the bonded (entangled) and nonbonded (disentangled) states of reactants in acid(A)–base(B) systems is stressed and generalized entropy concepts are used to determine the phase equilibria in molecular systems. The grand-canonical principles for the minima of electronic energy and overall gradient information allow one to explore relations between energetic and information criteria of chemical reactivity in open molecules. The populational derivatives of electronic energy and resultant gradient information give identical predictions of electronic flows between reactants. The role of electronic kinetic energy (resultant gradient information) in chemical-bond formation is examined, the virial theorem implications for the Hammond postulate of reactivity theory are explored, and changes of the overall structure information in chemical processes are addressed. The frontier-electron basis of the hard (soft) acids and bases (HSAB) principle is reexamined and covalent/ionic characters of the intra- and inter-reactant communications in donor-acceptor systems are explored. The complementary A–B coordination is compared with its regional HSAB analog, and polarizational/relaxational flows in such reactive systems are explored.

Information carriers and (reading them through) information theory in quantum chemistry

This Perspective discusses the reduction of the electronic wave function via the second-order reduced density matrix to the electron density ρ(r), which is the key ingredient in density functional theory (DFT) as a basic carrier of information. Simplifying further, the 1-normalized density function turns out to contain essentially the same information as ρ(r) and is even of preferred use as an information carrier when discussing the periodic properties along Mendeleev's table where essentially the valence electrons are at stake. The Kullback-Leibler information deficiency turns out to be the most interesting choice to obtain information on the differences in ρ(r) or σ(r) between two systems. To put it otherwise: when looking for the construction of a functional F(AB) = F[ζ(A)(r),ζ(B)(r)] for extracting differences in information from an information carrier ζ(r) (i.e. ρ(r), σ(r)) for two systems A and B the Kullback-Leibler information measure ΔS is a particularly adequate choice. Examples are given, varying from atoms, to molecules and molecular interactions. Quantum similarity of atoms indicates that the shape function based KL information deficiency is the most appropriate tool to retrieve periodicity in the Periodic Table. The dissimilarity of enantiomers for which different information measures are presented at global and local (i.e. molecular and atomic) level leads to an extension of Mezey's holographic density theorem and shows numerical evidence that in a chiral molecule the whole molecule is pervaded by chirality. Finally Kullback-Leibler information profiles are discussed for intra- and intermolecular proton transfer reactions and a simple S(N)2 reaction indicating that the theoretical information profile can be used as a companion to the energy based Hammond postulate to discuss the early or late transition state character of a reaction. All in all this Perspective's answer is positive to the question of whether an even simpler carrier of information than the electron density function ρ(r) can be envisaged: the shape function, integrating to 1 by construction fulfils this role. On the other hand obtaining the information (or information difference) contained in one (or two) systems from ρ(r) or σ(r) can be most efficiently done by using information theory, the Kulback-Leibler information deficiency being at the moment (one of) the most advisable functionals.

A generalized Fisher equation and its utility in chemical kinetics

A generalized Fisher equation (GFE) relates the time derivative of the average of the intrinsic rate of growth to its variance. The GFE is an exact mathematical result that has been widely used in population dynamics and genetics, where it originated. Here we demonstrate that the GFE can also be useful in other fields, specifically in chemistry, with models of two chemical reaction systems for which the mechanisms and rate coefficients correspond reasonably well to experiments. A bad fit of the GFE can be a sign of high levels of measurement noise; for low or moderate levels of noise, fulfillment of the GFE is not degraded. Hence, the GFE presents a noise threshold that may be used to test the validity of experimental measurements without requiring any additional information. In a different approach information about the system (model) is included in the calculations. In that case, the discrepancy with the GFE can be used as an optimization criterion for the determination of rate coefficients in a given reaction mechanism.