Stability Of Chemical Systems Research Articles

Three-centre two-electron bonds from the quantum interference perspective.

The nature of the three-center two-electron (3c2e) chemical bond is investigated by the Interference Energy Analysis (IEA) method and using a SC(2, 3) (spin coupled wave function with two electrons and three orbitals) approach for describing 3c2e bonds. In this approach, each center involved in the bonding contributes with a one-electron state for the interference process. The species H3+, Li3+, LiH2+, C3H5+, C3H3+, R2CBeCR2 (R = H, CH3), C7H11+ and CH5+ are considered in the study. The results show that 3c2e bonds have the same features of a 2c2e bond: the stability of the chemical systems exhibiting 3c2e bonds derives from quantum interference among electronic states. Other (quasi-classical) factors are always overall destabilizing, mostly because of the nuclear repulsion. The interference energy of a 3c2e bond is about three times higher than that of a 2c2e bond involving atoms of the same elements. In particular, concerning Li3+ and C3H3+ we found no evidence that the 'aromatic' character attributed to those species imparts any special features to their chemical structures, compared to other 3c2e bonds. Therefore, these species exhibit multicenter bonds, essentially equivalent to the other studied cases.

SWITCHES: Searchable Web Interface for Topologies of CHEmical Switches.

Bistable biochemical switches are key motifs in cellular state decisions and long-term storage of cellular 'memory'. There are a few known biological switches that have been well characterized, however, these examples are insufficient for systematic surveys of properties of these important systems. Here we present a resource of all possible bistable biochemical reaction networks with up to six reactions between three molecules, and three reactions between four molecules. Over 35000 reaction topologies were constructed by identifying unique combinations of reactions between a fixed number of molecules. Then, these topologies were populated with rates within a biologically realistic range. The Searchable Web Interface for Topologies of CHEmical Switches (SWITCHES, https://switches.ncbs.res.in) provides a bistability and parameter analysis of over seven million models from this systematic survey of chemical reaction space. This database will be useful for theoreticians interested in analyzing stability in chemical systems and also experimentalists for creating robust synthetic biological switches. Freely available on the web at https://switches.ncbs.res.in. Website implemented in PHP, MariaDB, Graphviz and Apache, with all major browsers supported.

Insight into the antioxidant and antiradical properties of colorotane sesquiterpenes extracted from Warburgia ugandensis: theoretical evaluation

The present work is focused on the examination of two biological activities (antioxidant and antiradical properties) of colorotane sesquiterpenes extracted from Warburgia ugandensis. The geometrical optimizations of structures studied were performed in gas phase and water at B3PW91/6-311+G(d,p)// B3PW91/6-31+G(d,p) level under stereochemical constraints. The stability of chemical systems has been elaborated according to thermodynamic and kinetic approaches. Additional descriptors referred to global reactivity descriptors (electronegativity, global hardness, global softness, and electrophilicity index) have also been integrated. Predictions of antioxidant power were exclusively based on the calculation of the enthalpy change of the single-electron transfer (SET) mechanism named IP. Electrodonating (ω−), electroaccepting (ω+) powers, donor Rd and Ra indexes are used as antiradical descriptors. Our results demonstrated that 1,4,4a,5,6,7,8,8a-octahydro-1,4-dihydroxy-4a,5,5,8a-tetramethylnaphthalene-1,2-dicarbaldehyde in the absolute configuration (1R,4R) bearing one hydrogen bond exhibits the highest antioxidant profile. This compound that exhibited the lowest hardness values η (1.517 eV) has shown to be the less stable. Collectively, all colorotane sesquiterpenes have exhibited a good electron donor than sodium (Na). The location of the vitamin C above the colorotane sesquiterpenes in the donor-acceptor map illustrates better antiradical behaviour than the vitamin C in the gas phase. But, these compounds have presented worse antiradical behaviour with respect to gallic acid in the gas phase. In water, the Rd of the compound examined is higher than that of gallic acid (0.178 eV) with exception of 1,4,4a,5,6,7,8,8a-octahydro-1,4-dihydroxy-4a,5,5,8a-tetramethylnaphthalene-1,2-dicarbaldehyde in the absolute configuration (1R,4R) that have shown to be the best antiradical activity due to its highest Ra value (0.904 eV) and lowest Rd value (0.169 eV).

Conformational analysis and vibrational study of daidzein by using FT-IR and FT-Raman spectroscopies and DFT calculations

Daidzein (C15H10O4) is a type of isoflavone. It was isolated from Butea monosperma that belongs to the Fabaceae family. Soybeans and soy products are the abundant source of daidzein. It is the subject of investigation for many reasons, as it has got wide applications, such as anti-tumor, anti-estrogen, weak pro-estrogen and anti-cancer activities.In the present study, a complete vibrational assignment is provided for the observed IR and Raman spectra of daidzein. Electronic properties have been analyzed using TD-DFT method for both gaseous and solvent phase. The optimized geometry, total energy, potential energy surface and vibrational wavenumbers of daidzein have been determined using density functional theory (DFT/B3LYP) method with 6-311++G(d,p) basis set and a good correlation was found between observed and calculated values. The double well potential energy curve of the molecule about three bonds, has been plotted, as obtained from DFT/6-31G basis. The HOMO–LUMO energy gap of possible conformers has been calculated for comparing their chemical activity. Global reactivity descriptors have been calculated for predicting the chemical reactivity and the stability of chemical systems. Electrostatic potential surface has been plotted for predicting the structure activity relationship. NBO analysis has also been performed to study the stability of the molecule. NLO study reveals the nonlinear properties of the molecule. 1H and 13C NMR spectra have also been studied. Finally, the calculated results were used to simulate infrared and Raman spectra of the title compound which showed a good agreement with the observed spectra.

Looking for chemical reaction networks exhibiting a drift along a manifold of marginally stable states

I recently reported some examples of mass-action equations that have a continuous manifold of marginally stable stationary states [Brogioli, D., 2010. Marginally stable chemical systems as precursors of life. Phys. Rev. Lett. 105, 058102; Brogioli, D., 2011. Marginal stability in chemical systems and its relevance in the origin of life. Phys. Rev. E 84, 031931]. The corresponding chemical reaction networks show nonclassical effects, i.e. a violation of the mass-action equations, under the effect of the concentration fluctuations: the chemical system drifts along the marginally stable states. I proposed that this effect is potentially involved in abiogenesis. In the present paper, I analyze the mathematical properties of mass-action equations of marginally stable chemical reaction networks. The marginal stability implies that the mass-action equations obey some conservation law; I show that the mathematical properties of the conserved quantity characterize the motion along the marginally stable stationary state manifold, i.e. they allow to predict if the fluctuations give rise to a random walk or a drift under the effect of concentration fluctuations. Moreover, I show that the presence of the drift along the manifold of marginally stable stationary-states is a critical property, i.e. at least one of the reaction constants must be fine tuned in order to obtain the drift.

Marginal stability in chemical systems and its relevance in the origin of life

Concentration fluctuations are always present in solutions; it has been noticed that, in chemical systems, they can lead to deviations from what is expected from mass-action equations. I recently described the class of the "marginally stable" chemical systems; namely, a system that have an infinity of stationary states forming a continuous curve, and I showed that they present such deviations, which appear as a drift along the stationary-state curve [Phys. Rev. Lett. 105, 058102 (2010)]. Here I describe various marginally stable chemical reaction networks, including replicating molecules, and I present numerical calculations based on reaction-diffusion master equations, showing that the thermodynamic fluctuations induce a drift. This drift can be interpreted in terms of evolution toward a more efficiently replicating system and is analogous to a Darwinian evolution. The concentration fluctuations observed during the drift are scale invariant. Relevance of this phenomenon to the origin of life is discussed. I propose that marginal stability is the mathematical property defining chemical reaction networks potentially involved in the origin of life.

Green and roasted coffee antiradical activity stability in chemical systems

The stability to storage at different temperature and oxygen exposure of green and roasted coffee either as coffee beans or as ground coffee antiradical activity, was evaluated. The results showed that the coffee solution antihydroxyl radical activity was constant, independently from the coffee species, from the roasting process, and moreover from the type of storage conditions, suggesting that temperature and oxygen exposure did not affect this antiradical activity. With regard to antiperoxyl radical activity, all green coffee solutions showed remarkable and stable activity. Conversely, the roasted coffee beans and roasted and ground coffee antiperoxyl radical activity started to increase after three month of storage, suggesting that Maillard reaction products affect the stability of such antiradical property.

On the stability of mass action reactions in open systems

We consider the stability of chemical systems whose evolution is governed by mass action reactions. We show, with no reference to the second law of thermodynamics, that the stability of equilibrium in a closed system follows from the fact that one can express the kinetic matrix for the linearized equations near equilibrium in the form of a matrix times its transpose. This is a necessary and sufficient condition that the matrix be positive indefinite (some of the eigenvalues are necessarily zero due to the existence of conservation relations in a closed system). We then extend this approach to open systems where one finds that a component of the kinetic matrix cannot be expressed as the product of a matrix times its transpose. It is this matrix, having a simple expression in terms of stoichiometric matrices, thus expressing the basic mechanisms of the chemistry, that is potentially responsible for instabilities, oscillations, and chaos far from equilibrium. Examination of this matrix leads naturally to autocatalytic reactions as candidates for interesting behavior far from equilibrium. We conclude that all of the interesting features of mass action kinetics can be determined directly from the kinetic equations and the principle of detailed balance with no additional constraints coming uniquely from thermodynamics.

Cellular systems—I. stability of chemical systems

In this work, we attempt to formulate and partially resolve the “complexity vs. stability” problem in open chemical systems, in the framework of Lyapunov's second method. Sufficient conditions are given for stability of the steady state of a chemical system under structural perturbations caused by interactions among the chemical species in the system. As a byproduct of this analysis, we will show important properties of the self-inhibitory chemical systems, and establish the tolerance of the stability to a broad class of perturbations. Finally, biological open systems are exhibited in order to show the scope of our stability analysis.

Mass balance laws and the decomposition, evolution and stability of chemical systems

The laws of mass balance (conservation of atomic species) for reacting, diffusing and conducting material bodies are shown to provide a direct and simple decomposition of the reaction and diffusion processes. They also provide significant simplifications in implementing the condition of charge neutrality of the reaction processes and yield a reduction in the number of independent variables (thermodynamic forces) that occur in the dissipation inequality. General solutions of dissipation inequality are obtained which include the Onsager forms as special cases. These solutions yield a complete system of nonlinear constitutive relations for the viscous stresses, heat flux, diffusion fluxes, and the mass supplies associated with the chemical reactions. It is shown that chemically closed systems in fixed containers evolve toward static states whenever (1) the entropy production function vanishes only when all of the thermodynamic forces vanish, (2) the total free energy at constant temperature, constant total mass, and constant total masses of the atomic constituents possesses an absolute lower bound in an equilibrium state (thermodynamic stability), (3) the body is in thermal contact with an external environment at constant temperature, and (4) the body forces which act on each chemical constituent possess a potential function. Asymptotic stability of the thermodynamic equilibrium point is shown under the additional assumption that the total free energy has one and only one minimum at constant temperature, constant total mass, and constant total masses of the atomic constituents.