Search results for "free-energy"

The transition state and cognate concepts

2019

Abstract This review aims firstly to clarify the meanings of key terms and concepts associated with the idea of the transition state, as developed by theoreticians and applied by experimentalist, and secondly to provide an update to the meaning and significance of the transition state in an era when computational simulation, in which complexity is being increasingly incorporated, is commonly employed as a means by which to bridge the realms of theory and experiment. The relationship between the transition state and the potential-energy surface for an elementary reaction is explored, with discussion of the following terms: saddle point, minimum-energy reaction path, reaction coordinate, acti…

2020

The course of organic chemical reactions is efficiently modelled through the concepts of “electrophiles” and “nucleophiles” (meaning electron-seeking and nucleus-seeking reactive species). On the one hand, an advanced approach of the correlation of the nucleophilicity parameters N and electrophilicity E has been delivered from the linear free energy relationship log k (20 °C) = s(N + E). On the other hand, the general influence of the solvent mixtures, which are very often employed in preparative synthetic chemistry, has been poorly explored theoretically and experimentally, to date. Herein, we combined experimental and theoretical studies of the solvent influence on pyrrolidine nucleophili…

Molecular basis of SARS-CoV-2 infection and rational design of potential antiviral agents: Modeling and simulation approaches

2020

International audience; The emergence in late 2019 of the coronavirus SARS-CoV-2 has resulted in the breakthrough of the COVID-19 pandemic that is presently affecting a growing number of countries. The development of the pandemic has also prompted an unprecedented effort of the scientific community to understand the molecular bases of the virus infection and to propose rational drug design strategies able to alleviate the serious COVID-19 morbidity. In this context, a strong synergy between the structural biophysics and molecular modeling and simulation communities has emerged, resolving at the atomistic level the crucial protein apparatus of the virus and revealing the dynamic aspects of k…

Monte Carlo simulations of the solid-liquid transition in hard spheres and colloid-polymer mixtures

2010

Monte Carlo simulations at constant pressure are performed to study coexistence and interfacial properties of the liquid-solid transition in hard spheres and in colloid-polymer mixtures. The latter system is described as a one-component Asakura-Oosawa (AO) model where the polymer's degrees of freedom are incorporated via an attractive part in the effective potential for the colloid-colloid interactions. For the considered AO model, the polymer reservoir packing fraction is eta_p^r=0.1 and the colloid-polymer size ratio is q=sigma_p/\sigma=0.15 (with sigma_p and sigma the diameter of polymers and colloids, respectively). Inhomogeneous solid-liquid systems are prepared by placing the solid fc…

Quantum Hopfield Model

2020

We find the free-energy in the thermodynamic limit of a one-dimensional XY model associated to a system of N qubits. The coupling among the &sigma

Azide Binding Controlled by Steric Interactions in Second Sphere. Synthesis, Crystal Structure, and Magnetic Properties of [Ni II 2 (L)(μ 1,1 -N 3 )]…

2016

International audience; The dinuclear Ni-II complex [Ni-2(L-2)][ClO4](2) (3) supported by the 28-membered hexaaza-dithiophenolate macro-cycle (L-2)(2-) binds the N-3(-) ion specifically end-on yielding [Ni-2(L-2)(mu(1,1)-N-3)] [ClO4] (7) or [Ni-2(L-2)(mu(1,1)-N-3)][BPh4] (8), while the previously reported complex [Ni2L1(mu(1,3)-N-3)][ClO4] (2) of the 24-membered macrocycle (L-1)(2-) coordinates it in the end-to-end fashion. A comparison of the X-ray structures of 2, 3, and 7 reveals the form-selective binding of complex 3 to be a consequence of its preorganized, channel-like binding pocket, which accommodates the azide anion via repulsive CH center dot center dot center dot pi interactions …

ACID-BASE INTERACTIONS AND THEIR ROLE IN FORECASTING OF POLYMER COMPOSITES ADHESION PROPERTIES

2010

Acid-base properties of wide range of polymers and adhesion systems based on polymers, polymer composites and metals were investigated. Composite materials based on high and low density polyethylenes, ethylene copolymers, other carbochain and heterochain polymers, synthetic rubber and their based on composites, epoxy composites, cured with a wide range of curing agents were used as adhesives. By using the contact angle of test liquids the values of the dispersion, acid-base, acid and base components of the surface free energy were calculated and the acidity parameter was estimated by means of van Oss-Chaudhury-Good and E. Berger methods respectively. Effect of composition on acidity and bas…

Linear free energyortho-correlations in the thiophene series. Part IX . Kinetics of esterification with diazodiphenylmethane of some 3-, 4-, and 5-su…

1981

The rate constants for the esterification of some 3-, 4-, and 5-substituted thiophene-2-carboxylic acids with diazodiphenylmethane in methanol at 25° have been measured. The reactivity of some para- and ortho-substituted benzoic acids has also been determined. Logarithmic kinetic constants for ortho-, meta-, and para-like substituted thiophene-2-carboxylic acids furnish an excellent linear free energy relationship when plotted versus Δpka (β 0.89, r 0.989, C.L. > 99.9%, n 18, i 0.04), thus confirming the peculiar behaviour of five-membered ring derivatives. The correlation with σH values offers an additional proof of the hyper-ortho character of the 2,3-relation in thiophene derivatives. pa…

The avidin-theophylline complex: A structural and computational study

2023

: The interaction between avidin and its counterpart biotin is one of central importance in biology and has been reproposed and studied at length. However, the binding pocket of avidin is prone to promiscuous binding, able to accommodate even non-biotinylated ligands. Comprehending the factors that distinguish the extremely strong interaction with biotin to other ligands is an important step to fully picture the thermodynamics of these low-affinity complexes. Here, we present the complex between chicken white egg avidin and theophylline (TEP), the xanthine derivative used in the therapy of asthma. In the crystal structure, TEP lies in the biotin-binding pocket with the same orientation and …