Thermodynamics of water confined in porous calcium-silicate-hydrates

Water within pores of cementitious materials plays a crucial role in the damage processes of cement pastes, particularly in the binding material comprising calcium-silicate-hydrates (C-S-H). Here, we employed Grand Canonical Monte Carlo simulations to investigate the properties of water confined at ambient temperature within and between C-S-H nanoparticles or "grains" as a function of the relative humidity (%RH). We address the effect of water on the cohesion of cement pastes by computing fluid internal pressures within and between grains as a function of %RH and intergranular separation distance, from 1 to 10 ?. We found that, within a C-S-H grain and between C-S-H grains, pores are completely filled with water for %RH larger than 20%. While the cohesion of the cement paste is mainly driven by the calcium ions in the C-S-H, water facilitates a disjoining behavior inside a C-S-H grain. Between C-S-H grains, confined water diminishes or enhances the cohesion of the material depending on the intergranular distance. At very low %RH, the loss of water increases the cohesion within a C-S-H grain and reduces the cohesion between C-S-H grains. These findings provide insights into the behavior of C-S-H in dry or high-temperature environments, with a loss of cohesion between C-S-H grains due to the loss of water content. Such quantification provides the necessary baseline to understand cement paste damaging upon extreme thermal, mechanical, and salt-rich environments.     

Single-molecule force spectroscopy of bimolecular reactions: system homology in the mechanical activation of ligand substitution reactions

The mechanochemistry of the bimolecular nucleophilic substitution of DMSO for substituted pyridines at a square-planar pincer Pd(II) center was investigated using single-molecule force spectroscopy (SMFS). The SMFS data are interpreted in terms of the Bell-Evans model, which gives thermal off-rates for two reactions that agree well with previous, stress-free measurements. The characteristic force dependency of the rupture rate, fbeta, is effectively constant for the two reactions examined (22 +/- 2 and 24 +/- 2 pN), and the system homology in the mechanical response is consistent with expected similarities in the reaction potential energy surfaces.     

Thermodynamics of d-dimensional hard sphere fluids confined to micropores

We derive an analytical expression of the second virial coefficient of d-dimensional hard sphere fluids confined to slit pores by applying Speedy and Reiss' interpretation of cavity space. We confirm that this coefficient is identical to the one obtained from the Mayer cluster expansion up to second order with respect to fugacity. The key step of both approaches is to evaluate either the surface area or the volume of the d-dimensional exclusion sphere confined to a slit pore. We, further, present an analytical form of thermodynamic functions such as entropy and pressure tensor as a function of the size of the slit pore. Molecular dynamics simulations are performed for d = 2 and d = 3, and the results are compared with analytically obtained equations of state. They agree satisfactorily in the low density regime, and, for given density, the agreement of the results becomes excellent as the width of the slit pore gets smaller, because the higher order virial coefficients become unimportant.     

Thermodynamics of industrially-important,enzyme-catalyzed reactions

The thermodynamics of 10 industrially-important, enzyme-catalyzed reactions are examined. The reactions discussed are: the conversions of penicillin G to 6-amino-penicillinic acid using the enzyme penicillin acylase; starch to glucose using amylases; glucose to fructose using glucose (xylose) isomerase; cellulose to glucose using cellulase; fumaric acid and ammonia to L-aspartic acid using L-aspartase; transcinnamic acid and ammonia to L-phenylalanine using L-phenylalanine ammonia lyase; L-histidine to urocanic acid and ammonia using L-histidine ammonia lyase; lactose to glucose and galactose using lactase; and the reactions catalyzed by amino acylases and proteases. The selection of these processes was based on the economic value of the products and their intrinsic industrial importance. The available thermodynamic properties, such as equilibrium constants, Gibbs energies (delta G degrees), enthalphies (delta H degrees), and heat capacity changes (delta Cp degrees) of these enzyme-catalyzed reactions, are reviewed and summarized. Recommendations are made for future research in this area.     

Scratching the (cell) surface: cytokine engineering for improved ligand/receptor trafficking dynamics

Cytokines can be engineered for greater potency in stimulating cellular functions. An obvious test criterion for an improved cytokine is receptor-binding affinity, but this does not always correlate with improved biological response. By combining protein-engineering techniques with studies of receptor trafficking and signaling, it might be possible to identify the ligand receptor-binding properties that should be sought.     

Reversible electrochemical monitoring of surface confined reactions at liquid-liquid interfaces by modulation of ion transfer fluxes

The adsorption of the neutral surfactant Brij35 at a liquid-liquid interface is reversibly monitored via its disturbance of an electrochemically imposed ion flux across the interface, forming a promising experimental tool for the detection of surface confined reactions at such liquids and polymers.     

Thermodynamics of redox reactions involving nicotinamide adenine dinucleotide

Literature data on the thermodynamics of redox nicotinamide adenine dinucleotide (NAD) dependent reactions have been analyzed. It has been established that for the redox reaction of NAD

where all substances except H₂ are in the aqueous buffer with the ionization enthalpy equal to zero, the most reliable thermodynamic parameters should be considered as: ΔH(298.15 K; pH 7)=?27.4±1.7 kJ mole^?1; ΔG (298.15K; pH 7)=±17.8 kJ mole^?1. From the above thermodynamic parameters of the reaction ΔH, ΔG and ΔS for reactions of NAD with natural substrates, synthetic mediators and some inorganic compounds have been calculated.     

Probing the behavior of confined water by proton-transfer reactions

The picosecond dynamics of a bifunctional and H-bonding molecule, 7-hydroxyquinoline (7HQ), has been studied in a reverse micelle with increasing water content. The fluorescence kinetics has a complex behavior as the water content is changed. All reactions are irreversible, and a two-step mechanism is invoked to explain the observations. H2O/D2O exchange and excitation energy effects show that the second step has a higher barrier and that the corresponding reaction occurs through tunneling. The results clearly indicate two regimes of water nanopool behavior switching at W0 approximately 5 (W0 = [water]/[surfactant]). Water collective dynamics explains these observations. The lower fluidity of confined water within the reverse micelle with respect to normal bulk water alters the related H-bond network dynamics and therefore is responsible for the slower proton-transfer processes.     

Prediction of the mechanisms of enzyme-catalysed reactions using hybrid quantum mechanical/molecular mechanical methods

The use of hybrid methods, involving both quantum mechanics and molecular mechanics, to model the mechanism of enzyme-catalysed reactions, is discussed. Two alternative approaches to treating the electrostatic interactions between the quantum mechanical and molecular mechanical regions are studied, involving either the inclusion of this term in the electronic Hamiltonian (QM/MM), or evaluating it purely classically (MO + MM). In the latter scheme, possible problems of using force fields that are standard for macromolecular modelling are identified. The use of QM/MM schemes to investigate the mechanism of the enzymes thymidine phosphorylase (ThdPase) and protein tyrosine phosphatase (PTP) is described. For both systems, transition states have been identified using a PM3 Hamiltonian. For ThdPase, concerted motion of the enzyme during the course of the reaction is suggested and, for PTP, a two-step dephosphorylation reaction is indicated, both with quite low barriers.     

Oxidation reactions of the phosphinidene oxide ligand

The (H-DBU)+ salt of the anionic phosphinidene oxide complex [MoCp(CO)2{P(O)R*}]- (1) (DBU = 1,8-diazabicyclo[5.4.0]undec-7-ene; R* = 2,4,6-C6H2tBu3) reacts with different oxidizing agents, displaying a multisite activity located at the Mo and P atoms or at the Mo=P bond. Thus, reaction of 1 with [FeCp2]BF4 gives the dimer [Mo2Cp2(CO)4{P(O)R*}2], and reaction with bromine gives the phosphinous acid complex [MoBrCp{P(OH)(CH2CMe2C6H2tBu2}(CO)2], the latter arising from an unprecedented C-H bond addition to the oxide P=O moiety. In contrast, reaction of 1 with p-benzoquinone occurs at the P site to give the P,O-bound phosphonite complex [MoCp{kappa2-OP(OC6H4OH)R*}(CO)2]. Finally, oxygen or sulfur atoms are added to the Mo=P bond by reaction of 1 with Me2CO2 and S8 to give the novel dioxophosphorane or thiooxophosphorane complexes [MoCp(CO)2{kappa2-EP(O)R*}]- (E = O, S). The thiooxophosphorane anion is a good nucleophile and is methylated at either the S or O positions depending on the electrophile used (MeI or (Me3O)BF4) to give the isomers [MoCp{kappa2-(MeS)P(O)R*}(CO)2] and [MoCp{kappa2-SP(OMe)R*}(CO)2], both having novel organophosphorus ligands.     

Ligand displacement reactions of dimer and trimer pyridyl ligand/transition metal complexes

Ligand exchange reactions of pyridyl ligand/transition metal complexes are examined in a quadrupole ion trap mass spectrometer to evaluate the ability of multidentate ligands to displace other pyridyl ligands in complexes where the charge is highly delocalized and there is a great degree of ligand repulsions. Partially or fully coordinated transition metal ions in dimer or trimer species involving small mono- or bidentate pyridyl ligands undergo ligand displacement reactions with larger bi- and tridentate pyridyl ligands. Larger ligands with greater chelation abilities, such as 1,10-phenanthroline and 2,2′:6,2″-terpyridine, are often able to simultaneously displace two nonchelating ligands from a partially coordinated metal ion. However, the analogous reactions involving displacement of bidentate chelating ligands from more fully coordinated transition metal ion complexes are nearly quenched. In other cases, mixed-ligand dimer and trimer complexes are observed, indicating step-wise displacement of the initially complexed ligands.     

Cell receptor and surface ligand density effects on dynamic states of adhering circulating tumor cells

Dynamic states of cancer cells moving under shear flow in an antibody-functionalized microchannel are investigated experimentally and theoretically. The cell motion is analyzed with the aid of a simplified physical model featuring a receptor-coated rigid sphere moving above a solid surface with immobilized ligands. The motion of the sphere is described by the Langevin equation accounting for the hydrodynamic loadings, gravitational force, receptor-ligand bindings, and thermal fluctuations; the receptor-ligand bonds are modeled as linear springs. Depending on the applied shear flow rate, three dynamic states of cell motion have been identified: (i) free motion, (ii) rolling adhesion, and (iii) firm adhesion. Of particular interest is the fraction of captured circulating tumor cells, defined as the capture ratio, via specific receptor-ligand bonds. The cell capture ratio decreases with increasing shear flow rate with a characteristic rate. Based on both experimental and theoretical results, the characteristic flow rate increases monotonically with increasing either cell-receptor or surface-ligand density within certain ranges. Utilizing it as a scaling parameter, flow-rate dependent capture ratios for various cell-surface combinations collapse onto a single curve described by an exponential formula.     

Thermodynamics of coupled reactions by the amplitudes of chemical relaxation

The amplitudes of the relaxation curves, as obtained by the Temperature-jump method have been used to measure simultaneously equilibrium constant and enthalpy for the reaction of complex formation of Ni²⁺ ion by 2,6-dihydroxobenzoic acid in the presence of a buffer. The experiments have been performed by changing the concentration of metal ion at constant ligand concentration andpH as in a complexometric titration. The points of such ‘dynamic titrations’ have been analysed by means of the concept of ‘normal reactions’ which enabled us to transform a set of coupled individual steps into a set of kinetically independent reactions. The potentialities of the dynamic titrations are discussed.     

A mixed-valence copper coordination polymer generated by hydrothermal metal/ligand redox reactions

A novel coordination polymer of mixed-valence copper(I,II) with 4,4'-bipyridine and in situ oxidized isophthalate, [Cu2(ipO)(4,4'-bpy)] (ipOH = 2-hydroxyisophthalate), was hydrothermally synthesized and crystallographically characterized to be a laminated structure via weak copper(II)--oxygen interactions.     

Thermodynamics of hydrogen-isotope-exchange reactions. Proton solvation inn-hexanol and water

This paper reports our results for the direct experimental determination of the equilibrium constant for the hydrogen-isotope-exchange reaction, 1/2D₂(g)+HCl(hexOH)=1/2H₂(g)+DCl(hexOD), where hexOH isn-hexanol and hexOD isn-hexanol with deuterium substitution in the alcohol function. The reaction was studied in electrochemical double cells without liquid junction for which the net cell reaction is the above isotope-exchange reaction. The experimentally determined value of ε° (296.0°K) for this cell is 4.03±0.95 mV (strong electrolyte standard states, mole-fraction composition scale); the value of the equilibrium constant for the reaction is 1.17±0.05. The contributions of isotope-exchange and transfer effects to the magnitude of the standard Gibbs energy change for the above reaction and for the analogous reaction 1/2D₂(g)+HCl(aq)=DCl(daq)+1/2H₂(g) are considered. Our results support the conclusion of Heinzinger and Weston that the formulation of the solvated proton in water as H₃O⁺, as opposed to H₉O₄ ⁺, is sufficient for the interpretation of the thermodynamics of hydrogen-isotope-exchange reactions in water. We also find that the formulation of the solvated proton inn-hexanol as ROH ₂ ⁺ is sufficient for the interpretation of our results on the thermodynamics of hydrogen-isotope-exchange inn-hexanol.     

Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach

Ligand docking to flexible protein molecules can be efficiently carried out through ensemble docking to multiple protein conformations, either from experimental X-ray structures or from in silico simulations. The success of ensemble docking often requires the careful selection of complementary protein conformations, through docking and scoring of known co-crystallized ligands. False positives, in which a ligand in a wrong pose achieves a better docking score than that of native pose, arise as additional protein conformations are added. In the current study, we developed a new ligand-biased ensemble receptor docking method and composite scoring function which combine the use of ligand-based atomic property field (APF) method with receptor structure-based docking. This method helps us to correctly dock 30 out of 36 ligands presented by the D3R docking challenge. For the six mis-docked ligands, the cognate receptor structures prove to be too different from the 40 available experimental Pocketome conformations used for docking and could be identified only by receptor sampling beyond experimentally explored conformational subspace.