Search results for "solvation"
showing 10 items of 157 documents
Theoretical and structural studies of lithium cyclic amide conformations. Monomers and aggregates
2000
High level ab initio calculations on the conformations of unsolvated and solvated lithium piperidide, 1, and lithium morpholide, 2, were carried out. It was found that both monomers exhibit a global minimum for a chair structure with a planar nitrogen, and 2 shows an additional stable pseudo boat conformation. Dimers and amine–lithium amide mixed aggregates were also calculated including discrete solvation; the role of aggregation is clearly shown both by the changes in geometries and in the stabilization energies. Semiempirical calculations carried out on a recently synthesized tetrameric mixed aggregate give a geometry very similar to the structure determined by X-ray diffraction. The pre…
Determination of Individual Gibbs Energies of Anion Transfer and Excess Gibbs Energies Using an Electrochemical Method Based on Insertion Electrochem…
2011
A method is presented to determine, individually and with minimal extra-thermodynamic assumptions, the Gibbs energy for anion transfer between two solvents using solid state electrochemistry of alkynyldiphosphine dinuclear Au(I) complexes (AuC2R)2PPh2C6H4PPh2 (L1, R = Fc; L2, R = C6H4Fc) and the heterometallic Au(I)–Cu(I) [{Au3Cu2(C2R)6}Au3(PPh2C6H4PPh2)3](PF6)2 (L3, R = Fc; L4, R = C6H4Fc) cluster complexes containing ferrocenyl units. These compounds exhibit a well-defined, essentially reversible solid-state oxidation in contact with different electrolytes, based on ferrocenyl-centered oxidation processes involving anion insertion. Voltammetric data can be used for a direct measurement of…
The effect of water on protein dynamics
2004
Neutron diffraction and spectroscopy were applied to describe the hydration and dynamics of a soluble protein and a natural membrane from extreme halophilic Archaea. The quantitative dependence of protein motions on water activity was clearly illustrated, and it was established that a minimum hydration shell is required for the systems to access their functional resilience, i.e. a dynamics state that allows biological activity.
The hydration shell of myoglobin.
1992
The space in the unit cell of a metmyoglobin crystal not occupied by myoglobin atoms was filled with water using Monte Carlo calculations. Independent calculations with different amounts of water have been performed. Structure factors were calculated using the water coordinates thus obtained and the known coordinates of the myoglobin atoms. A comparison with experimental structure factors showed that both the low and the high resolution regime could be well reproduced with 814 Monte Carlo water molecules per unit cell with a B-value of 50 A2. The Monte Carlo water molecules yield a smaller standard R-value (0.166) than using a homogeneous electron density for the simulation of the crystal w…
Oxygen K-shell spectroscopy of isolated progressively solvated peptide
2020
Gas-phase near-edge X-ray-absorption fine structure (NEXAFS) action spectroscopy around the oxygen K-edge and mass spectrometry were employed to probe isolated substance P (SP) molecular ions, both bare and progressively solvated with 4 and 11 water molecules. Detailed mass spectra of bare and hydrated precursors are presented for the resonant photon energy of 532 eV that corresponds to O1s --> pi(amide)* core excitation, triggering resonant Auger decay and fragmentation from the ionized radical molecular system. The fragmentation pattern of doubly protonated SP hydrated with 4 water molecules clearly shows a series of abundant doubly charged backbone fragments, as well as triply charged pr…
Free Energy, Enthalpy and Entropy from Implicit Solvent End-Point Simulations
2018
Free energy is the key quantity to describe the thermodynamics of biological systems. In this perspective we consider the calculation of free energy, enthalpy and entropy from end-point molecular dynamics simulations. Since the enthalpy may be calculated as the ensemble average over equilibrated simulation snapshots the difficulties related to free energy calculation are ultimately related to the calculation of the entropy of the system and in particular of the solvent entropy. In the last two decades implicit solvent models have been used to circumvent the problem and to take into account solvent entropy implicitly in the solvation terms. More recently outstanding advancement in both impli…
Internal dynamics and energy transfer in dansylated POPAM dendrimers and their eosin complexes.
2010
Internal dynamics of dansylated poly(propyleneamine) dendrimers (POPAM, G1-G4) in solution and excitation energy transfer from dansyls to eosin in POPAM-eosin complexes have been studied by time-resolved fluorescence spectroscopy and molecular dynamics (MD) simulations. Combining the results from fluorescence anisotropy and the MD simulation studies suggests three time domains for the internal dynamics of the G3 and G4 generations, about 60 ps for motions of the outer-sphere dansyls, 500-1000 ps for restricted motions of back-folded dansyls, and 1500-2600 ps for the overall rotation. For the smaller generations, the contribution from the restricted motions was not entirely evident. Eosin bi…
Determination of Kinetic and Thermochemical Parameters of a Substitution Reaction at a Square-Planar Palladium(II) Complex in Water/AOT/n-Heptane Mic…
1995
Abstract The substitution reaction [Pd(bipy)(en)] 2+ + en → [Pd(en) 2 ] 2+ + bipy (where bipy = 2,2′-bipyridine and en = ethylenediamine) has been studied in water and water/AOT/ n -heptane microemulsions at various values of the molar ratio R ( R = [water]/[AOT]) by flow microcalorimetry. From calorimetric data, molar enthalpies of reaction and rate constants were obtained. These quantities indicate that, by increasing R , the reaction becomes less exothermic and its rate constant decreases, trending to the value observed in water. These features can be reasonably rationalized in terms of the peculiar solvation state of reactants inside the AOT reversed micelles and/or the peculiar physico…
The mechanism of formamide hydrolysis in water from ab initio calculations and simulations.
2005
The neutral hydrolysis of formamide in water is a suitable reference to quantify the efficiency of proteolytic enzymes. However, experimental data for this reaction has only very recently been obtained and the kinetic constant determined experimentally is significantly higher than that predicted by previous theoretical estimations. In this work, we have investigated in detail the possible mechanisms of this reaction. Several solvent models have been considered that represent a considerable improvement on those used in previous studies. Density functional and ab initio calculations have been carried out on a system which explicitly includes the first solvation shell of the formamide molecule…
Impulsive solvent heating probed by picosecond x-ray diffraction
2006
The time-resolved diffraction signal from a laser-excited solution has three principal components: the solute-only term, the solute-solvent cross term, and the solvent-only term. The last term is very sensitive to the thermodynamic state of the bulk solvent, which may change during a chemical reaction due to energy transfer from light-absorbing solute molecules to the surrounding solvent molecules and the following relaxation to equilibrium with the environment around the scattering volume. The volume expansion coefficient alpha for a liquid is typically approximately 1 x 10(-3) K(-1), which is about 1000 times greater than for a solid. Hence solvent scattering is a very sensitive on-line t…