Search results for "Solvation shell"
showing 10 items of 23 documents
Computational Study of the Effect of Glyoxal–Sulfate Clustering on the Henry’s Law Coefficient of Glyoxal
2014
We have used quantum chemical methods to investigate the molecular mechanism behind the recently reported ( Kampf , C. J. ; Environ. Sci. Technol . 2013 , 47 , 4236 - 4244 ) strong dependence of the Henry's law coefficient of glyoxal (C2O2H2) on the sulfate concentration of the aqueous phase. Although the glyoxal molecule interacts only weakly with sulfate, its hydrated forms (C2O3H4 and C2O4H6) form strong complexes with sulfate, displacing water molecules from the solvation shell and increasing the uptake of glyoxal into sulfate-containing aqueous solutions, including sulfate-containing aerosol particles. This promotes the participation of glyoxal in reactions leading to secondary organic…
Surface charges at the CaF2/water interface allow very fast intermolecular vibrational-energy transfer
2020
Abstract We investigate the dynamics of water in contact with solid calcium fluoride, where at low pH, localized charges can develop upon fluorite dissolution. We use 2D surface‐specific vibrational spectroscopy to quantify the heterogeneity of the interfacial water (D2O) molecules and provide information about the sub‐picosecond vibrational‐energy‐relaxation dynamics at the buried solid/liquid interface. We find that strongly H‐bonded OD groups, with a vibrational frequency below 2500 cm−1, display very rapid spectral diffusion and vibrational relaxation; for weakly H‐bonded OD groups, above 2500 cm−1, the dynamics slows down substantially. Atomistic simulations based on electronic‐structu…
The Coordination of Uranyl in Water: A Combined Quantum Chemical and Molecular Simulation Study
2005
The coordination environment of uranyl in water has been studied using a combined quantum mechanical and molecular dynamics approach. Multiconfigurational wave function calculations have been performed to generate pair potentials between uranyl and water. The quantum chemically determined energies have been used to fit parameters in a polarizable force field with an added charge transfer term. Molecular dynamics simulations have been performed for the uranyl ion and up to 400 water molecules. The results show a uranyl ion with five water molecules coordinated in the equatorial plane. The U-O(H(2)O) distance is 2.40 A, which is close to the experimental estimates. A second coordination shell…
Molecular precursors of mesostructured silica materials in the atrane route: A DFT/GIAO/NBO theoretical study
2007
Abstract Quantum chemical calculations using density functional theory have been carried out to investigate two assumed molecular precursors and identified as silatranes (N[OCH2CH2]3Si–OCH2CH2N–(CH2CH2OH)2 and N[OCH2CH2]3Si–OCH2CH2N–(CH2CH2OH)2Na+) which are present in the synthesis of mesoporous silica based material namely “the atrane route”. One of the ways in this synthesis leads to the well-known MCM-41. Additionally, in this work has been also investigated two others molecules such as triethanolamine (TEAH3) and sodatrane which are present in the medium. Gas phase and solution equilibrium geometries of the previous molecules were fully optimized at B3LYP level, modeling solvent effect…
Study of percolation and clustering in supercritical water-CO2 mixtures
2008
The microscopic structure of supercritical water-CO(2) mixture is investigated by neutron diffraction experiments exploiting the isotopic HD substitution. The investigated water reach mixtures are in the liquidlike region of the phase diagram, according to the behavior of the radial distribution functions, yet a reduction of the average number of hydrogen bonds, compared to equivalent states of pure water, is found. As a consequence, the average dimension of water clusters is reduced and the system stays below the percolation threshold. These results, along with the shift of the main peaks of the site-site radial distribution functions, suggest that the excess volume in these supercritical …
A Microscopic Interpretation of Pump–Probe Vibrational Spectroscopy Using Ab Initio Molecular Dynamics
2018
What happens when extra vibrational energy is added to water? Using nonequilibrium molecular dynamics simulations, also including the full electronic structure, and novel descriptors, based on projected vibrational density of states, we are able to follow the flow of excess vibrational energy from the excited stretching and bending modes. We find that the energy relaxation, mostly mediated by a stretching-stretching coupling in the first solvation shell, is highly heterogeneous and strongly depends on the local environment, where a strong hydrogen bond network can transport energy with a time scale of 200 fs, whereas a weaker network can slow down the transport by a factor 2-3.
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…
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…