Biomedical subjects
Publications and source records attributed to V Buch.
On-the-fly dynamics is used to analyze the remarkably anharmonic infrared spectroscopy of crystalline HCl monohydrate, an ionic solid composed of H3O+ and Cl-. The dominant intense infrared feature is shown to originate from specific sections of the hydronium trajectory, in which one of the H-atoms interacts strongly with a neighboring Cl-.
Following an initial Communication [Buch et al., J. Chem. Phys. 123, 051108 (2005)], a new molecular-dynamics-based approach is explored to search for candidate crystal structures of molecular solids corresponding to minima of the enthalpy. The approach is based on the observation of phase transitions in an artificial periodic system with a small unit cell and relies on the existence of an optimal energy range for observing freezing to low-lying minima in the course of classical trajectories. Tests are carried out for O structures of nine H2O-ice polymorphs. NVE trajectories for a range of preimposed box shapes display freezing to the different crystal polymorphs whenever the box dimensions approximate roughly the appropriate unit cell; the exception is ice II for which freezing requires unit cell dimensions close to the correct ones. In an alternate version of the algorithm, an initial box shape is picked at random and subsequently readjusted at short trajectory intervals by enthalpy minimization. Tests reveal the existence of ice forms which are "difficult" and "easy" to locate in this way. The former include ice IV, which is also difficult to crystallize experimentally from the liquid, and ice II, which does not interface with the liquid in the phase diagram. On the other hand, the latter crystal search procedure located successfully the remaining seven ice polymorphs, including ice V, which corresponds to the most complicated structure of all ice phases, with a monoclinic cell of 28 molecules.
Molecular dynamics simulations are used to investigate typical coordination shells of molecules in the liquid water surface, for two potential energy surfaces. The major undercoordinated species found in the surface include three-coordinated H2O with either a dangling-H or a dangling-O atom and two-coordinated H2O with one hydrogen bond via H, and another via O. Vibrational signatures of the different coordinations are calculated. The 3400 cm(-1) band in the surface sum frequency generation (SFG) spectrum is assigned to four-coordinated molecules within the surface layer. The low-frequency wing of the OH-stretch band, near 3200 cm(-1) in the SFG spectrum, is proposed to be due to collective excitations of a relatively small number of intermolecularly coupled O-H bond vibrations.
A new molecular-dynamics based approach is proposed to search for candidate crystal structures of molecular solids. The procedure is based on the observation of spontaneous transitions between ordered and disordered states in molecular-dynamics simulations of an artificial periodic system with a small unit cell. In such a way only the most stable structures are automatically selected. The method can be applied to the solution of crystal structures from low-quality or very complex diffraction data. Tests are presented for H2O-ice polymorphs.
In addition to revealing the stretch-mode bands of the smallest mixed clusters of HCl and HBr (HX) with water, the ragout-jet FTIR spectra of dense mixed water-acid supersonic jets include bands that result from the interaction of HX with larger water clusters. It is argued here that low jet temperatures prevent the water-cluster-bound HX molecules from becoming sufficiently solvated to induce ionic dissociation. The molecular nature of the HX can be deduced directly from the observed influence of changing from HCl to HBr and from replacing H2O with D2O. Furthermore, the band positions of HX are roughly coincidental with bands assigned to molecular HCl and HBr adsorbed on ice nanocrystal surfaces at temperatures below 100 K. It is also interesting that the HX band positions and widths approximate those of HX bound to the surface of amorphous ice films at <60 K. Though computational results suggest the adsorbed HX molecules observed in the jet expansions are weakly distorted by single coordination with surface dangling-oxygen atoms, on-the-fly trajectories indicate that the cluster skeletons undergo large-amplitude low-frequency vibrations. Local HX solvation, the extent of proton sharing, and the HX vibrational spectra undergo serious modulation on a picosecond time scale.
Acid solvation states are investigated in the recently discovered mixed ether:acid crystalline solids. The solids are simulated using on-the-fly molecular dynamics as implemented in the density functional code QUICKSTEP employing Gaussian basis sets. The solids are shown to display a remarkably broad range of acid solvation states, depending on the ether:acid ratio, including proton sharing in the 1:1 case, proton transfer to the ether in 1:2, and perturbed molecular acid in 1:6. The observed variation of the infrared spectra with the composition is accounted for qualitatively with the help of the calculations.
The study focuses on nucleation and growth of a binary mixed crystal phase from two pure crystals in contact. Monte Carlo simulations of this process are conducted, with the dynamics proceeding via activated atom-vacancy exchanges. Intermolecular interactions, ranging up to next-nearest neighbors, are of size typical of hydrogen bonded systems. The process is driven by the formation of strong AB bonds at the expense of weaker AA and BB bonds. In the resulting model, the material is channeled and transported through the mixed phase crust along antiphase boundaries. The flow of molecules through the channels is directed, due to molecular energy lowering via gradual acquisition of an increasing number of nearest neighbors of the second species. On the other hand, defect motion is quasirandom. The model accounts partially for the t(1/alpha) (alpha>3) time dependence observed for conversion of nanoparticles of HBr dihydrate to monohydrate, by exposure to acid adsorbate.
Orientational defects in hexagonal ice were investigated using molecular dynamics simulations. Energy relaxation during L- and D-defect migration was shown to be associated with improved alignment of water molecules along the local electric fields. Two new forms of defects, an "L+D complex," and a "5+7 defect," were characterized. These forms appear in ice trajectories close to the melting point, and in the course of L- and D-pair recombination process. Defect pair recombination was shown to be a complex process, involving collective H-bond changes in groups of molecules.
Ionization and dissociation reactions play a fundamental role in aqueous chemistry. A basic and well-understood example is the reaction between hydrogen chloride (HCl) and water to form chloride ions (Cl(-)) and hydrated protons (H(3)O(+) or H(5)O(2)(+)). This acid ionization process also occurs in small water clusters and on ice surfaces, and recent attention has focused on the mechanism of this reaction in confined-water media and the extent of solvation needed for it to proceed. In fact, the transformation of HCl adsorbed on ice surfaces from a predominantly molecular form to ionic species during heating from 50 to 140 K has been observed. But the molecular details of this process remain poorly understood. Here we report infrared transmission spectroscopic signatures of distinct stages in the solvation and ionization of HCl adsorbed on ice nanoparticles kept at progressively higher temperatures. By using Monte Carlo and ab initio simulations to interpret the spectra, we are able to identify slightly stretched HCl molecules, strongly stretched molecules on the verge of ionization, contact ion pairs comprising H(3)O(+) and Cl(-), and an ionic surface phase rich in Zundel ions, H(5)O(2)(+).