Biomedical subjects
Publications and source records attributed to Chi-Kit Siu.
Comparison of the collision cross-section of the [Fe(III)-protoporphyrin IX]+ ion, hemin+, measured by means of ion-mobility experiments and the cross-sections calculated from theoretical structures based on density functional theory reveals that hemin+, in the gas phase, contains intramolecular hydrogen bonding between its two propionic acid side-chains.
An ab initio molecular dynamics method was used to compare the ionic dissolution of soluble sodium chloride (NaCl) in water clusters with the highly insoluble silver chloride (AgCl). The investigations focused on the solvation structures, dynamics, and energetics of the contact ion pair (CIP) and of the solvent-separated ion pair (SSIP) in NaCl(H(2)O)(n) and AgCl(H(2)O)(n) with cluster sizes of n = 6, 10 and 14. We found that the minimum cluster size required to stabilize the SSIP configuration in NaCl(H(2)O)(n) is temperature-dependent. For n = 6, both configurations are present as two distinct local minima on the free-energy profile at 100 K, whereas SSIP is unstable at 300 K. Both configurations, separated by a low barrier (<10 kJ mol(-1)), are identifiable on the free energy profiles of NaCl(H(2)O)(n) for n = 10 and 14 at 300 K, with the Na(+)/Cl(-) pairs being internally solvated in the water cluster and the SSIP configuration being slightly higher in energy (<5 kJ mol(-1)). In agreement with the low bulk solubility of AgCl, no SSIP minimum is observed on the free-energy profiles of finite AgCl(H(2)O)(n) clusters. The AgCl interaction is more covalent in nature, and is less affected by the water solvent. Unlike NaCl, AgCl is mainly solvated on the surface in finite water clusters, and ionic dissolution requires a significant reorganization of the solvent structure.
Explore the source record for details and available documents.
The conformers of gaseous bradykinin, BK, (Arg(1)-Pro(2)-Pro(3)-Gly(4)-Phe(5)-Ser(6)-Pro(7)-Phe(8)-Arg(9)) and its protonated forms, [BK + H](+), [BK + 2H](2+), and [BK + 3H](3+), were examined theoretically using a combination of the Merck molecular force field, Hartree-Fock, and density functional theory. Neutral BK, [BK + H](+), and [BK + 2H](2+) exist in zwitterionic forms that are stabilized by internal solvation and have compact structures; [BK + 3H](3+) differs by the absence of a salt bridge and adopts an elongated form. The common structural feature in all four BK species is a beta-turn in the Ser(6)-Pro(7)-Phe(8)-Arg(9) sequence. The gas-phase basicity of [BK + H](+) estimated from the calculated protonation energy is in accord with published experimental basicity; population-weighted collision cross-sections of the three ionic forms are in agreement with experimental cross-sections in the literature.
By a systematic examination on Na(H2O)n, with n = 4-7, 9, 10, and 15, we demonstrate that a hydrogen loss reaction can be initiated by a single sodium atom with water molecules. This reaction is similar to the well-known size-dependent intracluster hydrogen loss in Mg+(H2O)n, which is isoelectronic to Na(H2O)n. However, with one less charge on Na(H2O)n than that on Mg+(H2O)n, the hydrogen loss for Na(H2O)n is characterized by a higher barrier and a more flexible solvation shell around the metal ion, although the reaction should be accessible, as the lowest barrier is around 8 kcal/mol. Interestingly, the hydroxide ion OH- produced in the process is stabilized by the solvation of H2O molecules and the formation of an ion pair Na+(H2O)4(H2O)n-l-4[OH-(H2O)l]. The activation barrier is reduced as the unpaired electron in Na(H2O)n moves to higher solvation shells with increasing cluster size, and the reaction is not switched off for larger clusters. This is in sharp contrast to the reaction for Mg+(H2O)n, in which the OH- ion is stabilized by direct coordination with Mg2+ and the reaction is switched off for n > 17, as the unpaired electron moved to higher solvation shells. Such a contrast illustrates the important link between microsolvation environment and chemical reactivity in solvation clusters.
The gas-phase reactions of hydrated electrons with carbon dioxide and molecular oxygen were studied by Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry. Both CO2 and O2 react efficiently with (H2O)n- because they possess low-lying empty pi* orbitals. The molecular CO2- and O2- anions are concurrently solvated and stabilized by the water ligands to form CO2(-)(H2O)n and O2(-)(H2O)n. Core exchange reactions are also observed, in which CO2(-)(H2O)n is transformed into O2(-)(H2O)n upon collision with O2. This is in agreement with the prediction based on density functional theory calculations that O2(-)(H2O)n clusters are thermodynamically favored with respect to CO2(-)(H2O)n. Electron detachment from the product species is only observed for CO2(-)(H2O)2, in agreement with the calculated electron affinities and solvation energies.
We report computational studies on Al(+)(H(2)O)(n), and HAlOH(+)(H(2)O)(n-1), n = 6-14, by the density functional theory based ab initio molecular dynamics method, employing a planewave basis set with pseudopotentials, and also by conventional methods with Gaussian basis sets. The mechanism for the intracluster H(2) elimination reaction is explored. First, a new size-dependent insertion reaction for the transformation of Al(+)(H(2)O)(n), into HAlOH(+)(H(2)O)(n-1) is discovered for n > or = 8. This is because of the presence of a fairly stable six-water-ring structure in Al(+)(H(2)O)(n) with 12 members, including the Al(+). This structure promotes acidic dissociation and, for n > or = 8, leads to the insertion reaction. Gaussian based BPW91 and MP2 calculations with 6-31G* and 6-31G** basis sets confirmed the existence of such structures and located the transition structures for the insertion reaction. The calculated transition barrier is 10.0 kcal/mol for n = 9 and 7.1 kcal/mol for n = 8 at the MP2/6-31G** level, with zero-point energy corrections. Second, the experimentally observed size-dependent H(2) elimination reaction is related to the conformation of HAlOH(+)(H(2)O)(n-1), instead of Al(+)(H(2)O)(n). As n increases from 6 to 14, the structure of the HAlOH(+)(H(2)O)(n-1) cluster changes into a caged structure, with the Al-H bond buried inside, and protons produced in acidic dissociation could then travel through the H(2)O network to the vicinity of the Al-H bond and react with the hydride H to produce H(2). The structural transformation is completed at n = 13, coincident approximately with the onset of the H(2) elimination reaction. From constrained ab initio MD simulations, we estimated the free energy barrier for the H(2) elimination reaction to be 0.7 eV (16 kcal/mol) at n = 13, 1.5 eV (35 kcal/mol) at n = 12, and 4.5 eV (100 kcal/mol) at n = 8. The existence of transition structures for the H(2) elimination has also been verified by ab initio calculations at the MP2/6-31G** level. Finally, the switch-off of the H(2) elimination for n > 24 is explored and attributed to the diffusion of protons through enlarged hydrogen bonded H(2)O networks, which reduces the probability of finding a proton near the Al-H bond.
The mechanism of size-dependent intracluster hydrogen loss in the cluster ions Mg(+)(H(2)O)(n), which is switched on around n=6, and off around n=14, was studied by ab initio calculations at the MP2/6-31G* and MP2/6-31G** levels for n=1-6. The reaction proceeds by Mg(+)-assisted breaking of an H-O bond in one of the H(2)O molecules. The reaction barrier is dependent on both the cluster size and the solvation structure. As n increases from 1 to 6, there is a dramatic drop in the reaction barrier, from greater than 70 kcal mol(-1) for n=1 to less than 10 kcal mol(-1) for n=6. In the transition structures, the Mg atom is close to the oxidation state of +2, and H(2)O molecules in the first solvation shell are much more effective in stabilizing the transition structures and lowering the reaction barriers than H(2)O molecules in the other solvation shells. While the reaction barrier for trimer core structures with only three H(2)O molecules in the first shell is greater than 24 kcal mol(-1), even for Mg(+)(H(2)O)(6), it drops considerably for clusters with four-six H(2)O molecules in the first shell. The more highly coordinated complexes have comparable or slightly higher energy than the trimer core structures, and the presence of such high coordination number complexes is the underlying kinetic factor for the switching on of the hydrogen-loss reaction around n=6. For clusters with trimer core structures, the hydrogen loss reaction is much easier when it is preceded by an isomerization step that increases the coordination number around Mg(+). Delocalization of the electron on the singly occupied molecular orbital (SOMO) away from the Mg(+) ion is observed for the hexamer core structure, while at the same time this isomer is the most reactive for the hydrogen-loss reaction, with an energy barrier of only 2.7 kcal mol(-1) at the MP2/6-31G** level.