Yuxiang Bu

Solvation of excess electrons in LiF ionic pair matrix: evidence for a solvated dielectron from ab initio molecular dynamics simulations and calculations.

Ab initio molecular dynamics simulations and first-principles calculations reveal the existence of a solvated dielectron species, (2e)s, in an LiF ionic matrix. The nature of the solvation mechanism and the stability of the species was explored. In addition to electrostatic interactions, a hole-orbital coupling among solvent molecules may significantly enhance the stability of the solvated electrons and govern the extent of electron solvation. This hole-orbital coupling is different from either an electrostatic coupling or conventional chemical bonding, and it may be described as a transition between them.

Effect of metal ions on radical type and proton-coupled electron transfer channel: σ-Radical vs π-radical and σ-channel vs π-channel in the imide units

The mechanism of proton transfer (PT)/electron transfer (ET) in imide units, and its regulation by hydrated metal ions, was explored theoretically using density functional theory in a representative model (a nearly planar and cisoid complex between uracil and its N3‐dehydrogenated radical, UU). In UU (σ‐radical), PT/ET normally occurs via a seven‐center, cyclic proton‐coupled σ‐electron σ‐channel transfer (PCσEσT) mechanism (3.8 kcal/mol barrier height) with a N3→N3′ PT and an O4→O4′ ET. Binding of hydrated metal ions to the dioxygen sites (O2/O2′ or/and O4/O4′) of UU may significantly affect its PT/ET cooperative reactivity by changing the radical type (σ‐radical ↔ π‐radical) and ET channel (σ‐channel ↔ π‐channel), leading to different mechanisms, ranging from PCσEσT, to proton‐coupled π‐electron σ‐channel transfer (PCπEσT) to proton‐coupled π‐electron π‐channel transfer (PCπEπT). This change originates from an alteration of the ordering of the UU moiety SOMO/HDMO (the singly occupied molecular orbital and the highest doubly occupied molecular orbital), induced by binding of the hydrated metal ions. It is a consequence of three associated factors: the asymmetric reactant structure, electron cloud redistribution, and fixing role of metal ions to structural backbone. The findings regarding the modulation of the PT/ET pathway via hydrated metal ions may provide valuable information for a greater understanding of PT/ET cooperative mechanisms, and an alternative way for designing imide‐based molecular devices, such as molecular switches and molecular wires.

Remarkable metal counterion effect on the internucleotide J- couplings and chemical shifts of the N-H... N hydrogen bonds in the W-C base pairs

The effects of metal ion binding on the (2h) J(NN)-coupling and delta( (1)H)/Deltadelta( (15)N) chemical shifts of N-H...N H-bond units in internucleotide base pairs were explored by a combination of density functional theory calculations and molecular dynamics (MD) simulations. Results indicate that the NMR parameters vary considerably upon cation binding to the natural GC or AT base pairs, and thus can be used to identify the status of the base pairs, if cation-perturbed. The basic trend is that cation perturbation causes (2h) J(NN) to increase, Deltadelta( (15)N) to decrease, and delta( (1)H) to shift upfield for GC, and in the opposite directions for AT. The magnitudes of variation are closely related to the Lewis acidity of the metal ions. For both base pair series (M(z+)GC and M(z+)AT), these NMR parameters are linearly correlated among themselves. Their values depend strongly on the energy gaps (Delta(ELP-->sigma*)) and the second-order interaction energies ( E(2)) between the donor N lone pair (LP(N)) and the acceptor sigma* N-H localized NBO orbitals. In addition, the (2h) J NN changes are also sensitive to the amount of sigma charge transfer from LP(N) to sigma*(N-H) NBOs or from the purine to the pyrimidine moieties. The different trends are a consequence of the different H-bond patterns combined with the polarization effect of the metal ions in the cationized M(z+)AT series, M(z+) <-- A --> T, and the cationized GC series, M(z+) <-- G <-- C. The predicted cation-induced systematic trends of (2h) J(NN) and delta( (15)N, (1)H) in N-H...N H-bond units may provide a new approach to the determination of H-bond structure and strength in Watson-Crick base pairs, and provide an alternative probe of the heterogeneity of DNA sequences.

Electron bridging dihydrogen bond in the imidazole-contained anion derivatives

The large contact distance of electron bridging dihydrogen bond (EBDB), which is over 2.4 A, is the most prominent characteristic for the imidazole-contained anion derivatives. The elongation of N-H bond and the shortening of H...H distance can be observed upon hydration and hydrogenation. Transformation from EBDB to dissociative H2 is convenient upon sequential hydrogenation. The H...H distance decreases with the enhancement of the electronegativity of the heavy atom which contacts directly with one of these two hydrogen atoms. NMR shielding of the bonding N varies significantly upon hydration and hydrogenation. The spin-spin coupling constants, 1J(H-H), is dominated predominantly by the paramagnetic spin-orbit and diamagnetic spin-orbit contributions instead of the Fermi-contact term. Enhancement of electronegativity of the heavy atom leads to the increase of 1J(H-H) coupling constants. The stabilization is enhanced upon hydration predominantly for the formation of O-H...N H bond, while it is reversed upon hydrogenation for the cleavage of big pi bond, Pi5(6). Enhancement of the stability is demonstrated by the increase of stabilization energy and vertical electron detachment energy with the electronegativity of the heavy atom. The dominant contributions for the formation of such electron bridging dihydrogen bond are the high polarity of each fragment, large electron density between two fragments, and strong bonding interaction of the bridging electron with H(N) atoms. The H...H interaction can be formed by X-Hdelta+ and Hdelta- -Y polar molecules in Hdelta+...Hdelta- and Hdelta+...e...Hdelta+ of two forms.

Hydration effect on interaction mode between glutamic acid and Ca2+ and its biochemical implication: a theoretical exploration

The stepwise hydration effect on the glutamic acid–Ca2+ (GC) complexes in the gas phase has been investigated by density functional theory (DFT) calculations. The thermodynamics parameters for the hydration reactions, the stepwise hydration energies and accurate geometries have been explored. To elucidate the Ca2+–ligand interaction, the charge transfer, bonding analysis and IR spectroscopic characteristics have also been investigated. The correlating data have shown that all of the stepwise hydration reactions are enthalpy-driven because of the relatively small value of ΔS, but the number of coordinated water molecules in the first shell of Ca2+ is not limitless. In our study, the optimal coordination number (CN) of Ca2+ in the first shell is 6 or 7; the former value agrees well with the data reported in the Protein Data Bank (PDB), and the latter is the reflection of the most frequent Ca2+-binding motif, EF-hand, in soluble proteins. Furthermore, the self-consistent reaction field (SCRF) and higher-level MP2 calculations have confirmed our conclusions. Additionally and very importantly, the stepwise hydration in either the first or second coordination shell can weaken the glutamic acid–Ca2+ interaction gradually till the glutamic acid ligand is replaced by the added water molecules, resulting in the conversion of coordination mode of the glutamic acid to Ca2+ from the inner-sphere one to a peripheral interaction mode, just like the ligand exchange process in the Ca2+ release channel existing in the real biological system. Finally, the similarities and discrepancies between our model and the Ca2+-channel in vivo have been compared.