Zhiyuan Zhang

Cooperative vibrational properties of hydrogen bonds in Watson–Crick DNA base pairs

A detailed analysis of hydrogen bonding (H-bonding) nuclear motions is presented for adenine–thymine (AT) and guanine–cytosine (GC) Watson–Crick DNA base pairs. Using first-principles calculations, we investigated the infrared (IR) spectroscopy and nuclear vibrating patterns of multiple H-bond interactions, compared with those of the individual H-bonding base pairs. For the first time, we have shown that multiple H-bonds arouse collective nuclei vibrations, and retain “intensifying” and “bounding” effects on symmetric and asymmetric donor stretching, respectively. This gives the H-bonds an unexpectedly amplified effect. On the other hand, H-bonds that donate charge in different directions reinforce each other through enhanced orbital interactions, indicating a correlated fashion of electronic activities. The coordinated nuclei motion and electron transport constitutes a simple form of H-bond cooperation. This study brings a new perspective of H-bond cooperativity and should enhance our knowledge of the control of H-bonds. Due to their important universality, such properties can benefit experimental applications in spectroscopy, material designing, and biological processes for complex H-bonding systems.

Energetics competition in centrally four-coordinated water clusters and Raman spectroscopic signature for hydrogen bonding

Extending the electronic structure of four-coordinated hydrogen bonds (H-bonds) to medium sized water cages (H2O)n (n = 17, 19, 20, 21, 23 and 25), we separate the H-bonded neighbour molecules of their centrally four-coordinated water (C4CW) molecules from other molecules in outer cages and discover these two regions interact competitively with the central molecule, showing complementary interaction energy curves with respect to size changes. Raman spectral analyses clearly reveal the characteristic vibration response of water molecules to different H-bonding environment, where the C4CW structure is relatively sensitive. Our theoretical research advances a new perspective for the study of H-bonding interaction in liquid water.

Spin polarization and dispersion effects in emergence of roaming transition state for nitrobenzene isomerization

Since roaming was found as a new but common reaction path of isomerization, many of its properties, especially those of roaming transition state (TSR), have been studied recently on many systems. However, the mechanism of roaming is still not clear at the atomic level. In this work, we used first-principles calculations to illustrate the detailed structure of TSR in an internal isomerization process of nitrobenzene. The calculations distinctively show its nature of antiferromagnetic coupling between two roaming fragments. Moreover, the effect of dispersion is also revealed as an important issue for the stability of the TSR. Our work provides a new insight from the view of electronic structure towards the TSR and contributes to the basic understanding of the roaming systems.

The electron density delocalization of hydrogen bond systems

Abstract Recent experimental and theoretical researches have gradually proved that hydrogen bond (H-bond) interactions are not simple traditionally considered electrostatic interaction. Instead, they involve electron density delocalization. In this work, we outline the studies of electronic structures of the H-bond systems in water systems and biological organic molecules systems. Theoretical researches based on the first-principles method have found important evidences for electron density delocalization in H-bond region. Topological analysis based on natural bond orbital (NBO) analysis proves that during the formation of the H-bonds, electrons transfer from B orbitals to A–H anti-bond orbitals. Energy decomposition analyses revealed that the delocalized electronic structures show strong relations with orbital interactions. Moreover, penetrating molecular orbitals (MOs) are proved to contribute to the electron density delocalization of the H-bonds, and the quantitative contributions for such MOs could be obtained with the electronic density projected integral (EDPI) method. The electronic delocalization and the corresponding penetrating MOs could be visualized in water clusters, based on the first-principles method. These researches open a new sight for understanding the electronic structures of H-bonds from atomic level, and even contribute to further controlling proton tunneling as well as charge and energy transfer processes.

Structural Asymmetry-Facilitated Tunability of Spin Distribution in the (10,0) Carbon Nanotube Induced by Charging

Constructing the asymmetric electronic structure of low-dimensional carbon nanomaterials is significant for application of molecular devices, such as magnetic switches. In this work, we use density functional theory to investigate the asymmetric spin distribution in a typical (10, 0) carbon nanotube by capping one end with a fullerene hemisphere and saturating the dangling bonds with hydrogen atoms at the other end. Calculated results indicate that this geometry obviously modified the distribution of spin density along the tube axis, and the electrons present were antiferromagnetically coupled at both ends. Specifically, the change in magnetic order at the end of the cap can be changed with either the increase or decrease of the charge. In addition, the analysis of electron density difference shows that charge induces gain or loss of electrons not only at the open end, but also at the cap end. These findings provide a strategy for controlling spin distribution for nanoscale functional molecular devices through a simple charge adjustment.