A fluctuating charge interaction potential function for alanine-water was constructed in the spirit of newly developed ABEEMax/MM（atom-bond electronegativity equalization method at the azc level fused into molecular mechanics）. The properties of gaseous neutral alanine-（H20）n（n=l--7） clusters were systematically investigated by quantum mechanics（QM） and the constructed ABEEMax/MM potential, such as conformations, hydrogen bonds （H-bonds）, interaction energies, charge distributions, and so on. The results of ABEEM^rrc/MM model are in fair agreement with those of QM and available experimental data. For isolated alanine, compared with those of experi- mental structure, the average absolute deviations（AAD） of bond length and bond angle are 0.002 nm and 1.4~, re- spectively. For alanine-water clusters, the AAD of interaction energies and H-bond lengths are only 3.77 kJ/mol and 0.012 nm, respectively, compared to the results of MP2/aug-cc-pVDZ//MP2/6-31 I＋G＊＊ method. The ABEEMa charges fluctuate with the changing conformation of the system, and can accurately and reasonably reflect the inter- polarization between water and alanine. The presented alanine-water potential function may provide a basis for fur- ther simulations on related aqueous solutions ofbiomolecules.
Ab initio MP2 and DFT studies on the tautomers of cytosine and the related hydrated tautomers have been carried out. The ground-state structures of four tautomers of cytosine and related transition states were fully optimized. The vibrational frequency analysis was performed on all the optimized structures. Detailed intrinsic reaction coordinate （IRC） calculations were carded out to guarantee the optimized transition-state structures being connected to the related tautomers. We obtained the relative stability order for the tautomers of cytosine and the related hydrated tautomers. In the isolated and hydrated condition, the bond types of C（2）--O（7） and C（4）--N（8） greatly affect the stability of the cytosine tautomers. Moreover, we have explored the influence of the water molecules on the intramolecular proton transfer between the keto and enol forms of the cytosine tautomers. The first water molecule obviously decreases the isomerization activation energy for the monohydrated cytosine tautomers. It is shown that the isomerization energy barrier changes only a little when the second and third water molecules are added in the reaction loop. The solvent effects have an obvious influence on the proton-transfer barrier of the isolated cytosine. However, the solvent effects seem to be insignificant for the isomerization energy barriers of the monohydrated, dihydrated and trihydrated cytosine. The water molecule in these complexes can be looked on as the explicit water. Therefore, the explicit water model may be more credible to explore the intramolecular proton transfer, in comparison with the PCM which is the implicit water model.
Accepted theories predict that substitution reactions are controlled by the electronic nature of the attacked site for electrophilic aromatic substitution. Here it is shown that in addition the bond strength of the broken bond may also influence the regioselectivity of the substitution reaction, and that the Dpb is a good indicator of the strength of a chemical bond. The Dpb denotes the depth of the potential acting on one electron in a molecule at the bond center （bc）. In this letter, the values of Dpb along the C-H and N-H bonds have been investigated, and it is demonstrated that for aromatic compounds, the regioselectivity of the electrophilic substitution can well be rationalized in terms of Dpb values.
Carbon nanotubes（CNTs） have received wide application and investigation because of their unique electronic, chemical and mechanical properties. But the self-aggregation of CNTs limits their practical application and study. In order to disperse CNTs effectively, polymers, such as polyglycerol and its derivatives, are adopted as dispersants in view of their strong interaction with CNTs. In order to understand the interaction between CNTs and glycerol in water in detail, a series of simulations has been conducted to investigate the interaction between them and analyze the influences of CNTs diameter and temperature. All the analyses indicate that the glycerol molecules are prone to aggregate around CNTs with the addition of CNTs. This is mainly due to hydrophobic interaction. It is confirmed that this aggregation is influenced by CNTs diameter and the temperature to some degree. This work will establish the basis for the exploration of polyglycerol and its derivatives interacting with CNTs and provide an invaluable guide to seek for emergent dispersants for CNTs.
