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A comprehensive density functional theory (DFT) discussion of the hydration effect on the structures and reservation energy behaviors of the biologically relevant complexes glycine-H(super +)M(super +) (where M is Li, Na, or K) in the gas phase is presented. It is concluded that the REBs indeed exist in these biologically relevant systems and the reservation energy values in these systems would be >20 kcal/mol.

Tautomerization processes of amino–imino adenineisomer(A → A1) in five different environments are studied by thedensity functional theory (B3LYP) method. The five environments aremetal ion (M, M = K+, Na+, Cu+, Zn+, Ca2+, Mg2+, Cu2+, Zn2+) coordinated bidentate system, either monowater (W) or monoammonia(N) attached system, both metal ion and monowater cooperative system(M-W), and both metal ion and monoammonia cooperative system (M-N).Results show that the complexes formed by noncanonical rare iminoform A1 are more stable than those formed by the canonical amino onein most of these environments. The tautomerization of A → A1becomes quite easy in either M-W or M-N system. It is noteworthy thatunder divalent M-N environment the A → A1 process meets withparticularly lower and even free energy barrier, indicating the instabilityof the amino adenine isomer and probable existence of more stableimino adenine isomer. Expanding studies for the microhydration atthe metal ion of the M-N system predict the required number (n) of water molecules to remain the amino adenine isomerA (AMNnW) stable. The number of nis 2, 3, 3, and 4 for M = Ca2+, Zn2+, Cu2+, and Mg2+, respectively. The present study providesfurther understanding for the amino–imino tautomerization behaviorof the most stable adenine under the influence of several relatedclosely factors, and is useful for rational design of these differentenvironments for the purposes of prevention and control of pyrimidinesmispairing, which is responsible for the mutagenic properties of thenucleic acid bases. [ABSTRACT FROM AUTHOR]

In this work, the three most stable uracil isomers (U1, U2, and U3) and their neutral, positive, and negative charged multihydrates are chosen as research objects to investigate the tautomeric process between the most stable uracil, U1, and its two minor stable isomers, U2 and U3. By the study, deeper insight can be obtained regarding point mutations induced by uracil deformation. Toward the target, the activation energies of the intramolecular proton transfer (tautomeric process) as well as the catalysis effects of water molecules and of charges attached are investigated using density functional theory (DFT) calculations by means of the B3LYP exchange and correlation functions. Results reveal that water molecules hold a stronger catalysis effect on the proton transfer in these negative charged uracil hydrates than in the neutral counterparts. The optimal number of water molecules needed to catalyze the proton transfer is determined as two in the neutral hydrated systems, whereas it is three in the negative charged systems. Positive charge attachment, however, hinders the intramolecualr proton transfer of uracil, and the charge and the proton of uracil will transfer to the water clusters if water molecules are attached. Then the positive charged hydrates look more like U1a/b+[(H2O)n+H+] species in structure. Analysis reveals that it is the acceptance process of the last proton to determine the impossibility of proton transfer and result in the failure of tautomeric processes from cat-U1a-nw to cat-U2-nw and from cat-U1b-nw to cat-U3-nw. Detailed structural parameters and energy changes are discussed for the above different processes.

Adsorptions of nine tripeptides GXG, ranging from negatively (D) and positively (K) charged, to hydrophilic (N and S), and to hydrophobic (G, V, F, W, and Y) residues, on the two cluster models (C(54)H(18) and C(54)) of (10,0) single-walled carbon nanotubes (SWCNTs) are systemically investigated with the MPWB1K and MP2 methods. The solvent effects are taken into account with the implicit CPCM model. The objective is to provide novel insights into the interaction mechanism between proteins and SWCNTs. Results reveal that the adsorption strength of two charged tripeptides is greatly affected by the solvent effect and the hydrogen saturability of the SWCNT models. In the gas phase, on the surface of C(54)H(18), GKG has the strongest adsorption (adsorption energy (AE): -29.3 kcal/mol at the MP2 level), whereas the adsorption of the negatively charged GDG is the strongest on C(54) (AE: -30.4 kcal/mol with MP2). However, because of strong solvation, the adsorptions of the charged residues (D and K) on both C(54)H(18) and C(54) surfaces in aqueous solution are either rather weak or even unbound. The two neutral hydrophilic residues (N and S) exhibit adsorptions on C(54)H(18) in the gas phase (AE: -3.3 and -4.2 kcal/mol), yet are unable to adsorb on SWCNTs in aqueous solution (AE: +0.3 kcal/mol at MP2+CPCM). The five hydrophobic residues present relatively strong adsorption on SWCNTs, especially for the three aromatic residues (GFG, GYG, and GWG), regardless of the CNT model and whether they are in the gas phase or solution. These results indicate that in general the aromatic groups of proteins would play a very important role on functionalizing CNTs, which basically supports the relevant experimental observations. In addition, the electron correlation is essential for adsorptions of GXG on pristine SWCNTs, and the three aromatic residues have the highest electron correlation effects. The present investigation provides strong evidence that for the functionalization of CNTs via proteins it is most likely that hydrophobic interaction and van der Waals are the dominant driving forces.

The side-chain effects of metalated and protonated dipeptides, including GGH(+)M(+), GAH(+)M(+), AGH(+)M(+), AAH(+)M(+), GWH(+)M(+), GSH(+)M(+), GTH(+)M(+), GFH(+)M(+), GYH(+)M(+), and GVH(+)M(+) (G = glycine, A = alanine, W = tryptophan, S = serine, T = threonine, F = phenylalanine, and V = valine; M = Li, Na, and K), are theoretically explored in this paper on their positive binding energies (PBEs), which are derived from interactions of M+ with the carboxyl oxygen(s). The B3LYP/6-311++G(**)// B3LYP/6-31G(*) calculations suggest that the PBEs of dipeptides with side chain(s) are much smaller than those with no side chain (GGH(+)M(+)). Generally, larger side chains and smaller M(+) radii would lead to fewer PBEs for the M(+) involved systems. On the basis of the direct dependence of PBE on the electrostatic repulsion between two kinds of cations (H(+) and M(+)) in these dipeptide models, it could be reasonably expected that the side-chain effect on the electrostatic repulsion and consequently on the PBEs could offer one good insight, on a chemical-physical basis, into the origin of regular ordering of the amino acids when they form a filter in the K(+) channel protein (MacKinnon, et al. Science 1998, 280, 106).