Structures and properties of CdSe quantum dots (clusters) up to a diameter of approximately 2 nm were investigated by combining experimental absorption, photoluminescence (PL), and X-ray diffraction (XRD) spectroscopies as well as ab initio DFT calculations. These CdSe clusters were nucleated and grown from solutions containing respective cadmium and selenium precursors following the hot-injection technique that allows one to obtain size-controlled CdSe clusters having PL efficiency up to 0.5. The DFT calculations were performed at the B3LYP/Lanl2dz level and followed by time-dependent TDDFT calculations to estimate n energy singlet transitions. On the basis of the results of these experimental and theoretical studies, an approach to determine whether the proposed cluster with a mean diameter of approximately 2 nm is more physically reasonable is discussed. It was shown that the minimum nucleus of a CdSe cluster consists of (CdSe)(3) with a six-membered ring and planar structure. No PL is observed for this structure. The formation of the next stable cluster depends on whether hexadecylamine (HDA) was used for the growth of the CdSe clusters. In the absence of HDA, the second cluster was found to be (CdSe)(6) characterized by a broad PL spectrum, while in the presence of HDA, it was found to be (CdSe)(n) (where n > or = 14) with a sharp PL spectrum.

Ab initio quantum chemical studies at the HF level with the 6-31G* basis set were performed for three different Watson−Crick hydrogen bonded adenine−uracil complexes in the gas phase and in a water solution approximated by the first solvation shell. Full geometry optimizations without any constraints on the planarity of these complexes were carried out. The solvent effect was modeled by explicit inclusion of seven water molecules which creates the first coordination sphere around the adenine-uracil base pair. Single point calculations were also performed at the correlated MP2/6−31*//HF/6-31G* level. The interaction and solvation energies were corrected for the basis set superposition error. It was shown that base pair corresponding to the standard Watson−Crick pair (denoted as AU1) is the lowest energy structure on the potential energy surface both in the gas phase and in a water solution. Only a slight deviation from planarity is observed for these complexes in both phases. Furthermore, the relative stability order of the considered WC AU hydrogen bonded complexes remains unchanged upon interaction with the water cluster although the zwitterionic form (denoted as AU3) is stabilized more compared to a rare tautomer (denoted as AU2). Some similarities and differences between the title species and the isocytosine−cytosine complexes in both phases are also discussed.

The inclusion of the GC base pair into parallel stranded (ps) DNA requires a counterrotation of the two bases by 180° with respect to the standard Watson−Crick (WC) arrangement. This brings the two amino groups into close contact and leads also to a repulsive interaction between the two carbonyl groups. The repulsion can be eliminated by a transition to a base pair with two hydrogen bonds; however, such a structure significantly violates the backbone geometry of the ps DNA. The repulsion can also be partly relieved by involving amino group pyramidalization without major changes to the intermolecular geometry. In the present study we investigated another way to stabilize the GC base pair within ps DNA. Ab initio quantum chemical studies were performed for all three possible triply bonded hydrogen bonded reverse Watson−Crick isocytosine−cytosine (RWC iCC) base pairs with one or two minor tautomers of bases. The iCC base pair is a realistic model of the GC base pair since it has the same base pairing. The solvent effects were estimated using explicit inclusion of the first solvation shell of the base pair. Full geometry optimizations were carried out without any constraints at the HF/6-31G* level followed by single-point calculations at the correlated MP2/6-31G* level. The interaction and hydration energies were corrected for the basis set superposition error. The three base pairs investigated are higher on the potential energy surface both in the gas phase and in a water cluster as compared to the standard (antiparallel) WC base pair. However, for one structure the difference is only 9 kcal/mol in the gas phase, i.e., it is more stable than the previously postulated model with the amino−amino donor−acceptor interaction. Inclusion of hydration destabilizes the pair with respect to the standard WC pair by an additional 6 kcal/mol. The remaining two rare-tautomer RWC pairs are around 20 kcal/mol less stable than the WC base pair.

Ab initio quantum chemical studies at the Hartree−Fock (HF) level with the 6-31G* basis set were performed for four different hydrogen-bonded isocytosine−cytosine (iCC) complexes in the gas phase and in a water solution. Full geometry optimizations without any constraints on the planarity of these complexes were carried out. The water solution was modeled by explicit inclusion of different numbers of water molecules, up to six, which creates the first coordination sphere around the iCC base pair. Single point calculations were also performed at the correlated MP2/6-31G*//HF/6-31G* level. The interaction and solvation energies were corrected for the basis set superposition error by using the full Boys−Bernardi counterpoise correction scheme. It was shown that the base pair corresponding to the standard Watson−Crick pair (denoted as iCC1) is the global minimum on the potential energy surface both in the gas phase and in a water solution. Inclusion of six instead of four water molecules has crucial effects both on the geometries and relative stabilities of iCC complexes. Complexes involving six water molecules become strongly nonplanar, whereas in the case of four or fewer water molecules, only a slight deviation from planarity is observed. Moreover, the relative stability order changes when one considers six water molecules, and the zwitterionic form (denoted as iCC4) becomes the second most stable species after the Watson−Crick iCC1 base pair. Since the structure of isocytosine mimics the six-membered parts of guanine, the results of this study could provide important insights into the structures and properties of analogous guanine−cytosine complexes in a water solution.

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