Dimers of and tautomerism between 2-pyrimidinethiol and 2(1H)-pyrimidinethione: a density functional theory (DFT) study

Density functional theory (BLYP, B3LYP, B3P86, B3PW91) with the 6-31+G(d,p), 6-311+G(d,p), and cc-pVTZ basis sets has been used to calculate structural parameters, relative energies, and vibrational spectra of 2-pyrimidinethiol (1) and 2(1H)-pyrimidinethione (2) and their hydrogen-bonded homodimers (C(2) 3, C(2h) [4](double dagger), C(2h) 5), monohydrates, and dihydrates and a heterodimer (6). Several transition state structures proposed for the tautomerization process have also been examined. At the B3PW91/6-311+G(d,p)//B3PW91/6-31+G(d,p) level of theory 2-pyrimidinethiol (1) is predicted to be 3.41 kcal/mol more stable (E(rel)) than 2(1H)-pyrimidinethione (2) in the gas phase and 2 is predicted to be 6.47 kcal/mol more stable than 1 in aqueous medium. An unfavorable planar intramolecular strained four center transition state (TS1) for the tautomerization of 1 and 2 in the gas-phase lies 29.07 kcal/mol higher in energy than 2-pyrimidinethiol (1). The C(2) 2-pyrimidinethiol dimer (3) is 6.84 kcal/mol lower in energy than the C(2) homodimer transition state structure ([11](double dagger)) that connects dimers 3 and 4. Transition state [11](double dagger) provides a facile pathway for tautomerization between 1 and 2 in the gas phase (monomer-dimer promoted tautomerization). The hydrogen bonded 2-pyrimidinethiol- - -H(2)O and 2-pyrimidinethiol- - -2H(2)O structures are predicted to be 1.27 and 1.55 kcal/mol, respectively, higher in energy than 2(1H)-pyrimidinethione- - -H(2)O and 2(1H)-pyrimidinethione- - -2H(2)O. Water promoted tautomerization via cyclic transition states involving one water molecule (TS- - -H(2)O, [12](double dagger)) and two water molecules (TS- - -2H(2)O, [13](double dagger)) lie 11.42 and 11.44 kcal/mol, respectively, higher in energy than 2-pyrimidinethiol- - -H(2)O and 2-pyrimidinethiol- - -2H(2)O. Thus, the hydrated transition states [12](double dagger) and [13](double dagger) are involved in the tautomerism between 1 and 2 in aqueous medium.     

Effects of hydrogen bonding on the ring stretching modes of pyridine

The effects of hydrogen bonding on the ring stretching modes (both ring breathing and triangle) of pyridine are experimentally investigated using noisy light based coherent Raman scattering spectroscopy. Three systems, pyridine/formamide, pyridine/water, and pyridine/acetic acid, provide varying degrees of strength for the diluent-pyridine hydrogen bond complex. Formamide forms a relatively weaker hydrogen bond, while acetic acid essentially fully transfers a proton to pyridine. Both dilution studies and temperature studies are performed on the three systems. Together, these provide a broad context in which a very simple model for the electronic behavior of pyridine is formulated. This model is based on a molecular orbital picture and electrostatic arguments, and it well explains the observed experimental results. Additionally, a new mechanism for the line broadening of the ring breathing mode for the pyridine-water hydrogen bonded complex is proposed.     

Parallel acquisition of two-dimensional NMR spectra of several nuclear species

We show that two or more two-dimensional NMR correlation spectra can be recorded in a single shot, using a multicoil radio-frequency probe and receiver system designed for simultaneous parallel acquisition of signals from different nuclear species such as 1H, 13C, and 15N. Dubbed PANSY (parallel acquisition NMR spectroscopy), this new technique shows promise for recording several multidimensional NMR spectra of different nuclear species in a very short time.     

Conformational study of the natural iron chelator myo-inositol 1,2,3-trisphosphate using restrained/flexible analogues and computational analysis

myo-Inositol 1,2,3-trisphosphate [Ins(1,2,3)P₃], a component in mammalian cells, possesses the correct chemical properties of an intracellular iron transit ligand. Here we have examined the conformation of the Ins(1,2,3)P₃-Fe³⁺ complex. The synthesis and antioxidant properties of 4,6-carbonate-myo-inositol 1,2,3,5-tetrakisphosphate [4,6-carbonate Ins(1,2,3,5)P₄], which is locked in the unstable penta-axial chair conformation and 1,2,3-trisphosphoglycerol, a flexible acyclic analogue of Ins(1,2,3)P₃, are reported. 4,6-Carbonate Ins(1,2,3,5)P₄ caused complete inhibition of iron-catalysed hydroxyl radical (HO) formation at 100 μM, thereby resembling Ins(1,2,3)P₃ and supporting a penta-axial chair binding conformation. In contrast, 1,2,3-trisphosphoglycerol was shown to have incomplete antioxidant properties. In support of experimental observations, we have applied high-level density functional calculations to the binding of Ins(1,2,3)P₃ to iron. This study provides evidence that Fe³⁺ binds tightly to the less stable penta-axial conformation of Ins(1,2,3)P₃ using terminal and bridging phosphate oxygens, thought to also contain a tightly bound water molecule or hydroxyl ligand in the complex.     

Approaching Dianionic Tetraoxadiborecine Macrocycles: 10-Membered Bora-Crown Ethers Incorporating Borafluorenate Units

The addition of non-benzenoid quinones, acenapthenequinone or aceanthrenequinone, to the 9-carbene-9-borafluorene monoanion ( 1 ) affords the first examples of dianionic 10-membered bora-crown ethers ( 2 – 5 ), which are characterized by multi-nuclear NMR spectroscopy (¹H, ¹³C, ¹¹B), X-ray crystallography, elemental analysis, and UV/Vis spectroscopy. These tetraoxadiborecines have distinct absorption profiles based on the positioning of the alkali metal cations. When compound 4 , which has a vacant C₄B₂O₄ cavity, is reacted with sodium tetrakis[3,5-bis(trifluoromethyl)phenyl]borate, a color change from purple to orange serves as a visual indicator of metal binding to the central ring, whereby the Na⁺ ion coordinates to four oxygen atoms. A detailed theoretical analysis of the calculated reaction energetics is provided to gain insight into the reaction mechanism for the formation of 2 – 5 . These data, and the electronic structures of proposed intermediates, indicate that the reaction proceeds via a boron enolate intermediate.