Predicted crystal structures of tetramethylsilane and tetramethylgermane and an experimental low-temperature structure of tetramethylsilane

Isotope chirality in long-armed multifunctional organosilicon ("Cephalopod") molecules

Long-armed multifunctional organosilicon molecules display self-replicating and self-perfecting behavior in asymmetric autocatalysis (Soai reaction). Two representatives of this class were studied by statistical methods aiming at determination of probabilities of natural abundance chiral isotopomers. The results, reported here, show an astonishing richness of possibilities of the formation of chiral isotopically substituted derivatives. This feature could serve as a model for the evolution of biological chirality in prebiotic and early biotic stereochemistry.

Vibrational and structural properties of tetramethyltin under pressure

The vibrational and structural properties of a hydrogen-rich group IVa hydride, Sn(CH(3))(4), have been investigated by combining Raman spectroscopy and synchrotron x-ray diffraction measurements at room temperature and at pressures up to 49.9 GPa. Both techniques allow the obtaining of complementary information on the high-pressure behaviors and yield consistent phase transitions at 0.9 GPa for the liquid to solid and 2.8, 10.4, 20.4, and 32.6 GPa for the solid to solid. The foregoing solid phases are identified to have the orthorhombic, tetragonal, monoclinic crystal structures with space groups of Pmmm for phase I, P4/mmm for phase II, P2/m for phase III, respectively. The phases IV and V coexist with phase III, resulting in complex analysis on the possible structures. These transitions suggest the variation in the inter- and intra-molecular bonding of this compound.

Formation of an unusually short hydrogen bond in photoactive yellow protein

The photoactive chromophore of photoactive yellow protein (PYP) is p-coumaric acid (pCA). In the ground state, the pCA chromophore exists as a phenolate anion, which is H-bonded by protonated Glu46 (O(Glu46)-O(pCA)=~2.6Å) and protonated Tyr42. On the other hand, the O(Glu46)-O(pCA) H-bond was unusually short (O(Glu46)-O(pCA)=2.47Å) in the intermediate pR(CW) state observed in time-resolved Laue diffraction studies. To understand how the existence of the unusually short H-bond is energetically possible, we analyzed the H-bond energetics adopting a quantum mechanical/molecular mechanical (QM/MM) approach based on the atomic coordinates of the PYP crystal structures. In QM/MM calculations, the O(Glu46)-O(pCA) bond is 2.60Å in the ground state, where Tyr42 donates an H-bond to pCA. In contrast, when the hydroxyl group of Tyr42 is flipped away from pCA, the H-bond was significantly shortened to 2.49Å in the ground state. The same H-bond pattern reproduced the unusually short H-bond in the pR(CW) structure (O(Glu46)-O(pCA)=2.49Å). Intriguingly, the potential-energy profile resembles that of a single-well H-bond, suggesting that the pK(a) values of the donor (Glu46) and acceptor (pCA) moieties are nearly equal. The present results indicate that the "equal pK(a)" requirement for formation of single-well or low-barrier H-bond (LBHB) is satisfied only when Tyr42 does not donate an H-bond to pCA, and argue against the possibility that the O(Glu46)-O(pCA) bond is an LBHB in the ground state, where Tyr42 donates an H-bond to pCA.

H atom positions and nuclear magnetic resonance chemical shifts of short H bonds in photoactive yellow protein

Recent neutron diffraction studies on photoactive yellow protein (PYP) proposed that the H bond between protonated Glu46 and the chromophore-ionized p-coumaric acid (pCA) is a low-barrier H bond (LBHB) mainly because the H atom position was assigned at the midpoint of the O(Glu46)-O(pCA) bond. However, the (1)H nuclear magnetic resonance (NMR) chemical shift (δ(H)) was 15.2 ppm, which is lower than the values of 17-19 ppm for typical LBHBs. We evaluated the dependence of δ(H) on an H atom position in the O(Glu46)-O(pCA) bond in the PYP ground state by using a quantum mechanical/molecular mechanical (QM/MM) approach. The calculated chemical shift unambiguously suggested that a δ(H) of 15.2 ppm for the O(Glu46)-O(pCA) bond in NMR studies should correspond to the QM/MM geometry (δ(H) = 14.5 ppm), where the H atom belongs to the Glu moiety, rather than the neutron diffraction geometry (δ(H) = 19.7 ppm), where the H atom is near the midpoint of the donor and acceptor atoms.

High-pressure study of tetramethylsilane by Raman spectroscopy

High-pressure behavior of tetramethylsilane, one of the Group IVa hydrides, was investigated by Raman scattering measurements at pressures up to 142 GPa and room temperature. Our results revealed the phase transitions at 0.6, 9, and 16 GPa from both the mode frequency shifts with pressure and the changes of the full width half maxima of these modes. These transitions were suggested to result from the changes in the inter- and intra-molecular bonding of this material. We also observed two other possible phase transitions at 49-69 GPa and 96 GPa. No indication of metallization in tetramethylsilane was found with stepwise compression to 142 GPa.