Dynamics of Bacteriorhodopsin in the Dark-Adapted State from Solution Nuclear Magnetic Resonance Spectroscopy

To achieve efficient proton pumping in the light-driven proton pump bacteriorhodopsin (bR), the protein must be tightly coupled to the retinal to rapidly convert retinal isomerization into protein structural rearrangements. Methyl group dynamics of bR embedded in lipid nanodiscs were determined in the dark-adapted state, and were found to be mostly well ordered at the cytosolic side. Methyl groups in the M145A mutant of bR, which displays only 10 % residual proton pumping activity, are less well ordered, suggesting a link between side-chain dynamics on the cytosolic side of the bR cavity and proton pumping activity. In addition, slow conformational exchange, attributed to low frequency motions of aromatic rings, was indirectly observed for residues on the extracellular side of the bR cavity. This may be related to reorganization of the water network. These observations provide a detailed picture of previously undescribed equilibrium dynamics on different time scales for ground-state bR.     

Hydrodynamic Limit of the Symmetric Exclusion Process on a Compact Riemannian Manifold

Journal of Statistical Physics - We consider the symmetric exclusion process on suitable random grids that approximate a compact Riemannian manifold. We prove that a class of random walks on these...     

Unusual Bonding and Properties in Main Group Element Chemistry: Rational Synthesis,Characterization, and Experimental Electron Density Determination of Mixed‐Valent Tetraphosphetes

Five dispirocyclic λ³,λ⁵‐tetraphosphetes [{R₂Si(NR¹)(NR²)P₂}₂] (R¹ = R² and R¹ ≠ R²) are easily prepared in almost quantitative yields via photolysis of the respective bis(trimethylsilyl)phosphanyldiazaphosphasiletidines with intense visible light. These deep‐yellow low‐coordinate phosphorus compounds can be considered as the first higher congeners of the well‐known cyclodiphosphazenes. The tetraphosphetes are remarkably stable in air and show unexpected molecular properties related to the unique bonding situation of the central four‐π‐electron four‐membered phosphorus ring. The extent of rhombic distortion of the central P₄ ring is remarkable due to an unusually acute angle at the σ²‐phosphorus atoms. All of the P?P bonds are approximately equal in length. The distances are in the middle of the range given by phosphorus single and double bonds. The anisotropic absorption of visible light that can easily be observed in the case of the yellow/colorless dichroic crystals of [{Me₂Si(NtBu)(NtBu)P₂}₂] and the exceptional ³¹P NMR chemical shift of the σ²‐phosphorus atoms are the most remarkable features of the λ³,λ⁵‐tetraphosphetes. In the case of [{Me₂Si(NtBu)(NtBu)P₂}₂], the Hansen–Coppens multipole model is applied to extract the electron density from high‐resolution X‐ray diffraction data obtained at 100 K. Static deformation density and topological analysis reveal a unique bonding situation in the central unsaturated P₄ fragment characterized by polar σ‐bonding, pronounced out‐of‐ring non‐bonding lone pair density on the σ²‐phosphorus atoms, and an additional non‐classical three‐center back‐bonding contribution.     

Square‐Planar Ruthenium(II) Complexes: Control of Spin State by Pincer Ligand Functionalization

Functionalization of the PNP pincer ligand backbone allows for a comparison of the dialkyl amido, vinyl alkyl amido, and divinyl amido ruthenium(II) pincer complex series [RuCl{N(CH₂CH₂PtBu₂)₂}], [RuCl{N(CHCHPtBu₂)(CH₂CH₂PtBu₂)}], and [RuCl{N(CHCHPtBu₂)₂}], in which the ruthenium(II) ions are in the extremely rare square‐planar coordination geometry. Whereas the dialkylamido complex adopts an electronic singlet (S=0) ground state and energetically low‐lying triplet (S=1) state, the vinyl alkyl amido and the divinyl amido complexes exhibit unusual triplet (S=1) ground states as confirmed by experimental and computational examination. However, essentially non‐magnetic ground states arise for the two intermediate‐spin complexes owing to unusually large zero‐field splitting (D>+200 cm^?1). The change in ground state electronic configuration is attributed to tailored pincer ligand‐to‐metal π‐donation within the PNP ligand series.     

Base-Pairing Properties of Double-Headed Nucleotides

Nucleotides that contain two nucleobases (double-headed nucleotides) have the potential to condense the information of two separate nucleotides into one. This presupposes that both bases must successfully pair with a cognate strand. Here, double-headed nucleotides that feature cytosine, guanine, thymine, adenine, hypoxanthine, and diaminopurine linked to the C2′-position of an arabinose scaffold were developed and examined in full detail. These monomeric units were efficiently prepared by convergent synthesis and incorporated into DNA oligonucleotides by means of the automated phosphoramidite method. Their pairing efficiency was assessed by UV-based melting-temperature analysis in several contexts and extensive molecular dynamics studies. Altogether, the results show that these double-headed nucleotides have a well-defined structure and invariably behave as functional dinucleotide mimics in DNA duplexes.     

Benzyl Borane NHC Adducts: Beyond B−C Bond Scission

Benzyl-substituted boronates and borates are widely employed as mild sources in radical or anionic transfer reactions of benzyl entities. In this process the B−C bond to the benzyl moiety is essentially ruptured. In contrast, reactions with retention of the B−C bond are poorly investigated although several other reactive sites in benzyl–boron systems are clearly inherent. In this respect, the novel reactivity of the representative borane adduct IiPr−BH₂Bn [IiPr=:C{N(iPr)CH}₂, Bn=CH₂C₆H₅] is demonstrated. Dihalogenation of the BH₂ entity is observed with BCl₃ and BBr₃, whereas BI₃ either affords IiPr−BHI₂ or proceeds with borylation of the aromatic phenyl ring to give a hydride-bridged bisborylated species. The photochemical mono- and dihalogenation of the benzylic CH₂ group was demonstrated with elemental bromine Br₂. The brominated product IiPr−BBr₂−CHBr−C₆H₅ was borylated at the benzylic carbon atom in an umpolung event with BI₃ to afford the zwitterion IiPr−BI−CH(BI₃)−C₆H₅.     

Functionalized Silver-Ion-Mediated α-dC/β-dC Hybrid Base Pairs with Exceptional Stability: α-d-5-Iodo-2′-Deoxycytidine and Its Octadiynyl Derivative in Metal DNA

Silver-mediated α-dC–Ag⁺–β-dC hybrid base pairs decorated with 5-iodo- or 5-octadiynyl residues are well accommodated in duplex DNA. A strong T_m increase and favorable thermodynamic data for duplex DNA were observed after addition of silver ions. The phenomenon is particularly obvious when both nucleobases of the base pairs are functionalized. Neither the position of the base pair, nor the type of 5-substituent had a negative influence. On the contrary, functionalization of conventional silver-mediated β-dC–Ag⁺–β-dC homo base pairs showed a negative impact induced by the bulky substituents. To this end, cytosine modified 12-mer oligodeoxynucleotides were prepared by solid-phase synthesis employing new α-anomeric 2′-deoxycytidine phosphoramidites. A multigram scale synthesis was developed for 5-iodo-α-d -2′-deoxycytidine ( 1 ) employing the direct glycosylation of cytosine with Hoffer's α-d -halogenose followed by separation of anomeric DMT nucleosides. Regarding base-pair stability and functionalization silver-mediated α/β-dC hybrid base pairs were found to be superior to β/β-dC homo pairs. According to their extraordinary properties, they might find applications in DNA diagnostics, material science, or nanotechnology.