Nanoscale rotational dynamics of four independent rotators confined in crowded crystalline layers.

We report a study where Car-Parrinello molecular dynamics simulations and variable-temperature (30-300 K) 1H spin-lattice relaxation time experiments nicely complement each other to characterize the dynamics within a set of four crystalline 1,4-diethynylbicyclo[2.2.2]octane (BCO) rotors assembled in the metal-organic rotor, {Li+4(-CO2-Ph-BCO-py)4(H2O)8}·2DMF. The remarkable finding of this work is that, despite the individual rotational barriers of four rotors being indiscernible and superimposed in a broad relaxation process, we were able to unravel a strongly interrelated series of rotational motions involving disrotatory and conrotatory motions in pairs as well as rotational steps of single rotators, all three processes with similar, sizeable rotational barriers of 6 kcal mol-1. It is noteworthy that DFT molecular dynamics simulations and variable-temperature (30-300 K) proton spin-lattice relaxation time experiments deliver the same high value for the rotational barriers stressing the potential of the combined use of the two techniques in understanding rotational motion at the nanoscale.

Mercury(II) Binding to Metallothionein in Mytilus edulis revealed by High Energy-Resolution XANES Spectroscopy.

Of all divalent metals, mercury (HgII ) has the highest affinity for metallothioneins. HgII is considered to be enclosed in the α and ß domains as tetrahedral α-type Hg4 Cys11-12 and ß-type Hg3 Cys9 clusters similar to CdII and ZnII . However, neither the four-fold coordination of Hg nor the existence of Hg-Hg atomic pairs have ever been demonstrated, and the HgII partitioning among the two protein domains is unknown. Using high energy-resolution XANES spectroscopy, MP2 geometry optimization, and biochemical analysis, evidence for the coexistence of two-coordinate Hg-thiolate complex and four-coordinate Hg-thiolate cluster with a metacinnabar-type (ß-HgS) structure in the α domain of separate metallothionein molecules from blue mussel under in vivo exposure is provided. The findings suggest that the CXXC claw setting of thiolate donors, which only exists in the α domain, acts as a nucleation center for the polynuclear complex and that the five CXC motifs from this domain serve as the cluster-forming motifs. Oligomerization is driven by metallophilic Hg⋅⋅⋅Hg interactions. Our results provide clues as to why Hg has higher affinity for the α than the ß domain. More generally, this work provides a foundation for understanding how metallothioneins mediate mercury detoxification in the cell under in vivo conditions.

Static Modulation Wave of Arrays of Halogen Interactions Transduced to a Hierarchy of Nanoscale Change Stimuli of Crystalline Rotors Dynamics.

Here we present a study where what can be seen as a static modulation wave encompassing four successive arrays of interacting iodine atoms in crystalline 1,4-Bis((4'-(iodoethynyl)phenyl) ethynyl)bicyclo[2,2,2]octane rotors changes the structure from one-half molecule to three-and-a-half molecules in the asymmetric unit below a phase transition at 105 K. The remarkable finding is that the total 1H spin-lattice relaxation rate, T1-1, of unprecedented complexity to date in molecular rotors, is the weighted sum of the relaxation rates of the four contributing rotors relaxation rates, each with distinguishable exchange frequencies reflecting Arrhenius parameters with different activation barriers ( Ea) and attempt frequencies (τo-1). This allows us to show in tandem with rotor-environment interaction energy calculations how the dynamics of molecular rotors are able to decode structural information from their surroundings with remarkable nanoscale precision.

Structure, Bonding, and Stability of Mercury Complexes with Thiolate and Thioether Ligands from High-Resolution XANES Spectroscopy and First-Principles Calculations.

We present results obtained from high energy-resolution L3-edge XANES spectroscopy and first-principles calculations for the structure, bonding, and stability of mercury(II) complexes with thiolate and thioether ligands in crystalline compounds, aqueous solution, and macromolecular natural organic matter (NOM). Core-to-valence XANES features that vary in intensity differentiate with unprecedented sensitivity the number and identity of Hg ligands and the geometry of the ligand environment. Post-Hartree-Fock XANES calculations, coupled with natural population analysis, performed on MP2-optimized Hg[(SR)2···(RSR)n] complexes show that the shape, position, and number of electronic transitions observed at high energy-resolution are directly correlated to the Hg and S (l,m)-projected empty densities of states and occupations of the hybridized Hg 6s and 5d valence orbitals. Linear two-coordination, the most common coordination geometry in mercury chemistry, yields a sharp 2p to 6s + 5d electronic transition. This transition varies in intensity for Hg bonded to thiol groups in macromolecular NOM. The intensity variation is explained by contributions from next-nearest, low-charge, thioether-type RSR ligands at 3.0-3.3 Å from Hg. Thus, Hg in NOM has two strong bonds to thiol S and k additional weak Hg···S contacts, or 2 + k coordination. The calculated stabilization energy is -5 kcal/mol per RSR ligand. Detection of distant ligands beyond the first coordination shell requires precise measurement of, and comparison to, spectra of reference compounds as well as accurate calculation of spectra for representative molecular models. The combined experimental and theoretical approaches described here for Hg can be applied to other closed-shell atoms, such as Ag(I) and Au(I). To facilitate further calculation of XANES spectra, experimental data, a new crystallographic structure of a key mercury thioether complex, Cartesian coordinates of the computed models, and examples of input files are provided as Supporting Information .

Asymmetric 1,4-bis(ethynyl)bicyclo[2.2.2]octane rotators via monocarbinol functionalization. Ready access to polyrotors.

Asymmetric rotators with a 1,4-bis(ethynyl)bicyclo[2.2.2]octane (BCO) core are needed for engineering crystalline arrays of functional molecular rotors. Their synthesis uses carbinol, 2-methyl-3-butyn-2-ol, as a protecting group because of its polar character and its ability to sustain orthogonal functionalization with the further advantage of being readily removed. The synthesis in good yields of unprecedented asymmetric rotors and polyrotors demonstrates the efficiency of this strategy.

Formation of Mercury Sulfide from Hg(II)-Thiolate Complexes in Natural Organic Matter.

Methylmercury is the environmental form of neurotoxic mercury that is biomagnified in the food chain. Methylation rates are reduced when the metal is sequestered in crystalline mercury sulfides or bound to thiol groups in macromolecular natural organic matter. Mercury sulfide minerals are known to nucleate in anoxic zones, by reaction of the thiol-bound mercury with biogenic sulfide, but not in oxic environments. We present experimental evidence that mercury sulfide forms from thiol-bound mercury alone in aqueous dark systems in contact with air. The maximum amount of nanoparticulate mercury sulfide relative to thiol-bound mercury obtained by reacting dissolved mercury and soil organic matter matches that detected in the organic horizon of a contaminated soil situated downstream from Oak Ridge, TN, in the United States. The nearly identical ratios of the two forms of mercury in field and experimental systems suggest a common reaction mechanism for nucleating the mineral. We identified a chemical reaction mechanism that is thermodynamically favorable in which thiol-bound mercury polymerizes to mercury-sulfur clusters. The clusters form by elimination of sulfur from the thiol complexes via breaking of mercury-sulfur bonds as in an alkylation reaction. Addition of sulfide is not required. This nucleation mechanism provides one explanation for how mercury may be immobilized, and eventually sequestered, in oxygenated surface environments.

Crystalline arrays of pairs of molecular rotors: correlated motion, rotational barriers, and space-inversion symmetry breaking due to conformational mutations.

The rod-like molecule bis((4-(4-pyridyl)ethynyl)bicyclo[2.2.2]oct-1-yl)buta-1,3-diyne, 1, contains two 1,4-bis(ethynyl)bicyclo[2.2.2]octane (BCO) chiral rotators linked by a diyne fragment and self-assembles in a one-dimensional, monoclinic C2/c centrosymmetric structure where two equilibrium positions with large occupancy imbalance (88% versus 12%) are identified on a single rotor site. Combining variable-temperature (70-300 K) proton spin-lattice relaxation, (1)H T1(-1), at two different (1)H Larmor frequencies (55 and 210 MHz) and DFT calculations of rotational barriers, we were able to assign two types of Brownian rotators with different activation energies, 1.85 and 6.1 kcal mol(-1), to the two (1)H spin-lattice relaxation processes on the single rotor site. On the basis of DFT calculations, the low-energy process has been assigned to adjacent rotors in a well-correlated synchronous motion, whereas the high-energy process is the manifestation of an abrupt change in their kinematics once two blades of adjacent rotors are seen to rub together. Although crystals of 1 should be second harmonic inactive, a large second-order optical response is recorded when the electric field oscillates in a direction parallel to the unique rotor axle director. We conclude that conformational mutations by torsional interconversion of the three blades of the BCO units break space-inversion symmetry in sequences of mutamers in dynamic equilibrium in the crystal in domains at a mesoscopic scale comparable with the wavelength of light used. A control experiment was performed with a crystalline film of a similar tetrayne molecule, 1,4-bis(3-((trimethylsilyl)ethynyl)bicyclo[1.1.1]pent-1-yl)buta-1,3-diyne, whose bicyclopentane units can rotate but are achiral and produce no second-order optical response.

Design and evaluation of a crystalline hybrid of molecular conductors and molecular rotors.

Combining recent concepts from the fields of molecular conductivity and molecular machinery we set out to design a crystalline molecular conductor that also possesses a molecular rotor. We report on the structures, electronic and physical properties, and dynamics of two solids with a common 1,4-bis(carboxyethynyl)bicyclo[2.2.2]octane (BABCO) functional rotor. One, [nBu(4)N(+)](2)[BABCO][BABCO(-)](2), is a colorless insulator where the dicarboxylic acid cocrystallizes with two of its monoanionic conjugated bases. The other is self-assembled by electrocrystallization in the form of black, shiny needles, with highly conducting molecular slabs of (EDT-TTF-CONH(2))(2)(+) (EDT-TTF = ethylenedithiotetrathiafulvalene) and anionic [BABCO(-)] rotors. Using variable-temperature (5-300 K) proton spin-lattice relaxation, (1)H T(1)(-1), we were able to assign two types of Brownian rotators in [nBu(4)N(+)](2)[BABCO][BABCO(-)](2). We showed that neutral BABCO groups have a rotational frequency of 120 GHz at 300 K with a rotational barrier of 2.03 kcal mol(-1). Rotors on the BABCO(-) sites experience stochastic 32 GHz jumps at the same temperature over a rotational barrier of 2.72 kcal mol(-1). In contrast, the BABCO(-) rotors within the highly conducting crystals of (EDT-TTF-CONH(2))(2)(+)[BABCO(-)] are essentially "braked" at room temperature. Notably, these crystals possess a conductivity of 5 S cm(-1) at 1 bar, which increases rapidly with pressure up to 50 S cm(-1) at 11.5 kbar. Two regimes with different activation energies E(a) for the resistivity (180 K above 50 and 400 K below) are observed at ambient pressure; a metallic state is stabilized at ca. 8 kbar, and an insulating ground state remains below 50 K at all pressures. We discuss two likely channels by which the motion of the rotors might become slowed down in the highly conducting solid. One is defined as a low-velocity viscous regime inherent to a noncovalent, physical coupling induced by the cooperativity between five C(sp3)-H···O hydrogen bonds engaging any rotor and five BABCO units in its environment. The rotational barrier calculated with the effect of this set of hydrogen bonds amounts to 7.3 kcal mol(-1). Another is quantum dissipation, a phenomenon addressing the difference of dynamics of the rotors in the two solids with different electrical properties, by which the large number of degrees of freedom of the low dimensional electron gas may serve as a bath for the dissipation of the energy of the rotor motion, the two systems being coupled by the Coulomb interaction between the charges of the rotors (local moments and induced dipoles) and the charges of the carriers.

Amino acid derivatives of perylenediimide and their N-H···O peptide bond dipoles-templated solid state assembly into stacks.

A methodology is proposed to provide direct access in good yields to peptide residues-appended perylenediimides PDI-(Cl(4))-[Gly-Ala(OEt)](2), 2a, PDI-(Cl(4))-[Gly-Val(OEt)](2), 2b and PDI-(Cl(4))-[Gly-Gly(OEt)](2), 2c from a generic perylenediimide (PDI) platform symmetrically functionalized with carboxylic acids at the imide sites, PDI-(Cl(4))-[Gly(OH)](2), 1. The latter is obtained in good purity by a non classical two-steps route avoiding the many, notoriously cumbersome successive chromatography steps typical of PDI chemistry, and including a single final purification allowing to crystallize the water soluble pure diacid 1, of great interest in its own right for further developments in a variety of fields. Then, the synthesis, crystallization and analysis of the crystal structures of 2a and 2b reveal a common pattern of self-assembly of the outer peptide residues based on collections of parallel N-H···O peptidic hydrogen bonds running alongside stacks where the constraints imposed upon on the inner PDI skeletons by long range interaction of these parallel electric dipoles reduce the dihedral angles around the bay regions by as much as 11% down to 32°.

Ultra-fast rotors for molecular machines and functional materials via halogen bonding: crystals of 1,4-bis(iodoethynyl)bicyclo[2.2.2]octane with distinct gigahertz rotation at two sites.

As a point of entry to investigate the potential of halogen-bonding interactions in the construction of functional materials and crystalline molecular machines, samples of 1,4-bis(iodoethynyl)bicyclo[2.2.2]octane (BIBCO) were synthesized and crystallized. Knowing that halogen-bonding interactions are common between electron-rich acetylenic carbons and electron-deficient iodines, it was expected that the BIBCO rotors would be an ideal platform to investigate the formation of a crystalline array of molecular rotors. Variable temperature single crystal X-ray crystallography established the presence of a halogen-bonded network, characterized by lamellarly ordered layers of crystallographically unique BIBCO rotors, which undergo a reversible monoclinic-to-triclinic phase transition at 110 K. In order to elucidate the rotational frequencies and the activation parameters of the BIBCO molecular rotors, variable-temperature (1)H wide-line and (13)C cross-polarization/magic-angle spinning solid-state NMR experiments were performed at temperatures between 27 and 290 K. Analysis of the (1)H spin-lattice relaxation and second moment as a function of temperature revealed two dynamic processes simultaneously present over the entire temperature range studied, with temperature-dependent rotational rates of k(rot) = 5.21 × 10(10) s(-1)·exp(-1.48 kcal·mol(-1)/RT) and k(rot) = 8.00 × 10(10) s(-1)·exp(-2.75 kcal·mol(-1)/RT). Impressively, these correspond to room temperature rotational rates of 4.3 and 0.8 GHz, respectively. Notably, the high-temperature plastic crystalline phase I of bicyclo[2.2.2]octane has a reported activation energy of 1.84 kcal·mol(-1) for rotation about the 1,4 axis, which is 24% larger than E(a) = 1.48 kcal·mol(-1) for the same rotational motion of the fastest BIBCO rotor; yet, the BIBCO rotor has three fewer degrees of translational freedom and two fewer degrees of rotational freedom! Even more so, these rates represent some of the fastest engineered molecular machines, to date. The results of this study highlight the potential of halogen bonding as a valuable construction tool for the design and the synthesis of amphidynamic artificial molecular machines and suggest the potential of modulating properties that depend on the dielectric behavior of crystalline media.