Self-assembling a molecular pegboard

This paper describes the design, construction, and application of a self-assembled, chemically addressable DNA nanogrid composed of DNA tiles of nanometer dimensions. This self-assembled structure permits precise placement of molecules at predetermined locations on a "molecular pegboard". We used the indexed DNA nanogrids to identify single molecules of DNA that hybridize at particular locations.     

Diels-Alder via molecular recognition in a crystalline molecular flask

In the pore of a porous coordination network, Diels-Alder reactants, a diene and a dienophile, are recognized by donor-acceptor and multiple H-bond interactions, respectively, and fixed at ideal positions for the reaction. Heating the crystals promoted the Diels-Alder reactions with enhanced reactivity and controlled regioselectivity as clearly monitored by in situ X-ray crystallography.     

Control of rotor motion in a light-driven molecular motor: towards a molecular gearbox

Controlled intramolecular movement and coupling of motor and rotor functions is exerted by this new molecular device. The rate of rotation of the rotor part of the molecule can be adjusted by alteration of the conformation of the motor part of the molecule. For all states of the motor part, different rates of rotation were measured for the rotor part. Conversion between the four propeller orientations was achieved by irradiation and heating.     

Anharmonicity of a molecular oscillator

The phenomenon of anharmonicity has been proved to be an effect of coupling between the change of nuclear positions in molecular vibrations ( Q ) and the electronic degrees of freedom as represented by the chemical potential (μ) at constant number of electrons (N). The coupling parameters have well‐founded meaning in the conceptual density functional theory (DFT), first approximations to their numerical values have recently become available. The effect of coupling between normal vibrational modes also appears to be the direct consequence of the electron‐nuclear coupling. To show the pure anharmonic effect, calculations for a collection of diatomic molecules have been presented. The anharmonicity, described in the present work as d³E/d Q ³ ≠ 0, has been proved to be the intrinsic property of every oscillating molecular system. A small anharmonic contribution exists even for the “strong harmonic” oscillator, when for the force constant k both a = (?k/? Q )_N = 0 and λ = (?k/?N) _Q = 0. The latter derivative of the force constant appears to be primary factor determining the anharmonic property of a molecule. An estimate of its values has been provided from the experimental data on the anharmonicity of diatomic molecules. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Orientational melting and reorientational motion in a cubane molecular crystal: a molecular simulation study

Detailed molecular simulations are carried out to investigate the effect of temperature on orientational order in cubane molecular crystal. We report a transition from an orientationally ordered to an orientationally disordered plastic crystalline phase in the temperature range 425-450 K. This is similar to the experimentally reported transition at 395 K. The nature of this transition is first order and is associated with a 4.8% increase in unit cell volume that is comparable to the experimentally reported unit cell volume change of 5.4% (Phys. Rev. Lett. 1997, 78, 4938). An orientational order parameter, eta(T), has been defined in terms of average angle of libration of a molecular 3-fold axis and the orientational melting has been characterized by using eta(T). The orientational melting is associated with an anomaly in specific heat at constant pressure (C(P)) and compressibility (kappa). The enthalpy of transition and entropy of transition associated with this orientational melting are 20.8 J mol(-1) and 0.046 J mol(-1) K(-1), respectively. The structure of crystalline as well as plastic crystalline phases is characterized by using various radial distribution functions and orientational distribution functions. The coefficient of thermal expansion of the plastic crystalline phase is more than twice that of the crystalline phase.     

二维分子晶体的研究进展

二维分子晶体具有超薄、长程有序、无晶界和缺陷密度低等优点,是构建多种高性能光电器件的理想材料.实现二维分子晶体的低成本、大面积制备是二维分子晶体走向应用的关键.目前,人们开发了多种方法,在气相和液相中实现了二维分子晶体的可控制备,并揭示了这类二维有机体系独特的光电性能.本文综述了二维分子晶体的制备方法及其在有机场效应晶...     

Observing a molecular knife at work

Sum frequency generation (SFG) vibrational spectroscopy has been employed to study the molecular interactions between a single substrate supported lipid bilayer and an amphiphilic antibiotic compound 1, with a design based on the common structural motif of natural antimicrobial peptides. The interfacial sensitivity of SFG allows real-time in situ monitoring of ordering changes in both leaflets of the bilayer and orientation of 1 simultaneously. A critical concentration of about 0.8 microg/mL of 1 is found, above which the inner leaflet of the bilayer is significantly perturbed. This concentration corresponds well to the minimum inhibition concentration of 1 that is obtained from bacterial experiments. Orientation of 1 in the bilayer is shown to be perpendicular to the bilayer surface, in agreement with simulation results. SFG can be developed into a very informative technique for studying the cell membrane and the interactions of membrane-active molecules.     

Self-assembly of a molecular figure-of-eight strip

A hexanuclear copper(ii) complex with a figure-of-eight strip topology is formed by metal-directed self-assembly of tritopic ligand L, bis-bidentate glycine hydroxamic acid and Cu(ii) ions in a 2:2:6 ratio.     

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.     

Assembly of a supramolecular capsule on a molecular printboard

A molecular capsule based on ionic interactions between two oppositely charged calix[4]arenes, 1 and 2, was assembled both in solution and on a surface. In solution, the formation of the equimolar assembly 1.2 was studied by (1)H NMR, ESI-MS, and isothermal titration calorimetry, giving an association constant (K(a)) of 7.5 x 10(5) M(-1). A beta-cyclodextrin self-assembled monolayer (beta-CD SAM) on gold was used as a molecular printboard to anchor the tetraguanidinium calix[4]arene (2). The binding of tetrasulfonate calix[4]arene 1 was monitored by surface plasmon resonance spectroscopy. Rinsing of the surface with a high ionic strength aqueous solution allows the removal of the tetrasulfonate calix[4]arene (1), while by rinsing with 2-propanol it is possible to achieve the complete desorption of the tetraguanidinium calix[4]arene (2) from the beta-CD SAM. The K(a) for the capsule formation on a surface is 3.5 x 10(6) M(-1), thus comparing well with the K(a) determined in solution.     

Time-resolved vibrational spectroscopy of a molecular shuttle

Time-resolved vibrational spectroscopy is used to investigate the inter-component motion of an ultraviolet-triggered two-station molecular shuttle. The operation cycle of this molecular shuttle involves several intermediate species, which are observable in the amide I and amide II regions of the mid-IR spectrum. Using ab initio calculations on specific parts of the rotaxane, and by comparing the transient spectra of the normal rotaxane with that of the N-deuterated version, we can assign the observed vibrational modes of each species occurring during the shuttling cycle in an unambiguous way. The complete time- and frequency-dependent data set is analyzed using singular value decomposition (SVD). Using a kinetic model to describe the time-dependent concentrations of the transient species, we derive the absorption spectra associated with each stage in the operation cycle of the molecular shuttle, including the recombination of the charged species.     

Phonon spectrum of a fluorene molecular crystal

The dynamics of the fluorene molecular crystal lattice is calculated by the atom-atom potential method. The fundamental lattice vibration frequencies are determined, their assignment is made, and shapes of the vibrations are studied over a pressure range of from 1 bar to 30 kbar. For acoustic phonon vibrations, the distribution of Debye frequencies over directions of the wave vector is estimated. The results obtained are used to discuss the photochemical reaction of detachment of a hydrogen atom in a fluorene crystal, a process occurring by the tunneling mechanism.     

High frequency excitations in a molecular glass

Neutron inelastic triple-axis spectra of CD₃OD/6%D₂O in the glassy and liquid phases are reported. Both the dispersion and damping of the sound modes show characteristic features as the temperature is lowered to the glassy regime. Furthermore, analysis of the observed scattering intensities reveals the presence in the glass of a second component centred at zero frequency which is not observed in the liquid.