Parking and restarting a molecular shuttle in situ

Herein we report an easy-to-synthesize [2]rotaxane, which incorporates two ionic monopyridinium stations and one 2,2'-bipyridine station as the shaft of the dumbbell-shaped component and a bis-p-xylyl[26]crown-6 (BPX26C6) unit as the macrocyclic component. In this molecular shuttle, the BPX26C6 unit can be docked selectively on either the central 2,2'-bipyridine station or one of the two terminal pyridinium stations, and subsequently, returned to its shuttling molecular motion through the in situ addition of simple reagents (acid/base or metal ion/metal-ion-complexing ligand pairs).     

Probing molecular environments with a fictitious isotopic dipole

A HD-like (HD: mono-deuterated hydrogen molecule) isotopic dipole moment is proposed as a sensible probe for molecular environments, in particular for electrostatic fields and polarizable (reactive) sites of molecules. Fictitious nuclear masses are chosen in order to yield a rigid dipole with a small appropriate magnitude. Upon subtracting the Born-Oppenheimer energy, the interaction is reduced to field-dipole-like and dipole-polarizability-like terms, the last one being particularly informative since connected to potentially reactive sites. Possible asymmetries of this term appear as signatures of charged sites in the molecule. The field strength and orientation are easily obtained by identifying the minimum field-dipole energy configuration and flipping the dipole from it. Tests with hydrogen, water, benzene, and chlorobenzene molecules confirm the good performance of the method. In an application to test the present models for hydrogen activation by a frustrated Lewis pair, the full potential of the method is assessed.     

Interactions between chlorinated dioxins and a positively charged molecular probe: New molecular interaction potential

Interaction with the ligand binding domain of receptors for natural chemicals present one potential mechanism for the biological effects of environmental chemicals. Evidence suggests that the electrostatic interaction between the ligand and the receptor is an important component for binding to some of the relevant receptors. The presence of charged residues near the binding site suggests that the charge distribution of the free ligand may be different from the charge distribution of the ligand as it approaches the binding domain of the protein. In this study a new type of potential is computed for a series of dibenzo-p-dioxin (dioxin) ligands. This quantum mechanically computed potential results from interaction between the ligand and a trimethyl ammonium probe at a set of grid points. This interaction potential is compared with the molecular electrostatic potential computed from the wave function of the isolated ligands. Three types of local minima are found: (1) above the oxygen; (2) above the conjugated ring; and (3) above the chlorine(s). The molecular electrostatic potential emphasizes the minima associated with the chlorine atoms and, in that potential, the minima associated with the oxygen atoms disappear with chlorination. In the new potential, the minima over the oxygen atoms are maintained even in tetrachlorodioxin. As chlorination is increased the differences between the two potentials increases. The new potential shows the influence of the π-cation interaction, which is largest when there is little substitution on the ring. The presence of the probe induces a dipole component of 1 debye perpendicular to the plane of the ligand. Local minima in the interaction potential are then used as starting structures for the determination of the most stable ligand–probe complexes. The most stable structures are obtained from the minima associated with the oxygen atoms. These structures are stabilized by a hydrogen bond formation between the probe and the oxygen and the molecule is bent by 30° about the O(SINGLE BOND)O axis. For this series of molecules, the new potential retains some of the features that determine the hydrogen bond whereas the molecular electrostatic potential does not. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 673–684, 1998     

IMiCMO: a new integrated ab initio multicenter molecular orbitals method for molecular dynamics calculations in solvent cluster systems

A new computational scheme integrating ab initio multicenter molecular orbitals for determining forces of individual atoms in large cluster systems is presented. This method can be used to treat systems of many molecules, such as solvents by quantum mechanics. The geometry parameters obtained for three models of water clusters by the present method are compared with those obtained by the full ab initio MO method. The results agree very well. The scheme proposed in this article also intended for use in modeling cluster systems using parallel algorithms. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1107–1112, 2001     

Minimum sequence requirements for selective RNA-ligand binding: a molecular mechanics algorithm using molecular dynamics and free-energy techniques

In vitro evolution techniques allow RNA molecules with unique functions to be developed. However, these techniques do not necessarily identify the simplest RNA structures for performing their functions. Determining the simplest RNA that binds to a particular ligand is currently limited to experimental protocols. Here, we introduce a molecular-mechanics based algorithm employing molecular dynamics simulations and free-energy methods to predict the minimum sequence requirements for selective ligand binding to RNA. The algorithm involves iteratively deleting nucleotides from an experimentally determined structure of an RNA-ligand complex, performing energy minimizations and molecular dynamics on each truncated structure, and assessing which truncations do not prohibit RNA binding to the ligand. The algorithm allows prediction of the effects of sequence modifications on RNA structural stability and ligand-binding energy. We have implemented the algorithm in the AMBER suite of programs, but it could be implemented in any molecular mechanics force field parameterized for nucleic acids. Test cases are presented to show the utility and accuracy of the methodology.     

New approach for representation of molecular surface

A new algorithm is proposed for approximation to the molecular surface. It starts with a triangular mesh built on an ellipsoid embracing the whole molecular surface. The triangular mesh is obtained from an icosahedron subdivision sphere with highly uniform vertex distribution, and the embracing surface is deflated stepwise to the best adherence of its triangles onto the surface of the molecule. The deflating direction of each vertex of a triangle is defined by the vector normal at this point to the previous deflated embracing surface. Our results show that the speed of the triangulation embracing ellipsoid method and the quality of the surface obtained by the method are faster and better than the method that starts with a quadrilateral mesh built from meridian and parallel representations on an embracing sphere to get the molecular surface. Furthermore, the surface obtained by the method can be used directly to approximate the molecular surface by spherical harmonic expansions. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1805–1815, 1998     

A macrocycle/molecular-clip complex that functions as a quadruply controllable molecular switch

Herein, we report the synthesis of a molecular clip with TTF side-walls and its binding behavior towards electron-deficient guests, namely the formation of macrocycle/molecular-clip supramolecular complexes in solution. Four different sets of external stimuli--the K(+)/[2.2.2]cryptand, NH(4) (+)/Et(3)N and (p-BrPh)(3)NSbCl(6)/Zn pairs, and heating/cooling cycles-control the movement of this molecular switch between its threaded and unthreaded states and provide color changes that are observable by the naked eye. This macrocycle/molecular-clip complex system can be considered not only as a quadruple-use molecular switch, but can also be operated by three of these stimuli as a three-input molecular NOR-functioning logic gate that may be monitored by UV-visible spectroscopy.     

Halide anion capture and recognition by a tetrahedral tetraammonium receptor in water: a molecular dynamics investigation

We report molecular dynamics potential of mean force (PMF) simulations on the capture of halide anions X(-) (F(-), Cl(-), Br(-)) by a tetrahedral receptor L(4+) built from four quaternary ammonium sites connected by six (CH(2))(n) chains, leading to the formation of inclusion complexes X(-) subset L(4+). Simulations performed with a reaction field correction of the electrostatics and with PME-Ewald summation gave very similar energy profiles. In aqueous solution, an energy barrier of 12-17 kcal mol(-1) was found for the three anions, mainly due to their dehydration when they enter through the largest triangular face of L(4+). In the inclusion complexes, the anion is anchored near the center of the cavity due to the electrostatic field of the four positively charged ammonium sites, shielded from the surrounding water molecules. It was predicted that L(4+) is selective for Cl(-) over Br(-) which both form stable inclusion complexes, while the F(-) complex should dissociate. The comparison of PMFs in aqueous solution and in the gas phase and the energy component analysis demonstrates the importance of solvent on the nature of these complexes and on the complexation energy profiles. The Cl(-)/Br(-) selectivity obtained from the dissociation pathways in water was in good agreement with the results of free energy perturbation simulations based on the "alchemical route" of a thermodynamic cycle, and consistent with experimental observations.     

Polyatomic molecular liquids under extreme compression: facts,models, and a few predictions

Early work by Siringo, Pucci and March (Phys. Rev. B, 37, 2491 (1988)) studied solid I₂ under high pressure at T = 0. Their conclusion was that insulating crystalline I₂ at low pressures eventually transformed into a molecular metal. This has subsequently been confirmed experimentally. Later studies by Weir et al. (Phys. Rev. Lett., 76, 1860 (1996)) on solid H₂ under pressure point in the same direction, though in the solid phase the metallic state has still not been achieved at low temperatures. However, in the liquid phase, an insulating metallic transition has been proposed, as in solid iodine, again on the basis of experimental high-pressure studies. Here, attention is shifted to some polyatomic molecules, such as the 10-electron series H₂O, NH₃ and CH₄. Particular attention is focused on the measured Hugoniots of the polyatomic molecular liquids.     

Cylindrical molecular brushes with a loose grafting density

A cylindrical molecular brush with a low graft density was synthesized by two steps. Firstly, free radical alternating copolymerization of styrene (St) and N‐[2‐(2‐bromoisobutyryloxy)ethyl] maleimide (BiBEMI) gave a macroinitiator where pendant initiating sites for atom transfer radical polymerization (ATRP) being positioned along the backbone with an interval of four C? C bonds. The backbone‐to‐be with an alternating sequence was verified by elemental analysis (EA). Secondly, grafting poly(tert‐butyl acrylate) chains from the macroinitiator by ATRP produced the novel molecular brush. Size exclusion chromatography, static light scattering (SLS), and ¹H NMR and atomic force microscopy (AFM) were used to characterize the macroinitiator and the molecular brush. The results show that the backbone contains an average 730 repeat units (1 repeat unit = a pair of St and BiBEMI) and the absolute molecular weight of the brush, M_w,SLS, was 4.88 × 10⁶ Da. The brush reveals a number average length L_n to be 96 nm under AFM observation on carbon coated mica, corresponding to the length per main chain monomer unit (L_unit) of 0.066 nm, indicating a less extended conformation due to the low grafting density. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 5527–5533, 2009     

Intramolecular spin alignment in photomagnetic molecular devices: a theoretical study

Ground- and excited-state magnetic properties of recently characterized pi-conjugated photomagnetic organic molecules are analyzed by the means of density functional theory (DFT). The systems under investigation are made up of an anthracene (An) unit primarily acting as a photosensitizer (P), one or two iminonitroxyl (IN) or oxoverdazyl (OV) stable organic radical(s) as the dangling spin carrier(s) (SC), and intervening phenylene connector(s) (B). The magnetic behavior of these multicomponent systems, represented here by the Heisenberg-Dirac magnetic exchange coupling (J), as well as the EPR observables (g tensors and isotropic A values), are accurately modeled and rationalized by using our DFT approach. As the capability to quantitatively assess intramolecular exchange coupling J in the excited state makes it possible to undertake rational optimization of photomagnetic systems, DFT was subsequently used to model new compounds exhibiting different connection schemes for their functional components (P, B, SC). We show in the present work that it is worthwhile considering the triplet state of anthracene, that is, P when promoted in its lowest photoexcited state, as a full magnetic site in the same capacity as the remote SCs. This framework allows us to accurately account for the interplay between transient ((3)An) and persistent (IN, OV) spin carriers, which magnetically couple according to a sole polarization mechanism essentially supported by phenyl connector(s). From our theoretical investigations of photoinduced spin alignment, some general rules are proposed and validated. Relying on the analysis of spin-density maps, they allow us to predict the magnetic behavior of purely organic magnets in both the ground and the excited states. Finally, the notion of photomagnetic molecular devices (PMMDs) is derived and potential application towards molecular spintronics disclosed.