Extremely strong and readily accessible AAA-DDD triple hydrogen bond complexes.
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Chloroform↗
Biomedical subjects
Francesco Zerbetto
Publications and source records attributed to Francesco Zerbetto.
Molecular dynamics of nanobubbles' collapse in ionic solutions.
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Journal Article↗
Synthetic molecular motors and mechanical machines.
The widespread use of controlled molecular-level motion in key natural processes suggests that great rewards could come from bridging the gap between the present generation of synthetic molecular systems, which by and large rely upon electronic and chemical effects to carry out their functions, and the machines of the macroscopic world, which utilize the synchronized movements of smaller parts to perform specific tasks. This is a scientific area of great contemporary interest and extraordinary recent growth, yet the notion of molecular-level machines dates back to a time when the ideas surrounding the statistical nature of matter and the laws of thermodynamics were first being formulated. Here we outline the exciting successes in taming molecular-level movement thus far, the underlying principles that all experimental designs must follow, and the early progress made towards utilizing synthetic molecular structures to perform tasks using mechanical motion. We also highlight some of the issues and challenges that still need to be overcome.
Journal Article↗
Self-organization of nano-lines and dots triggered by a local mechanical stimulus.
When a local mechanical perturbation is applied to the surface of a thin film of a mechanically interlocked molecule (a rotaxane), the molecules self-organize into periodic arrays of discrete dots or lines. The dimensionality of the nanostructures depends on whether the mechanical stimulus acts along a 1D line or over a 2D area. The size (50-500 nm) and periodicity (100-600 nm) of the patterns are controlled solely by the film thickness. This self-organization at the mesoscopic scale occurs via a nucleation-ripening mechanism eased by the relatively low energy barriers of the intramolecular rearrangement introduced by the mechanical bond. The phenomenon can be exploited as a bottom-up nanofabrication method.
Journal Article↗
Adsorption of fumaramide [2]rotaxane and its components on a solid substrate: a coverage-dependent study.
The coverage-dependent adsorption on Au(111) of a fumaramide [2]rotaxane and its components, a benzylic amide macrocycle and a fumaramide thread, is studied using high-resolution electron energy loss spectroscopy (HREELS). Up to monolayer coverage, the relative intensity of out-of-plane to in-plane phenyl ring vibrational modes indicates that the macrocycle adopts an orientation with the phenyl rings largely parallel to the surface. The formation of a chemisorption bond is evidenced by the presence of a Au-O stretching vibration. In contrast, the thread shows no evidence of chemisorption or a preferential orientation. The introduction of the thread into the macrocycle partly disrupts the film order so that the resulting chemisorbed rotaxane shows intermediate behavior with a preferential orientation up to 0.5 ML coverage. A decrease in film order and the absence of a preferred molecular orientation is observed for all three molecules at multilayer coverages. The spectral differences are addressed by molecular dynamics simulations in terms of the mobility of the phenyls of the three molecules on Au(111).
Journal Article↗
Interactions in single wall carbon nanotubes/pyrene/porphyrin nanohybrids.
This work provides an in-depth look at a range of physicochemical aspects of (i) single wall carbon nanotubes (SWNT), (ii) pyrene derivatives (pyrene(+)), (iii) porphyrin derivatives (ZnP(8)()(-)() and H(2)()P(8)()(-)()), (iv) poly(sodium 4-styrenesulfonate), and (v) their combinations. Implicit in their supramolecular combinations is the hierarchical integration of SWNT (as electron acceptors), together with ZnP(8)()(-)() or H(2)()P(8)()(-)() (as electron donors), in an aqueous environment mediated through pyrene(+). This supramolecular approach yields novel electron donor-acceptor nanohybrids (SWNT/pyrene(+)/ZnP(8)()(-)() or SWNT/pyrene(+)/H(2)()P(8)()(-)()). In particular, we report on electrochemical and photophysical investigations that as a whole suggest sizeable and appreciable interactions between the individual components. The key step to form SWNT/pyrene(+)()/ZnP(8)()(-)() or SWNT/pyrene(+)()/H(2)()P(8)()(-)() hybrids is pi-pi interactions between SWNT and pyrene(+), for which we have developed for the first time a sensitive marker. The marker is the monomeric pyrene fluorescence, which although quenched is (i) only present in SWNT/pyrene(+) and (ii) completely lacking in just pyrene(+). Electrostatic interactions help to immobilize ZnP(8)()(-)() or H(2)()P(8)()(-)() onto SWNT/pyrene(+) to yield the final electron donor-acceptor nanohybrids. A series of photochemical experiments confirm that long-lived radical ion pairs are formed as a product of a rapid excited-state deactivation of ZnP(8)()(-)() or H(2)()P(8)()(-)(). This formation is fully rationalized on the basis of the properties of the individual moieties. Additional modeling shows that the data are likely to be relevant to the SWNTs present in the sample, which possess wider diameters.
Microscopy, Electron, Transmission↗
Molecular dynamics study of onset of water gelation around the collagen triple helix.
The onset of water gelation around a collagen-like triple helix peptide was studied at ambient temperature and pressure by performing Molecular Dynamics simulations. The radial distribution functions of the oxygen and hydrogen atoms of water are distorted below 4 A from the peptide. The distortion is accompanied by the breakdown of the tetrahedral coordination of the hydrogen-bonded network of water molecules. The water shell around the peptide consists of alternating regions of higher and lower density. In agreement with experiments we find that the first hydration shell is kinetically labile, with a residence time in the order of picoseconds for a water molecule. From the computed diffusion coefficient, a key measure of the collective dynamics, we estimate the average diffusion speed decreases by a factor of 1.5 close to the peptide compared to the liquid. Our results give new insight in gel formation and structure on a molecular level.
Collagen↗
Application of the Poisson-Nernst-Planck theory with space-dependent diffusion coefficients to KcsA.
The Poisson-Nernst-Planck electrodiffusion theory serves to compute charge fluxes and is here applied to the ion current through a protein channel. KcsA was selected as an example because of the abundance of experimental and theoretical data. The potassium channels MthK and KvAP were used as templates to define two open channel models for KcsA. Channel boundary surfaces and protein charge distributions were defined according to atomic radii and partial atomic charges. To establish the sensitivity of the results to these parameters, two different sets were used. Assigning the potassium diffusion coefficients equal to the value for free-diffusion in water (1.96 x 10(-9) m(2)/s), the computed currents overestimated the experimental data. Ion distributions inside the channel suggest that the overestimate is not due to an excess of charge shielding. A good agreement with the experimental data was achieved by reducing the potassium diffusion coefficient inside the channel to 1.96 x 10(-10) m(2)/s, a value of substantial motility but nonetheless in accord with the intuitive notion that the channel has a high affinity for the ions and therefore slows them down. These results are independent of the open channel model and the parameterization adopted for atomic radii and partial atomic charges. The method offers a reliable estimate of the channel current with low computational effort.
Bacterial Proteins↗
Clay-fulleropyrrolidine nanocomposites.
In this work, we describe the insertion of a water-soluble bisadduct fulleropyrrolidine derivative into the interlayer space of three layered smectite clays. The composites were characterized by a combination of powder X-ray diffraction, transmission electron microscopy, X-ray photoemission and FTIR spectroscopies, and laser flash photolysis measurements. The experiments, complemented by computer simulations, give insight into the formation process, structural details, and properties of the fullerene/clay nanocomposites. The reported composite materials constitute a new hybrid system, where C(60) differs from its crystals or its solutions, and open new perspectives for the design and construction of novel C(60)-based organic/clay hybrid materials.
Aluminum Silicates↗
Surface enhanced second harmonic generation from macrocycle, catenane, and rotaxane thin films: experiments and theory.
Surface enhanced second harmonic generation (SE SHG) experiments on molecular structures, macrocycles, catenanes, and rotaxanes, deposited as monolayers and multilayers by vacuum sublimation on silver, are reported. The measurements show that the molecules form ordered thin films, where the highest degree of order is observed in the case of macrocycle monolayers and the lowest in the case of rotaxane multilayers. The second harmonic generation activity is interpreted in terms of electric field induced second harmonic (EFISH) generation where the electric field is created by the substrate silver atoms. The measured second order nonlinear optical susceptibility for a rotaxane thin film is compared with that obtained by considering only EFISH contribution to SHG intensity. The electric field on the surface of a silver layer is calculated by using the Delphi4 program for structures obtained with TINKER molecular mechanics/dynamics simulations. An excellent agreement is observed between the calculated and the measured SHG susceptibilities.
Journal Article↗
Mono- and bichromatic electron dynamics: LiH, a test case.
This paper describes an electron dynamics method where the time dependence of an external oscillating electric field is the perturbing part of the Hamiltonian. Application of the electric field induces charge movement inside the molecule and electronic transitions between the molecular orbitals. The test system is the neutral LiH molecule. The method is applied to wave functions calculated using the B3LYP (hybrid) density functional, with the STO-3G and the 6-31+G basis sets. The molecule undergoes full population inversion between the HOMO and the LUMO when the electric field is in resonance with the HOMO-LUMO energy gap. The magnitude of the electric field directly affects the rate at which electronic transitions occur and the rate at which charges move between lithium and hydrogen atoms. The method is used to model both monochromatic and bichromatic multiphoton effects in LiH. Monochromatic one-, two- and three-photon transitions occur between the HOMO, LUMO and two other virtual orbitals. There is evidence of both [1+2] direct and [1+1+1] stepwise multiphoton transitions. Bichromatically, two "laser" pulses are applied at different frequencies. Electronic transitions can be fine-tuned to occur via pre-specified pathways of virtual molecular orbitals.
Journal Article↗
Interaction model for the adsorption of organic molecules on the silver surface.
Adsorption of organics on a silver surface is simulated. An Embedded Atom Model is used for the metal, a standard force field for the organics, and a combination of the charge equilibration model and the Morse potential for their electrostatic and nonbonding interactions. The only adjustable parameters of this approach appear in the Morse potential. They are tuned to reproduce experimental and high level quantum chemical data. The adsorption energies of 13 molecules on the Ag(111) surface are obtained with an average error of less than 1 kcal mol(-1). The model should be transferable to molecules with the same chemical groups used in regressing the potential parameters when physisorption or weak chemisorption, i.e., no bond breaking, occur, and also to other Ag surfaces. When used to simulate perylene tetracarboxylic acid dianhydride (PTCDA) on Ag(111), correct geometry of mono- and multilayers are observed in molecular dynamics simulations at room temperature.
Journal Article↗
Self-organization of rotaxane thin films into spatially correlated nanostructures: morphological and structural aspects.
The self-organization of rotaxane thin films into spatially correlated nanostructures is shown to occur upon a thermal stimulus. The mechanism of formation of nanostructures and their organization has been investigated using atomic force microscopy, bright field transmission electron microscopy, selected area electron diffraction, and molecular mechanics simulations. The evolution of the nanostructures follows a complex pathway, where a rotaxane thin film first dewets from the substrate to form nanosized droplets. Droplets coalesce by ripening, generating spatially correlated motifs. In a later stage, the larger droplets change shape, nucleate, and coalesce to yield crystallites that grow into larger crystals by incorporating the surrounding droplets. The results show the following: (i) the nanostructures represent a metastable state of a crystallization process; (ii) spatial correlations emerge during ripening, but they are destroyed as stable nuclei are formed and crystallization proceeds to completion; iii) crystallization, either on graphite or amorphous carbon films, leads to a precise basal plane, viz. (010), which has minimum surface energy. The inherent degrees of freedom permitted in the rotaxane architecture favors the re-organization and nucleation of the film in the solid state. Low-energy trajectories leading to crystallites with stable surfaces and minimum energy contact plane are found to occur via concerted, small amplitude, internal motions without disruption of packing and intermolecular contacts.
Journal Article↗
Ejection dynamics of a simple liquid from individual carbon nanotube nozzles.
Molecular dynamics simulations show that the flow of a high pressurized atomic liquid inside carbon nanotube "pipets" occurs in one-atom-thick well-defined laminae. Fluxes and velocities at ejection are a function of the inlet diameter and the type of outlet. In the conditions investigated here, the force of the ejected liquid is similar in value to that of biomotors, while the output per second is of the order of picoliters.
Nanotechnology↗
Interactions in concentric carbon nanotubes: the radius vs the chirality angle contributions.
In multiwall carbon nanotubes in general, and in double wall carbon nanotubes, DWCNTs, in particular, the guest-host interactions depend primarily on the difference of the nanotubes radii, Deltar. The chirality angle mismatch of the two tubes, Deltatheta, also matters since it determines the pattern of pi-stacking interactions that ultimately is responsible for the shift of graphite layers into the so-called A-B structure. Here we calculate the minimum energy structures of 198 DWCNTs and construct two functions of Deltar and Deltatheta that fit the calculated data. Cross terms exists between Deltar and Deltatheta. The shape of the functions is rationalized in simple physical terms and can be used to construct minimum energy multiwall nanotubes.
Computer Simulation↗
Experimental and theoretical study of the adsorption of fumaramide [2]rotaxane on Au(111) and Ag(111) surfaces.
Thin films of fumaramide [2]rotaxane, a mechanically interlocked molecule composed of a macrocycle and a thread in a "bead and thread" configuration, were prepared by vapor deposition on both Ag(111) and Au(111) substrates. X-ray photoelectron spectroscopy (XPS) and high-resolution electron-energy-loss spectroscopy were used to characterize monolayer and bulklike multilayer films. XPS determination of the relative amounts of carbon, nitrogen, and oxygen indicates that the molecule adsorbs intact. On both metal surfaces, molecules in the first adsorbed layer show an additional component in the C 1s XPS line attributed to chemisorption via amide groups. Molecular-dynamics simulation indicates that the molecule orients two of its eight phenyl rings, one from the macrocycle and one from the thread, in a parallel bonding geometry with respect to the metal surfaces, leaving three amide groups very close to the substrate. In the case of fumaramide [2]rotaxane adsorption on Au(111), the presence of certain out-of-plane phenyl ring and Au-O vibrational modes points to such bonding and a preferential molecular orientation. The theoretical and experimental results imply that the three-dimensional intermolecular configuration permits chemisorption at low coverage to be driven by interactions between the three amide functions of fumaramide [2]rotaxane and the Ag(111) or Au(111) surface.
Journal Article↗
Asymmetric indolylmaleimide derivatives and their complexation with zinc(II)-cyclen.
The spectroscopic properties of two asymmetric indolylmaleimide derivatives, 4-bromo-3-(1'H-indol-3'-yl)maleimide and 4-methyl-3-(1'H-indol-3'-yl)maleimide, are investigated. The bromo derivative was crystallized and its X-ray structure was determined. Both compounds are strongly colored while their separate components (indole and maleimide) absorb in the UV region only. To understand the ground- and excited-state behavior, the photophysical properties of the two compounds were studied in detail by steady state and time-resolved absorption and emission spectroscopy. Their solvatochromic behavior was investigated by using the Kamlet-Taft approach, which indicates some charge transfer (CT) character in the excited state. Nano- and femtosecond transient absorption spectroscopy was used for the identification and investigation of the CT state. Furthermore, the effect of the complexation with zinc(II) 1,4,7,11-tetraazacyclododecane (Zn-cyclen) on the photophysical properties of these two compounds was studied. An enhancement of the fluorescence intensity upon self-assembly (up to 90 times) and high association constants were observed, which illustrate the potential use of these compounds as luminescent sensors. DFT calculations indicate that HOMO-1 to LUMO excitation is mainly responsible for the charge transfer character and that this transition changes its character drastically when Zn-cyclen complexation occurs, thus giving it sensor properties.
Computer Simulation↗
Simple models for hydrophobic hydration.
This tutorial review compares models that describe DeltaG(cavitation). Their qualitative agreement suggests the use of the simple, time-honored Pierotti equation. Its coefficients, fine-tuned with atomistic simulations, give a revised Pierotti approach, rPA. A discussion of the extension of the rPA model to non-spherical solutes is presented and the different roles of molecular volume and surface area of the solute are brought together. The tutorial review is aimed at experimentalists and theoreticians interested in the description of solvent effects.
Hydrophobic and Hydrophilic Interactions↗