Chemically Induced Mismatch of Rings and Stations in [3]Rotaxanes

The mechanical interlocking of molecular components can lead to the appearance of novel and unconventional properties and processes, with potential relevance for applications in nanoscience, sensing, catalysis, and materials science. We describe a [3]rotaxane in which the number of recognition sites available on the axle component can be changed by acid-base inputs, encompassing cases in which this number is larger, equal to, or smaller than the number of interlocked macrocycles. These species exhibit very different properties and give rise to a unique network of acid-base reactions that leads to a fine pKa tuning of chemically equivalent acidic sites. The rotaxane where only one station is available for two rings exhibits a rich coconformational dynamics, unveiled by an integrated experimental and computational approach. In this compound, the two crown ethers compete for the sole recognition site, but can also come together to share it, driven by the need to minimize free energy without evident inter-ring interactions

Constraint methods for determining pathways and free energy of activated processes

Activated processes from chemical reactions up to conformational transitions of large biomolecules are hampered by barriers which are overcome only by the input of some free energy of activation. Hence, the characteristic and rate-determining barrier regions are not sufficiently sampled by usual simulation techniques. Constraints on a reaction coordinate r have turned out to be a suitable means to explore difficult pathways without changing potential function, energy or temperature. For a dense sequence of values of r, the corresponding sequence of simulations provides a pathway for the process. As only one coordinate among thousands is fixed during each simulation, the pathway essentially reflects the system's internal dynamics. From mean forces the free energy profile can be calculated to obtain reaction rates and insight in the reaction mechanism. In the last decade, theoretical tools and computing capacity have been developed to a degree where simulations give impressive qualitative insight in the processes at quantitative agreement with experiments. Here, we give an introduction to reaction pathways and coordinates, and develop the theory of free energy as the potential of mean force. We clarify the connection between mean force and constraint force which is the central quantity evaluated, and discuss the mass metric tensor correction. Well-behaved coordinates without tensor correction are considered. We discuss the theoretical background and practical implementation on the example of the reaction coordinate of targeted molecular dynamics simulation. Finally, we compare applications of constraint methods and other techniques developed for the same purpose, and discuss the limits of the approach

Electron Localization in the Insulating State

The insulating state of matter is characterized by the excitation spectrum, but also by qualitative features of the electronic ground state. The insulating ground wavefunction in fact: (i) sustains macroscopic polarization, and (ii) is localized. We give a sharp definition of the latter concept, and we show how the two basic features stem from essentially the same formalism. Our approach to localization is exemplified by means of a two--band Hubbard model in one dimension. In the noninteracting limit the wavefunction localization is measured by the spread of the Wannier orbitals.Comment: 5 pages including 3 figures, submitted to PR

On the Fragmentation of Ni(II) β-Diketonate-Diamine Complexes as Molecular Precursors for NiO Films: A Theoretical and Experimental Investigation

NiO-based nanomaterials have attracted considerable interest for different applications, which have stimulated the implementation of various synthetic approaches aimed at modulating their chemico-physical properties. In this regard, their bottom-up preparation starting from suitable precursors plays an important role, although a molecular-level insight into their reactivity remains an open issue to be properly tackled. In the present study, we focused on the fragmentation of Ni(II) diketonate-diamine adducts, of interest as vapor-phase precursors for Ni(II) oxide systems, by combining electrospray ionization mass spectrometry (ESI-MS) with multiple collisional experiments (ESI-MSn) and theoretical calculations. The outcomes of this investigation revealed common features in the fragmentation pattern of the target compounds: (i) in the first fragmentation, the three complexes yield analogous base-peak cations by losing a negatively charged diketonate moiety; in these cations, Ni-O and Ni-N interactions are stronger and the Ni positive charge is lower than in the parent neutral complexes; (ii) the tendency of ligand electronic charge to migrate towards Ni further increases in the subsequent fragmentation, leading to the formation of a tetracoordinated Ni environment featuring an interesting cation-pi intramolecular interaction

Toward molecular wires confined in zeolite channels for an effective transport of electronic excitation energy.

Sunlight is the fundamental energy source sustaining life on Earth. Green plants are provided of very sophisticated and highly efficient tools to exploit light, they are able to harvest sunlight and to transport electronic excitation energy by means of a particular “antenna system” to reaction centres (natural photosynthesis). The antenna consists of regular arrangements of chlorophyll molecules held at fixed positions by means of proteins. Light absorbed by any of these molecules is transported - by radiationless energy transfer (FRET) - to reaction centres, providing the energy necessary for the chemical processes to be initiated. A green leaf consists of millions of such well-organized antenna devices. A long-standing challenge has been the development of an artificial system able to mimic the photosynthetic system. Artificial antenna systems can be realized once several organized chromophores are able to absorb the incident light and to channel the excitation energy to a common acceptor component1-3. Artificial antenna can be built by incorporating dyes into the one-dimensional channels of zeolite L (ZL). ZL crystals feature strictly parallel nano sized channels arranged in hexagonal symmetry. These channels can be filled with high concentration of suitable guests. The geometric constraints imposed by the host structure allow achieving supramolecular organization of photoactive guests1. It has been shown2,that the properties of the dye-ZL systems depend on the molecular packing inside the channels, controlling the intermolecular and the dyes/framework interactions In this work we presents a study on the optical properties of a two –dyes antenna system in which fluorenone molecules (donor molecule) and thionine(acceptor molecule) are organized in Zeolite L porosities. To interpret the optical properties of the hybrids a detailed structural study at atomistic level was mandatory. Due to the impossibility of studying from the structural point of view a two –dyes systems, two “one-dye” hybrids (ZL/fluorenone and ZL/thionine) were firstly synthesized and characterized to investigate the intermolecular and the dyes/framework interactions4. The results of thermogravimetric, IR, and X-ray structural refinements carried out for the one-dye system ZL/FL established that 1.5 molecules per unit cell is the maximum FL loading , in contrast with the data reported previously in literature5 and that the FL carbonyl group strong interact with a K+ of the ZL. The FL distribution at maximum loading can be consider as a self-assembly of planar dye molecules into a noncovalent nanoladder. FL molecules organized in such a single, continuous nanostructure of dye molecules did not exhibit significant electronic interactions. Indeed, both absorption (recorded in the diffuse reflectance mode) and photoemission electronic spectra of ZL/FL systems with different FL loading scaled almost linearly in intensity with the amount dye hosted in the unit cell (ranging from 0.5 to 1.5), without significant changes of the spectral profiles. Noticeably, the combination and steady state and time resolved photoluminescence data indicated that even at the maximum loading ca. 90% of FL molecules are photoluminescent, with significant increase in the average quantum yield with respect to FL molecules in solution. Such a finding clearly indicates that excited states coupling (Davydov splitting) is not contributing to the optical properties of the material. The structural study of the ZL/TH system revealed that the maximum possible loading of TH is equal to 0.3 molecules per unit cell in agreement with the TGA and literature data6. Short distances between the carbon, sulfur and nitrogen atoms and two water molecule sites , in turn at bond distance from the oxygen atoms of the main channel, suggested a water-mediated Th-ZL interactions7. Moreover, IR spectroscopy provided evidence of the interaction of the aromatic rings with the environment. This likely resulted in an increase of the rate of non-radiative decay of Th molecules in the electronic excited state, because only ca. 5% of Th molecules hosted in the ZL channel appeared photoluminescent. The occurrence of energy transfer from excited FL molecules forming the noncovalent nanoladder in the ZL channels and Th, in the ground state, deposited on the external surface of ZL particles are currently under investigation. In conclusion, we have here presented a study on the physico-chemical properties of dense molecular wires encapsulated in the one-dimensional pores arrays of Zeolite L. Concerning the optical properties of our composites, no evidence of Davydov splitting emerged from our study, indicating that one of the main competitors of the FRET mechanism is not operative notwithstanding the close packed arrangement of FL. We believe that this feature is of overwhelming relevance in view of application of such a system in artificial antenna systems

The Quantum-Mechanical Position Operator in Extended Systems

The position operator (defined within the Schroedinger representation in the standard way) becomes meaningless when periodic boundary conditions are adopted for the wavefunction, as usual in condensed matter physics. We show how to define the position expectation value by means of a simple many-body operator acting on the wavefunction of the extended system. The relationships of the present findings to the Berry-phase theory of polarization are discussed.Comment: Four pages in RevTe

Molecular wires confined in zeolite L channels for an effective transport of electronic excitation energy: a synchrotron structural study.

Sunlight is the fundamental energy source sustaining life on Earth. Green plants are provided of very sophisticated and highly efficient tools to exploit light, they are able to harvest sunlight and to transport electronic excitation energy by means of a particular \u201cantenna system\u201d to reaction centers (natural photosynthesis).The development of an artificial system able to mimic the natural phenomenon has been a long-standing challenge. Artificial antenna systems can be realized once several organized chromophores are able to absorb the incident light and to channel the excitation energy to a common acceptor component [1-3]. The optical properties of the systems depend on the molecular packing inside the channels. Artificial antenna can be built by incorporating suitable guests into the one-dimensional channels of zeolite L (ZL). In this work we present a detailed structural study of two hybrid systems in which dyes (fluorenone and thionine) are encapsulated in zeolite L channels. These two molecules were chosen since it has been demonstrated that a \u201ctwo \u2013dyes antenna system\u201d - in which fluorenone (FL) (donor molecule) and thionine (Th) (acceptor molecule) are organized in Zeolite L porosities - shows remarkable optical properties. Due to the impossibility of studying, from the structural point of view a \u201ctwo \u2013dyes systems\u201d, two \u201cone-dye\u201d hybrids (ZL/fluorenone and ZL/thionine) were firstly synthesized and characterized [4]. The results of thermogravimetric, IR, and X-ray structural refinements carried out for the one-dye ZL/FL and ZL/Th systems established that 1.5 molecules of FL and 0.3 molecules of Th per unit cell is the maximum loading, respectively. The FL carbonyl group strong interacts with a K+ of the ZL. On the other hand, short distances between the carbon, sulfur and nitrogen atoms of Th and two water molecule sites, in turn at bond distance from the oxygen atoms of the main channel, suggested a water-mediated Th-ZL interactions. The energy transfer from excited FL molecules, forming the non-covalent nano-ladder in the ZL channel, and Th, deposited on the external surface of ZL particles, is currently under investigation. In conclusion concerning the optical properties of our composites, no evidence of Davydov splitting emerged from our study, indicating that one of the main competitors of the FRET mechanism is not operative notwithstanding the close packed arrangement of FL. We believe that this feature is of overwhelming relevance in view of application of such a system in artificial antenna devices. The authors acknowledge the Italian Ministry of Education, MIUR-Project: \u201cFuturo in Ricerca 2012 - ImPACT- RBFR12CLQD\u201d

Topology of amorphous tetrahedral semiconductors on intermediate lengthscales

Using the recently-proposed ``activation-relaxation technique'' for optimizing complex structures, we develop a structural model appropriate to a-GaAs which is almost free of odd-membered rings, i.e., wrong bonds, and possesses an almost perfect coordination of four. The model is found to be superior to structures obtained from much more computer-intensive tight-binding or quantum molecular-dynamics simulations. For the elemental system a-Si, where wrong bonds do not exist, the cost in elastic energy for removing odd-membered rings is such that the traditional continuous-random network is appropriate. Our study thus provides, for the first time, direct information on the nature of intermediate-range topology in amorphous tetrahedral semiconductors.Comment: 4 pages, Latex and 2 postscript figure