Electronic structure and properties of isoreticular metal-organic frameworks: the case of M-IRMOF1 (M = Zn, Cd, Be, Mg, and Ca)

We investigate the possibility of tailoring the electronic properties of isoreticular metal-organic materials by replacing the metal atom in the metal-organic cluster and by doping. The electronic structure of M-IRMOF1, where IRMOF1 stands for isoreticular metal-organic framework 1 and M = Be, Mg, Ca, Zn, and Cd, was examined using density-functional theory. The results show that these materials have similar band gaps (ca. 3.5 eV) and a conduction band that is split into two bands, the lower of which has a width that varies with metal substitution. This variation prompted us to investigate whether doping with Al or Li could be used to tailor the electronic properties of the Zn-IRMOF1 and Be-IRMOF1 materials. It is shown that replacing one metal atom with Al can effectively be used to create IRMOFs with different metallic properties. On the other hand, adding Li produces structural changes that render this approach less suitable.     

Prediction of Complexation Properties of Crown Ethers Using Computational Neural Networks

A computational neural network method was used for the prediction of stability constants of simple crown ether complexes. The essence of the method lies in the ability of a computer neural network to recognize the structure-property relationships in these host-guest systems. Testing of the computational method has demonstrated that stability constants of alkali metal cation (Na+, K+, Cs+)-crown ether complexes in methanol at 25 °C can be predicted with an average error of ±0.3 log K units based on the chemical structure of the crown ethers alone. The computer model was then used for the preliminary analysis of trends in the stabilities of the above complexes.     

Nonvolatile memory elements based on the intercalation of organic molecules inside carbon nanotubes

We propose a novel class of nonvolatile memory elements based on the modification of the transport properties of a conducting carbon nanotube by the presence of an encapsulated molecule. The guest molecule has two stable orientational positions relative to the nanotube that correspond to conducting and nonconducting states. The mechanism, governed by a local gating effect of the molecule on the electronic properties of the nanotube host, is studied using density functional theory. The mechanisms of reversible reading and writing of information are illustrated with a F4TCNQ molecule encapsulated inside a metallic carbon nanotube. Our results suggest that this new type of nonvolatile memory element is robust, fatigue-free, and can operate at room temperature.     

Efficient computation of potential energy first and second derivatives for molecular dynamics,normal coordinate analysis,and molecular mechanics calculations

By using two- and three-body internal coordinates and their derivatives as intermediates, it is possible to enormously simplify formulas for three- and four-body internal coordinates and their derivatives. Using this approach, simple formulas are presented for stretch (two-body), two types of bend (three-body), and wag and two types of torsion (four-body) internal coordinates and their first and second derivatives. The formulas are eminently suitable for economizing molecular dynamics and molecular mechanics calculations and normal coordinate analysis of complicated potential energy surfaces. Efficient methods for computing derivatives of entire potential energy terms, and in particular cross terms with switching functions, are presented.     

The origins of avoided crossings in polymer dispersion curves

A purely mathematical heuristic model is examined in order to explain the existence of an avoided crossing between two dispersion curves calculated for a certain potential energy surface designed to simulate the dynamics of a linear polyethylene chain. The model shows that a third mode coupled to a two-mode Fermi-resonant system is able to create a marked instability in a vibrational spectrum. It is noted that such an explanation would require a fourth-order coupling term, which is the reason given for the failure of normal mode analysis to properly identify this dynamical effect.     

Development of Nanosensors and Bioprobes

We describe the development and application of nanosensors having bioreceptor probes for bioanalysis. The nanoprobes were fabricated with optical fibers pulled down to tips having distal end sizes of approximately 30–60nm. The use of two different types of receptors was investigated. Fiberoptic nanoprobes were covalently bound either with bioreceptors, such as antibodies, or with other receptors, such as cyclodextrins that are selective for the size and chemical structure of the analyte molecules. Theoretical calculations were performed to model the binding of beta-cyclodextrin with pyrene and 5,6-benzoquinoline, and to illustrate the possibility of comparing experimental data with theoretical data. The antibody-based nanoprobe was used for in situ measurements of benzopyrene tetrol in single cells. The performance of the nanosensor is illustrated by intracellular measurements performed on a rat liver epithelial cell line (Clone 9) used as the model cell system. The usefulness and potential of these nanotechnology-based biosensors in biological research and applications are discussed.     

Isomeric effects on the self‐assembly of a plausible prebiotic nucleoside analogue: A theoretical study

The self‐assembly properties of N(9)‐(2,3‐dihydroxypropyl adenine) (DHPA), a plausible prebiotic nucleoside analogue of adenosine, were investigated using density functional theory. Two different isomers were considered, and it is found that while both isomers can form a variety of structures, including chains, one of them is also able to form cages and helixes. When these results were put in the context of substrate supported molecular self‐assembly, it is concluded that gas‐phase self‐assembly studies that consider isomer identity and composition not only can aid interpreting the experimental results, but also reveal structures that might be overlooked otherwise. In particular, this study suggest that a double‐helical structure made of DHPA molecules which could have implications in prebiotic chemistry and nanotechnology, is stable even at room temperature. For example electrical properties (energy gap of 4.52eV) and a giant permanent electrical dipole moment (49.22 Debye) were found in our larger double‐helical structure (3.7 nm) formed by 14 DHPA molecules. The former properties could be convenient for construction of organic dielectric‐based devices.