Protein supramolecular systems for molecular information processing

Several protein supramolecular systems have been assembled for processing molecular information through intramolecular transfer of conformational change on the model of the biomolecular information network in biological systems. Intermolecular conformation transfer systems consist of calmodulin and phosphodiesterase. Calmodulin selectively binds calcium ions with a resulting change in its conformation that causes phosphodiesterase to change its conformation on being activated. Intermolecular transfer of conformational change has been successfully performed in response to the calcium ion by three different supramolecular systems: (1) calmodulin covalently conjugated with phosphodiesterase and immobilized on solid matrix; (2) lipid-conjugated calmodulin of monolayer on the water surface and coupled with phosphodiesterase in solution and (3) genetically engineered calmodulin self-assembled on a solid matrix and coupled with phosphodiesterase in solution. These supramolecular systems were found to be responsive to such environmental conditions as calcium ion concentration in the reversible alteration of enzyme activity.     

Tautomerism in chemical information management systems

Tautomerism has an impact on many of the processes in chemical information management systems including novelty checking during registration into chemical structure databases; storage of structures; exact and substructure searching in chemical structure databases; and depiction of structures retrieved by a search. The approaches taken by 27 different software vendors and database producers are compared. It is hoped that this comparison will act as a discussion document that could ultimately improve databases and software for researchers in the future.     

A combined quantum chemical/molecular mechanical study of hydrogen-bonded systems

A computational approach, which involves the combination of the OPLS force field and molecular orbital MNDO , AM 1, and PM 3 methods, has been developed to describe the effects of a large, molecular mechanically simulated environment on the Hamiltonian of a quantum chemical system. To test the validity of the combined quantum mechanical/molecular mechanical (QM /MM ) potential, a systematic study of the structures and energies of neutral and charged hydrogen-bonded complexes has been carried out, including comparisons with pure semiempirical calculations and available experimental and ab initio data. It is shown that, in many cases, the hybrid QM /MM potential behaves better than do related MNDO /M , AM 1, and PM 3 methods. As a case in point, the draw-back of AM 1 favoring bifurcated H-bonded structures over single ones is not presented in the combined AM 1/OPLS scheme. Possible ways of improvement of the combined QM /MM potential are discussed. © 1992 John Wiley & Sons, Inc.     

Topological/chemical distances and graph centers in molecular graphs with multiple bonds

A set of priority rules is defined for obtaining the graph center in multigraphs, i.e. in molecular graphs with multiple bonds. In order to obtain closer agreement between experimental bond distances in molecules and the relative magnitudes of entries in the distance matrix, a new type of distance is defined, called the “chemical distance”: CD = b^t-14, where b is the conventional bond multiplicity.     

Problems of hardware and software in chemical information systems

Three key problems are identified (independent of computer hardware) that must be solved before economically viable chemical information systems can be achieved. Solutions exist for all three problems. One solution, a high-speed data-management system, is discussed here in some detail. Examples are given for its use in chemistry and electrical engineering.     

Analytical chemical methods as systems producing chemical information by inference

Summary Analytical chemical methods as systems produce chemical information about the material to be analyzed. Analytical chemical systems as semiosis consist of analytical signal production and analytical chemical signal interpretation and produce chemical information by inference in an indirect way through analytical information. From the logical point of view the chemical information produced by analytical chemical systems is only credible. Generalizing the results the idea of diagnostic systems can be introduced and the analytical chemical methods as systems are a special type of diagnostic systems.

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Chemisch-analytische Systeme zur Erlangung chemischer Informationen

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Presented at the First International Symposium on History and Philosophy in Analytical Chemistry, Vienna, November 22–23, 1985     

Multiple expression of molecular information: enforced generation of different supramolecular inorganic architectures by processing of the same ligand information through specific coordination algorithms

The multisubunit ligand 2 combines two complexation substructures known to undergo, with specific metal ions, distinct self-assembly processes to form a double-helical and a grid-type structure, respectively. The binding information contained in this molecular strand may be expected to generate, in a strictly predetermined and univocal fashion, two different, well-defined output inorganic architectures depending on the set of metal ions, that is, on the coordination algorithm used. Indeed, as predicted, the self-assembly of 2 with eight CuII and four CuI yields the intertwined structure D1. It results from a crossover of the two assembly subprograms and has been fully characterized by crystal structure determination. On the other hand, when the instructions of strand 2 are read out with a set of eight CuI and four MII (M = Fe, Co, Ni, Cu) ions, the architectures C1-C4, resulting from a linear combination of the two subprograms, are obtained, as indicated by the available physico-chemical and spectral data. Redox interconversion of D1 and C4 has been achieved. These results indicate that the same molecular information may yield different output structures depending on how it is processed, that is, depending on the interactional (coordination) algorithm used to read it. They have wide implications for the design and implementation of programmed chemical systems, pointing towards multiprocessing capacity, in a one code/ several outputs scheme, of potential significance for molecular computation processes and possibly even with respect to information processing in biology.     

Liquid crystal devices for optical communication and information processing systems

This paper reviews liquid crystal optical devices including tunable filters, photonic switches and spatial light modulators, and examines their application to optical communication and information processing systems. Optical processing has three major advantages: massive parallelism, high speed and broad wavebands. Compared with typical optical materials including silica, semiconductors and inorganic electrooptic crystals used in communication systems, a liquid crystal has a number of outstanding features including its large refractive index change and large polarization rotation power at a low voltage. These features make it possible to develop new optical components.     

Joule-Thomson coefficient in systems with multiple chemical equilibria

Multiple chemical equilibria under adiabatic conditionsH, P = const. are considered. It is shown that in this case the Joule-Thomson coefficient may also be expressed in terms of response equilibria, which were previously introduced in the study of equilibria achieved underT, P = const. Nevertheless, our approach reveals some noteworthy differences between the isothermic and adiabatic equilibria.     

Thermodynamic stability of chemical species in multiple reaction systems

A general thermodynamic and stoichiometric method, recently developed by us to study subtle forms of stability/instability relations among chemical species, such as resonance and strain energies (Fishtik, I.; Datta, R. J. Phys. Chem. A 2004, 108, 5727-5739), is extended to stability relations in multiple chemical reaction systems. Namely, a new definition as well as a new algorithm of evaluation of the stabilities of chemical species, referred to as the overall stabilities, is proposed. It is further shown that the overall stabilities may be partitioned into a sum of contributions associated with a complete set of stoichiometrically unique response reactions (RERs). This finding reveals that the conventional stability analysis is stoichiometrically and thermodynamically inconsistent in that it involves only a part of RERs.     

Relative molecular mass information from aliphatic nitro compounds: A chemical ionization study

The mass spectra of a number of aliphatic nitro compounds have been studied using electron Ionization (EI) and a variety of chemical Ionization (CI) techniques in attempts to obtain relative molecular mass information. The use of positive ion ammonia chemical Ionization techniques gave very satisfactory results, providing abundant [M + NH4]⁺ ions, not only from both primary and secondary nitro compounds, but also from the much more labile tertiary nitro compounds. However, the use of methane and isobutane positive ion CI or EI conditions resulted in facile fragmentation with little relative molecular mass information being made available. Negative ion CI using methane, isobutane or ammonia as moderating gases all gave abundant [M ? 1]^? ions with primary and secondary nitro compounds but at much reduced sensitivity.     

Quantum chemical approach to electron transfer in molecular systems

A theoretical treatment of electron transfer in and between molecules is presented. The nuclei are assumed to move classically. A time-dependent electron probability density is calculated using general equations given by Nikitin. Variational methods of different kinds may be employed in these equations. In the present paper some examples are studied at the extended Hückel level for the systems H₂-H ₂ ⁺ , H₂-O^2–-H ₂ ⁺ , H₂-S^2–-H ₂ ⁺ and H₂-H₂-H ₂ ⁺ .     

Multiconfigurational quantum chemical methods for molecular systems containing actinides

Recent advances in computational actinide chemistry are reported in this tutorial review. Muticonfigurational quantum chemical methods have been employed to study the gas phase spectroscopy of small actinide molecules. Examples of actinide compounds studied in solution are also presented. Finally the multiple bond in the diuranium molecule and other diactinide compounds is described.     

Molecular recognition in molecular tweezers systems: quantum-chemical calculation of NMR chemical shifts

Quantum-chemical calculations for molecular tweezers systems are presented, where the focus is not only on the recognition process in the host-guest systems, but on the self aggregation of the tweezers host as well. Such intermolecular interactions influence the corresponding NMR spectra strongly by up to 6 ppm for proton chemical shifts, since ring-current effects are particularly important. The quantum-chemical results allow one to reliably assign the spectra and to gain information both on the structure and on the importance of intra- and intermolecular interactions. In addition, we study the accuracy of a variety of density functionals for describing the present host-guest systems, where we observe a considerable underestimation of ring-current effects on (1)H NMR chemical shifts at the density functional theory (DFT) level using smaller basis sets such as 6-31G**, so that larger bases like TZP are required. This stands in contrast to the behavior of the Hartree-Fock scheme, where small basis sets, such as 6-31G**, provide reliable (1)H NMR shieldings for molecular tweezers systems.     

Optical chemosensor for Ag+, Fe3+, and cysteine: information processing at molecular level

A thiacalix[4]arene based chemosensor 3 bearing two pyrene groups has been synthesized which demonstrates ratiometric sensing with Ag(+) and fluorescence quenching with Fe(3+) ions in mixed aqueous media. The 'in situ' prepared Ag(+) and Fe(3+) complexes showed high selectivity toward cysteine. The molecular switching between three chemical inputs (Ag(+), Fe(3+), cysteine) results in various molecular logic gates which have been integrated sequentially to generate a sequential information processing device.     

Configurational and constitutional information storage: multiple dynamics in systems based on pyridyl and acyl hydrazones

The C=N group of hydrazones can undergo E/Z isomerization both photochemically and thermally, allowing the generation of a closed process that can be tuned by either of these two physical stimuli. On the other hand, hydrazine-exchange reactions enable a constitutional change in a given hydrazone. The two classes of processes: 1) configurational (physically stimulated) and 2) constitutional (chemically stimulated) give access to short-term and long-term information storage, respectively. Such transformations are reported herein for two hydrazones (bis-pyridyl hydrazone and 2-pyridinecarboxaldehyde phenylhydrazone) that undergo a closed, chemically or physically driven process, and, in addition, can be locked or unlocked at will by metal-ion coordination or removal. These features also extend to acyl hydrazones derived from 2-pyridinecarboxaldehyde. Similarly to the terpydine-like hydrazones, such acyl hydrazones can undergo both constitutional and configurational changes, as well as metal-ion coordination. All these types of hydrazones represent dynamic systems capable of acting as multiple state molecular devices, in which the presence of coordination sites furthermore allows the metal ion-controlled locking and unlocking of the interconversion of the different states.