Molecular Resonance Energy Research Articles

Study on the Interaction between Lanthanide Cationic Porphyrin Complex and Bovine Serum Albumin

AbstractThe interaction between lanthanide cationic porphyrin and bovine serum albumin (BSA) was studied by fluorescence and UV‐Vis spectrum. The static quenching of BSA was observed in the presence of YbTMPyP. According to the thermodynamic parameters, this binding was regarded as "enthalpy‐driven" reaction. Furthermore, YbTMPyP is so close to the residues of BSA that molecular resonance energy transfer occurs between them. Besides, the red drift and hypochromicity of absorption spectrum of YbTMPyP were accompanied with the binding reaction.

Detection of single nucleotide variations by a hybridization proximity assay based on molecular beacons and luminescence resonance energy transfer.

A powerful combination of molecular beacon and luminescence resonance energy transfer technology reveals alterations in nucleic acid structure by as little as a single nucleotide in a novel hybridization proximity assay. The assay measures the length of a single-stranded target when a terbium chelate-labeled molecular beacon hybridizes to one side of the nucleic acid segment to be measured and an acceptor probe carrying a convention fluorophore hybridizes to the opposite end of the target. Using a test sequence shortened incrementally by deleting single nucleotides, this assay reports a nearly linear relationship between sequence length and the distance separating acceptor and donor probes. Consequently, this assay can be used to detect alternative splicing, allele types, rearrangements, insertion, and deletion events by measuring separation distances within a predefined region. Furthermore, the use of terbium chelates in molecular beacons can produce exceptionally high signal-to-background ratios compared to the use of conventional fluorophores. Principles of optimal probe design are investigated experimentally and by computational simulations of plausible molecular beacon folding. Some molecular beacon designs form dimers that reduce their maximal response to target sequences. A simple assay to detect such dimers is reported as a tool to help improve the design of molecular beacons. Optimally designed molecular beacons with terbium chelates and hybridization proximity assays are expected to expand their applications in the analysis and screening of genetic diseases.

Long-range resonance energy transfer in molecular systems.

The current state of understanding of molecular resonance energy transfer (RET) and recent developments in the field are reviewed. The development of more general theoretical approaches has uncovered some new principles underlying RET processes. This review brings many of these important new concepts together into a generalization of Förster's original theory. The conclusions of studies investigating the various approximations in Förster theory are summarized. Areas of present and future activity are discussed. The review covers Förster theory for donor-acceptor pairs and electronic coupling for singlet-singlet, triplet-triplet, and superexchange-mediated energy transfer. This includes the transition density picture of Coulombic coupling as well as electronic coupling between molecular aggregates (excitons). Spectral overlaps and ensemble energy transfer rates in disordered aggregates, the role of dielectric properties of the medium, weak versus strong coupling, and new models for energy transfer in complex molecular assemblies are also described.

Giant Benzenoid Hydrocarbons. Superphenalene Resonance Energy

We calculated molecular resonance energy for “0superphenalene”, a recently reported giant benzenoid which can be viewed as obtained from three fused “superbenzenes” (hexa-peri-hexabenzocoronenes). Using the Method of Conjugated Circuits we derived quantitative characterization of Clar's qualitative description of the considered benzenoids as composed from disjoint “π-sextets”. The calculations show the degree of differentiation between neighboring rings which decreases as we move more towards the central part of the molecule.

Dynamic polarization potential of 12C+12C system at molecular-resonance energies

The nuclear reaction dynamics leading to the formation of recently discovered resonance in the mutual-02+ channel of the 12C+12C inelastic scattering around Ec.m.≃ 32 MeV is studied in terms of the dynamic polarization potential (DPP) induced by the channel coupling among various excited states in 12C. The microscopic 3α cluster-model wave functions are used to generate the 12C−12C diagonal and coupling potentials in the double-folding model. It is found that DPP for the 02++ 02+ channel is an unusually strong attractive potential which even exceeds the zeroth-order folding-model potential of this channel around the nuclear surface region and that the strong coupling between the 02+ and 22+ states is predominantly responsible for the unusual DPP in this channel. The effective potential, the sum of the original folding-model potential and the attractive DPP, is found to generates resonance states in the same energy region as that of the resonance states generated by the original folding-model potential but the former states are found to be higher-nodal states having four additional radial nodes. Similar but more moderate property of DPP is also found in the entrance (elastic) channel. These results suggest that the reaction dynamics of generating the resonance in the 12C(02+) +12C(02+) channel may rather differ from that of the simple crossing of the zeroth-order molecular band generated by the potentials in the entrance and exit channels suggested by the standard band-crossing model.

Resonance energy of giant benzenoid hydrocarbon C78H26

We calculated the molecular resonance energy for a recently synthesized giant benzenoid hydrocarbon C78H26 having 27 fused benzene rings. Using the method of conjugated circuits, we derived the expression for the molecular resonance energy (RE) in terms of contributing conjugated circuits of size 6, 10, and 14. The method of conjugated circuits makes it possible to express the qualitative method of Clar into a quantitative form by deriving the contributions to RE of the individual benzene rings of a molecule. The results support the π-sextet model of Clar in which the contributions to the molecular resonance energy of rings depends on the assignment of π-sextets to a selection of individual benzene rings. The ring RE is sensitive to the immediate geometrical environment of the individual benzene rings which allows classification of benzene rings according to their relative contributions to the molecular RE. Such classification facilitates the calculation of reasonably accurate RE for even larger systems built from fused benzene rings. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 74: 697–708, 1999

Resonance energy of giant benzenoid hydrocarbon C78H26

We calculated the molecular resonance energy for a recently synthesized giant benzenoid hydrocarbon C78H26 having 27 fused benzene rings. Using the method of conjugated circuits, we derived the expression for the molecular resonance energy (RE) in terms of contributing conjugated circuits of size 6, 10, and 14. The method of conjugated circuits makes it possible to express the qualitative method of Clar into a quantitative form by deriving the contributions to RE of the individual benzene rings of a molecule. The results support the π-sextet model of Clar in which the contributions to the molecular resonance energy of rings depends on the assignment of π-sextets to a selection of individual benzene rings. The ring RE is sensitive to the immediate geometrical environment of the individual benzene rings which allows classification of benzene rings according to their relative contributions to the molecular RE. Such classification facilitates the calculation of reasonably accurate RE for even larger systems built from fused benzene rings. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 74: 697–708, 1999

Overview of laser microbeam applications as related to antibody targeting.

This chapter reviews several techniques which combine the use of laser microbeams with antibodies to study molecular and cellular biology. An overview of the basic properties of lasers and their integration with microscopes and computers is provided. Biophysical applications, such as fluorescence recovery after photobleaching to measure molecular mobility and fluorescence resonance energy transfer to measure molecular distances, as well as ablative applications for the selective inactivation of proteins or the selective killing of cells are described. Other techniques, such as optical trapping, that do not rely on the interaction of the laser with the targeting antibody, are also discussed.

Giant benzenoid hydrocarbons. Superphenalene resonance energy

We have calculated the molecular resonance energy for "‘superphenalene,’' a recently reported giant benzenoid that can be viewed as obtained from three fused "‘superbenzenes’' (hexa-peri-hexabenzocoronenes). Using the method of conjugated circuits we derived quantitative characterization of Clar's qualitative description of the considered benzenoids as composed from disjoint "‘π-sextets.'' The calculations show the degree of differentiation between neighboring rings, which decreases as we progressively move towards the center of the molecule.

On the difference in bond orders between HMO and PPP methods

AbstractWe have examined variations in bond orders in conjugated hydrocarbons that follow improvement in MO calculations on going from topological Hückel MO to self‐consistent Pariser‐Parr‐Pople–type calculations. Differences in individual bond orders can be interpreted as pointing to increased weights of selected Kekulé valence structures. Significantly, so indicated valence structures are those with the largest number of formal Kekulé benzene rings or the largest contribution to molecular resonance energy in terms of conjugated circuits.

Aromaticity in polycyclic conjugated hydrocarbon dianions

Dianions of polycyclic conjugated hydrocarbons are classified into aromatic, partially aromatic and anti-aromatic types. The classification has been based on a single structural concept: the conjugated circuits model. The negative charge in dianions is formally treated as a “double” bond contracted to a single carbon atom. Most dianions have been found to belong to the type “partially aromatic”, the degree of aromaticity being rather small, even zero or corresponding to weakly antiaromatic systems. The degree of aromaticity has been determined by the relative roles of RE (4 n + 2) and RE (4 n) which represent the positive and the negative contributions to molecular resonance energy, respectively. Our approach is contrasted to the still occasionally used peripheral model, the limitations of which are more serious than generally recognized. Its premise is that large (peripheral) conjugation is dominant, whilst in fact small conjugated cycles (circuits) play the dominant role in aromaticity and conjugation.

Conjugation and aromaticity of macrocyclic systems

Using a graph theoretical approach we have analyzed the aromatic stability of macrocylic systems having ten and fewer fused benzene rings. The approach requires construction and examination of Kekule valence structures of the macrocyclic systems considered. The Kekule valence structures for a molecule were systematically derived and the conjugated circuits in the individual Kekule formulas were enumerated subsequently. The counting results is the expression for molecular resonance energy, from which relative aromatic stabilities can be established. We report also on molecular local features, including ring benzene characters and Pauling bond orders.

ChemInform Abstract: Critical Test for Resonance Energies.

AbstractThe concept of conjugated circuits is used to formulate minimal conditions for theoretical models which have been designed to provide molecular resonance energies for benzenoid hydrocarbons.

Resonance energies of large conjugated hydrocarbons by a statistical method

AbstractWe developed a theoretical method for studying the aromatic stability of large molecules, molecules having a dozen and more fused benzene rings. Such molecules have so far often been outside the domain of theoretical studies. Combining the statistical approach and a particular graph theoretical analysis, it is possible to derive the expressions for molecular resonance energy for molecules of any size. The basis of the method is enumeration of conjugated circuits in random Kekulé valence structures. The method has been applied to evaluation of the resonance energies of conjugated hydrocarbons having about a dozen fused benzene rings. The approach consists of (1) construction of random Kekulé valence structures, (2) enumeration of conjugated circuits within the generated random valence structures, and (3) application of standard statistical analysis to a sufficiently large sample of structures. The construction of random valence forms is nontrivial, and some problems in generating random structures are discussed. The random Kekulé valence structures allow one not only to obtain the expression for molecular resonance energies (RE) and numerical estimates for RE, but also they provide the basis for discussion of local molecular features, such as ring characterization and Pauling bond orders.

A statistical approach to resonance energies of large molecules

For large conjugated molecules, resonance energies of SCF MO quality are not available. Here we outline a method of determining molecular resonance energies by combining a graph theoretical approach to aromaticity with a statistical analysis of random Kekule valence structures. The approach involves construction of random Kekule valence forms and subsequent enumeration of conjugated circuits within each such structure.

Average carbon-13 chemical shifts in benzenoid dications

The resonance energies and the average carbon-13 chemical shifts for a number of dications of benzenoid hydrocarbons are examined. The resonance energies have been derived by applying a graph theoretical approach based on enumeration of conjugated circuits present in the collection of Kekulé valence structural formulas for the dications, while carbon-13 chemical shifts have been taken from the literature. Average carbon-13 chemical shifts decrease sharply with increase in the molecular resonance energy. The derived correlation allows one to discuss the relative changes in the average carbon-13 chemical shifts and relative differences in resonance energies at a quantitative level.

Origin of Radio-resistance of Paired Substituted Bases : 9-Ethyl-guanine and 1-Methyl-cytosine

SOME years ago, Duchesne1 suggested that the greater the degree of delocalization of π-electrons, the greater the radio-resistance of solid phase compounds of aromatic type. This was verified by radiolytic yield measurements, using quadrupole spectroscopy and electron spin resonance methods2. B. Pullman3 developed similar views in the special field of biomolecules, with particular emphasis on nucleic acid bases, but using molecular resonance energy instead of diamagnetic anisotropy, as had been used, previously, to measure the delocalization effect.