Determination of the helix-coil transition heats from the melting curves of deoxyribonucleic acid containing additional linkages

Permogorov, V. I.; Frank‐Kamenetskii, Maxim D.; Serdyukova, L.A.; Lazurkin, Yu. S.

doi:10.1016/0032-3950(65)90071-7

Cited by 3 publications

(4 citation statements)

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“…Thus, a distinguishing feature of polymethine dyes is the transfer of electron density during the transition to the first excited state from the p centers at the odd positions in the chain to the atoms at the even positions, whereas in the neutral polyenes there are no changes in the charges during excitation, and only the orders of the p bonds change [12,[135][136][137][138]. Change in the charge distribution affects the intensity of the electronic transitions, while change in the bond orders and, accordingly, their lengths during subsequent vibrational relaxation in the excited state determines the width of the absorption bands [139][140][141], the magnitude of the Stokes shifts in the fluorescence spectra [142][143][144][145], and the paths for nonradiative degradation of the excited state [142,146]. A number of authors have postulated that the main reason for the decrease in the quantum yields of fluorescence is trans-cis conformational transformations both in the polymethine dyes [147][148][149][150][151][152][153][154][155] and in polyenes, stilbenes, and their substituted derivatives and hetero analogs [156,157].…”

Section: Soliton Waves In the Excited Statementioning

confidence: 99%

The Solitonic Nature of the Electronic Structure of the Ions of Linear Conjugated Systems

Kachkovskii

2005

Theor Exp Chem

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Features of the electron density distribution in the ground and excited states, the position of the energy levels, and the equilibrium molecular geometry of the ions of linear p-electron systems, including conjugated polymers and oligomers, cationic and anionic polymethine dyes, and the radical-ions of a,w-substituted polyenes, are reviewed. By using the soliton concept it was possible to explain many unusual properties of this type of organic compound: The quasimetallic conductivity, the marked change in the spectral characteristics of ionic dyes absorbing and emitting light in the near IR region of the spectrum, etc. It was shown on the basis of semiempirical and nonempirical calculations that the charges in collective p-electronic systems form soliton waves, the width of which does not depend on the length of the molecule. In the excited state the size of the solitons increases significantly. The introduction of donor and acceptor terminal groups can destroy the symmetry of the charge distribution and molecular geometry at a conjugation chain of critical length exceeding the dimensions of the soliton. It was established that the injection of electrons/holes not only leads to the appearance of a soliton level at the center of the energy gap but is also accompanied by significant displacement of the top of the valence band and the bottom of the conduction band.

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Section: Soliton Waves In the Excited Statementioning

confidence: 99%

The Solitonic Nature of the Electronic Structure of the Ions of Linear Conjugated Systems

Kachkovskii

2005

Theor Exp Chem

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“…However, the shoulder around (525) nm is usually ascribed to the dimmer. The bands below 450 nm represent the transitions to the mesomeric limit structures with shorter conjugation units and originate from n-π* transitions from the NHOMO (next highest occupied molecular orbital) to the LUMO [15]. Moreover, as shown in the inset, the absorption peak values increased with increasing Rh-B content, due to the increase of the number of the absorbing species according to Beer's law [18,19].…”

Section: Resultsmentioning

confidence: 99%

“…Levshin and Gorskov [14] concluded that the dye absorption spectrum is pH independent. Permogorov et al [15] attributed secondary maxima in the absorption spectrum to vibrational structure and disputed the existence of dimmers in ethanol solution. Selwyn and Steinfeld [16]…”

Section: Introductionmentioning

confidence: 99%

Optical properties of Rhodamine B Dye mixed with Polyvinylpyrrolidone (PVP ) as a matrix

Abdullah¹

2017

JK-Physics

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In the present work, the spin casting method has been utilized for preparing different concentrations of Rhodamine B (Rh B) (5%,10% and 15%) mixed with a transparent polymer Polyvinylpyrrolidone (PVP) as a matrix. The spectral characteristics of the prepared samples are studied by absorption, transmission, reflection (the wavelength region from 300 nm to 900 nm) and fluorescence spectroscopy (the wavelength region from 550 nm to 800 nm). The calculated Stokes shift between the absorption and emission of Rh.B reflects the displacement in potential surface between the ground and the excited states. The analysis of the spectral behavior of the absorption coefficient in the absorption region reveals an direct allowed transition with a band gap of 2.07 eV . The values of some important parameters (refractive index n and extinction coefficient K ) of polymer thin film are determined from these spectra.

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“…In the boundary case when all binding sites are occupied by ligands, the melting interval width increment tends to zero. In the observed case, it is assumed that each pairofbasesinpolymermaybeabindingsitefor ligand [12].…”

Section: Main Body 21 Theorymentioning

confidence: 99%

“Tie Calorimetry” as a Tool for Determination of Thermodynamic Parameters of Macromolecules

Karapetyan¹,

Vardevanyan²

2018

Calorimetry - Design, Theory and Applications in Porous Solids

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Determination of free energy of double helix formation from two single-stranded polynucleotides and estimation of energetics of different low-molecular compounds binding to nucleic acids provide valuable tools for understanding of mechanisms that govern noncovalent binding of ligands to their receptor targets. In order to completely understand the molecular forces that drive and stabilize double helix formation and its complexes with ligands, thermodynamic studies are needed to complement the structural data. Structural characterization of a number of DNA-ligand complexes by X-ray and high-resolution NMR method provides key insight relating to the properties of complex formation, but structural data alone, even when coupled with the most sophisticated current computational methods, cannot fully define the driving forces for binding interactions (or interactions) or even accurately predict their binding affinities. Thermodynamics provides quantitative data of use in elucidating these driving forces and for evaluating and understanding at a deeper level the effects of substituent changes on binding affinity.

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Determination of the helix-coil transition heats from the melting curves of deoxyribonucleic acid containing additional linkages

Cited by 3 publications

References 1 publication

The Solitonic Nature of the Electronic Structure of the Ions of Linear Conjugated Systems

The Solitonic Nature of the Electronic Structure of the Ions of Linear Conjugated Systems

Optical properties of Rhodamine B Dye mixed with Polyvinylpyrrolidone (PVP ) as a matrix

“Tie Calorimetry” as a Tool for Determination of Thermodynamic Parameters of Macromolecules

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