Generalized Susceptibility Theory I. Theories of Hypochromism

Rhodes, William C.; Chase, Malcolm

doi:10.1103/revmodphys.39.348

Cited by 110 publications

(46 citation statements)

References 18 publications

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“…2 was calculated from the isotropic atom polarizabilities (Table 111, set VI) computed by the interaction theory.24 Spectrum 2 also represents the results of calculations done with isotropic atom polarizabilities computed by the additivity assumption. 24 The greatest effect of using these various Table 111 for the "zero-frequency" polarizability sets which correspond to each curve as follows: (1) set I; (2) set I1 ( C -0 equals C-C) and set VI1; (-3) set 111; (4) set I\'; (5) set V, C -0 equals C-C; set VI is represented by the broken line.…”

Section: Group Polarizability Evaluationmentioning

confidence: 99%

“…: [3][4] Though classically derived, the DeVoe polarizability theory has been shown to be equivalent to the quantum-mechanical, time-dependent Hartree approximation. 5 The most distinguishing feature of this theory is the use of complex, frequency-dependent polarizabilities. Thus it has the advantage of using, as starting data, empirical monomer absorption properties.…”

Section: Introductionmentioning

confidence: 99%

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Circular dichroism of nucleic acid monomers. I. Calculated adenosine and 2′‐deoxyadenosine CD spectra

Moore

1980

Biopolymers

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SynopsisA comhination of the DeVoe and Kirkwood polarizahility concepts is developed to calculate CD spectra of nucleic acid monbmers. The method is perfectly general and applies t o any system where the constituents have absorption properties which are widely separated in terms o f frequency. T h e theory is applied to calculate the C I j spectra of adenosine and 2'-deoxyadenosine conformers. Bond polarizahilities are evaluated for the rihosyl moiety of adenosine, as a function of glycosidic rotational angles and polarizahility anisotropies. It is found that a wide range of C-C and C -0 bond polarizahilities give similar CD results. Isotropic atom polarizabilities are also evaluated. It is found that the CD results using these polarizahilities d o not differ significantly from those obtained with bond polarizabilities. T h e ('I) spectra of adenosine and Tdeoxyadenosine are calculated for three x-ray diffraction determined geometries: A-form RNA, B-form DNA, and C-form DNA. T h e results indicate that the monomer CD spectra are strongly dependent on the precise geometry and appear t o he o f importance in understanding the spectra of oligomcrs and polymers. T h e deoxyadenosine conformers are found to have calculated CD spectra which are less intense than those o f t he rihosyl conformers. These results indicate that the measured differences hetween the ('1) magnitudes of riho-and deoxyrihoadenositie are due to the presence o r ahsence of the 2'-hydroxyl. Weighted averaged adenosine CL) spectra are calculated with the aid of prohahility distributions from conformational energy calculations. The results suggest a new method tor obtaining empirical monomer parameters for use in optical calculations. The calculations in this paper indicate for the first time that DeVoe theory, in comhination with the Kirkwood theory, provides a useful method for the calculation of the CD spectra of nonpolvnieric tnolecules.

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Section: Group Polarizability Evaluationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Circular dichroism of nucleic acid monomers. I. Calculated adenosine and 2′‐deoxyadenosine CD spectra

Moore

1980

Biopolymers

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“…Похожая модель была независимо введена W. Rhodes [45]. Теория гипохромизма получила дальнейшее развитие в ряде исследований, где предлагались различные модели [46][47][48][49][50][51].…”

Section: ранние экспериментальные и теоретические исследования денатуunclassified

Theoretical and Experimental Investigations of DNA Open States

Shigaev¹,

Ponomarev²,

Лахно³

2013

Math.Biol.Bioinf.

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Аннотация. Работа посвящена обзору и анализу литературных данных, касающихся свойств открытых состояний ДНК. Данные состояния возникают вследствие крупных флуктуаций дуплекса и оказывают большое влияние на целый ряд биохимических процессов, в том числе на перенос электрического заряда в ДНК. Проведён сравнительный анализ экспериментальных данных по кинетике и термодинамике открытых состояний ДНК в широком интервале температур. Объяснены противоречия между результатами разных экспериментов. На основе различия термодинамических свойств и других характеристик выделено три типа открытых состояний ДНК, а также дано современное определение термина «открытое состояние». Представлен краткий обзор простых математических моделей ДНК, в большинстве которых состояние каждой пары оснований описывается одной-двумя переменными. Рассмотрены основные проблемы исследования гетерогенной ДНК в рамках подходов данного уровня. Обсуждается роль каждой из групп моделей в интерпретации экспериментальных данных. Особое внимание уделено изучению процессов переноса и локализации энергии колебаний нуклеотидных пар в дуплексе при помощи механических моделей. Показано, что данные процессы играют ключевую роль в динамике гетерогенного дуплекса, а их теоретическое исследование крайне важно для развития современной молекулярной биологии и биофизики. Рассмотрены основные особенности теоретических подходов, благодаря которым удалось описать различные экспериментальные данные. Описаны перспективы развития моделей, предложены конкретные детали оптимизации, а также возможные способы модернизации некоторых экспериментальных методик.

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“…The significance of a polarizability of ±• is that the molecule is in a state of resonance and absorbs energy from the applied field. This behaviour of the model can be understood from its close relation to the classical system of N coupled oscillators, which likewise shows resonance under conditions other than the resonance conditions of the isolated oscillators [53][54][55][56].…”

Section: Interacting Induced Dipoles Polarization Model For Molecularmentioning

confidence: 99%

Polarization by the effect of a small torsional change in the benzothiazole (A)-benzobisthiazole (B) oligomer A-B13-A

1999

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Abstract:We use a method for the calculation of the molecular dipole ( µ ) and quadrupole ( θ ) moments and dipole-dipole ( α ), dipole-quadrupole ( A ) and quadrupole-quadrupole ( C ) polarizabilities which we have successfully applied to the benzothiazole (A)-benzobisthiazole (B) linear oligomer A-B 13 -A. Two model rotational isomers have been characterized: (1) the fully-planar (000) conformation; and (2) a rotational isomer with each unit rotated in the range 1 − 10° in the same direction (+++). For isomer 000, µ is smaller than for +++. The calculation of α , A and C has been carried out by the interacting induced dipoles polarization model that calculates tensor effective anisotropic point polarizabilities (method of Applequist et al.). The values of A are specially sensitive to µ which varies under rotation. This fact explains the great values of A x xx , for the +++ polar isomer. It is found that small torsional changes can enhance solubility by a clear increasing of the hydrophilic accessible surface area. However, the torsion of the oligomer varies the value of µ and so modifies α , C , and, specially, A . For conformer +++, polarization effects occur even when each unit is rotated only φ = 1°. The observed effect is an increase in µ and, hence, in α , C , and, specially, A .

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Generalized Susceptibility Theory I. Theories of Hypochromism

Cited by 110 publications

References 18 publications

Circular dichroism of nucleic acid monomers. I. Calculated adenosine and 2′‐deoxyadenosine CD spectra

Circular dichroism of nucleic acid monomers. I. Calculated adenosine and 2′‐deoxyadenosine CD spectra

Theoretical and Experimental Investigations of DNA Open States

Polarization by the effect of a small torsional change in the benzothiazole (A)-benzobisthiazole (B) oligomer A-B13-A

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