Circular dichroism of nucleoside derivatives. IX. Vicinal effects on the circular dichroism of pyrimidine nucleosides

Miles, Daniel W.; Inskeep, Warren H.; Robins, Morris J.; Winkley, Michael W.; Robins, Roland K.; Eyring, Henry

doi:10.1021/ja00716a007

Cited by 79 publications

(27 citation statements)

References 4 publications

(6 reference statements)

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“…The theoretical diagrams predicted a positive CD band for fl-pyrimidine nu-cleosides in the anti conformation, a negative CD band for the syn conformation, and a large negative CD band for-the high-anti conformation (5). The conformations assigned from the theoretical diagrams have since been substantiated by several independent sources of conformational information.…”

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confidence: 81%

“…These studies have yielded some useful rules and diagrams (1)(2)(3)(4)(5)(6)(7)(8)(9)(10) relating the sign of the first CD band to anomeric configuration and to sugar-base torsion angle. Several excellent reviews in this area are now available (11)(12)(13)(14)(15).…”

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confidence: 99%

“…The program was adapted to give the desired spectral properties of the base such as the electric and magnetic transition moments and the transition monopoles of the Ath nucleus, QA: QA = /2e F, Ka,i--k X C#iCpk. [5] i Ok…”

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Calculations of the circular dichroism of adenosine derivatives constrained in the syn form

Miles¹,

Farmer²,

Eyring³

1980

Proc. Natl. Acad. Sci. U.S.A.

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The rotational strengths of the four longer wavelength transitions, BsU, Bju, and the two El , of adenosine derivatives constrained in the syn form have been investigated theoretically and experimentally. The theory combines a complete neglect of differential overlap version S (CNDO/S) description of the base with a generalized bond exciton metho by means of a matrix method. Rotational strength wheels for these transitions showing the rotational strength as a function of the glycosidic rotational angles are presented and sector rules discussed. Similar sector rules are predicted for purine nucleoside derivatives containing the 6-amino substituent, regardless of heteroatom content at positions 1 or 3 of the base. The sector rules for the Bs" rotational strength of purine nucleosides lacking the 6-amino substituent are strongly influenced by aza substitution. The circular dichroism spectra of 3-deazaadenosine, 8-a-hydroxyisopropyl)adenosine, and other purine nucleosides having a strong preference for the syn conformation are presented and compared with the theoretical results.Circular dichroism (CD) has been used extensively to study the conformation of nucleosides and nucleotides in solution. These studies have yielded some useful rules and diagrams (1-10) relating the sign of the first CD band to anomeric configuration and to sugar-base torsion angle. Several excellent reviews in this area are now available (11)(12)(13)(14)(15) We report here a theoretical CD study of some purine nucleosides closely related to adenosine which are conformationally restricted more or less to the syn conformation. The complete neglect of differential overlap version S (CNDO/S) procedure of Del Bene and Jaffe (27, 28) is used to calculate the optical parameters of the purine bases instead of our PariserParr-Pople method used in previous calculations (17,18). This and other modifications of the theoretical procedure have improved agreement between experimental data and theoretical results.COMPUTATIONAL METHODS The self-consistent field method has been widely used for the study of the electronic structure of molecules. The molecular orbitals 0t are expressed as linear combination of atomic orbitals 4u according to the equationThe coefficients Ct of the molecular orbital matrix are the solutions of the Hartree-Fock-Roothaan equations 3398The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U. S. C. §1734 solely to indicate this fact.

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Calculations of the circular dichroism of adenosine derivatives constrained in the syn form

Miles¹,

Farmer²,

Eyring³

1980

Proc. Natl. Acad. Sci. U.S.A.

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“…The evidence that the anti conformations of U and dU are favored over syn in the solid state as well as in solution is not disputed (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11). That syn conformations are not present to any detectable extent is generally agreed to be a consequence of unfavorable steric interactions (between the 2-keto oxygen and the endo ribose substituents) not present when the molecules are anti.…”

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confidence: 99%

Long-range Spin–Spin Coupling in Pyrimidine Nucleosides

Hruska¹

1971

Can. J. Chem.

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A study has been made of the 100 MHz p.m.r. spectra of a number of pyrimidine nucleosides in aqueous solution. Long-range five-bond spin–spin coupling interactions between the H-5 and H-1′ hydrogens were noted in uridine, 2′-deoxyuridine, 6-azauridine, and 6-azacytidine and rationalized by a predominantly anti conformation for each nucleoside. The absence of a detectable five-bond coupling in orotidine suggested that the syn conformation is preferred in this instance. The relative magnitudes of the four-bond and five-bond interactions in uridine and pseudouridine were shown to be consistent with the calculated mobile π-bond orders of the C6—N1 and C6—C5 bonds of the uracil base.

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“…Along with difficulties associated with treating the weak perturbation effects of the nonchromophoric sugar, this incomplete knowledge has hindered the development of theoretical models for calculating the rotatory parameters and extracting stereochemical information from them. In spite of these problems, CD studies of nucleosides have produced some useful rules and diagrams relating the sign of the first CD band to anomeric configuration and to conformation (10,(31)(32)(33)(34)(35)(36)(37)(38)(39)(40)(41)(52)(53)(54)(55)(56)(57)(58)(59)(60)(61).…”

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Optical activity and electronic absorption spectra of some simple nucleosides related to cytidine and uridine: all-valence-shell molecular orbital calculations.

Miles¹,

Redington²,

Miles³

et al. 1981

Proc. Natl. Acad. Sci. U.S.A.

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The circular dichroism and electronic absorption of three simple model systems for cytidine and uridine have been measured to 190 nm. The molecular spectral properties (excitation wavelengths, oscillator strengths, rotational strengths, and polarization directions) and electronic transitional patterns were investigated by using wave functions of the entire nucleoside with the goal of establishing the reliability of the theoretical method. The computed electronic absorption quantities were shown to be in satisfactory agreement with experimental data. It was found that the computed optical rotatory strengths of the B2. and El.electronic transitions and lowest observed n-ir* transition are in good agreement with experimental values. Electronic transitions were characterized by their electronic transitional patterns derived from population analysis of the transition density matrix.The theoretical rotational strengths associated with the B2. and El. transitions stabilize after the use of just a few singly excited configurations in the configuration interaction basis and, hypothetically, are more reliable as indicators of conformation in pyrimidine nucleosides related to cytidine.Spectroscopic studies of the nucleic acid bases and their derivatives have appeared continuously over the past quarter century (1-40). Many of these studies were motivated by the prospect of obtaining stereochemical information from changes in the absorption and optical rotation spectra of the nucleic acids and their models (41-51). More recently, the increasing importance of slightly modified versions of the nucleic acid monomers as potential therapeutic agents has accentuated the importance of optical studies in this area, particularly circular dichroism (CD) studies, which indirectly give one stereochemical information (10-18, 31-41, 52-61). The biological significance of the conformational aspects ofnucleosides and nucleotides has been sufficiently documented (60-63).Of the two main aspects of CD studies, stereochemical and spectroscopic, the spectroscopic problem is currently the more fundamental because incomplete knowledge of the electronic transitions that give rise to the absorption of radiation and the rotatory power has limited attempts to determine optically the chirality of nucleosides. Along with difficulties associated with treating the weak perturbation effects of the nonchromophoric sugar, this incomplete knowledge has hindered the development of theoretical models for calculating the rotatory parameters and extracting stereochemical information from them. In spite of these problems, CD studies of nucleosides have produced some useful rules and diagrams relating the sign of the first CD band to anomeric configuration and to conformation (10, 31-41, 52-61).The major goal of this study is to use the experimental data on 3-deaza-4-deoxyuridine, 3-deazauridine, and 3-deazacytidine to evaluate a new theoretical method for calculating and interpreting the optical properties of nucleosides. The method uses wave functions of...

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Circular dichroism of nucleoside derivatives. IX. Vicinal effects on the circular dichroism of pyrimidine nucleosides

Cited by 79 publications

References 4 publications

Calculations of the circular dichroism of adenosine derivatives constrained in the syn form

Calculations of the circular dichroism of adenosine derivatives constrained in the syn form

Long-range Spin–Spin Coupling in Pyrimidine Nucleosides

Optical activity and electronic absorption spectra of some simple nucleosides related to cytidine and uridine: all-valence-shell molecular orbital calculations.

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