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  • 1
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The probability distributions of the torsional angles (Φ′, ω′, ω, Φ, and ψ), which fix the structure of nucleotide backbone, have been calculated using the results of energy calculations based on extended Huckel theory (EHT), complete neglect of differential overlap (CNDO), perturbative configuration interaction using localized orbitals (PCILO), and classical potential functions (CPF) methods. Statistical average values of the vicinal 1H—1H, 1H—31P, and 13C—31P nmr coupling constants 〈J〉 have been calculated from the generalized Karplus relations using the probability distribution in the Φ′, Φ, and ψ space. Experimental 〈J〉 values for polyribouridylic acid (polyU) support the theoretical predictions for these torsional angles. Using Monte Carlo technique, random coils of single-stranded polynucleotides have been simulated and the mean-square end-to-end distance 〈r2〉 has been calculated. Molecular orbital methods (EHT, CNDO, and PCILO) suggest considerable flexibility around O—P bonds, leading to fairly small values for the characteristic ratio (C∞ ∼ 4). Observed values of the unperturbed characteristic ratio for polynucleotides are quite large (C∞ ∼ 18) suggesting a relatively rigid nucleotide backbone. The results based on molecular orbital calculations can be reconciled with the experimental values by introducing an additional stabilization of ∼2 kcal mol-1 for the predicted minimum energy ragion (Φ′ ∼ 240°, ω′ ∼ 290°, ω 290°, Φ 180°, and ψ 60°). Such a stabilization may arise from the association of water molecules and metal ions with the phosphate group and (or) Coulomb interaction between neighboring phosphate groups. The calculations provide a semiquantitative estimate of torsional rigidity in the nucleotide backbone.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The influence of accepting the hydrogen bond by N(3) of adenine on the conformational preferences of the N(6) substituent in modified nucleic acid base N6-(N-glycylcarbonyl)adenine (gc6Ade) has been modeled by the protonation of N(3). The preferred orientation of the glycylcarbonyl substituent changes on the protonation of N(3). The preferred conformation for the N(3) protonated base is the planar, intramolecular bifurcated hydrogen-bonded structure involving the interaction of the ureido N(11)H with the N(1) of the purine and the O(13b) of the amino acid carboxyl. Another conformation of nearly equal stability, having the internal hydrogen bonding of O(13b) with the N(6)H, is also predicted. Such protonation or hydrogen-bonding-induced conformational flipping may enable the structural reorientation of the anticodon loop required for the functioning of tRNA. © 1994 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
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  • 3
    ISSN: 0020-7608
    Keywords: modified nucleic acid base ; N(6)-substituted adenine ; N(1)-protonation-induced ; conformational flipping ; hydrogen bonding ; PCILO ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The influence of protonation at N(1) on the conformational preferences of the N(6) substituent in the modified nucleic acid base N6-(N-glycylcarbonyl) adenine, gc6Ade, was investigated by the quantum chemical perturbative configuration interaction using localized orbitals (PCILO) method. The preferred orientation of the glycylcarbonyl substituent changes on the protonation of N(1). In the preferred conformation, the carbonyl oxygen O(10) is placed on the same side as N(1)H and provides stabilization through intramolecular hydrogen bonding of O(10) with HN(1). The amino acid component is so oriented that the carboxyl oxygen O(13b) is aligned closely with the N(6)H direction. Thus, the preferred molecular orientation is further stabilized by intramolecular hydrogen bonding involving HN(6) with O(13b). The alternative conformation has 0.5 kcal/mol higher energy than has the preferred conformation. The preferred conformation is about 1 kcal/mol more stable than is the conformation obtained by the flipping of torsion angle β alone, from the favored orientation for the unprotonated gc6Ade. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 62: 551-556, 1997
    Additional Material: 5 Ill.
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  • 4
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A comparative study has been made of the configurational effects on the conformational properties of α- and β-anomers of purine and pyrimidine nucleoside 3′,5′,-cyclic monophosphates and their 2′-arabino epimers. Correlation between orientation of the base and the 2′-hydroxyl group have been studied theoretically using the PCILO (Perturbative Configuration Interaction using Localized Orbitals) method. The effect of change in ribose puckering on the base-hydroxyl interaction has also been studied. The result show that steric repulsions and stabilizing effects of intramolecular hydrogen bonding between the base and the 2′-hydroxyl (OH) group are of major importance in determining configurations of α-anomers and 2′-arabino-β-epimers. For example, hydrogen bonding between the 2′-hydroxyl group and polar centers on the base ring is clearly implicated as a determinant of syn-anti preferences of the purine (adenine) or pyrimidine (uracil) bases in α-nucleoside 3′,5′-cyclic monophosphates. Moreover, barrier heights for interconversion between conformers are sensitive to ribose pucker and 2′-OH orientations. The result clearly show that a change in ribose-ring pucker plays an essential role in relieving repulsive interaction between the base and the 2′-hydroxyl group. Thus a C2′-exo-C3′-endo (2T3) pucker is favored for α-anomers in contrast with the C4′-exo-C3′-endo (4T3) from found in β-compounds.
    Additional Material: 6 Ill.
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  • 5
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Conformational preferences of model modified nucleic acid base N6-(N-alanylcarbonyl) adenine, ac6Ade, have been investigated using the quantum chemical PCILO (perturbative configuration interaction using localized orbitals) method. The multidimensional conformational space has been searched using selected grid points formed by combining the various torsion angles that take favored values derived from energy variation with respect to each torsion angle individually.The preferred molecular structure is stabilized by an intramolecular hydrogen bond from N(11)H of the amino acid to N(1) of the adenine. The observed crystal structure conformations for the naturally occurring, anticodon adjacent, threonyl analogs, tc6Ade, correspond to the predicted most stable conformation for the model modified base ac6Ade. Three stable, low energy conformations differing in the orientations of the carboxyl group and the amino acid side chain are predicted within 1 kcal/mol of the most stable structure. The possible bifurcated hydrogen bonding of N(11)H with N(1) and either of the carboxyl oxygens is of minor significance.The indicated orientational flexibility for the carboxyl group and the amino acid side chain may enable convenient probing of the molecular environment, in the vicinity of the anticodon in tRNA, by the amino acid substituent, with only modest changes in energy stabilization.
    Additional Material: 6 Ill.
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  • 6
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Conformational preferences of N6-furfurylamino purine (kinetin) and N6-benzyl amino purine (BAP) have been investigated theoretically by the quantum chemical perturbative configuration interaction using localized orbitals method. The predicted most stable conformations for these molecules are quite similar. The N6 substituents in both these molecules are oriented toward N(1) and away from the imidazole moiety of the purine. The furfuryl ring in kinetin as well as the aromatic benzene ring in BAP are not coplanar with the purine ring. Comparison of these results with the preferred conformation of another compound N6-(Δ2-isopentenyl) adenine reveals striking similarity in the orientations of the N6 substituents in these cytokinin-active plant-growth-stimulating substances.
    Additional Material: 8 Ill.
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  • 7
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Conformational preferences of modified nucleic acid base N6-(N-glycylcarbonyl) adenine, gc6Ade, have been investigated using the quantum chemical PCILO (Perturbative configuration interaction using localized orbitals) method. The multidimensional conformational space has been searched using selected grid points formed by combining various torsion angles that take favored values derived from energy variation with respect to each torsion angle individually. The theoretically predicted most stable, minimum energy conformation of the molecule is such that the substituent on N(6) spreads away from the imidazole moiety of the adenine ring, thus keeping distal orientation. The preferred molecular orientation is stabilized by an intramolecular hydrogen bond from N(11)H of the amino acid to N(1) of the adenine. The carboxylic group of the substituent is trurned away in relation to N(11)H…N(1) and is perpendicular to the plane through the rest of the moleculeThe alternative stable conformation corresponding to an 0.8 kcal/mol higher energy has a coplanar carboxylic group turned towards the same side as N(11)H…N(1) and is exhibited in the crystal structure of the nucleoside derivative, gc6A. Energetically, the carboxyl group may change its orientation over a wide range, without much destabilization. This suggests probing by the carboxyl group of the molecular environment in the vicinity of the anticodon in tRNA.
    Additional Material: 6 Ill.
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  • 8
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Conformational preferences of the hypermodified nucleic acid bases N6-(Δ2-isopentenyl) adenine, (i6Ade) and its 2-methylthio derivative (ms2i6Ade) have been investigated theoretically by the quantum chemical perturbative configuration interaction using localized orbitals (PCILO) method.The predicted most stable conformation of i6Ade and ms2i6Ade are such that the isopentenyl substituent is oriented away from the imidazole moiety of the adenine ring. The atoms N(6), C(10), and C(11) remain coplanar with the adenine ring for both molecules. However, in contrast to the predicted cis orientation of the C(10)—C(11) bond with respect to the C(6)—N(6) bond in i6Ade, the trans orientation is favored for ms2i6Ade. The plane of the isopentenyl group is rotated by 120° from that of the purine base in i6Ade, whereas rotation by 60° is favored in ms2i6Ade. The favored orientation of the methylthio group with respect to the C(2)—N(3) bond is trans; however, the alternative cis arrangement is also quite probable. The conformational implications of the methylthiolation of the isopentenyladenine are brought out in the context of the considerably large range of accessible (β,γ) and χ orientations. The compatible roles of i6Ade and ms2i6Ade in tRNA are thus understood, besides their distinguishing features.
    Additional Material: 5 Ill.
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