2005
DOI: 10.1021/jp051218g
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Simulations of Structure and Vibrational Spectra of Deoxyoctanucleotides

Abstract: Combined molecular dynamics and ab initio computations were applied for analysis of infrared absorption and vibrational circular dichroism spectra of deoxyoctanucleotides. Unlike for previous idealized models, molecular geometries of these shorter DNA fragments in solutions were obtained as dynamic averages from simulations in a periodic water box. Vibrational spectra for the whole octamers including hydrogen-bonded solvent molecules were simulated on the basis of density-functional calculations on small fragm… Show more

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Cited by 28 publications
(30 citation statements)
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“…Typically, the CdO stretching contributes most to the strongest IR signal within ∼1650-1750 cm -1 . 29,36,39,40 The carbonyl vibrations are also the most sensitive to the hydration. For an isolated carbonyl group or in peptidic systems, the hydrogen binding to water molecules shifts down the CdO stretching vibration by tens of centimeters -1 .…”
Section: Resultsmentioning
confidence: 99%
“…Typically, the CdO stretching contributes most to the strongest IR signal within ∼1650-1750 cm -1 . 29,36,39,40 The carbonyl vibrations are also the most sensitive to the hydration. For an isolated carbonyl group or in peptidic systems, the hydrogen binding to water molecules shifts down the CdO stretching vibration by tens of centimeters -1 .…”
Section: Resultsmentioning
confidence: 99%
“…115 The most interesting outcome is described in the next two sections. The computed spectra will be compared to the experimental results for the same set of octanucleotides measured earlier.…”
Section: Accounting For Explicit Solvent and Dynamical Averagingmentioning
confidence: 99%
“…The details of the procedure can be found elsewhere. 115 For the fragment selection and following ab initio computations only water molecules closer than 3.6 Å (the first hydration shell) and hydrogen-bound to DNA were retained.…”
Section: Accounting For Explicit Solvent and Dynamical Averagingmentioning
confidence: 99%
See 1 more Smart Citation
“…IR [53][54][55][56][57] and VCD [58][59][60][61][62][63][64] band assignments for DNA and its constituents (nitrogen bases and sugar-phosphate backbone) have been extensively described in the literature. They are summarized in Table I based on a recent review 46 and two analyses of DNA interacting with manganese ions.…”
Section: Ir Experimentsmentioning
confidence: 99%