Electronic structure and partial charge distribution of Doxorubicin in different molecular environments.
The electronic structure and partial charge of doxorubicin (DOX) in three different molecular environments-isolated, solvated, and intercalated in a DNA complex-are studied by first-principles density functional methods. It is shown that the addition of solvating water molecules to DOX, together with the proximity to and interaction with DNA, has a significant impact on the electronic structure as well as on the partial charge distribution. Significant improvement in estimating the DOX-DNA interaction energy is achieved. The results are further elucidated by resolving the total density of states and surface charge density into different functional groups. It is concluded that the presence of the solvent and the details of the interaction geometry matter greatly in determining the stability of DOX complexation. Ab initio calculations on realistic models are an important step toward a more accurate description of the long-range interactions in biomolecular systems.
Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110 (USA).
Lokendra
L
Poudel
Department of Biomedical Engineering, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106 (USA).
Amy M
AM
Wen
Department of Radiology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106 (USA).|Department of Materials Science and Engineering, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106 (USA).
Roger H
RH
French
Department of Physics, University of Massachusetts, Amherst, Massachusetts 01003 (USA).
V Adrian
VA
Parsegian
Department of Physics, University of Massachusetts, Amherst, Massachusetts 01003 (USA).|Department of Theoretical Physics, J. Stefan Institut, SI-1000 Ljubljana (Slovenia).|Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana (Slovenia).
Rudolf
R
Podgornik
Department of Biomedical Engineering, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106 (USA).|Department of Radiology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106 (USA).|Department of Materials Science and Engineering, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106 (USA).|Department of Macromolecular Science and Engineering, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
Nicole F
NF
Steinmetz
Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110 (USA). chingw@umkc.edu.
Wai-Yim
WY
Ching
D004247:DNA / Q000737:chemistry*; D004317:Doxorubicin / Q000737:chemistry*; D004583:Electrons; D008958:Models, Molecular; D015394:Molecular Structure; D011789:Quantum Theory
D004317:Doxorubicin; D004247:DNA
DNA; ab initio calculations; electronic structure; intercalations; solvent effects