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TD-DFT Investigation of the Magnetic Circular Dichroism Spectra of Some Purine and Pyrimidine Bases of Nucleic Acids
Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
CNR, Italy.
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2015 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 119, no 21, 5476-5489 p.Article in journal (Refereed) Published
Abstract [en]

We present a computational study of the Magnetic circular dichroism (MCD) spectra in the 200-300 nm wavelength region of purine and its derivative hypoxanthine, as well as of the pyrimidine bases of nucleic acids uracil,thymine, and cytosine, Using the B3LYP and CAM-B3LYP functionals. Solvent effects, are investigated within the polarizable continuum model and by inclusion of explicit water molecules. In, general; the computed spectra are found to be in good agreement with the experimental ones, aprt from some overall blue shifts. Both the pseudo-A term shape of the MCD spectra of the purines and the B term shape of the spectra of pyrimidine base are reproduced. Our calculations also correctly reproduce the reversed phase of the MCD bands in purine compared to,that of its derivatives present in nucleic acids. Solvent effects are sizable and system specific,but they do not in general alter the qualitative shape of the spectra. The bands are dominated the-bright pi -greater than pi* transitions; and our calculations in solution nicely reproduce theft energy differences, improving the estimates obtained in the gas phase. Shoulders are predicted for purine and uracil due to n -greater than pi* excitations, but they are too weak to be observed in the. experiment.

Place, publisher, year, edition, pages
American Chemical Society , 2015. Vol. 119, no 21, 5476-5489 p.
National Category
Theoretical Chemistry
Identifiers
URN: urn:nbn:se:liu:diva-119800DOI: 10.1021/jp512468kISI: 000355495100043PubMedID: 25648759OAI: oai:DiVA.org:liu-119800DiVA: diva2:827229
Note

Funding Agencies|PRIN [2010ERFKXL_008]; University of Trieste [CHIM02-Ricerca]

Available from: 2015-06-26 Created: 2015-06-26 Last updated: 2016-01-15
In thesis
1. Development and characterization of damped cubic response functions with application to two-photon absorption
Open this publication in new window or tab >>Development and characterization of damped cubic response functions with application to two-photon absorption
2015 (English)Licentiate thesis, comprehensive summary (Other academic)
Abstract [en]

Molecular response to electromagnetic fields - static or optical - within a framework of perturbation theory diverges close to resonance with molecular transitionen energies, and need work-around solutions for real-valued response functions. This licentiate thesis deals with nonlinear response, with focus being on cubic polarizaibilities, and outlines the underlying mathematics for exact-state and approximatestate, complex-valued response functions applicable to quantum chemical computation. Such a complex-valued response theory is commonly known as dampedresponse theory, for which the response functions consists of a real and an imaginary component, each of them representing various spectroscopies in nature. In addition to the mathematics, the formulas have been implemented in the quantum chemical package DALTON, and several tests determining the integrity of the implementation has been conducted.

The fourth and final major part of the thesis is concerned with applied nonlinear response theory, including not only cubic response functions, but also quadratic and linear response functions, some of which are of the more exotic character. Three spectroscopies have been investigated for small and medium-sized organic molecules and the neon atom: two-photon absorption (TPA), Jones birefringence (JB), and magnetic circular dichroism (MCD).

The TPA part is a simple demonstration of capability of the damped cubic response code, for which neon is the example system. Perfect agreement is shown for the Ehrenfest approach and an independent implementation based on the quasienergy formalism.

JB is an optical eect in which induced refractive anisotropy, by means of external electric and magnetic static elds, results in ellipticity of linearly polarized light beams. This part mainly discuss implications from a paper which the current author took part in. The paper ultimately attempts to indentify the general observable strength of the effect, and coincidentaly pin-point some particular system suitable for experiments. Among other finds, JB is found to be correlated to the electric dipole moment, and for monosubstituted benzenes, the para-Hammett constant.

Finally, MCD is discussed based on three papers in which the present author is included. The elegant MCD solution to broad absorption peaks, for which it is desired to distinguish individual states, is demonstrated on adenine and three additional purine derivatives. A drawn out debate regarding relative stability of certain low-lying states could be settled by this method. Furthermore, appropriate description of solvation environment in conjunction with the exchange-correlation functionals B3LYP and CAM-B3LYP is investigated on purine and pyrimidine derivatives. CAM-B3LYP is found to be superior in terms of general prole shapes, while results regarding solvation model are rather inconclusive, although the results suggests some level of solvation model is appropriate, such as a polarizable continuum model or explicit solvation molecules.

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2015. 67 p.
Series
Linköping Studies in Science and Technology. Thesis, ISSN 0280-7971 ; 1742
National Category
Theoretical Chemistry Chemical Sciences
Identifiers
urn:nbn:se:liu:diva-123972 (URN)978-91-7685-844-8 (Print) (ISBN)
Supervisors
Available from: 2016-01-15 Created: 2016-01-15 Last updated: 2016-01-15Bibliographically approved

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