Applications of the Cartesian coordinate tensor transfer technique in the simulations of vibrational circular dichroism spectra of oligonucleotides

Abstract

The application of the Cartesian coordinate tensor transfer (CCT) technique for simulations of the IR absorption and vibrational circular dichroism (VCD) spectra of relatively large nucleic acid fragments is demonstrated on several case studies. The approach is based on direct ab initio calculations of atomic tensors, determining molecular properties, for relatively small fragments, and subsequent transfer of these tensors to the larger systems in Cartesian coordinates. This procedure enables precise computations of vibrational spectra for large biomolecular systems, currently with up to several thousands of atoms. The versatile ability of the CCT methods is emphasized on the examples of VCD and IR absorption spectra calculations for B- and Z-forms of DNA, single-, double-, and triple-stranded RNA helices and DNA structures with different base content and sequences. The development and recent improvements of the methodology are followed, including utilization of the constrained normal mode optimization (NMO) strategy and combined quantum mechanics and molecular dynamics simulations. Advantages, drawbacks, and recommendations for future improvements of the CCT method as applied to nucleic acid spectra calculations are discussed.

Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial

“…Nowadays, density functional theory (DFT) allows a calculation of the VCD spectrum of a chiral molecule, which then can be compared with the measured VCD spectrum and by this the absolute configuration (AC) of a chiral molecule can be determined [ 37 ]. Furthermore, an oligonucleotide VCD spectrum calculation was described recently [ 38 ].…”

Studying the stereostructures of biomolecules and their analogs by vibrational circular dichroism

“…[7][8][9] Alternatively, when the entire secondary structure of a polymer is uniform, the VCD spectrum of an entire polymer can be simulated by transferring several parameters derived from density functional theory calculations of a small fragment to larger molecules via a Cartesian coordinate transfer technique. 10,11 However, a computational approach for the Comparison of the observed and calculated VCD (top) and IR (bottom) spectra of (a) α-pinene (1) and (b) methyl 2-deoxy-β-D-threo-pentopyranoside (2) as well as (c) the structure of homooligomers of unnatural amino acids (3a-3d). (a) Observed spectra were measured as neat liquid using a JASCO FVS-6000 spectrometer (Tokyo, Japan).…”

Vibrational Circular Dichroism: A Valuable Tool for Conformational Analysis and Absolute Configuration Assignment of Chiral 1‐Aryl‐2,2,2‐Trifluoroethanols

“…Vibrational circular dichroism (VCD) is a relatively recent technique that allows one to define the absolute configuration (AC) of chiral molecules. [1] At the same time, ab initio methods, in particular density functional theory (DFT) [2,3] have progressed enormously. The concerted use of the two techniques has proven ideal for solving intricate problems of AC assignment of compounds possessing more than one stereo-centre.…”

“…The concerted use of the two techniques has proven ideal for solving intricate problems of AC assignment of compounds possessing more than one stereo-centre. [1,3] It is relevant to mention two instances where VCD was important. In one study Stephens et al [4] corrected by VCD a previous AC assignment based on electronic circular dichroism (ECD) and in another study VCD was claimed to be competitive with X-ray crystallography.…”