NMR chemical shifts are highly sensitive probes of local molecular conformation and environment and form an important source of structural information. In this study, the relationship between the NMR chemical shifts of nucleic acids and the glycosidic torsion angle, χ, has been investigated for the two commonly occurring sugar conformations. We have calculated by means of DFT the chemical shifts of all atoms in the eight DNA and RNA mono-nucleosides as a function of these two variables. From the DFT calculations, structures and potential energy surfaces were determined by using constrained geometry optimizations at the BP86/TZ2P level of theory. The NMR parameters were subsequently calculated by single-point calculations at the SAOP/TZ2P level of theory. Comparison of the (1)H and (13)C NMR shifts calculated for the mono-nucleosides with the shifts determined by NMR spectroscopy for nucleic acids demonstrates that the theoretical shifts are valuable for the characterization of nucleic acid conformation. For example, a clear distinction can be made between χ angles in the anti and syn domains. Furthermore, a quantitative determination of the χ angle in the syn domain is possible, in particular when (13)C and (1)H chemical shift data are combined. The approximate linear dependence of the C1' shift on the χ angle in the anti domain provides a good estimate of the angle in this region. It is also possible to derive the sugar conformation from the chemical shift information. The DFT calculations reported herein were performed on mono-nucleosides, but examples are also provided to estimate intramolecularly induced shifts as a result of hydrogen bonding, polarization effects, or ring-current effects.

Calculated indirect NMR spin-spin coupling constants (J-couplings) between (31)P, (13)C, and (1)H nuclei were related to the backbone torsion angles of nucleic acids (NAs), and it was shown that J-couplings can facilitate accurate and reliable structural interpretation of NMR measurements and help to discriminate between their distinct conformational classes. A proposed stepwise procedure suggests assignment of the J-couplings to torsion angles from the sugar part to the phosphodiester link. Some J-couplings show multidimensional dependence on torsion angles, the most prominent of which is the effect of the sugar pucker. J-couplings were calculated in 16 distinct nucleic acid conformations, two principal double-helical DNAs, B- and A-, the main RNA form, A-RNA, as well as in 13 other RNA conformations. High-level quantum mechanics calculations used a baseless dinucleoside phosphate as a molecular model, and the effect of solvent was included. The predicted J-couplings correlate reliably with available experimental data from the literature.

We describe a novel, fundamental property of nucleobase structure, namely, pyramidilization at the N1/9 sites of purine and pyrimidine bases. Through a combined analyses of ultra-high-resolution X-ray structures of both oligonucleotides extracted from the Nucleic Acid Database and isolated nucleotides and nucleosides from the Cambridge Structural Database, together with a series of quantum chemical calculations, molecular dynamics (MD) simulations, and published solution nuclear magnetic resonance (NMR) data, we show that pyramidilization at the glycosidic nitrogen is an intrinsic property. This property is common to isolated nucleosides and nucleotides as well as oligonucleotides—it is also common to both RNA and DNA. Our analysis suggests that pyramidilization at N1/9 sites depends in a systematic way on the local structure of the nucleoside. Of note, the pyramidilization undergoes stereo-inversion upon reorientation of the glycosidic bond. The extent of the pyramidilization is further modulated by the conformation of the sugar ring. The observed pyramidilization is more pronounced for purine bases, while for pyrimidines it is negligible. We discuss how the assumption of nucleic acid base planarity can lead to systematic errors in determining the conformation of nucleotides from experimental data and from unconstrained MD simulations.

The l-alanyl-l-alanine (AA) molecule behaves differently in acidic, neutral, and basic environments. Because of its molecular flexibility and strong interaction with the aqueous environment, its behavior has to be deduced from the NMR spectra indirectly, using statistical methods and comparison with ab initio predictions of geometric and spectral parameters. In this study, chemical shifts and indirect spin-spin coupling constants of the AA cation, anion, and zwitterion were measured and compared to values obtained by density functional computations for various conformers of the dipeptide. The accuracy and sensitivity of the quantum methods to the molecular charge was also tested on the (mono)-alanine molecule. Probable AA conformers could be identified at two-dimensional potential energy surfaces and verified by the comparison of the computed parameters with measured NMR data. The results indicate that, whereas the main-chain peptide conformations of the cationic (AA+) and zwitterionic (AAZW) forms are similar, the anion (AA-) adopts also another, approximately equally populated conformer in the aqueous solution. Additionally, the NH2 group can rotate in the two main chain conformations of the anionic form AA-. According to a vibrational quantum analysis of the two-dimensional energy surfaces, higher-energy conformers might exist for all three charged AA forms but cannot be detected directly by NMR spectroscopy because of their small populations and short lifetimes. In accord with previous studies, the NMR parameters, particularly the indirect nuclear spin-spin coupling constants, often provided an excellent probe of a local conformation. Generalization to peptides and proteins, however, has to take into account the environment, molecular charge, and flexibility of the peptide chain.

We combined various experimental (scanning tunneling microscopy and Raman spectroscopy) and theoretical (density functional theory and molecular dynamics) approaches to study the relationships between the base-pairing patterns and the charge transfer properties in DNA 32-mer duplexes that may be relevant for identification and repair of defects in base pairing of the genetic DNA and for DNA use in nanotechnologies. Studied were two fully Watson-Crick (W-C)-paired duplexes, one mismatched (containing three non-W-C pairs), and three with base pairs chemically removed. The results show that the charge transport varies strongly between these duplexes. The conductivity of the mismatched duplex is considerably lower than that of the W-C-paired one despite the fact that their structural integrities and thermal stabilities are comparable. Structurally and thermally much less stable abasic duplexes have still lower conductivity but not markedly different from the mismatched duplex. All duplexes are likely to conduct by the hole mechanism, and water orbitals increase the charge transport probability.

Determination of nucleic acid (NA) structure with NMR spectroscopy is limited by the lack of restraints on conformation of NA phosphate. In this work, the (31)P chemical shielding tensor, the Γ(P,C5'H5'1) and Γ(P,C5'H5'2) cross-correlated relaxation rates, and the (2)J(P,C3'), (2)J(P,C5'), and (3)J(P,C4') coupling constants were calculated in dependence on NA backbone torsion angles ζ and α. While the orientation of the (31)P chemical shielding tensor was almost independent of the NA phosphate conformation, the principal tensor components varied by up to ~40 ppm. This variation and the dependence of the phosphate geometry on torsion angles ζ and α had only a minor influence on the calculated Γ(P,C5'H5'1) and Γ(P,C5'H5'2) cross-correlated relaxation rates, and therefore, the so-called rigid tensor approximation was here validated. For the first time, the (2)J(P,C) spin-spin coupling constants were correlated with the conformation of NA phosphate. Although each of the two J-couplings was significantly modulated by both torsions ζ and α, the (2)J(P,C3') coupling could be structurally assigned to torsion ζ and the (2)J(P,C5') coupling to torsion α. We propose qualitative rules for their structural interpretation as loose restraints on torsion angles ζ and α. The (3)J(P,C4') coupling assigned to torsion angle β was found dependent also on torsions ζ and α, implying that the uncertainty in determination of β with standard Karplus curves could be as large as ~25°. The calculations provided a unified picture of NMR parameters applicable for the determination of NA phosphate conformation.

The measured NMR scalar coupling constants (J-couplings) in the XpY, (X,Y = adenine (A) or cytosine (C)) RNA dinucleoside monophosphates (DMPs) were assigned to the backbone (alpha, beta, gamma, delta, epsilon, zeta) and glycosidic (chi) torsion angles in order to resolve the global structure of the DMP molecules. The experimental J-couplings were correlated with the theoretical J-couplings obtained as the dynamical averages of the Karplus equations relevant to the torsion angles. The dynamical information was captured using the molecular dynamics (MD) calculation method. The individual conformational flexibility of the four DMP molecules was thus consistently probed with the NMR J-couplings. The calculated structure and flexibility of the DMP molecules depend on the sequence considered with respect to the 5' and 3' end of the DMP molecules (5'-XpY-3'). The dynamical characteristics of the two nucleosides are not equivalent even for the ApA and CpC homologues. An enhancement of the sampling in the MD calculations was achieved using five different starting structural motives classified previously for the RNA backbone in the solid phase (Richardson et al. RNA 2008, 14, 465-481). The initial structures were selected on the basis of a database search for RNA oligonucleotides. Frequent interconversions between the conformers during the MD calculations were actually observed. The structural interpretation of the NMR spectroscopic data based on the MD simulations combined with the Karplus equations indicates that the dominant conformation of the DMP molecules in solution corresponds to the A-RNA form. For 52% of the total simulation time (1000 ns), the zeta(g-)-alpha(g-)-gamma(g+) backbone topology corresponding to the canonical A-RNA form was observed, with roughly equally populated C2'- and C3'-endo sugar puckers interconverting on the nanosecond time scale. However, other noncanonical patterns were also found and thus indicate their relatively high potential to be populated in the dynamical regime. For approximately 72% of the time portion when the A-RNA of the zeta-alpha-gamma combination occurred, the nucleobases were classified as being mutually stacked. The geometries of the nucleobases classified in this work as stacked were significantly more populated for the DMP molecules with adenosine at the 3' end (ApA and CpA DMPs) than the ApC or CpC RNA molecules with C at the 3' end.

In this study, the most important kinds of pigments (chlorophylls, bacteriochlorophylls, phycobilins, and carotenoids) from various photosystems were explored. For the most stable conformations, electronic transitions were determined at the TDDFT/6-31+G(d) level with the B3PW91 functional and compared to measured spectra. The group of carotenoids was also investigated at the TDA/TDDFT level with the BLYP functional. The energies of Qy transitions are systematically blue-shifted by about 50-100 nm in the case of (bacterio)chlorophyll and pheophytin molecules. Nevertheless, the correct relative order of the Q lines among various chlorophyll types was obtained through comparison with experimental results. Much better agreement was obtained for the Soret band, for which the differences between calculated and measured transitions were at most 35 nm. In the case of phycobilins, the first transition line was estimated to be at lower frequencies (around 500 nm) with a very similar blue shift of about 100 nm from experimental values. The influence of anchoring cysteine side chain(s) was found to be marginal. A dominant effect of the linear polyene chain on the determined spectral lines was found in the case of carotenoids. Nevertheless, the impact of beta-cycles and epoxy and keto groups is clearly visible as well. The high intensity of the first allowed transition matches different characters of the HOMO and LUMO. In the case of fucoxanthin, the TDA method also predicts the Bu- state to lie below the 1Bu+ state. Because the shift of electron transitions is approximately proportional to the size of the pi-conjugated system, the shift of the calculated transitions compared to experimental values is practically constant for the same excitations of (bacterio)chlorophyll and phycobilin molecules. However, this is not true for carotenoids, for which both the transition energy and the shift of the transition vary with the number of conjugated double bonds.