Assessment of the Accuracy of DFT-Predicted Li+-Nucleic Acid Binding Energies

Assessing Computational Methods to Calculate the Binding Energies of Dimers of Five-Membered Heterocyclic Molecules

Computational electronic structure methods, including ab initio and density functional theory (DFT), have been assessed in calculating the binding energies of 14 five-membered heterocyclic dimers. The configurations were generated using classical molecular dynamics before optimization at the MP2/aug-cc-pVTZ. Benchmark binding energies are calculated at the CCSD(T)/CBS level of theory. Among the ab initio methods, the DLPNO-CCSD(T)/CBS method has the best performance, reproducing CCSD(T)/CBS with a mean absolute deviation (MAD) of 0.17 kcal/mol. In addition, a schematic CCSD(T)/CBS approach perfectly reproduces the canonical CCSD(T)/CBS with a mean absolute error of 0.08 kcal/mol. Regarding DFT functionals, it has been found that counterpoise corrections have negligible effects on the accuracy of the functionals. Furthermore, including the D3 empirical dispersion considerably enhances the accuracy of the DFT functionals. As a result, outstanding performance is noted for the double hybrid functional B2K-PLYP, with a mean absolute error of 0.25 kcal/mol. In addition to the B2K-PLYP double hybrid functional, M05-D3, B97D, M05-2X-D3, M05-2X, M06-HF, M08-HX, M11, TPSSh-D3, and RSX-0DH-D3(BJ) have MAD values lower than 0.5 kcal/mol. These functionals are recommended for further investigations of five-membered heterocyclic clusters.

Intermolecular hydrogen bonding in DNA base pairs interacting with different numbers of bare and hydrated Li+: NBO, QTAIM, and computational spectroscopic studies

In this study, the effect of different numbers of Li+ interacting with various sites of DNA base pairs (adenine-thymine (AT) and cytosine-guanine (GC)) on the base pair structures, the strength of hydrogen bonding between the bases, and spectroscopic properties (IR and absorption spectra) of the base pairs was investigated. Two quantum computational analyses, the natural bonding orbitals (NBO) and the quantum theory of atoms in molecules (QTAIM), were used to follow the change in the strength of hydrogen bonds between the bases in each pair. The type of base pair's site interacting with Li+ showed different effects on the change in the strength of the hydrogen bonds between the bases. The IR and absorption spectra of the lithiated base pairs were calculated and compared with those of bare base pairs. This comparison provided the changes in the spectra as a fingerprint for the structural identification of different lithiated base pairs. Also, the determination of the change in the strength of hydrogen bonds in the lithiated base pairs compared to their bare base pairs. In the other part of this study, the effect of the hydration of the attached Li+ in the structure of lithiated base pairs on the strength of their hydrogen bonds and spectra was investigated.

Generation of an accurate CCSD(T)/CBS data set and assessment of DFT methods for the binding strengths of group I metal-nucleic acid complexes

Accurate information about interactions between group I metals and nucleic acids is required to understand the roles these metals play in basic cellular functions, disease progression, and pharmaceuticals, as well as to aid the design of new energy storage materials and nucleic acid sensors that target metal contaminants, among other applications. From this perspective, this work generates a complete CCSD(T)/CBS data set of the binding energies for 64 complexes involving each group I metal (Li+, Na+, K+, Rb+, or Cs+) directly coordinated to various sites in each nucleic acid component (A, C, G, T, U, or dimethylphosphate). This data have otherwise been challenging to determine experimentally, with highly accurate information missing for many group I metal-nucleic acid combinations and no data available for the (charged) phosphate moiety. Subsequently, the performance of 61 DFT methods in combination with def2-TZVPP is tested against the newly generated CCSD(T)/CBS reference values. Detailed analysis of the results reveals that functional performance is dependent on the identity of the metal (with increased errors as group I is descended) and nucleic acid binding site (with larger errors for select purine coordination sites). Over all complexes considered, the best methods include the mPW2-PLYP double-hybrid and ωB97M-V RSH functionals (≤1.6% MPE; <1.0 kcal/mol MUE). If more computationally efficient approaches are required, the TPSS and revTPSS local meta-GGA functionals are reasonable alternatives (≤2.0% MPE; <1.0 kcal/mol MUE). Inclusion of counterpoise corrections to account for basis set superposition error only marginally improves the computed binding energies, suggesting that these corrections can be neglected with little loss in accuracy when using larger models that are necessary for describing biosystems and biomaterials. Overall, the most accurate functionals identified in this study will permit future works geared towards uncovering the impact of group I metals on the environment and human biology, designing new ways to selectively sense harmful metals, engineering modern biomaterials, and developing improved computational methods to more broadly study group I metal-nucleic acid interactions.

Stochastic dynamic ultraviolet photofragmentation and high collision energy dissociation mass spectrometric kinetics of triadimenol and sucralose

The major goal of the paper is to provide empirical proof of view that innovative stochastic dynamic mass spectrometric equation D″_SD = 2.6388·10^-17·(< I² >  -  < I > ²) determines the exact analyte concentration in solution via quantifying experimental variable intensity (I) of an analyte ion per any short span of scan time of any measurement, which also appears applicable to quantify laser-induced ultraviolet photofragmentation and high energy collision dissociation mass spectrometric processes. Triadimenol (1) and sucralose (2) using positive and negative polarity are examined. Laser irradiation energy λ_ex = 213 nm is utilized. The issue is of central importance for monitoring organic micro-pollutants in surface, ground, and drinking water as well as tasks of risk assessment for environment and human health from contamination with organics. Despite the significant importance of the topic, answering the question of functional kinetic relations of such processes is by no means straightforward, so far, due to a lack of in-depth knowledge of mechanistic aspects of fragment paths of analytes in environment and foods as well as kinetics of processes under ultraviolet laser irradiation. Although there is truth in the classical theory of first-order reaction kinetics, it does not describe all kinetic data on analytes (1) and (2). A new damped sine wave functional response to a large amount of kinetics is presented. High-resolution mass spectrometric data and chemometrics are used. The study provides empirical evidence for claim that temporal behavior of mass spectrometric variable intensity under negative polarity obeys a certain scientific law written by means of equation above. It is the same for positive and negative soft-ionization mass spectrometric conditions.