Orbital interactions and charge redistribution in weak hydrogen bonds: The Watson-Crick AT mimic adenine-2,4-difluorotoluene

An overview is given of results that reestablish hydrogen bonding as an essential factor in DNA replication involving natural bases as well as less polar mimics and they also confirm the importance of steric factors, in line with Kool's experimental work. In addition they show that knowledge of the hydrogen bonding mechanism helps understanding the behavior of these bonds if they are deformed

Structure and Bonding in DNA. Development and Application of Parallel and Order-N DFT Methods

Baerends, E.J. [Promotor]Snijders, J.G. [Promotor]Bickelhaupt, F.M. [Copromotor

Hydrogen Bonding in DNA Base Pairs: Reconciliation of Theory and Experiment

Up till now, there has been a significant disagreement between theory and experiment regarding hydrogen bond lengths in Watson - Crick base pairs. To investigate the possible sources of this discrepancy, we have studied numerous model systems for adenine - thymine (AT) and guanine - cytosine (GC) base pairs at various levels (i.e., BP86, PW91, and BLYP) of nonlocal density functional theory (DFT) in combination with different Slater-type orbital (STO) basis sets. Best agreement with available gas-phase experimental A - T and G - C bond enthalpies (-12.1 and -21.0 kcal/mol) is obtained at the BP86/TZ2P level, which (for 298 K) yields -11.8 and -23.8 kcal/mol. However, the computed hydrogen bond lengths show again the notorious discrepancy with experimental values. The origin of this discrepancy is not the use of the plain nucleic bases as models for nucleotides: the disagreement with experiment remains no matter if we use hydrogen, methyl, deoxyribose, or 5'- deoxyribose monophosphate as the substituents at N9 and N1 of the purine and pyrimidine bases, respectively. Even the BP86/DZP geometry of the Watson- Crick-type dimer of deoxyadenylyl-3',5'-deoxyuridine including one N

SARS-CoV spike proteins can compete for electrolytes in physiological fluids according to structure-based quantum-chemical calculations

The trimeric spike (S) glycoprotein is the trojan horse and the stronghold of the severe acute respiratory syndrome coronaviruses. Although several structures of the S-protein have been solved, a complete understanding of all its functions is still lacking. Our multi-approach study, based on the combination of structural experimental data and quantum-chemical DFT calculations, led to identify a sequestration site for sodium, potassium and chloride ions within the central cavity of both the SARS-CoV-1 and SARS-CoV-2 spike proteins. The same region was found as strictly conserved, even among the sequences of the bat-respective coronaviruses. Due to the prominent role of the main three electrolytes at many levels, and their possible implication in the molecular mechanisms of COVID-19 disease, our study can take the lead in important discoveries related to the SARS-CoV-2 biology, as well as in the design of novel effective therapeutic strategies.Theoretical Chemistr

Adenine versus Guanine Quartets in Aqueous Solution. Dispersion-Corrected DFT Study on the Differences in π-Stacking and Hydrogen-Bonding Behavior

We have investigated the performance of the dispersion-corrected density functionals (BLYP-D, BP86-D and PBE-D) and the widely used B3LYP functional for describing the hydrogen bonds and the stacking interactions in DNA base dimers. For the gas-phase situation, the bonding energies have been compared to the best ab initio results available in the literature. All dispersion-corrected functionals reproduce well the ab initio results, whereas B3LYP fails completely for the stacked systems. The use of the proper functional leads us to find minima for the adenine quartets, which are energetically and structurally very different from the

Medium perturbations on the molecular polarizability calculated within a localized dipole interaction model

We have studied the medium effects on the frequency-dependent polarizability of water by separating the total polarizability of water clusters into polarizabilities of the individual water molecules. A classical frequency-dependent dipole–dipole interaction model based on classical electrostatics and an Unsöld dispersion formula has been used. It is shown that the model reproduces the polarizabilities of small water clusters calculated with time-dependent density functional theory. A comparison between supermolecular calculations and the localized interaction model illustrate the problems arising from using supermolecular calculations to predict the medium perturbations on the solute polarizability. It is also noted that the solute polarizability is more dependent on the local geometry of the cluster than on the size of the cluster

B-{DNA} Structure and Stability: The Role of Nucleotide Composition and Order

We have quantum chemically analyzed the influence of nucleotide composition and sequence (that is, order) on the stability of double-stranded B-DNA triplets in aqueous solution. To this end, we have investigated the structure and bonding of all 32 possible DNA duplexes with Watson-Crick base pairing, using dispersion-corrected DFT at the BLYP-D3(BJ)/TZ2P level and COSMO for simulating aqueous solvation. We find enhanced stabilities for duplexes possessing a higher GC base pair content. Our activation strain analyses unexpectedly identify the loss of stacking interactions within individual strands as a destabilizing factor in the duplex formation, in addition to the better-known effects of partial desolvation. Furthermore, we show that the sequence-dependent differences in the interaction energy for duplexes of the same overall base pair composition result from the so-called "diagonal interactions" or "cross terms". Whether cross terms are stabilizing or destabilizing depends on the nature of the electrostatic interaction between polar functional groups in the pertinent nucleobases

Electronic and magnetic properties of Fe clusters inside finite zigzag single-wall carbon nanotubes

Density functional calculations of the electronic structure of the Fe12 cluster encapsulated inside finite singlewall zigzag carbon nanotubes of indices (11,0) and (10,0) have been performed. Several Fe12 isomers have been considered, including elongated shape isomers aimed to fit well inside the nanotubes, and the icosahedral minimum energy structure. We analyze the structural and magnetic properties of the combined systems, and how those properties change compared to the isolated systems. A strong ferromagnetic coupling between the Fe atoms occurs both for the free and the encapsulated Fe12 clusters, but there is a small reduction (3–7.4μB) of the spin magnetic moment of the encapsulated clusters with respect to that of the free ones (μ = 38μB). The reduction of the magnetic moment is mostly due to the internal redistribution of the spin charges in the iron cluster. In contrast, the spin magnetic moment of the carbon nanotubes, which is zero for the empty tubes, becomes nonzero (1–3μB) because of the interaction with the encapsulated cluster. We have also studied the encapsulation of atomic Fe and the growth of small Fen clusters (n = 2, 4, 8) encapsulated in a short (10,0) tube. The results suggest that the growth of nanowires formed by distorted tetrahedral Fe4 units will be favorable in (10,0) nanotubes and nanotubes of similar diameter

Redox conversion of cobalt(II)‐diselenide to cobalt(III)‐selenolate compounds: comparison with their sulfur analogs

The synthesis of the selenium-based ligand (LSeSeL1)-Se-1 (2,2'-diselanediylbis(N,N-bis(pyridin-2-ylmethyl)ethan-1-amine) is described along with its reactivity with cobalt(II) salts. The cobalt(II)-diselenide complex [Co-2((LSeSeL1)-Se-1)Cl-4] was obtained in good yield, and its spectroscopic properties closely resemble that of its sulfur analog. Reaction of (LSeSeL1)-Se-1 with Co(II) thiocyanate results in the formation of the cobalt(III) compound [Co((LSe)-Se-1)(NCS)(2)], similar to reaction of (LSSL1)-S-1. The redox-conversion reactions from the Co(II)-diselenide compound [Co((LSeSeL1)-Se-1)Cl-4] using external triggers such as removal of the halide ions or the addition of the strong-field ligand 8-quinolinolate resulted in good yields of the Co(III)-selenolate complexes [Co((LSe)-Se-1)(MeCN)(2)](SbF6)(2) and [Co((LSe)-Se-1)(quin)]Cl. Our computational studies show that the ligand-field splitting energy of the selenium compounds is smaller than their sulfur analogs, indicating that redox-conversion of cobalt(II)-diselenide to cobalt(III)-selenolate complexes may be more arduous than that for the related sulfur compounds.Theoretical ChemistryMetals in Catalysis, Biomimetics & Inorganic Material