For the first time, a complete implementation of coupled perturbed density functional theory (CPDFT) for calculation NMR spin–spin coupling constants (SSCCs) with pure and hybrid DFT is presented. By applying this method to several hydrides, hydrocarbons, molecules multiple bonds, performance SSCCs analyzed in dependence XC used. The importance electron correlation effects demonstrated it shown that B3LYP leads best accuracy calculated SSCCs. Also, CPDFT compared sum-over-states (SOS) where...

Abstract We have determined the three-dimensional (3D) structure of DNA duplex that includes tandem HgII-mediated T–T base pairs (thymine–HgII–thymine, T–HgII–T) with NMR spectroscopy in solution. This is first 3D metallo-DNA (covalently metallated DNA) composed exclusively ‘NATURAL’ bases. The T–HgII–T whose chemical was 15N were well accommodated a B-form double helix, mimicking normal Watson–Crick pairs. Hg atoms aligned along helical axis shielded from bulk water. complete dehydration...

The structure of an Ag(I) -mediated cytosine-cytosine base pair, C-Ag(I) -C, was determined with NMR spectroscopy in solution. observation 1-bond (15) N-(109) Ag J-coupling ((1) J((15) N,(109) Ag): 83 and 84 Hz) recorded within the -C pair evidenced N3-Ag(I) -N3 linkage -C. triplet resonances N4 atoms demonstrated that each exocyclic atom exists as amino group (-NH2 ), any isomerization and/or N4-Ag(I) bonding can be excluded. 3D -DNA complex NOEs classified a B-form conformation notable...

The conductive polymer-electrolyte interface plays an important role in many electrochemical devices. An unusual situation arises when a solvent-free ionic liquid (SF-IL) is used as the electrolyte because it behaves molten salt rather than solution. On basis of Raman spectra, was found that presence ion pairs SF-IL vicinity poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) results decrease oxidation level polymer and increase HOMO-LUMO gap. process "dedoping" modification...

Abstract NMR chemical shifts are highly sensitive probes of local molecular conformation and environment form an important source structural information. In this study, the relationship between nucleic acids glycosidic torsion angle, χ , has been investigated for two commonly occurring sugar conformations. We have calculated by means DFT all atoms in eight DNA RNA mono‐nucleosides as a function these variables. From calculations, structures potential energy surfaces were determined using...

Abstract A reaction mechanism that describes the substitution of two imino protons in a thymine:thymine (T:T) mismatched DNA base pair with Hg II ion, which results formation (T)N3‐Hg ‐N3(T) metal‐mediated was proposed and calculated. The assumes key steps: first N3(T) bond is triggered by deprotonation N3 atom thymine hydroxo ligand on ion. second proceeds through water‐assisted tautomerization remaining, metal‐nonbonded or ion already coordinated to base. thermodynamic parameters Δ G R...

Abstract The synthesis of a hyperpolarized molecule was developed, where the polarization and singlet state were preserved over two controlled chemical steps. Nuclear singlet‐state lifetimes close to 6 min for protons are reported in dimethyl fumarate. Owing high symmetry (AA′X 3 X ′ A 2 systems), readout requires either desymmetrization or long repeated spin lock. Using DFT calculations relaxation models, we further determine nuclear lifetime limiting factors, which include intramolecular...

Developing applications for metal-mediated base pairs (metallo-base-pair) has recently become a high-priority area in nucleic acid research, and physicochemical analyses are important designing fine-tuning molecular devices using metallo-base-pairs. In this study, we characterized the Hg II -mediated T-T (T-Hg -T) pair by Raman spectroscopy, which revealed unique physical chemical properties of . A characteristic marker band at 1586 cm −1 was observed assigned to C4=O4 stretching mode. We...

DNA-Hg complexes may play an important role in sensing DNA defects or detecting the presence of Hg environment. A fundamental way characterizing is to study electric charge transferred through molecular chain. The main goal this contribution was investigate impact a mercury metal cation that links two thymine bases T-T mismatched base pair (T-Hg-T) on transfer molecule. We compared efficiencies standard DNA, with pairs, and T-Hg(II)-T pair. For purpose, we measured temperature dependence...

One-bond ¹⁹⁹Hg–¹⁵N <italic>J</italic>-coupling.

Zika virus is a global health threat due to significantly elevated risk of fetus malformations in infected pregnant women. Currently, neither an effective therapy nor prophylactic vaccination available for clinical use, desperately necessitating novel therapeutics and approaches obtain them. Here, we present structural model the RNA-dependent RNA polymerase (ZIKV RdRp) complex with template nascent RNAs, Mg2+ ions accessing nucleoside triphosphate. The allowed docking studies aimed at...

Cis and trans sugar edge/sugar edge (SE/SE) binding patterns are essential building units of RNAs. For example, SE/SE interactions form the A-minor motifs, most important tertiary interaction type in functional This study provides an in-depth structure stability analysis for these two base pair families. Gas-phase-optimized geometries reported 12 cis 7 pairs contrasted to their X-ray counterparts. Interaction energies computed at RIMP2 level theory using density-functional-theory-optimized...

Complex molecular shapes of ribosomal RNA molecules are stabilized by recurrent types tertiary interactions involving highly specific and conserved non-Watson−Crick base pairs, triplets, quartets. We analyzed the intrinsic structure stability P-motif four basic A-minor (types I, II, III, 0), which represent most prominent interaction patterns refined in course evolution. In studied interactions, electron correlation component stabilization usually exceeds Hartree−Fock (HF) term, leading to a...

We combined various experimental (scanning tunneling microscopy and Raman spectroscopy) theoretical (density functional theory molecular dynamics) approaches to study the relationships between base-pairing patterns charge transfer properties in DNA 32-mer duplexes that may be relevant for identification repair of defects base pairing genetic use nanotechnologies. Studied were two fully Watson−Crick (W-C)-paired duplexes, one mismatched (containing three non-W-C pairs), with pairs chemically...

Nuclear magnetic resonance (NMR) and Raman optical activity (ROA) spectra of the cyclic dipeptide were measured analyzed with respect to their ability sense molecular structure conformation. Data obtained by both techniques simulated using ab initio quantum mechanical computations. Calculated chemical shifts, hydrogen−hydrogen spin−spin coupling constants ROA intensities agreed well experimental values. The NMR found be most suitable for estimating conformational ratio. provided additional...

With the aid of labeling with stable isotopes ((15)N and (13)C) a complete set chemical shifts indirect spin-spin coupling constants was obtained for zwitterionic form L-alanyl-L-alanine in aqueous solution. Different sensitivities NMR parameters to molecular geometry were discussed on basis comparison ab initio (DFT) calculated values. An adiabatic two-dimensional vibrational wave function constructed used determination main chain torsion angle dispersions conformational averaging...

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 backbone (α, β, γ, δ, ε, ζ) and glycosidic (χ) torsion angles order resolve global structure of DMP molecules. experimental J-couplings correlated with theoretical obtained as dynamical averages Karplus equations relevant angles. information was captured using molecular dynamics (MD) calculation method. individual conformational...

We describe a novel, fundamental property of nucleobase structure, namely, pyramidilization at the N1/9 sites purine and pyrimidine bases. Through combined analyses ultra-high-resolution X-ray structures both oligonucleotides extracted from Nucleic Acid Database isolated nucleotides nucleosides Cambridge Structural Database, together with series quantum chemical calculations, molecular dynamics (MD) simulations, published solution nuclear magnetic resonance (NMR) data, we show that...

Metal atoms with a closed-shell electronic structure and positive charge as for example the Au(I), Pt(II), Ag(I), Tl(I) or Hg(II) do not in some compounds repel each other due to so-called metallophilic attraction (P. Pyykkö, Chem. Rev., 1997, 97, 597-636). Here we highlight role of Hg(II)Hg(II) between consecutive metal-mediated mismatched base pairs nucleic acids. Usually, stacking dominates non-covalent interactions steps native In presence these are enriched by metal-base attraction. The...

A benchmark for structural interpretation of the 31P NMR shift and 2JP,C spin-spin coupling in phosphate group was obtained by means theoretical calculations measurements diethylphosphate (DEP) 5,5-dimethyl-2-hydroxy-1,3,2-dioxaphosphinane 2-oxide (cDEP). The parameters were calculated employing B3LYP, BP86, BPW91, M06-2X, PBE0, KT2, KT3, MP2, HF methods, 6-31+G(d), Iglo-n (n = II, III), cc-pVnZ D, T, Q, 5), aug-cc-pVnZ T Q), pcS-n pcJ-n 1, 2, 3, 4) bases, including solvent effects described...

The calculated intermolecular and intramolecular indirect NMR spin-spin coupling constants shifts were used for the discrimination between inner-shell outer-shell binding motif of hydrated divalent cations Mg(2+) or Zn(2+) with a guanine base. (1)J(X,O6) (1)J(X,N7) (X = Mg(2+), Zn(2+)) can be unambiguously assigned to specific cation either oxygen O6 nitrogen N7 guanine. (1)J(Mg,O6) (1)J(Zn,O6) 6.2 -17.5 Hz, respectively, complex directly interacting For coordination at N7, (1)J(Mg,N7)...

Binding modes of hydrated Zn2+ and Mg2+ cations to the N7 O6 positions guanine have been characterized by state-of-the-art ab initio model calculations. We show how differences in electronic structure cationic complexes, as revealed gas-phase computations, translate into biological function two studied metals. The thermodynamic driving force metal binding process is estimated on basis interaction energies total energies. computed results unambiguously reveal that position exhibits a greater...

Dependence of NMR (31)P shielding tensor and (2)J(P,C) coupling constants on solvation nucleic acid phosphate by Mg(2+) water was studied using methods bioinformatic structural analyses crystallographic data DFT B3LYP calculations parameters. The effect solvent dynamics parameters calculated molecular dynamic. for representative patterns determined in crystals B-DNA A-RNA molecules pointed out the crucial importance local coordination geometry, including hydration explicit necessity...