Modeling Metal Cation−Phosphate Interactions in Nucleic Acids in the Gas Phase via Alkali Metal Cation−Triethyl Phosphate Complexes

Formation of Porous Structures and Crystalline Phases in Poly(vinylidene fluoride) Membranes Prepared with Nonsolvent-Induced Phase Separation-Roles of Solvent Polarity

PVDF membranes were prepared with nonsolvent-induced phase separation, using solvents with various dipole moments, including HMPA, NMP, DMAc and TEP. Both the fraction of the polar crystalline phase and the water permeability of the prepared membrane increased monotonously with an increasing solvent dipole moment. FTIR/ATR analyses were conducted at the surfaces of the cast films during membrane formation to provide information on if the solvents were present as the PVDF crystallized. The results reveal that, with HMPA, NMP or DMAc being used to dissolve PVDF, a solvent with a higher dipole moment resulted in a lower solvent removal rate from the cast film, because the viscosity of the casting solution was higher. The lower solvent removal rate allowed a higher solvent concentration on the surface of the cast film, leading to a more porous surface and longer solvent-governed crystallization. Because of its low polarity, TEP induced non-polar crystals and had a low affinity for water, accounting for the low water permeability and the low fraction of polar crystals with TEP as the solvent. The results provide insight into how the membrane structure on a molecular scale (related to the crystalline phase) and nanoscale (related to water permeability) was related to and influenced by solvent polarity and its removal rate during membrane formation.

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

Understanding how lithium interacts with complex biosystems is crucial for uncovering the roles of this alkali metal in biology and designing extraction techniques for battery production and environmental remediation. In this light, fundamental information about Li⁺ binding to nucleic acids is required. Herein, a new database of Li⁺-nucleic acid interactions is presented that contains CCSD(T)/CBS benchmark energies for all nucleobase and phosphate binding locations. Furthermore, the performance of 54 DFT functionals in combination with three triple-zeta (TZ) basis sets (6-311+G(3df,2p), aug-cc-pVTZ, and def2-TZVPP) is tested. The results identify a range of functionals across different families (B2-PLYP, PBE-QIDH, ωB97, ωB97X-D, MN15, B3PW91, B97-2, TPSS, BP86-D3(BJ), and PBE) that can accurately describe coordinated Li⁺-nucleic acid interactions, with the average mean percent error (AMPE) across binding positions and basis sets being below 2%. Nevertheless, only three functionals tested (B2-PLYP, PBE-QIDH, and ωB97X-D) preserve this accuracy for metal cation-π interactions, suggesting that caution is warranted when choosing a functional to describe a diverse range of Li⁺-nucleic acid complexes. Removal of counterpoise corrections has very little impact on the reliability of most functionals, while the effect of empirical dispersion corrections varies depending on the functional choice and interaction type. While increasing the basis set to quadruple-zeta quality had little impact on the AMPE, the accuracy of double-zeta basis sets varies with family. Importantly, DFT methods reproduce the CCSD(T)/CBS trend in the preferred binding position for a given nucleic acid component and the global trend across components (phosphate ≫ G > C ≫ A ∼ T = U), as well as the geometries of the metal-nucleic acid complexes. The overall top performing functional is PBE-QIDH, which results in deviations from CCSD(T)/CBS values as small as ∼0.1 kcal/mol for nucleobase contacts and ∼1 kcal/mol for phosphate interactions. The most accurate DFT methods identified in the present work are recommended for future investigations of lithium interactions in larger nucleic acid systems to provide insights into the biological roles of this metal and the design of novel biosensing strategies.

Ligand-mediated reversal of the oxidation state dependent ROS scavenging and enzyme mimicking activity of ceria nanoparticles

Enzymatic activity of cerium oxide nanoparticles modified by phosphine ligands.

Cationic Noncovalent Interactions: Energetics and Periodic Trends

In this review, noncovalent interactions of ions with neutral molecules are discussed. After defining the scope of the article, which excludes anionic and most protonated systems, methods associated with measuring thermodynamic information for such systems are briefly recounted. An extensive set of tables detailing available thermodynamic information for the noncovalent interactions of metal cations with a host of ligands is provided. Ligands include small molecules (H2, NH3, CO, CS, H2O, CH3CN, and others), organic ligands (O- and N-donors, crown ethers and related molecules, MALDI matrix molecules), π-ligands (alkenes, alkynes, benzene, and substituted benzenes), miscellaneous inorganic ligands, and biological systems (amino acids, peptides, sugars, nucleobases, nucleosides, and nucleotides). Hydration of metalated biological systems is also included along with selected proton-based systems: 18-crown-6 polyether with protonated peptides and base-pairing energies of nucleobases. In all cases, the literature thermochemistry is evaluated and, in many cases, reanchored or adjusted to 0 K bond dissociation energies. Trends in these values are discussed and related to a variety of simple molecular concepts.

Thermochemistry of non-covalent ion-molecule interactions

The thermochemistry of non-covalent ion-molecule complexes has been examined by measuring quantitative bond dissociation energies using threshold collision-induced dissociation in guided ion beam tandem mass spectrometers (GIBMS). The methods used are briefly reviewed and several examples of the types of information and insight that can be obtained from such thermodynamic information are discussed. The hydration of metal cations, both singly and doubly charged, is reviewed and the trends elucidated, mainly on the basis of electrostatic contributions. The binding of alkali metal cations to amino acids has been examined for a range of systems, with both the overall polarizability of the amino acid and the local dipole moment of heteroatomic side-chains shown to be important contributors. The gas-phase interactions of the 12-crown-4 (12C4) polyether with alkali metal cations, classic molecular recognition systems in solution, have been newly compared to previous GIBMS work. These results validate the previous hypothesis that excited conformers were present for Rb(+)(12C4) and Cs(+)(12C4) and offer clues as to how and why they are formed.

Infrared multiple photon dissociation action spectroscopy and theoretical studies of triethyl phosphate complexes: effects of protonation and sodium cationization on structure

The gas-phase structures of protonated and sodium cationized complexes of triethyl phosphate, [TEP + H](+) and [TEP + Na](+), are examined via infrared multiple photon dissociation (IRMPD) action spectroscopy using tunable IR radiation generated by a free electron laser, a Fourier transform ion cyclotron resonance mass spectrometer with an electrospray ionization source, and theoretical electronic structure calculations. Measured IRMPD action spectra are compared to linear IR spectra calculated at the B3LYP/6-31 G(d,p) level of theory to identify the structures accessed in the experimental studies. For comparison, theoretical studies of neutral TEP are also performed. Sodium cationization and protonation produce changes in the central phosphate geometry, including an increase in the alkoxy ∠OPO bond angle and shortening of the alkoxy P-O bond. Changes associated with protonation are more pronounced than those produced by sodium cationization.

Infrared multiple photon dissociation action spectroscopy and theoretical studies of diethyl phosphate complexes: effects of protonation and sodium cationization on structure

The gas-phase structures of deprotonated, protonated, and sodium-cationized complexes of diethyl phosphate (DEP) including [DEP - H](-), [DEP + H](+), [DEP + Na](+), and [DEP - H + 2Na](+) are examined via infrared multiple photon dissociation (IRMPD) action spectroscopy using tunable IR radiation generated by a free electron laser, a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) with an electrospray ionization (ESI) source, and theoretical electronic structure calculations. Measured IRMPD spectra are compared to linear IR spectra calculated at the B3LYP/6-31G(d,p) level of theory to identify the structures accessed in the experimental studies. For comparison, theoretical studies of neutral complexes are also performed. These experiments and calculations suggest that specific geometric changes occur upon the binding of protons and/or sodium cations, including changes correlating to nucleic acid backbone geometry, specifically P-O bond lengths and ∠OPO bond angles. Information from these observations may be used to gain insight into the structures of more complex systems, such as nucleotides and solvated nucleic acids.

Modeling metal cation-phosphate interactions in nucleic acids: activated dissociation of Mg+, Al+, Cu+, and Zn+ complexes of triethyl phosphate

Threshold collision-induced dissociation techniques are employed to determine the activation energies (AEs) and bond dissociation energies (BDEs) of metal cation-triethyl phosphate complexes, M(+)(TEP), where M(+) = Mg(+), Al(+), Cu(+), and Zn(+). Activated dissociation resulting in loss of ethene, C(2)H(4), corresponds to the primary and lowest energy pathway for all four systems examined. Sequential loss of additional C(2)H(4) molecules and loss of the intact TEP ligand is also observed at elevated energies. Theoretical calculations at the B3LYP/6-31G* level of theory are used to determine the structures, vibrational frequencies, and rotational constants of neutral TEP and the M(+)(TEP) complexes, transition states, intermediates, and products of the activated dissociation of these complexes. Theoretical AEs and BDEs are determined from single point energy calculations at the B3LYP/6-311+G(2d,2p) level using the B3LYP/6-31G* optimized geometries. The agreement between the calculated and measured AEs for elimination of C(2)H(4) is excellent for all four systems. In contrast, less satisfactory agreement between theory and experiment is found for the M(+)-TEP BDEs and may indicate limitations in the competitive model used to analyze these high energy dissociation pathways. The influence of the valence orbital occupation of the metal cation on the binding and activation propensities for elimination of ethene from TEP is examined. The binding of metal cations to TEP is compared to that of the nucleobases to assess the binding preferences of metal cations to nucleic acids.

Interaction of metal ions and DNA films on gold surfaces: an electrochemical impedance study

Electrochemical impedance spectroscopy (EIS) has been used to investigate the effects of a number of metal ions with DNA films on gold surfaces exploiting [Fe(CN)6](3-/4-) as a solution-based redox probe. Alkaline earth metal ions Mg2+, Ca2+, trivalent Al3+, La3+ and divalent transition metal ions Ni2+, Cu2+, Cd2+ and Hg2+ have been selected in this study and the results are compared with previous studies on the effects of Zn2+ on the EIS of DNA films. All experimental results were evaluated with the help of equivalent circuits which allowed the extraction of resistive and capacitive components. For all metal ions studied here, addition of the metal ions causes a decrease in the charge transfer resistance. The difference of charge transfer resistance (DeltaR(ct)) of ds-DNA films in the presence and absence of the various metal ions is different and particular to any given metal ion. In addition, we studied the EIS of ds-DNA films containing a single A-C mismatch in the presence and absence of Ca2+, Zn2+, Cd2+ and Hg2+. DeltaR(ct) values for ds-DNA films with a single A-C mismatch is smaller than those of fully matched ds-DNA films.